title: Gene array analysis of langerhans cells and macrophages from human skin and pDCs from human spleen

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

institute: Singapore Immunology Network

summary: Langerhans cells and macrophages were isolated from adult skin that was collagenase digeseted overnight by FACS.  Adult spleen was collagenase digested for 1hr and the pDCs were isolated by FACS. Gene expression analysis using total RNA from specific cell subsets was performed.

overall_design: Totally 9 samples: 3 langerhans cell samples and 3 macrophage samples from adult skin; 3 pDC samples from adult lung

first: Naomi

last: Mc Govern

first: Michael

last: Poidinger


title: Circulating CD1c+ myeloid dendritic cells are precursors to Langerhans cell histiocytosis (LCH) lesion CD1a+CD207+cells

status: Public on Jan 21 2020

country: Singapore

summary:
Expression data from LCH lesion subpopulations and healthy donors' peripheral blood specimens
Langerhans cell histiocytosis (LCH) is a myeloproliferative disorder that is characterized by the inflammatory lesions with pathogenic CD1a+CD207+ dendritic cells (DCs).  BRAFV600E and other somatic activating MAPK gene mutations have been identified in differentiating bone marrow and blood myeloid cells, but the origin of the LCH lesion CD1a+CD207+DCs and mechanisms of lesion formation remain incompletely defined. In order to identify candidate LCH CD1a+CD207+DCs’ precursor populations, gene expression profiles of LCH lesion CD1a+CD207+DCs were first compared to established gene signatures from human myeloid cell subpopulations. Interestingly, the CD1c+ myeloid DC (mDC) gene signature was most enriched in the LCH CD1a+CD207+DC’ transcriptome.  Additionally, the BRAFV600E allele was not only localized to CD1a+CD207-DCs and CD1a+CD207+DCs, but it was also identified in CD1c+mDCs in LCH lesions. Transcriptomes of CD1a+CD207-DCs were nearly indistinguishable from CD1a+CD207+DCs (both CD207low and CD207high subpopulations).  Transcription profiles of LCH lesion CD1a+CD207+DCs and peripheral blood CD1c+mDCs from healthy donors were compared to identify potential LCH DC-specific biomarkers. HLADQB2 expression was significantly increased in LCH lesion CD1a+CD207+DCs compared to circulating CD1c+mDCs from healthy donors, and HLA-DQB2 antigen was identified on LCH lesion CD1a+CD207- and CD1a+CD207+DCs as well as on CD1c+(CD1a+CD207-) mDCs, but not in any other lesion myeloid subpopulations. Interestingly, HLADQB2 expression was specific to peripheral blood of patients with BRAFV600E+ peripheral blood mononuclear cells (PBMC), and HLA-DQB2+CD1c+blood cells were highly enriched for the BRAFV600E in these patients. These data support a model where blood CD1c+mDCs with activated ERK migrate to lesion sites where they differentiate into pathogenic CD1a+CD207+ DCs.

overall_design: 12 samples: 12 LCH lesion subpopulation specimens

first: Karen Phaik Har

last: Lim

first: Florent

last: Ginhoux


title: Exogenous melatonin promotes rice seed germination under salinity through regulating reactive oxygen species and phytohormones

status: Public on Jan 20 2020

city: yangzhou

first: hflx

middle: hflx

last: hflx

state: jiangsu

address: 88 University South Road

department: Agricultural College

country: China

institute: yangzhou university

type: Expression profiling by high throughput sequencing

summary: Melatonin plays a potential role in multiple plant developmental processes and stress response. However, there are no reports regarding exogenous melatonin promoting rice seed germination under salinity and nor about the underlying molecular mechanisms at genome-wide. Here, we revealed that exogenous application of melatonin conferred roles in promoting rice seed germination under salinity. The putative molecular mechanisms of exogenous melatonin in promoting rice seed germination under high salinity were further investigated through metabolomic and transcriptomic analyses. The results state clearly that the phytohormone contents were reprogrammed, the activities of SOD, CAT, POD were enhanced, and the total antioxidant capacity was activated under salinity by exogenous melatonin. Additionally, melatonin-pre-treated seeds exhibited higher concentrations of glycosides than non-treated seeds under salinity. Furthermore, exogenous melatonin alleviated the accumulation of fatty acids induced by salinity. Genome-wide transcriptomic profiling identified 7160 transcripts that were differentially expressed in NaCl, MT100 and control. Pathway and GO term enrichment analysis revealed that genes involved in the response to oxidative stress, hormone metabolism, heme building, mitochondrion, tricarboxylic acid transformation were altered after melatonin pre-treatment under salinity. This study provides the first evidence of the protective roles of exogenous melatonin in increasing rice seed germination under salt stress, mainly via activation of antioxidants and modulation of metabolic homeostasis.

overall_design: A total of nine samples, including three treatments. Each treatment was detected  at a time point with 3 replicates.

first: Liexiang

last: Huangfu


title: Differentially expressed genes after siRNA transfection or gene knockdown in human cancer cell lines

status: Public on Jan 17 2020

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

summary: To identify differentially expressed genes by specific gene silencing (via siRNAs or knockout) in human cancer, several cell lines (esophageal cancer and gastric cancer) were subjected to Agilent whole genome microarrays.

overall_design: Human cell lines (TE-8 and MKN45) were treated with siRNAs (si-HMGA2 and si-SERPINH1, respectively). TE-8 was also subjected to HMGA2 knockdown by CRISPR-Cas9 system.

first: Reona

last: Okada


title: Molecular changes during progression from early stage to advanced urothelial carcinoma

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

summary: It is unclear how urothelial carcinoma of the urinary bladder change, genetically and phenotypically, as patients progress from recurrent non muscle-invasive (NMI) to muscle-invasive (MI) disease or disease that require radical cystectomy. This data set contains gene expression data from 200 samples in a longitudinal study of such patients. Overlap with previously GEO-published cohorts from our lab is described in the metadata.

overall_design: Total RNA isolated from FFPE-blocks containing tissue from trans-urethral resection of the bladder extracted using the High Pure FFPET RNA isolation kit (Roche), assessed for quality using Nanodrop ND-1000, and labeled using SensationPlus FFPE Amplification and WT labeling kit. Labeled sample was hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix) at the SCIBLU genomics facility in Lund, Sweden. Several samples may be derived from different tumors from the same pateints, see publication and metadata. Tumor stage in this study was determined using available pre-operative information (pathological stage from radical cystectomy not considered). The full dataset of 200 CEL files were normalized using RMA by labeling batches. Batches were combined and RMA normalized. The data was filtered for probes with signal intensity less than the median of negative control probes for >80% of the values. Gene symbols and EntrezID were appended using Bioconductor (hugene10stprobeset.db Version 8.6.0). Probes not mapping to a gene symbol were removed. The probes were median merged by gene symbol, log-transformed, and median centered for the final normalized data set. The patient-level and tumor-level overlap with previous GEO submissions and publications from our lab (GSE83586) is described in a dedicated column in the metadata.

last: Sjödahl


title: MGA represses MYC-target genes [RNA-seq]

status: Public on Jan 18 2020

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

country: USA

institute: University of Utah

summary: Using RNA-seq to identify genes that regulated by MGA and MYC

overall_design: RNA-seq of A549 cells over-expressing empty vector or MGA; RNA-seq of A549 cells treated with siNC or siMYC


title: Gene changes over aging in the C.elegans rrf-3(pk1426) mutant

city: Mainz

first: Holger

last: Richly

address: Ackermannweg 4

country: Germany

institute: Institute of molecular Biology

summary: The goal of this experiment is to asses quantative changes to gene expression over aging in worms grown in liquid culuture. Using this method allows us to generate more tightly synchornised worm poplulations with larger sample sizes for each time point analysed

overall_design: C.elegans rrf-3(pk1436) mutant worms were grown in liquid culture and harvested for RNAsequencing at the following ages, day 3, day 6, day 9, day 12, and day 15. RNA libraries were sequenced on a HiSeq2500 with a read length of 51 bp single read.

first: Jonathan

last: Byrne

first: Rebeca

last: Medina

first: Thomas

last: Wilhelm


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [RNA-seq_CPT]

city: Tsuruoka

first: Junko

last: Murai

state: Yamagata

address: 246-2 Kakuganji Mizugami

institute: Keio University

summary: Schlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication stress. Here we show that SLFN11 increases chromatin accessibility genome-wide, dominantly at promoters in response to replication stress induced by the CHK1 inhibitor prexasertib and the topoisomerase I inhibitor, camptothecin. Concomitantly SLFN11 selectively activates cellular stress response pathways by inducing the transcription of the Immediate Early Genes (IEGs) including JUN, FOS, EGR1, NFKB2 and ATF3. Both chromatin opening and IEG activation require the putative helicase activity of SLFN11 whereas extrinsic IEG activation by serum induction is SLFN11-independent. SLFN11-dependent IEG activation is also observed across 55 non-isogenic NCI-60 cell lines by comparing transcriptome data before and after camptothecin treatment. We conclude that SLFN11 acts as a global regulator of chromatin structure and an intrinsic IEG activator with the potential to engage the native immune activation in response to replicative stress.

overall_design: SLFN11-positive parent cells (leukemia CCRF-CEM) and their SLFN11-knockout cells were treated with camptothecin (CPT 100 nM) a DNA damaging agents, and their transcriptome were compared to the basal transcriptome.

first: Lorinc

last: Pongor

first: Yves

last: Pommier


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [ChIP-seq_H3K27ac_CPTO]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: SLFN11-positive parent cells (leukemia CCRF-CEM) and their SLFN11-knockout cells were treated with camptothecin (CPT 100 nM) a DNA damaging agents, and ChIP-seq against H3K27ac was performed.

first: Hongliang


title: LncRNA SNHG5 suppresses cell migration and invasion of human lung adenocarcinoma via regulation of epithelial-mesenchymal transition

city: Shijiazhuang

first: Zhirong

last: Li

state: Hebei

address: 12# Jiankang road, Shijiazhuang, China

department: Research Center

institute: The Fourth Hospital of Hebei Medical University

summary: Long noncoding RNAs (lncRNAs) are emerging as important regulators in cellular processes. In the present study, the effects of the long non-coding RNA, SNHG5 was investigated in lung adenocarcinoma (LAD) and we also revealed the underlying mechanisms of it. Overexpressed SNHG5 suppressed migration and invasion of LAD cell line A549 in vitro. Transcriptome sequencing analysis supported the inhibitory effects of SNHG5 were associated with cell adhesion molecules. In addition, western blot and immunofluorescence showed that the expression of SNHG5 was associated with epithelial-mesenchymal transition (EMT) markers. Furthermore, we determined the effects of SNHG5 in EMT procession of A549 induced by TGF-β1. Consistent with previous results, overexpression of SNHG5 suppressed the migration and invasion, and also the expression of EMT-related transcription factors including Snail, SLUG and ZEB1 in EMT of A549 reduced by TGF-β1. Moreover, qRT-PCR demonstrated expression of SNHG5 was positively correlated with E-cadherin protein expression, but negatively correlated with N-cadherin and Vimentin in LAD tissues. In summary, our study demonstrated that lncRNA SNHG5 could suppress cell migration and invasion of LAD cancer by inhibiting EMT procession, highlighting the potential of SNHG5 as a therapy strategy for lung adenocarcinoma.

overall_design: Examination of 6 samples including 3 repeats of SNGH5-overexpressed A549 cells and 3 control repeats.

first: Yipeng

last: Wu

first: Cong

first: Suli

last: Dai

first: Lianmei

last: Zhao

first: Baoen

last: Shan


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [ATAC-seq_K562]

overall_design: Three lines of gene modified K562 cells were treated with drugs for the indicated time. Genome-wide mapping of chromatin accessibility was done by Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq).


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [ATAC-seq_CPTO]

overall_design: SLFN11-positive parent cells (leukemia CCRF-CEM) and their SLFN11-knockout cells were treated with drugs for the indicated time. Genome-wide mapping of chromatin accessibility was done by Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq).


title: Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase

status: Public on Jan 19 2020

city: SAN FRANCISCO

first: Hiten

last: Madhani

state: CA

institute: University of California San Francisco

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles, yet has been lost many times in diverse eukaryotic lineages. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase, Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 MYA. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 MY through a process analogous to Darwinian evolution of the genome.

overall_design: Bisulfite-sequencing, ChIP-seq and MeDIP-seq to investigate DNA methylation in C. neoformans

first: Sandra

last: Catania


title: Single cell RNA sequencing of cells treated with a KRAS G12C specific inhibitor

city: NY

first: Piro

last: Lito

state: NY

address: 1275 York

institute: Memorial Sloan Kettering Cancer Center

summary: KRAS GTPases are activated in one-third of cancers and KRASG12C is the most common activating alteration in lung adenocarcinoma. KRASG12C inhibitors are in Phase-I clinical trials and early data show partial responses in ~50% of lung cancer patients. How cancer cells bypass inhibition, to prevent maximal response to therapy, is not understood. By studying the effect of treatment at single-cell resolution here we found that shortly after treatment, some cancer cells are sequestered in a quiescent state with low KRAS activity, while others bypass this effect to resume proliferation. We then identified adaptive changes that lead to this rapid divergent response and how these differ between cancer cell subpopulaitons. This study uncovers a flexible non-uniform fitness mechanism that enables groups of cells within a population to rapidly bypass the effect of treatment. This adaptive process must be overcome if we are to achieve complete and durable responses in the clinic.

overall_design: KRAS G12C-mutant tumor cell models (H358, H2122 and SW1573) were treated with the KRAS G12C (ARS1620, 10µM) inhibitor for 0, 4, 24 and 72h, followed by rapid collection of attached cells in cryopreservation medium. The cells were stored in -80oC until the completion of the experiment. scRNAseq was carried out using the Chromium 10X platform (3-prime v1 kit), as described in the manufacturer’s protocol.

first: Jeny

last: Xue

first: Yulei

last: Zaho

first: Jordan

last: Aronowitz

first: Trang

last: Mai

first: Alberto

last: Vides

first: Dongsung

last: Kim

first: Chuanchuan

first: Besnik

last: Qeriqi

first: Elisa

last: de Stanchina

first: Linas

last: Mazutis

first: Davide

last: Risso


title: Global temporal gene expression of Nematostella vectensis in-situ

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: We assessed genome-wide temporal transcript expression patterns in the sea anemone, Nematostella vectensis, in Great Sippewissett Marsh in Massachusetts, where anemones experienced a natural light cycle with intensity varying from 0-200 lum/ft2, daily temperature fluctuations of ~9C. We measured ‘in situ’ gene expression from recaptured anemones every hour from 0800 to 1700 and identified six time-dependent gene clusters, represented by several genes involved in metabolism, stress, and transcription-translation related functions.

overall_design: We measured gene expression from anemones every hour from 0800 to 1700 for a total of 10 time points in both single individuals and pooled samples

middle: B

first: Adam

middle: M

last: Reitzel


title: Gene expression profiling of Tg(14xUAS:GFP-EWSR1-ERG) x Et(E1b:Gal4-VP16)s1101t, Tg(UAS:Kaede) s1999t zebrafish embryos at 3 days post fertilization

city: Leiden

first: Wietske

last: van der Ent

address: Einsteinweg 55

country: Netherlands

institute: Leiden University, Institute of Biology Leiden

summary: We use next generation sequencing of embryos with neuronally expressed EWSR1-ERG at 3 dpf to investigate overlap between these embryos' regulated gene set and  that of other Ewing sarcoma models

overall_design: This deep sequence study was designed to determine the gene expression profile regulated by EWSR1-ERG. Samples were obtained at 3 days post fetilisation from Tg(14xUAS:GFP-EWSR1-ERG) x Et(E1b:Gal4-VP16)s1101t, Tg(UAS:Kaede) s1999tRNA embryos expressing EWSR1-ERG neuronally, or wild-type siblings. RNA was isolated from 15 embryos per sample using the RNeasy Micro Kit (Qiagen).

first: W

first: P

middle: J

last: Schoonheim

first: K

last: Szuhai

first: H

middle: P

last: Spaink

middle: C

last: Hogendoorn

first: B

middle: E

last: Snaar-Jagalska


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [ATAC-seq_CHPTCHK1i]

first: Junko

last: Murai

overall_design:
SLFN11-positive parent cells (leukemia CCRF-CEM) and their SLFN11-knockout cells were treated with drugs for the indicated time. Genome-wide mapping of chromatin accessibility was done by Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq).

***Please note that the raw data for the 'GSM4190680 Parent_CHK1i4h' sample is truncated and the submitter is unable to provide the intact replacement file.

first: Lorinc

last: Pongor

first: Yves

last: Pommier


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [RNA-seq_CHK1i]

overall_design: SLFN11-positive parent cells (leukemia CCRF-CEM) and their SLFN11-knockout cells were treated with prexasertib (clinical check 1 inhibitor, 100 nM), and their transcriptome were compared to the basal transcriptome.


title: Gene-expression profiles of  HepG2.2.15 cells induced by  overexpression of Complement 2

city: Guangzhou

first: Gang

last: Ning

state: Guangdong

address: 600 Tianhe Road, Guangzhou

department: Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-Sen University

institute: sun yat-sen university

summary: To explore the effect of overexpression of complement component 2 (C2) on HepG2.2.15 cells, we established HepG2.2.15-mock cells and C2-overexpressing HepG2.2.15 cells (HepG2.2.15-shC2) to identify differentially expressed genes and then performed GO and KEGG analysis to identified the altered pathways caused by over-expression of C2.

overall_design: 2x10e5 HepG2.2.15-shC2 (n=3) and 2x10e5 HepG2.2.15-mock cells (n=3) were seeded in 6-well plates and inoculated for 48 hours, then total RNA was isolated from cell samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).

first: Ning

last: Gang

first: Limin

last: Zhen


title: Changes in rumen fermentation and transcriptomes of liver tissue in Holstein cows with and those without subacute ruminal acidosis during the periparturient period

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: We investigated changes in rumen fermentation, peripheral blood metabolites and hormones, and hepatic transcriptomic dynamics in Holstein cows with and those without subacute ruminal acidosis (SARA) during the periparturient period.

overall_design: SARA was diagnosed when ruminal pH was < 5.6 for more than 3 h per day (Gozho et al., 2005) during the 2 weeks following parturition. Based on these criteria, cows were assigned to the SARA (n = 8) or Control (n = 8) group.

first: Yo-Han

last: Kim


title: Transcriptional analysis of the GlnR regulon of Listeria monocytogenes

city: Boston

first: Rajesh

middle: K

last: Biswas

state: MA

address: 136 Harrison Avenue

department: Molecular Biology and Microbiology

institute: Tufts University Schoolof Medicine

summary: RNA-Seq analysis of L. monocytogenes wild-type and glnR null mutant strains was performed in a defined medium

overall_design: Wild-type and glnR null mutant strains were grown in a defined medium, LDM, containing NH4Cl or glutamine as a principal nitrogen source

first: Boris

middle: R

last: Belitsky

first: Abraham

middle: L

last: Sonenshein


title: Next Generation Sequencing  Analysis of wild-type and transgenic beta-synuclein reactive T cells

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: We report the expression profile of beta-synuclein reactive CD4+ T cells isolated from blood and brain in animals affected by Experimental autoimmune encephalomyelitis

overall_design: WIld-type or  transgenic beta-synuclein reactive  CD4+ T cells were sorted from blood, brain meninges and brain parenchyma 3 days after i.v. T-cell transfer. mRNA profiles  were generated by deep sequencing, in triplicate, using Illumina platform.

first: Francesca

last: Odoardi

first: Moritz

last: Hermann


title: Adult bone marrow-derived progenitors give rise to decidual cells and are essential for implantation and pregnancy maintenance

city: New Haven

first: Myles

middle: H

last: Alderman III

state: Ct

address: 10 Amistad St

department: Cell Biology

institute: Yale University School of Medicine

summary: Bone marrow (BM)-derived progenitor cells (BMDPCs) are known to migrate and give rise to endometrial cells however their functional contribution to implantation and pregnancy are unknown . Here we show that implantation and pregnancy are strong stimuli for BMDPCs recruitment to the uterine decidua where BMDPCs differentiate into functional non-hematopoietic prolactin-producing decidual cells. Transcriptome analysis of implantation sites demonstrated that Hoxa11+/- mice transplanted with WT BM clustered hierarchically more closely with normal WT mice than with control Hoxa11+/- mice, showing normalized expression of numerous implantation-related genes. These findings reveal that BMDPCs have a major non-hematopoietic physiologic contribution to the decidual stroma, and thereby play an essential and previously unproven role in the establishment and maintenance of pregnancy.

overall_design: Female Hoxa11 knockout, heterozygotes or wild type mice were given Hoxa11 knockout or wild type bone marrow transplants. After mating, uterine implantation sites were collected and total RNA was extracted on ED 5.5. 14 samples were sequenced by single-end next generation sequencing and differential transcriptome analysis.

first: Reshef

last: Tal

first: Shafiq

last: Shaikh

first: Ying

last: Liu

first: Nicola

last: Pluchino

first: Harvey

last: Kliman

last: Alderman

first: Jehanzeb

last: Kayani

first: Ramanaiah

last: Mammillapalli

first: Hugh

middle: S

last: Taylor


title: Single-cell RNA of multiregional sampling in hepatocellular carcinoma

city: New York

first: Augusto

last: Villanueva

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: The purpose of this experiment is to detect and characterize heterogeneity in single cell sequence data from liver cancer

overall_design: Three and four tumor samples coming from different regions of two different individuals were analyzed

first: Carlos

last: Villacorta-Martin


title: DNA methylation arrays for 8 Surgical specimens (DNA extracted from FFPE slides) after cetuximab treatment

city: Brussels

first: Sandra

last: Schmitz

address: Avenue Hippocrate, 54

department: Medical Oncology

country: Belgium

institute: Universite catholique de louvain

type: Methylation profiling by genome tiling array

summary: DNA methylation arrays for 8 Surgical specimens(DNA extracted from FFPE slides) after cetuximab treatment

overall_design: DNA methylation arrays for 8 HNSCC tumors following cetuximab treatment

first: Elana

last: Fertig


title: Characterization of Sheep Milk Extracellular Vesicle-miRNA by Sequencing and Comparison with Cow milk

city: Beijing

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: Milk can mediate maternal-neonatal signal transmission by the bioactive component-extracellular vesicles (EVs), which select specific types of miRNA to encapsulate. The miRNA profiling of sheep milk EVs was characterized by sequencing and compared with that of cow milk. Sheep milk EVs contained various small RNAs, including tRNA, Cis-regulatory element, rRNA, snRNA, other Rfam RNA, and miRNA, which held about 36% of all the small RNAs. Totally 84 types of miRNAs were annotated with Ovis aries by miRBase (version 22.0) in sheep milk EVs, with 75 shared types of miRNAs in all samples. Fourteen sheep milk EV-miRNAs in the top 20, occupying 98% of the total expression, were immune-related.

sample_organism:
Bos taurus
Ovis aries

platform_organism:
Bos taurus
Ovis aries

overall_design: The miRNA profiling of sheep milk EVs was characterized by sequencing and compared with that of cow milk in our prior study.

first: Suyu

last: Quan

first: Xuemei


title: Expression data from SCA3 and genetically corrected iPSCs

first: Guoxu

last: Song

address: No. 15, Datun Road, Chaoyang District, Beijing

institute: Institute of Biophysics, Chinese Academy of Science

summary:
The neurodegenerative disease spinocerebellar ataxia type 3 (SCA3; also called Machado-Joseph disease, MJD) is a trinucleotide repeat disorder caused by expansion of CAG repeats which encoding an abnormal long polyglutamine (polyQ) tract in ataxin-3 of the ATXN3 gene. Even now the pathogenic mechanism has remained elusive and no cure method is currently available.
In this study, we first applied CRISPR/Cas9-mediated approach using homologous recombination to achieve one-step genetic correction in SCA3-specific induced pluripotent stem cells (iPSCs) by adjusting pathological 80 CAG repeats to normal 13 CAG repeats, without detectable off-target based on whole exon sequencing or polyacrylamide gel electrophoresis (PAGE). The correction normalized SCA3 pathogenic signal pathways (like transcription, apoptosis, and ubiquitin-dependent protein catabolic process) and reversed disease-associated phenotypes. Our strategy provides deep insights into pathogenic mechanism of SCA3 disease and suggests potential therapeutic applications of trinucleotide repeat disorders.

overall_design: 6 experimental samples were used overall. There were 3 replicates per group, with one group being the control (SCA3 iPSCs), and the other being the experimental (corrected iPSCs).

first: Yong

last: Tian


title: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [microarray]

first: Junko

last: Murai

overall_design: SLFN11-positive parent cells (prostate DU145 and leukemia CCRF-CEM) and their SLFN11-knockout cell lines were treated with camptothecin (CPT) a DNA damaging agents, and their transcriptome were compared to the basal transcriptome.

first: Yves

last: Pommier


title: USP22 functions as an oncogenic driver in prostate cancer by regulating cell proliferation and DNA repair

status: Public on Jan 16 2020

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

institute: Thomas Jefferson University

summary: The deubiquitinase USP22 is a member of the SAGA transcriptional activation complex. This study used models of USP22 overexpression and depletion to identify differentially expressed gene networks.

overall_design: Transcriptional alterations upon USP22 overexpression or shRNA-mediated depletion were assessed  through RNA-Seq of LNCaP prostate cancer cells

first: Karen

last: Knudsen

first: Jennifer

last: McCann


title: Single-cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2-deficient vascular progenitors into skeletal muscle

city: Tampa

first: Saulius

last: Sumanas

state: Florida

address: 560 Channelside Dr

institute: University of South Florida

summary: An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single-cell transcriptomic analysis of hematovascular development in wild-type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line, in which the Gal4 transcriptional activator is integrated into the etv2 gene locus. Unexpectedly, a cell population with a skeletal muscle signature was observed in etv2-deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites, elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2-deficient embryos.

overall_design: GFP+ cells FACS sorted from etv2^ci32Gt; UAS:GFP embryos at 20ss were analyzed using 10X single-cell RNA-seq

first: Satish

last: Casie Chetty

first: Andrew

last: Koenig


title: Gene expression changes in cervical motor neuron transcriptomes after loss of Hox5 transcription factors

city: Cleveland

first: Polyxeni

last: Philippidou

state: OH

address: 2109 Adelbert Rd

department: Neurosciences

institute: Case Western Reserve University

summary: The goal of this study was to identify potential Hox5 target genes in cervical motor neurons (C3-C6) using unbiased genomic screens (RNA-seq). We examined expression changes independently of motor neuron cell death by deleting the pro-apoptotic gene Bax in both control and experimental mice.

overall_design: Examination of cervical (C3-C6) motor neuron transcriptomes from 3 e12.5 control Bax-/- mouse embryos and 3 e12.5 Hox5MNdelta Bax-/- embryos. Embryos also had Hb9::GFP for isolation of MNs via FACS.

first: Alicia

middle: N

last: Vagnozzi


title: Effect of Calcium Chloride Concentrations on the Transcriptome of Brevibacterium lines

city: Qingdao

first: Ning

last: Ma

address: No.7 Nanhai Road

institute: The Institute of Oceanology, Chinese Academy of Sciences

summary: A urease positive marine actinobacterium Brevibacterium lines was demonstrated to form and dissolve calcite precipitation in conditions with different concentration of Ca2+. Next-generation sequencing (NGS) was used to analyze the transcriptome of B. lines under 0, 50 and 150 mM Ca2+ after 24 h incubation to discover the differentially expressed genes involved. Results provide insight into the molecular response of B. lines stressed with different concentration of Ca2+.

overall_design: mRNA profiles of Brevibacterium lines under 0 mM, 50 mM and 150 mM Ca2+.

first: Chaomin

last: Sun


title: Ffar2 modulates dendritic cell-derived IL-27 and CD8+ T cell exhaustion in colorectal cancer

city: MA

first: Sena

last: Bae

address: Boston

institute: Harvard T.H. Chan School of Public Health

summary: Background and aims: Gut microbial metabolites and their host signaling pathways hold therapeutic potential for colorectal cancer (CRC). One example is short-chain fatty acids (SCFA), which are microbial metabolites generated from dietary fiber. This study aims to determine the pathogenesis of CRC from the host-microbiota perspective and the contributions of Ffar2, a SCFA receptor, to CRC. Methods: We have employed Apc-based models of CRC in conjunction with Ffar2 knock-out (ko) mice, Ffar2 conditional ko mice, and Ffar2 chemical agonism to reveal how a microbial metabolite receptor influences tumorigenesis in the colon. Utilizing human CRC datasets from The Cancer Genome Atlas aided our discovery of the links between Ffar2 function in dendritic cells and tumoral T cell dysfunction. Herein, we also used preclinical CRC models to test IL-27p28 neutralization or Ffar2 agonism as proof of concept for CRC prevention and treatment. Results: We have identified a mechanism by which Ffar2 deficiency potentiates tumorigenesis by affecting gut barrier integrity that increases tumor bacterial load and then altering IL-27+ dendritic cell populations and tumor CD8+ T cell phenotype and function. These events create a tumor immune milieu notable for dying and over-activated DCs and exhausted CD8+ T cells, which enables tumor growth. Proof-of-concept experiments in mice employing IL-27p28 neutralization or Ffar2 agonism reduced tumor burden. Conclusions: Our data support that loss of Ffar2 signaling potentiates tumorigenesis via a “two-hit” model, first by gut barrier breach and then by immune cell dysfunction. Our work supports that altering Ffar2 signaling or neutralizing IL-27 represent potential immunotherapy CRC treatment strategies.

overall_design: mRNA profiles of MLNs from WT C57BL/6J mice, with/without Ffar2 agonist treatment, were generated by deep sequencing, in duplicate, using Illumina NextSeq 500.

first: Sydney

last: Lavoie


title: RNA-sequencing of mouse intestinal stem cells (ISCs)

status: Public on Jan 15 2020

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: We previously demonstrated that SRCAP regulates the self-renewal of ESCs and modulates lymphoid lineage commitment. We further validated that SRCAP was mainly distributed in liver, spleen and intestine by Northern blot. SRCAP was also highly expressed in Lgr5+ ISCs. We then sought to explore the physiological role of SRCAP in the regulation of self-renewal maintenance of ISCs.We then generated Srcapflox/flox mice through insertion of loxP sequences flanking at the exon5 of Srcap gene locus. We established Srcapflox/flox;Lgr5GFP-CreERT2 mice through crossing Srcapflox/flox mice with Lgr5GFP-CreERT2 mice. With administration of tamoxifen (TAM), Srcap was completely deleted in Lgr5+ ISCs. We identified that Srcap deficiency impairs the self-renewal of ISCs and intestinal epithelial regeneration. Through RNA-sequencing, we sough to identify the key gene regulated by SRCAP in ISC self-renewal.

overall_design: Total RNAs were isolated from WT or SRCAP-deficient ISCs and used for RNA sequencing

first: Buqing

last: Ye


title: Single-cell transcriptional profiles in human skeletal muscle

first: Gregory

middle: Robert

last: Smith

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Mount Sinai Hospital

summary: Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using single-cell RNA-seq of dissections from vastus lateralis. We generate transcriptome profiles of 11 mononuclear human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells.  We delineate two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance training study using the human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell subtypes will resolve cell type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.

overall_design: Single cell RNA sequencing was conducted on four samples of mononuclear muscle cells isolated from a single vastus lateralis biopsy.

first: Aliza

last: Rubenstein

first: Ulrika

last: Raue

first: Frederique

last: Ruf-Zamojski

first: Venugopalan

last: Nair

first: Lan

last: Zhou

first: Elena

last: Zaslavksy

first: Scott

last: Trappe

first: Stuart

last: Sealfon


title: Haspin-dependent and independent effects of the kinase inhibitor 5-Iodotubercidin on self-renewal and differentiation.

city: Ioannina

first: Katerina

middle: Periklis

last: Soupsana

address: Dourouti

department: Medical School

country: Greece

institute: University of Ioannina

summary: The kinase Haspin phosphorylates histone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC). CPC plays a pivotal role in preventing chromosome misalignment. Here, we have examined the effects of 5-Iodotubercidin (5-ITu), a commonly used Haspin inhibitor, on self-renewal and differentiation of mouse embryonic stem cells (ESCs). Treatment with low concentrations of 5-ITu eliminates the H3T3ph mark during mitosis, but does not affect the mode or the outcome of self-renewal divisions. Interestingly, 5-ITu causes sustained accumulation of p53, increases markedly the expression of histone genes and results in reversible upregulation of the pluripotency factor Klf4. However, the properties of 5-ITu treated cells are distinct from those observed in Haspin-knockout cells generated by CRISPR/Cas9 genome editing, suggesting "off-target" effects. Continuous exposure to 5-ITu allows modest expansion of the ESC population and growth of embryoid bodies, but release from the drug after an initial treatment aborts embryoid body or teratoma formation. The data reveal an unusual robustness of ESCs against mitotic perturbants and suggest that the lack of H3T3ph and the "off-target" effects of 5-ITu can be partially compensated by changes in expression program or accumulation of suppressor mutations.

overall_design: E14 cells were treated for 26 hours either with DMSO only, 0.1uM 5-ITU or 1 uM 5-ITU under undifferentiated conditions (serum&LIF).

first: Eleftheria

last: Karanika

first: Anastasia

last: Christogianni

first: Dimitris

last: Stellas

first: Apostolos

last: Klinakis

last: Politou

first: Spyros

last: Georgatos


title: Epigenetic Memory of HSC after LPS injection (ATAC-Seq)

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

summary: Here we show that immune challenge can induce epigenetic memory in HSC.   We show that LPS, a gram-negative bacterial component, induces changes in HSC differentiation and gene expression that returned rapidly to normal but also establish novel open chromatin regions (OCR) that persist long term. These OCR are associated with genes involved in myeloid lineage commitment and innate immunity, that become more highly expressed upon a secondary bacterial challenge and enable LPS-exposed HSCs to mount an increased myeloid differentiation and accelerated immune response.

overall_design: Mice were injected with 125 ug of LPS IP or PBS. ATAC-seq was performed on HSC KSL Flt3- sorted 0, 4 weeks or 12 weeks after LPS injection. Samples are from pool of 4-8 mice.

first: Bérengère

last: de Laval

first: Orit

last: Matcovitch-Natan

first: Eyal

last: David

first: Ido

last: Amit

first: Sandrine

last: Sarrazin

first: Michael

last: Sieweke


title: Epigenetic Memory of HSC after LPS injection (RNA-Seq)

overall_design: Mice were injected with 125 ug of LPS IP or PBS. RNA-seq was performed on LT-HSC sorted one day after the first or the second LPS stimulation (second challenge has been done 4 or 12 weeks after the first one). Duplicates or triplicated from pool of 3-8 mice mice are provided.


title: Determining the role of serum progesterone monitoring by comparing endometrial transcriptomics in women with low progesterone versus women with normal progesterone during the receptive phase of the menstrual cycle

city: nottingham

first: Sutham

last: Suthaporn

state: UK

address: Derby road

department: Ob&Gyn

country: United Kingdom

institute: University of Nottingham

summary: Abnormally low progesterone results in an aberrance of endometrial gene expression affecting the chance of implantation. Therefore, serum progesterone monitoring for embryo transfer in the natural cycle is useful and it seems to be potentially applicable for artificial cycles with using similar thresholds.

overall_design: The participants were categorized into two groups based on their progesterone level: normal progesterone (>15 ng/ml) and low progesterone (<15 ng/ml). Global endometrial gene expression between the two groups was compared by microarray technique

first: S

first: K

last: Jayaprakasan

first: J

middle: G

last: Thornton

middle: F

last: Walker

last: Hernandez-Medrano

first: M

last: Castellanos

middle: T

last: May

first: I

last: Khanc

first: W

last: Maalouf


title: Expression data of ex vivo and stimulated p14 TE (day 8) and p14 TM (day 46)

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

summary: The spectrum of pathogen-specific CD8+T cell functionalities, including their chemokine production profiles, remains incompletely defined. Here, we have employed microarray analyses to determine the gene expression profiles of lymphocytic choriomeningits virus- (LCMV-) specific effector (TE) and memory (TM) CD8+T cells in the established p14 chimera model; analyses of p14 TE and TM expression profiles were conducted directly ex vivo and after 3h TCR engagement using aCD3 and aCD28 antibodies (note that the present ex vivo p14 TE and TM data have previously been uploaded in the context of a related study [GSE38462] and are included here due to analyses now conducted together with stimulated p14 TE and TM data).

overall_design: Congenic LCMV Armstrong-immune p14 chimeras were generated in a staggered fashion to allow for concurrent sample collection at the effector and early memory stage. In brief, splenic CD90.1+ effector p14 TE (8 days post infection/dpi) and memory p14 TM (46 dpi) were magenetically pre-enriched from individual p14 chimeras (n=3-4) using an anti-PE selection kit (EasySep, StemCell Technologies), and further purified by FACS-sorting of CD8+CD90.1+ cells (FACSAria, BDBiosciences) achieveing >99% purity; each sorted sample was then divided into two aliquots and processed either for direct extraction of total DNA-digested RNA (ex vivo), or 3h stimulation with aCD3/aCD28 prior to RNA extraction (stimulated).

first: Jens

last: Eberlein

first: Dirk

last: Homann


title: DNA methylation profiles of IRAK-M gene in untreated or drug-treated human melanoma cell lines

city: Aurora

first: Eduardo

last: Davila

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: Genome-wide DNA methylation analysis of over 850,000 methylation sites was performed using the Infinium MethylationEPIC BeadChip (Illumina) in RPMI7951, C32, Malme-3M, SK-MEL-28, EPZ-6438-treated C32, azacytidine-treated Malme-3M, and DMSO- or NU7441-treated Mb3429 cells.

overall_design: Genomic DNA from the 8 samples was sodium bisulfite treated and hybridized to the Infinium MethylationEPIC BeadChip

first: Degui

last: Geng


title: Transcriptome analysis of contrasting resistance to herbivory by empoasca fabae in two shrub willow species and their hybrid progeny

city: University Park

first: John

last: Carlson

state: Pennsylvania

address: 323 Forest Resources Building

department: Ecosystem Science and Management

institute: Pennsylvania State University

summary: Shrub willow (Salix spp.), a short rotation woody biomass crop, has superior properties as a perennial energy crop for the Northeast and Midwest US. However, the insect pest potato leafhopper Empoasca fabae (Harris) (PLH) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display  varying levels of susceptibility under PLH infestation. However, genes and markers for resistance to PLH are not yet available for marker-assisted selection in breeding. In this  study, transcriptome differences between a resistant genotype 94006 (S. purpurea) and a susceptible cultivar ‘Jorr’ (S. viminalis), and their hybrid progeny were determined.  Over 600 million RNA-Seq reads were generated and mapped to the Salix purpurea reference transcriptome. Gene expression analyses revealed the unique defense  mechanism in resistant genotype 94006 that involves PLH-induced secondary cell wall modification. In the susceptible genotypes, genes involved in programed cell death were highly expressed, explaining the necrosis symptoms after potato leafhopper feeding. Overall, the discovery of resistance genes and defense mechanisms provides new resources for shrub willow breeding and research in the future.

overall_design: Leaf tissue mRNA profiles of two shrub willow species and their 7 progenies, before and after PLH infestation at four time points, were generated by deep sequencing, in duplicate/triplicate, using Illumina HiSeq 2500

first: Wanyan

last: Wang

first: Lawrence

middle: B

last: Smart

first: Craig


title: Inhibition of Mitochondria NADH–Ubiquinone Oxidoreductase (Complex I) Sensitizes the Radioresistant Glioma Cells to Radiation

city: Dalian

first: Weifeng

last: Mao

address: 9 Lvshun South Rd,

institute: Dalian Medical University

summary: We cumulatively radiated a glioblastoma cell line, U87MG, and screened radioresistant glioma cells. A transcriptome sequencing was performed to analyze the transcription differences between the raidoresistant and control cells.

overall_design: U87MG cells (1×10^6) in 10 cm culture dishes were irradiated them with 2 Gy of X-rays for 5 times. The radioresistant U87MG cells were named as U87MG_F. The U87MG and U87MG_F cells were perfomred RNA sequencing through Illumina Hiseq xten Sequencing.

first: Yanqin

last: Yang

first: Jia

first: Lu

last: Zhang

first: Caifeng

last: Sun

first: Ying

first: Haoyu

last: Dong

first: Han

first: Xingjie

last: Gao

first: Chuanzhou

first: Bin

last: Feng


title: The function of DP cells during the development of hair follicles in cashmere goats

city: Hohhot

first: Feng

state: Inner Mongolia

address: 306 Zhaowuda Road

institute: Inner Mongolia Agricultural University

summary:
OBJECTIVE: To study the function of DP cells during the development of hair follicles in cashmere goats, we used single-cell sequencing to perform transcriptome sequencing of skin samples from different periods.
Method: Single cell barcoding and library preparation were performed based on 10x Genomics single-cell RNA sequencing platform, CellRanger (v2.2.0) software was used for analyzing raw sequencing data, the quality control (QC) and cell clustering were analyzed with single- Cell RNA seq Seurat software (v2.3.0) based on R environment, Monocle (v 2.4.0) was used to order single cells along pseudotime according, Metascape (http://metascape.org/gp/index.html#/main /step1) was used to perform gene ontology (GO) analysis
Conclusion: we show the function of four different intermediate DP cells: Intermediate cells 10 show important functions in the growth of villi and maintenance of villus attachment to the skin, and intermediate cell 1 shows important functions in the process of apoptosis and villous shedding of hair Follicles, intermediate cell 0 initiates a new follicular cycle, completes the migration of hair follicles and the occurrence of villi, and intermediate cell 15 maybe DP progenitor cells, In addition, we speculated the apoptotic order of different bulge cells. More importantly, we provided a molecular landscape for the mechanism of DP cells in the process of hair follicle cycle initiation.
Skin samples from telogen, anagen, and catagen were used to sequence single-cell transcriptomes, revealing the function and evolution of DP cells.

overall_design: Feng, Yang

first: Zhihong

last: Liu


title: Mechanism of in vivo activation of the MutL-Exo1 complex for meiotic crossover formation

city: NEW YORK

first: Xiaojing

last: Mu

state: New York

address: 1275 York Ave

department: Molecular Biology

institute: Memorial Sloan kettering cancer center

summary: Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination and their subsequent repair culminates in crossover (CO) formation. COs result from the asymmetric cleavage of double-Holliday junction (dHJ) intermediates, that requires the MutLγ endonuclease and a non-catalytic function of Exo1, an activity essential for fertility but at risk of generating unwanted chromosome rearrangements. Here we show how crossover formation by MutLγ is activated at the right time and at the right place. MutLγ forms a constitutive complex with Exo1, and in meiotic cells transiently contacts the upstream MutSγ (Msh4-Msh5) heterodimer. MutLγ associates with DSB hotspots only once recombination intermediates have been stabilized and engaged in the crossover repair pathway. MutLγ-Exo1 is recruited to DSB hotspots independently of the polo-like Cdc5 kinase, but to activate dHJ resolution, Cdc5 is recruited to the recombination intermediates and interacts individually with both MutLγ and Exo1, suggesting their direct modification. in vivo, MutLγ occupancy is restrained on recombination intermediates, and MutLγ associates with the vast majority of DSB hotspots, but at a lower frequency in centromeres, consistent with a strategy to reduce at-risk crossover events in these regions, and in late replicating regions. Our data highlight the tight temporal and spatial control of the activity of this constitutive, potentially harmful, nuclease.

overall_design: Two biological replicate Spo11-oligo maps of Saccharomyces cerevisiae strain mlh3 at meiotic 5 hr time point

first: Aurore

last: Sanchez

first: Valérie

last: Borde

first: Scott

last: Keeney


title: Epigenetic Memory of HSC after LPS injection

first: Julien

last: Maurizio

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

overall_design: Refer to individual Series


title: Wound epidermis-dependent transcriptional programs

city: Cambridge

first: Douglas

middle: A.

last: Melton

address: 7 Divinity Ave.

institute: Harvard University

summary: The wound epidermis is required for limb regeneration. To elucidate the roles of the wound epidermis during early regeneration, we examined how the transcriptional programs of early dividing cells (enriched for blastemal progenitors) and non-dividing cells in regenerating stump tissues as well as epithelial cells change when we prevented wound epidermis formation.

overall_design: To prevent wound epidermis formation, we performed full skin flap surgeries to inhibit epithelial migration over the exposed stump tissues post-amputation. We separately sequenced stump-derived 4N, stump-derived 2N, and epithelial cells from the sutured full skin flap at 5 days post-amputation (dpa). We sequenced a total of 9 samples, 3 biological replicates per timepoint. These samples were multiplexed and sequenced on 6 lanes on a Hiseq 2500. (dataset from Tsai et al. (2019), accession number: GSE111213)

first: Stephanie

last: Tsai

middle: A


title: Sequencing of iMDK-treated regenerating limbs

summary: Treatment with midkine inhibitor iMDK inhibits limb regeneration. To elucidate the transcriptional mechanisms of iMDK treatment, we sequenced regenerating limbs treated with either DMSO or iMDK (bulk) in biological triplicate at 11 days post-amputation (dpa).

overall_design: Limbs were treated with iMDK or DMSO beginning immediately post-amputation up until the collection point at 11 dpa.


title: Tissue-engineered bone tumor as a reproducible human in vitro model for studies of anti-cancer drugs

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

summary: We investigated changes in bone and Ewing’s Sarcoma transcriptomes among control and treated cells grown in 2D plates, or within engineered bone scaffolds.

overall_design: This study was made up of 2 main tiers of testing—in tier 1, TE-Bone (Scaffold with human osteoblasts) and TE-Tumor (human osteoblasts and Ewing’s sarcoma aggregates) scaffolds were exposed to Linsitinib (3 week treatment, 12uM), Doxorubicin (2 week treatment, 4.16uM), or vehicle controls. Treatments were carried out in 1 week cycles with 3 days of drug treatment, followed by 4 days of rest period. In the second tier of testing, TE-Tumor scaffolds were treated with vehicle, cisplatin (3, 10, or 30uM), dexamethasone (0.1, 1, or 10uM), methotrexate (0.1, 1, or 10uM), vincristine (0.1, 1, or 10uM), or MAP (cisplatin, doxorubicin and methotrexate mixture) at a high or low concentration. Scaffolds were treated over 2 one week cycles, followed by a 2 week recovery period with no drug treatment. In addition to the studies with the tissue engineered scaffolds, Ewings sarcoma cells were grown in 2D (96-well plate) as a comparator, and treated on the same regimens.

first: Courtney

last: Sakolish

first: Alan

last: Chramiec

first: Yizhong

first: Zunwei

last: Chen

first: Susan

middle: P

last: Halligan

first: Gordana

last: Vunjak-Novakovic

first: Ivan

last: Rusyn


title: DNA methylation of colorectal cancer stem cells

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

summary: Colorectal cancer stem cells (CR-CSCs) are implicated in tumor development, metastasis, and therapy resistance, however little is known about their epigenetic features. Here we describe the DNA methylation profiles of eight CR-CSC lines and their distinctive patterns, which are maintained following in vivo passages in immune-compromised mice.

overall_design: DNA was bisulfite-converted using the EZDNA Methylation-Gold Kit (Zymo Research) and analysed using the Infinium HumanMethylationEPIC BeadChip (Illumina) following manufacturer's instructions.

first: Angelo

last: Veronese


title: Toxoplasma gondii bradyzoites manipulate host cell transcription

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

sample_organism:
Toxoplasma gondii
Homo sapiens

platform_organism:
Toxoplasma gondii
Homo sapiens


title: RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with Toxoplasma gondii bradyzoites, with and without myr1 (myc regulation 1)

summary: The purpose of these data is to determine if the impact bradyzoites have on the host transcripton is dependent on the export of parasite effector proteins via Myr1. We found that the expression of 3,068 host genes (~42%) were dependent on Myr1. A further 4,312 were altered in the same direction when comparing both the wild type and knock-out infected samples to the uninfected group. We can therefore conclude that Myr1 has an impact on the host transcriptional response to bradyzoite infection.

overall_design: Five groups of human foreskin fibroblasts are compared which are either uninfected or infected with the bradyzoite stage of the Toxoplasma gondii parasite. These data consist of 15 samples, all taken from a single donor, with 3 samples per group. All samples have been incubated for 1 week in iM: RPMI-HEPES  supplemented with 5% v/v fetal calf serum at pH 8.1-8.2. The samples are either uninfected host,  wild-type (WT) bradyzoite infected, Myr1 knock-out (KO) bradyzoite infected, bystander WT bradyzoite, or bystander Myr1 KO bradyzoite. A bystander sample is a sample generated from cells that have been in the presence of the bradyzoite form of Toxoplasma but are not infected by it.

first: Simona

last: Seizova

first: Chris

middle: J

last: Tonkin


title: RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with either bradyzoites and tachyzoite of Toxoplasma gondii

summary: The purpose of this data set is to determine if bradyzoites impact the host transcripton in a similar manner as tachyzoites. We found that 3853 differentially expressed genes (DEGs) are shared between tachyzoite infected cells and bradyzoite infected cells (41%; 2161 up-reg., 1692 down-reg.) when compared to uninfected host samples, leaving 3356 tachyzoite specific DEGs (1488 up-reg., 1868 down-reg.), and 1951 DEGs specific to bradyzoite infection (1075 up-reg., 876 down-reg).  We conclude therefore that bradyzoites manipulate the host cell and that this is unique when compared to tachyzoites.

overall_design: Four groups of human foreskin fibroblasts are compared. These samples are either uninfected or infected with Toxoplasma gondii. These data comprize 12 samples, all taken from a single donor, with 3 samples per group. The samples are either uninfected host (24 hour incubation), uninfected host (1 week incubation), infected with the tachyzoite stage of Toxoplasma (24 hour incubation), or infected with the bradyzoite stage of Toxoplasma (1 week incubtion)


title: RNA-seq analyses of Fusarium graminearum wild-type GZ03639 and toxoflavin-sensitive mutant under toxoflavin condition

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: Bacterial pathogen Burkholderia glumae and fungal pathogen Fusarium graminearum cause similar disease symptoms and are often co-isolated from rice heads, inferring interactions between the two pathogens. F. graminearum is resistant to the bacterial toxin toxoflavin, a strong anti-microbial activity, produced by B. glumae. We isolated a toxoflavin-sensitive mutant from transcription factor deletion mutant library of F. graminearum. To understand genome-wide transcriptional profiling, we performed RNA-seq analyses of F. graminearum wild-type strain GZ03639 and toxoflavin-sensitive mutant strain, ∆GzZC190, under toxoflavin condition.

overall_design: Two libraries constructed: fungal culture containing toxoflavin (100 mg l-1) of Fusarium graminearum GZ03639 wild-type and ∆GzZC190 mutant strain.

first: Boknam

last: Jung

first: Jungkwan

last: Lee

first: Young-su

last: Seo


title: Early Angiogenic Proteins Associated with High Risk for Bronchopulmonary Dysplasia and Pulmonary Hypertension in Preterm Infants

city: Groningen

first: Sanne

last: Arjaans

address: Hanzeplein 1

institute: University Medical Center Groningen

summary:
Introduction: Early pulmonary vascular disease in preterm infants is associated with the subsequent development of bronchopulmonary dysplasia (BPD) and pulmonary hypertension (PH), however, mechanisms that contribute to or identify infants with increased susceptibility for BPD and/or PH are incompletely understood. Therefore, we tested if changes in circulating angiogenic peptides during the first week of life are associated with the later development of BPD and/or PH. We further sought to determine alternate peptides and related signalling pathways with the risk for BPD or PH.
Methods: We prospectively enrolled infants with gestational age <34 weeks gestation and collected blood samples during their first week of life.  BPD and PH were assessed at 36 weeks postmenstrual age. Samples were assayed for each of the 1121 peptides included in the SOMAscanTM technology, with subsequent pathway analysis.
Results: Of 102 study infants, 82 had BPD and 13 had PH. Multiple angiogenic proteins  (PF-4, VEGF121, ANG-1, BMP10, HGF, ANG2) were associated with the subsequent diagnosis of BPD, and FGF-19,  PF-4, CTAP-III and PDGF-AA levels were associated with BPD severity. Early increases in BMP10 was strongly associated with the late risk for BPD and PH.
Conclusion: We found that early alterations of circulating angiogenic peptides and others were associated with the subsequent development of BPD. We further identified  peptides that were associated with BPD severity and BPD-associated PH, including BMP10. We speculate that proteomic biomarkers during the first week of life may identify infants at risk for BPD and/or PH to enhance care and research.

overall_design: A prospective cohort study. Included 102 infants, with extracted blood samples. Protein profiles existing of 1121 peptides, have been acquired by SOMAscan technology.

first: Brandie

middle: D

last: Wagner

first: Peter

middle: M

last: Mourani

first: Erica

middle: W

last: Mandell

first: Brenda

last: Poindexter

first: Rolf

last: Berger

first: Steven

last: Abman


title: Differential gene expression in articular cartilage and subchondral bone of neonatal and adult horses

city: Urbana

first: Ann

middle: Marie

last: Kemper

state: IL

address: 1008 W Hazelwood Dr

institute: University of Illinois

summary: We report differential expression analysis of RNAseq data in joint-related tissues (articular cartilage and subchondral bone) in healthy foals (4 weeks of age or younger) and healthy adult horses. We find that 1115 genes are differentially expressed in cartilage and 3574 in bone between these two groups. Functional annotation suggests that differences primarily lie in genes involved in growth/turnover of tissue and cell signaling.

overall_design: Six individuals were included in each group (foals and adults). Articular cartilage and subchondral bone were collected in each individual from the metatarsophalangeal joint, tarsocrural joint, and femoropatellar joint, resulting in a total of 56 samples for RNAseq and subsequent analysis.

first: Jenny

last: Drnevich

first: Molly

middle: E

last: McCue

first: Annette

last: McCoy


title: Study of the TRa1-dependent intestinal tumorigenesis

city: Lyon

first: Michelina

last: Plateroti

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

summary: The aim of the study was to analyse the impact of the TRa1 nuclear receptor on Apc+/1638N-dependent intestinal tumorigenesis

overall_design: mRNA from vil-TRa1/Apc and Apc adenocarcinomas were prepared and compared

first: Joel

last: Uchuya-Castillo


title: mRNA profiles in gastrointestinal stromal tumor (GIST) cell lines and GIST-associated fibroblast

status: Public on Jan 14 2020

city: La Jolla

first: Jason

last: Sicklick

state: CA

address: 3855 Health Sciences Dr

institute: UCSD, Moores Cancer Center

summary: To identify mRNA profiles in GIST and CAFs, we performed RNA sequencing analysis (RNA-seq) using GIST cell lines, GIST-T1 and GIST882, and CAFs.

overall_design: Differential mRNA expression of human GIST and CAF was generated by deep sequencing using Illumina HiSeq 2500.

middle: K

first: Hyunho

last: Yoon


title: Novel technique for the simultaneous isolation of cardiac fibroblasts and epicardial stromal cells from the infarcted murine heart

city: Duesseldorf

first: Christoph

last: Owenier

address: Universitätsstraße 1

department: Molecular Cardiology

institute: Uniklinik Duesseldorf

summary:
Myocardial infarction (MI) leads to activation of cardiac fibroblasts (aCFs) and at the same time induces the formation of epicardium-derived cells at the heart surface. To discriminate between the two cell populations, we elaborated a fast and efficient protocol for the simultaneous isolation and characterization of aCFs and epicardial stromal cells (EpiSCs) from the infarcted mouse heart. For the isolation of aCFs and EpiSCs, infarcted hearts (50 min ischaemia/reperfusion) were digested by perfusion with a collagenase-containing medium for only 8 min, while EpiSCs were enzymatically removed from the outside by applying mild shear forces via a motor driven device.
Cardiac fibroblasts (CFs) isolated from unstressed hearts served as control. Microarray analysis of CFs, aCFs, and EpiSCs on day 5 post-MI revealed a unique gene expression pattern in the EpiSC fraction, which was enriched for epithelial markers and epithelial to mesenchymal transition-related genes. Compared to aCFs, 336 significantly altered gene entities were identified in the EpiSC fraction. Microarray data identified Ddah1 and Cemip to be highly up-regulated in aCFs compared to CFs.  In this study, several differentially expressed markers for aCFs and EpiSCs were identified, underlining the importance of cell separation to study heterogeneity of stromal cells in the healing process after MI.

overall_design: 15 total samples (five biological replicates each) were analyzed. aCF and EpiSC samples were compared to each other and CF samples were compared to aCF samples. Data analyses on Affymetrix CEL files obtained from the microarray experiment were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by GeneSprings’ ExonRMA16 algorithm after quantile normalization of probe-level signal intensities across all samples to reduce interarray variability. Input data preprocessing was concluded by baseline transformation to the median of all samples. After grouping of samples according to their respective experimental condition, a given probe set had to be expressed above background (i.e., fluorescence signal of that probe set was detected within the 20th and 100th percentiles of the raw signal distribution of a given array) in all five replicates in at least one of three conditions to be further analyzed in pairwise comparisons. Differential gene expression was statistically determined by Moderated t test. The Resulting P values were  corrected for multiple testing by Bonferroni-correction. A P<0.05 was considered significant.

first: Julia

last: Hesse

first: Christina

last: Alter

first: Zhaoping

last: Ding

first: Aseel

last: Marzoq

first: Patrick

last: Petzsch

first: Karl

last: Köhrer

first: Jürgen

last: Schrader


title: Genomic Landscape and Therapeutic Targets of Adenosquamous Carcinoma of the Pancreas

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

type: Genome variation profiling by genome tiling array


title: RNA sequencing data of peripheral blood isolated from Korean patients with Crohn's disease.

city: Seoul

first: Seulgi

last: Jung

address: 88 Olympic-ro 43-gil

department: Department of Biochemistry and Molecular Biology

institute: University of Ulsan College of Medicine

summary: We performed RNA sequencing to produce expression quantitative trait loci (eQTL) database of Crohn's disease patients. Using this eQTL data, we tried to determine the most functionally relevant genes at the established Crohn’s disease loci identified in genome-wide association studies (GWAS) involving Asian populations and to find novel disease-associated genes.

overall_design: eQTL analysis was pefromed using whole-blood RNA-sequencing of 101 Korean patients with Crohn’s disease. The Crohn's disease patients were recruited from the IBD Clinic of Asan Medical Center. Whole blood was taken and immediately store in a PAXgene Blood RNA tube at room temperature for > 4h. The total RNA was extracted using the PAXgene Blood RNA kit, following the manufacturer’s instructions. RNA quality and quantity were checked using a 2100 Bioanalyzer (Agilent Technologies, CA, USA) and the samples with an RNA integrity number ≥ 7 were deep-sequenced. Sequencing libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-ZeroTM Globin (Illumina, CA, USA) and paired-end RNA sequencing of 101 bp reads was performed using Illumina HiSeq 2500 platform. FastQTL was used for a pair-wise genome analysis of ~ 6.5 M SNPs and ~ 22 K transcripts.

first: Wenting

last: Liu

first: Jiwon

last: Baek

first: Jung

last: Moon

first: Byong

last: Ye

first: Ho-Su

last: Lee

first: Sang

last: Park

first: Suk-Kyun

last: Yang

first: Buhm

last: Han

first: Jianjun

first: Kyuyoung

last: Song


title: RNA-Seq of wild-type (WT) and smn2 mutants for quantitative analysis of transcriptomes and mapping SMN2-dependent degraded regions

city: Tsukuba

first: Fuminori

last: Takahashi

state: Ibaraki

address: 3-1-1 Koyadai

institute: RIKEN

summary: To compare expression of defense-related genes between WT and smn2 mutant, we performed the RNA-seq analysis using the total RNA prepared from Arabidopsis WT and smn2 seedlings. RNA-seq profiling showed 250 Differentially Expressed Genes (DEGs) detected in smn2 compared to WT. Genome-wide mapping of DEG regions was also performed to elucidate SMN2-dependent degraded regions in defense-related genes.

overall_design: Fourteen-day old WT and smn2 seedlings were treated with 0.1 uM flg22 for 0hr or 4hr with two biological replicates.

first: Momoko

last: Takagi

first: Kazuya

last: Ichimura


title: Knockdown PTPRN expression inhibits U87 cell line growth

city: Beijing

first: Liwei

last: Zhang

address: South 4th Ring West Road

department: Neurosurgery

institute: Beijing Tian Tan Hospital, Capital Medical University

summary: Protein Tyrosine Phosphatase Receptor Type N (PTPRN) plays an important role in diabetes and many cancers but its role in glioma remain poorly defined. Here, we firstly verified PTPRN expression was negatively correlated with overall survival of glioblastoma patients. Moreover, suppression of PTPRN expression reduced both U87 and U343 cell viability, suppressed proliferation, induced cell cycle arrest and inhibited glioma growth in vivo. Furthermore, KEGG and GO analysis demonstrated that PTPRN was involved in cell cycle signaling pathway, which were then confirmed by Western blot. In summary, we are the first to demonstrate that PTPRN inhibits glioma proliferation by targeting cell cycle signaling pathway. These data highlight PTPRN as a novel target for glioma treatment.

overall_design: U87 glioma cell line mRNA profiles of H1-RFP (WT) and shPTPRN-3 were generated by deep sequencing, two biological replicates, using Illumina Xten Platform

first: Yibo

last: Geng


title: Endometrial Axin2+ cells drive epithelial homeostasis and regeneration, and develop endometrial cancer following oncogenic transformation

city: Callaghan

first: Shafiq

middle: Mukhtar

last: Syed

state: NSW

address: University Drive, Callaghan-2308

department: School of Biomedical Sciences and Pharmacy

institute: University of Newcastle

summary:
Summary: RNAseq analysis of Axin2+ and Axin2- endometrial epithelial cells shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- cells.
Methods: Four-week-old Axin2rtTA; tetOH2BJGFP mice (n=3) were ovariectomized. After 2 weeks of rest, H2BJGFP was induced in Axin2+ cells by a single dose of doxycycline administered intraperitoneally and uteri were collected 4 days post-doxycycline administration. Endometrial epithelial cells were isolated, digested into single cell suspension and Axin2+ (GFPhigh) and Axin2- (GFP-) cells were FACS sorted. The respective Axin2+ and Axin2- cells from each of the three mice used in this experiment were pooled together (Axin2- cells = C1, C2, C3; Axin2+ cells = M1, M2, M3, Arabic numeral represents the mouse number). Total RNA was isolated using RNeasy Micro kit (Qiagen) as per manufacturer instructions. RNA quality and concentration were determined using Nanodrop ND-1000 Spectrophotometer. RNAseq profiles were generated using Illumina NovaSeq platform. The reads were mapped to the mouse genome (Build version mm10) using the STAR aligner (v2.5.3a) and differential gene expression analysis was performed using edgeR (version 3.22.5) tool.
Results: Differential gene expression analysis using edgeR identified 4458 genes that were differentially expressed by more than twofold in the Axin2high population compared with Axin2- population. Several of these differentially expressed genes include some of the well-known stem cell markers.

overall_design: mRNA profiles of Axin2+ and Axin2- endometrial epithelial cells from ovariectomized mice were analysed by deep sequencing, in triplicate, using Illumina NovaSeq platform

first: Pradeep

middle: S

last: Tanwar


title: Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial [methylation]

city: Columbus

first: Daniel

middle: Yui

last: Weng

address: 420 W. 12th Ave. Room 390

department: Comprehensive Cancer Center

institute: The Ohio State University

summary: E-cig use is continuing to increase, particularly among youth never-smokers, and is used by some smokers to quit. The acute and chronic toxicity of e-cig use is unclear generally in the context of increasing reports of inflammatory-type pneumonia in some e-cig users. To assess lung effects of e-cigs without nicotine or flavors, we conducted a pilot study with serial bronchoscopies over 4 weeks in 30 never-smokers, randomized either to a four-week intervention with the use of e-cigs containing only 50% propylene glycol (PG) and 50% vegetable glycerine (VG) or to a no-use control group. Compliance to the e-cig intervention was assessed by participants sending daily puff counts and by urinary propylene glycol (PG). Inflammatory cell counts and cytokines were determined in bronchoalveolar lavage (BAL) fluids. Genome-wide expression, microRNA, and mRNA were determined from bronchial epithelial cells. There were no significant differences in changes of BAL inflammatory cell counts or cytokines between baseline and follow-up, comparing the control and e-cig groups. However, in the intervention but not the control group, change in urinary PG as a marker of e-cig use and inhalation, was significantly correlated with change in cell counts (cell concentrations, macrophages, and lymphocytes) and cytokines (IL-8, IL-13, and TNF-α), although the absolute magnitude of changes was small. There were no significant changes in mRNA or microRNA gene expression. Although limited by study size and duration, this is the first experimental demonstration of an impact of e-cig use on inflammation in the human lung among never-smokers.

overall_design: Bisulphite converted DNA from the 58 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchips

first: Min-Ae

middle: Y

first: Peter

middle: G

last: Shields


title: Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

institute: VIB - KU Leuven

summary: Polygenic risk scores have identified that genetic variants without genome-wide significance still add to the genetic risk of developing Alzheimer’s disease (AD). Whether and how subthreshold risk loci translate into relevant disease pathways, is unknown. We investigate here the involvement of AD risk variants in the transcriptional responses of two mouse models: APPswe/PS1L166P and Thy-TAU22. A unique gene expression module, highly enriched for AD risk genes, is specifically responsive to Aβ but not TAU pathology. We identify in this module 7 established AD risk genes (APOE, CLU, INPP5D, CD33, PLCG2, SPI1 and FCER1G) and 11 AD GWAS genes below the genome-wide significance threshold (GPC2, TREML2, SYK, GRN, SLC2A5, SAMSN1, PYDC1, HEXB, RRBP1, LYN and BLNK), that become significantly upregulated when exposed to Aβ. Single microglia sequencing confirms that Aβ, not TAU, pathology induces marked transcriptional changes in microglia, including increased proportions of activated microglia. We conclude that genetic risk of AD functionally translates into different microglia pathway responses to Aβ pathology, placing AD genetic risk downstream of the amyloid pathway but upstream of TAU pathology.

overall_design: Single cell sequencing on FACS-sorted CD11b+/CD45+ mouse hippocampal microglia, examing APPswe/PSEN1L166P and Thy-TAU22 mice and their respective WT littermates, at 4 and 11 months of age (8 groups in total; 2-3 mice per experimental group).

first: Annerieke

last: Sierksma

first: Ashley

last: Lu

first: Renzo

last: Mancuso

first: Nicola

last: Fattorelli

last: Thrupp

first: Evgenia

last: Salta

first: Jesus

last: Zoco

first: David

last: Blum

first: Luc

last: Buée

first: Mark

last: Fiers


title: Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial

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

overall_design: Refer to individual Series


title: Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial [expression]

overall_design: Gene expression in human bronchial epithelium from 58 patients undergoing bronchoscopy was analyzed by Affymetrix arrays

last: Song


title: A fully defined protocol for differentiation of human pluripotent stem cells into forebrain neural progenitors

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

institute: Lund University

summary: Human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) were differentiated into forebrain neural progenitors using a fully defined protocol with dual SMAD-inhibition. Cells were taken at four time points to monitor temporal changes in the transcriptome over the course of differentiation.

overall_design: Bulk RNA-seq was performed on ES and iPS-derived forebrain progenitor cells at four time points of differentiation (day 13, 14, 15, and 16). Two differentiation replicates were used at each of the time points.

first: Daniela

last: Grassi

first: Per

middle: L

last: Brattås

first: Marie

last: Jönsson

first: Ofelia

last: Karlsson

first: Diahann

last: Atacho

first: Sara

last: Nolbrant

first: Malin

last: Parmar


title: Direct RNA sequencing enables single-nucleotide m6A detection in endogenous transcript isoforms

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: We report the direct RNA sequencing of HEK293 and a primary human mammary epithelial cell (HMEC) line using Oxford Nanopore based sequencing. Using this data, we built an algorithm to detect m6A modifications within the DRACH motif context. Evaluation of m6A sites was carried out with HEK METTL3 knockdown and HMEC ALKBH5 over expression cell lines.

overall_design: Total RNA was isolated from HEK and HMEC cell lines using Trizol or Direct-zol, respectively. RNA was then poly-A selected using oligo-dT magnetic resin before library preparation using Oxford Nanopore’s direct RNA-sequencing kit and protocol. Sequencing output was mapped to reference genomes and resquiggled using Tombo. Tombo’s fraction modified and coverage files were subsequently combined and used as input for m6A detection.

first: Daniel

middle: A

last: Lorenz

first: Shashank

last: Sathe

first: Jacyln

last: Einstein


title: PRMT1-dependent Arginine methylation regulates replication stress response through DNA-protein kinase

city: Cambridge

first: SRIGANESH

last: JAMMULA

address: University of Cambridge, Li Ka Shing Centre, Robinson Way

institute: CRUK CI

summary: PRMT1 is the major Arginine methyltransferase in mammalian cells and its over-expression in human cancer has been linked to poor response to cancer therapy.  Here, combining mass spectrometry-based global methyl-proteomics with genome-wide mRNA expression profiling, we identify PRMT1 and its associated Arginine methylation as a regulatory hubs controlling cancer cell response to replicative stress agents. We show that DNA-PK binds to PRMT1 and regulates both its subcellular localization and activity, leading to PRMT1 recruitment to drug-stalled replication forks and channelling its methyl-transferase activity from its soluble targets towards Arginine 3 of histone H4. This DNA-PK-PRMT1 axis is required for the induction of the Senescence-Associated Secretory Phenotype, which sustains cell cycle arrest and protects cells from apoptosis.  Our data show that Arginine-methylation regulates the adaptive response of cancer cell to replicative stress agents and might be targeted to sensitize cancer cells to genotoxic chemotherapeutics

overall_design: 8 samples of SK-OV-3 ovarian cancer cells differentially treated were analyzed; two biological replicates were performed for each sample. "Emp" indicates shScramble cells that is the control used as a reference. "C20"indicates cell treatment with cisplatin (20 micromolar for 24 hours), whereas B6, B8 and B10 represent three different shRNA sequences used to knock down PRMT1 expression.

first: Daniele

last: Musiani

first: Marica-Rosaria

last: Ippolito

first: Enrico

last: Massignani

first: Sri-Ganesh

last: Jammula

first: Tiziana

last: Bonaldi


title: Cochlear transcriptome at 3 hours post-noise trauma in mice

city: Okayama

first: Yukihide

last: Maeda

address: 2-5-1 Shikata, Kita-Ku

department: Department of Otolaryngology-, Head and Neck Surgery

institute: Okayama University Hospital

summary: In order to elucidate molecular mechanisms of noise-induced hearing loss in the cochlea (inner ear), transcriptome of the cochlear sample was analyzed after induction of hearing loss by exposure to intense noise in mice. Cochlear transcriptome was analyzed at 3 hours following the noise exposure.

overall_design: The samples included cochlear RNA from “Noise3h” at 3 hours post-noise exposure and “Baseline 0707” without noise exposure (control).

first: Shin

last: Kariya

first: Junko

last: Takahara

first: Shohei

last: Fujimoto

first: Akiko

last: Sugaya

first: Kazunori

last: Nishizaki


first: Bart

last: De Strooper

overall_design: mRNAseq on 96 biological samples (mouse hippocampus), n=12 per experimental group, examining APPswe/PSEN1L166P and Thy-TAU22 mice and their respective WT littermates, at 4 and 10 months of age (8 groups in total)

first: Annerieke

last: Sierksma

first: Ashley

last: Lu

first: Renzo

last: Mancuso

first: Nicola

last: Fattorelli

last: Thrupp

first: Evgenia

last: Salta

first: Jesus

last: Zoco

first: David

last: Blum

first: Luc

last: Buée

first: Mark

last: Fiers


title: Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp2]

status: Public on Jan 13 2020

city: Lodz

first: Konrad

last: Pagacz

address: Mazowiecka 15

department: Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

summary: The samples were drawn from patients with diagnosed oropharyngeal cancer. We used blood samples (10ml) collected from patients after diagnosis, before treatment. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles. MicroRNA was extracted from 200 μL serum using miRCURY RNA Isolation kit (Qiagen) following the manufacturer’s protocol and stored at −80°C.

overall_design: miRNA qPCR assays from 70 patients with HnN cancer before irradiation. Equal amount of RNA was used from each patient.

first: Bartłomiej

last: Tomasik


title: Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors.


title: Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp1]

summary: The samples were drawn from patients with diagnosed oropharyngeal cancer treated with irradiation. We used blood samples (10ml) collected from patients 7 days after receiving 20Gy dose of irradiation. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles. MicroRNA was extracted from 200 μL serum using miRCURY RNA Isolation kit (Qiagen) following the manufacturer’s protocol and stored at −80°C.

overall_design: miRNA qPCR assays from 20 patients from after 20Gy irradiation due to oropharyngeal cancer. Equal amount of RNA was used from each patient.


title: Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture [GRO-seq]

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

summary: Our laboratory identified robust recurrent DNA double-strand break (DSB) cluster (“RDC”) genes in mouse neural stem/progenitor cells (NSPCs) by applying the high-throughput, genome-wide, translocation sequencing (HTGTS) method. Genomic alterations of most of the identified RDC-genes have been associated with psychiatric disorders such as autism and schizophrenia and several are altered in brain cancer. The most robust mouse RDCs are all in genes that tend to be very long, actively transcribed and were enhanced after mild inhibition of replication stress. The common transcription and replication characteristics we observe in RDC-genes suggest that frequent RDC DSBs might be generated by collision between transcription and replication processes. However, the underlying mechanism of RDC formation is still unknown.  To elucidate mechanisms that generate and resolve DSBs in these cells, we established an in vitro system of induced neural progenitor cells derived from embryonic stem cells. HTGTS bait-DSBs introduced by CRISPR/Cas9 on three mouse chromosomes identified only 5 RDC-genes in embryonic stem cells and 27 RDC-genes in the neural progenitor cells differentiated from them. All RDC-genes identified in induced neural progenitor cells belonged to the group of genes identified in primary neural and progenitor cells. These results indicate that our in vitro differentiation system is both effective and robust in terms of recapitulating our previous findings and facilitating mechanistic studies.

overall_design: GRO-seq libraries were performed to assess transcription activity in embryonic stem cells and embronic stem cell-derived neural progenitor cells RDC-genes.

first: Aseda

last: Tena


title: mRNA expression modification after XRN1 depletion in Hela Cells

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: RNA homeostasis, a process maintained through a balance between transcription and decay, plays a critical role for most cellular functions. The conserved XRN and DIS3 families are major exoribucleases involved in this RNA turnover. Very little information is currently available about their physiological and physiopathological functions in humans.  The aim of this study was to identify the possible advantage and the subsequent modification changes associated with XRN1 invalidation (siXRN1).

overall_design: Cells were plated at 200 000 cells/well in 6-well plates. After 24 h, cells were transfected with siRNA negative Control or Silencer Pre-designed siRNA XRN1 at 50 nM using Lipofectamine RNAiMAX (Life Technologies) according to the manufacturer’s instructions. Forty-eight hours after transfection, cells were lysed for RNA analysis as described below.

first: P

last: Brest


title: nsp1 acts on HEK-293T

city: Wuhan

first: Zhou

last: Shen

state: Hubei

address: 1 Shi-zi-shan Street

institute: Huazhong agriculture university

summary: Idenrify the function of NSP1

overall_design:
3 groups in triplicates;
HEK 293T transfected with empty backbone
HEK 293T transfected with SADS-CoV oriented NSP1 contained PCAGGS
HEK 293T transfected with FIPV oriented NSP1 contained PCAGGS


title: Expression data from SOX9 knockdown in HCC cells

city: Shanghai

first: mengchao

last: wang

state: China

address: No225, Changhai Rd,

institute: second military medical university

summary: Sorafenib is a multi-kinase blocker and one of the few suggested drug treatments for aggressive hepatocellular carcinoma (HCC) patients. However, drug resistance to sorafenib may often occur over time and cause further tumor aggression. Recently, cancer stem cells were found in HCC and were speculated to be involved in tumor progression. SOX9 is highly expressed in HCC cancer stem cells and promotes cell proliferation and self-renewal. Meanwhile, HCC patients with higher SOX9 expression show poorer prognosis [1]. Whether SOX9 is involved in sorafenib resistance in HCC is still unclear. Here, we found that sorafenib treatment increased SOX9 expression in HCC cell lines. Overexpression of exogenous SOX9 in HCC increased sorafenib resistance both in vitro and in vivo, whereas down-regulation led to inhibition of sorafenib resistance. Knock-down of SOX9 by RNA interference caused down-regulation of downstream genes, including ATP binding cassette subfamily G member 2 (ABCG2).  The drug resistance to sorafenib caused by SOX9 overexpression could be ameliorated by overexpression of SOX9 in combination withby ABCG2 inhibition in HCC cell lines. In the cohort of patients resistant to sorafenib, we found that patients with lower SOX9 expression had more prolonged overall survival (OS) and progression-free survival (PFS). Cox analysis shows that SOX9 expression exerts as an independent risk factor for HCC, and logistic regression analysis reveals that SOX9 expression, tumor capsule deficiency, tumor diameters, and microvascular invasion are risk factors for poor prognosis of HCC patients. These findings demonstrate that SOX9 enhances sorafenib resistance and may regulate this process by modulating ABCG2 expression.

overall_design: To examine the cellular pathways that result from SOX-9 knockdown, we performed microarray expression analysis between the SOX9-knockdown HepG2 cell line and the empty virus control cell line. Their respective RNA was extracted for Affymetrix microarrays.

first: Mengchao

last: Wang

first: Gang

last: Huang


title: MiR-765 functions as a tumour suppressor and eliminates lipids in clear cell renal cell carcinoma by downregulating PLP2

first: Wen

last: Xiao

address: 1277 Jiefang Avenue

department: Department of Urology

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

summary: MicroRNAs (miRNAs) expression profiles are widely investigated in the major cancers, but their expression in patients plasmas of cancers have not yet to be fully elucidated. We investigated expression profiles of miRNAs in patients preoperative/postoperative plasmas of clear cell renal cell carcinomas (ccRCCs) by using a miRNAs microarray platform which covers a total of 1,523 human miRNAs.

overall_design: Plasma samples were extracted from EDTA-K 2 tubes and centrifuged at 800g for 10 minutes at 40C to remove cells and centrifuged again at 12,000g for 15 minutes at 40C to remove cellular debris, and then stored in a deep freezer at -80°C.  All plasmas were obtained within 4 hours after drawing blood and stored at -80°C for further RNA extraction. 5 patients plasma samples  with ccRCC preoperatively and at day 7 postoperatively were used and expression profiles of miRNAs were screened by using a miRNA microarray platform.

first: Xiaoping

last: Zhang


title: obtain complete transcriptome data

city: Xiamen

first: Runwei

state: Fujian

address: No.43, yindou road

department: Fisheries College

institute: Jimei University

summary: In order to obtain complete transcriptome data of epinephelus coioides

overall_design: Pooled of five fish，Heart, muscle, gill filament, spleen, intestine, liver, gonad, kidney,hepatopancreas

first: Kai

last: Song

first: Chunxiao


title: Single cell RNA sequencing of day 6 and day 13 endodermal progenitors

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: Efficient generation of human induced pluripotent stem cell (hiPSC)-derived human intestinal organoids (HIOs) would facilitate the development of in vitro models for a variety of diseases that affect the gastrointestinal tract, such as inflammatory bowel disease or Cystic Fibrosis.

overall_design: Here, we report a novel directed differentiation protocol for the generation of mesenchyme-free HIOs that can be primed towards more colonic or proximal intestinal lineages in serum-free defined conditions. Using a novel CDX2eGFP iPSC “knock-in” reporter line to track the emergence of hindgut progenitors, we followed the kinetics of CDX2 expression throughout directed differentiation, enabling the purification of intestinal progenitors and robust generation of mesenchyme-free organoids expressing characteristic markers of small intestinal or colonic epithelium. We employed HIOs generated in this way to measure CFTR function using cystic fibrosis patient-derived iPSC lines before and after correction of the CFTR mutation, demonstrating their future potential for disease modeling and therapeutic screening applications.

first: Aditya

last: Mithal

first: Jed

last: Mahoney

first: Gustavo

last: Mostoslavsky


title: B cell-intrinsic epigenetic modulation of antibody responses by dietary fiber-derived short-chain fatty acids

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

type: Non-coding RNA profiling by high throughput sequencing

summary: Short-chain fatty acids (SCFAs) butyrate and propionate are metabolites from dietary fibers fermentation by gut microbiota that can affect differentiation or functions of T cells, macrophages and dendritic cells. We show here that these SCFAs directly impact B cells to modulate in a dose-dependent fashion AID and Blimp1 expression, class-switch DNA recombination, somatic hypermutation and plasma cell differentiation, thereby impairing, through B cell-intrinsic activity, local (intestinal) and systemic T-dependent and T-independent antibody responses. In human and mouse B cells, butyrate and propionate upregulate select miRNAs that target Aicda and Prdm1 mRNA-3’UTRs through epigenetic inhibition of histone deacetylation of the respective miRNA host genes. Further, they modulate B cell Aicda and Prdm1 by acting as HDAC inhibitors, not as energy substrate or through GPR-engagement signaling. Finally, butyrate and propionate epigenetic impact on B cells extends to inhibition of autoantibody production and autoimmunity in lupus MRL/Faslpr/lpr and NZB/WF1 mice.

overall_design: Analysis of the mRNA and micrRNA expression profiles in human B cells stimulated with CD154 plus IL-4 and IL-21 in the presence of nil or short-chain fatty acid butyrate

first: Paolo

last: Casali

first: Hong

last: Zan

first: Tabrez

last: Mohammad


title: Silencing Xrn1 by dox-inducible shRNA

city: Paris

first: Dominika

last: Foretek

address: 26 rue d'Ulm

institute: Institut Curie

summary: Xrn1 is a cytoplasmic 5’-3’ exoribonuclease responsible for degradation of multiple types of RNA. Data obtained on yeast model described Xrn1 function in degradation of messenger (m)RNA, Rapid transfer (t)RNA Decay (RTD) of hypomodified and unstable tRNA transcripts as well as maturation of 25S ribosomal (r)RNA and small nucleolar (sno)RNAs. Our group discovered previously that deletion of Xrn1 gene results in stabilization of a group of long non-coding RNAs which are often transcribed antisense to protein-coding genes and may regulate their expression on transcriptional level. However much less is known about human (h)Xrn1 function. Data available from human cell lines confirm involvement of hXrn1 in degradation of mRNA, initiator tRNA methionine and some miRNA. The high sequence similarity of Xrn1 between yeast and man suggests that also its function should be well conserved for hXrn1. Therefore, in this experiment using inducible shRNA we want to define hXrn1 targets by analyzing RNAs that are stabilized after Xrn1 silencing with focus on both coding and non-coding transcripts.

overall_design: The total RNA-seq was performed on technical duplicates for eachdoxocycline induced non-silencing shRNA  and shRNA against Xrn1

first: Marina

last: Pinskaya

first: Marc

last: Gabriel

first: Antonin

last: Morillon