title: Real-time quantitative PCR analysis of mouse colon samples

status: Public on Mar 07 2019

city: Rome

first: Roberta

last: Vitali

state: Italy

address: Via Anguillarese 301

country: Italy

institute: ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development

summary: Gut mucosal healing (MH) is considered a key therapeutic target and prognostic parameter in the management of inflammatory bowel disease (IBD). The dipotassium glycyrrhizate (DPG), a salt of the glycoconjugated triterpene glycyrrhizin, has been shown to inhibit the High Mobility Group Box 1 (HMGB1) protein, an allarmin strongly implicated in the pathogenesis of most inflammatory and auto-immune disorders, included IBD. The aims of the present study is to identify genes involved in MH pathways modulated by DPG in mouse model of chemical induced acute colitis.

overall_design: To induce colitis C57BL/6 female mice were treated 3% dextran sodium sulphate (DSS) for 7 days and then sacrificed. Mice, were randomly divided into three groups: 1) control group received regular drinking water; 2) mice treated with 3% DSS; 3) mice treated with 3% DSS and 8 mg/kg/day DPG. RNA obtained from colon tissue of controls (Untreated), DSS-induced colitis and mice co-treated with DSS and DPG, were analyzed by RT2 PCR array. PCR-Array was repeated in triplicate using a pool of RNA obtained from 5 animals for each group.

first: Francesca

last: Palone

first: Vincenzo

last: Cesi


title: Formative transition of human naïve pluripotent stem cells

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

type: Expression profiling by high throughput sequencing

summary: Human naïve pluripotent stem cells (PSC) share features with pre-implantation epiblast. They thus provide an unmatched opportunity for characterising the developmental programme of pluripotency in Homo sapiens. Here we confirm that naïve PSC do not respond directly to germ layer induction, but must first acquire competence. Capacitation for multi-lineage differentiation occurs without exogenous growth factor stimulation and is facilitated by inhibition of Wnt signalling. Whole transcriptome profiling during this formative transition highlights dynamic changes in gene expression, affecting many cellular properties, including metabolism and epithelialisation. Notably, naïve pluripotency factors are exchanged for post-implantation factors, but competent cells remain devoid of lineage primed transcription. The gradual pace of transition for human naïve PSC is consistent with the timespan of primate development from blastocyst to gastrulation. Transcriptome trajectory during in vitro capacitation of human naïve cells tracks the progression of epiblast during embryogenesis in Macaca fascicularis, but shows greater divergence from mouse development. Thus the formative transition of naïve PSC in a simple culture system may recapitulate essential and specific features of pluripotency dynamics during an inaccessible period of human embryogenesis.

overall_design: 2 lines of human naïve pluripotent stem cells (embryo-derived HNES1 and chemically reset cR-H9-EOS) were cultured in N2B27 and 2uM XAV939 for 10 days. After that the cells were split into two conditions: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF), or E8 medium, for extended maintenance. The experiment was performed in biological triplicates for each cell line. RNAseq was performed with the cells on day 0, 1, 2, 3, 7, 10, when the cells were cultured in XAV939; and one time point after transfer to maintenance conditions, at not less than 22 days of culture from the start of the experiment. Conventional hES cell line H9-EOS, which was a parental line for the chemically reset cR-H9-EOS was used as a control (in biological triplicate).

first: Austin

middle: G

last: Smith

first: Maria

last: Rostovskaya


title: Transcriptome-wide Profiling of Multiple RNA Modifications Simultaneously at Single-base Resolution

status: Public on Mar 08 2019

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

country: USA

institute: University of Utah School of Medicine

summary: We report RBS-Seq, a new RNA bisulfite sequencing method enabling the sensitive and simultaneous detection of m5C, pseudouridine, and m1A at single-base resolution transcriptome-wide. For each, we detect ‘signature’ base mismatches (for m5C and m1A), or 1-2 base deletions (for pseudouridine) structurally explained by ribose ring-opened pseudouridine-mono-bisulfite adducts.  Our profiles for pseudouridine reveal clear signatures at known sites in tRNAs and rRNAs, and provide hundreds of new targets in non-coding RNAs and mRNAs. However, our results diverge greatly from prior work, suggesting ~10-fold fewer m5C sites, and the absence of substantial m1A in mRNAs.

overall_design: Application of a modified RNA bisulfite sequencing approach on RNA samples from HeLa cells for simultaneous detection of m5C, pseudouridine, and m1A at single-base resolution transcriptome-wide.

first: Vahid

last: Khoddami

first: Archana

last: Yerra

first: Timothy

middle: L

last: Mosbruger

first: Aaron

middle: M

last: Fleming

first: Cynthia

middle: J

last: Burrows

first: Bradley

middle: R

last: Cairns


title: Genome-wide maps of ΔNLef1 in primary mouse keratinocytes

city: London

first: Giacomo

last: Donati

address: Guy's Hospital, Great Maze Pond

institute: King's College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In adult K14ΔNLef1 mouse, the overexpression of ∆NLef1, a ß-catenin dominat negative, in basal keratinocytes leads to the conversion of hair follicles into multilayered epithelial cysts and ectopic sebaceous gland. To uncover direct target genes of ΔNLef1 we performed ChIP-Seq experiments.

overall_design: Examination of ∆NLef1 genomic targets in mouse primary keratinocytes

first: Fiona

last: Watt


title: YAP/TAZ as new regulatory hub of VEGF signaling [RNA]

status: Public on Mar 12 2019

city: Heidelberg

first: Carmen

last: Ruiz de Almodovar

address: Im Neuenheimer Feld 328

country: Germany

institute: Heidelberg University Biochemistry Center (BZH)

summary:
VEGF is a major driver of blood vessel formation.
However, the signal transduction pathways culminating into the biological consequences of VEGF signaling are partially understood.
Here we show that the Hippo pathway effectors YAP and TAZ, work as a regulatory hub in mediating VEGF-VEGFR2 signaling during angiogenesis.
We demonstrate that YAP/TAZ are essential for vascular development as endothelium specific deletion of YAP/TAZ leads to impaired vascularization and embryonic lethality.
Mechanistically, we show that VEGF activates YAP/TAZ via its effects on actin cytoskeleton remodeling, and that activated YAP/TAZ induce a transcriptional program that results in the expression of a set of genes to further control cytoskeleton dynamics, and thus ensure a proper angiogenic response.
YAP/TAZ deletion also results in VEGFR2 trafficking defects from the Golgi to the plasma membrane.
Together, our study establishes YAP/TAZ as a central regulatory hub that mediates VEGF signaling, and hence, regulates angiogenesis.

overall_design: RNA-seq on WT and YAP/TAZ ecKO mouse brain endothelial cells, with 3 replicates of ecKO and 4 of WT.

first: Xiaohong

last: Wang

first: Aida

last: Freire

first: Géza

last: Schermann

first: Ivan

last: Moya

first: Ying

last: Shen

first: Laura

last: Castro

first: Severino

last: Urban

first: Gergely

last: Solecki

first: Frank

last: Winkler

first: Alba

last: Diz-Muñoz

first: Thomas

last: Schmidt

first: Tamás

last: Fischer

first: Georg

last: Halder

last: de Almodóvar


title: 4Cseq analysis of neural stem/progenitor cells (NSC) from wild type and Sox2-deleted mouse neonatal forebrain

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

institute: University of Milan

summary: We report the application of 4Cseq technology for the profiling of chromatin interactions in wild type and Sox2-deleted NSC, for 9 different loci (viewpoints): Olig2 promoter, Olig1 promoter, Tcf4 promoter, Kat2b promoter, Sox3 promoter, Stox2 promoter, c-fos 5' enhancer, c-fos 3' enhancer and c-fos promoter.

overall_design: NSC from wild type and mutant littermates individual mouse forebrains were cultured, and expanded for 3-7 passages (as in Favaro et al., Nature Neuroscience 2009, 12:1248-56, and Zhang et al., Nature 2013, 504:306-10). Cells were fixed as in Zhang et al., 2013, and processed for 4Cseq analysis. For 7 viewpoints analyzed, three wild type and three mutant cultures, each derived from individual P0 brains of littermate mice, were used; for 2 viewpoints analyzed, one wild type and one mutant culture were used.

first: Yanfen

last: Zhu

first: Harianto

last: Tjong

first: Giulio

last: Pavesi


title: Next Generation Sequencing of polyA+ RNA of cultured neural stem/progenitor cells (NSC) from mouse neonatal forebrain [RNA-seq]

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of NSC transcriptome.

overall_design: Wild type and Sox2-deleted NSC were sequenced; three independent samples from wild type, and three from Sox2-deleted brains (different individual mice).

first: Chew

middle: Y

last: Ngan

first: Miriam

last: Pagin


title: Sox2 is required for global chromatin interactions in brain-derived neural stem cells [ChIP-seq]

summary: Genome wide mapping of Sox2 binding sites in neural progenitor cells

overall_design: ChIP-Seq experiment on transcription factor Sox2  in neural progenitor cells. Cells were collected as small neurospheres and fixed either directly ("Spheres") or after dissociation ("Singles"). Cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate-buffered saline and then lysed, sonicated and immunoprecipitated as described previously (Mateo et al., 2015 and references therein). SOX2 was immunoprecipitated with 3mg of goat anti-SOX2 (Santa Cruz sc-17320).

first: Ben

last: Martynoga


title: miR-155 enhances PRC2 activity via polycomb-like protein Phf19 to sustain T cell antitumor immunity [RNA-Seq]

city: Bethesda

first: Luca

last: Gattinoni

state: MD

address: 10 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

summary: The microRNA miR-155 is essential for CD8+ T cell antiviral and antitumor immunity but the mechanisms behind its activity remain unresolved. Here, we show that miR-155 increased CD8+ T cell antitumor function by restraining T cell senescence and functional exhaustion through epigenetic silencing of key drivers of effector differentiation. miR-155 enhanced the function of polycomb repressor complex 2 (PRC2) indirectly by promoting the expression of the PRC2 cofactor Phf19 via AKT signaling. Phf19 orchestrated a transcriptional program extensively shared with miR-155 to enhance T cell engraftment, polyfunctionality, and antitumor immunity. These effects were dependent on the histone-binding capacity of Phf19 which is critical for the PRC2 recruitment to chromatin. These findings establish miR-155–Phf19–PRC2 as a pivotal axis regulating CD8+ T cell differentiation. Targeting the microRNA–polycomb-group protein circuitry is a promising route to potentiate cancer immunotherapy through epigenetic reprogramming of CD8+ T cell fate.

overall_design: We compared the gene expression profiles of Pmel-1 CD8+ T cells overexpressing with miR-155 or Controls 5 days after transduction or 5 days after transfer into C57BL/6 in conjunction with gp100-VV.

first: Yun

last: Ji


title: Genome-wide maps of chromatin state in neural stem/progenitor cells (NSC) from mouse neonatal forebrain [ChIP-seq]

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in NSC. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of NSC. We compared histone modifications between wild type and Sox2-deleted NSC.

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Marit

last: Vermunt

first: Rebecca

last: Favaro


title: Withdrawal of MEK1/2 inhibitor reverses acquired resistance driven by BRAF amplification but drives EMT and chemoresistance in cells with amplified KRAS

status: Public on Mar 11 2019

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

summary: Acquired resistance to MEK1/2 inhibitors can arise through amplification of BRAFV600E or KRASG13D to reinstate ERK1/2 signalling. Here we show that BRAFV600E amplification and selumetinib resistance are fully reversible following drug withdrawal. Resistant cells with BRAFV600E amplification become addicted to selumetinib to maintain a precise level of ERK1/2 signalling (2-3% of total ERK1/2 active, here quantified by mass spectrometry), that is optimal for cell survival and proliferation.  The magnitude of ERK1/2 activation following selumetinib withdrawal (~20% active) drives a p57KIP2-dependent G1 cell cycle arrest and senescence or expression of NOXA and cell death, which selects against those cells with amplified BRAFV600E. ERK1/2-dependent p57KIP2 expression is required for loss of BRAFV600E amplification and determines the rate of reversal of selumetinib resistance. Furthermore, growth of selumetinib-resistant cells with BRAFV600E amplification as tumour xenografts is inhibited in mice that do not receive selumetinib.  Thus, BRAFV600E amplification confers a selective disadvantage during drug withdrawal, providing a rationale for intermittent dosing to forestall resistance. In striking contrast, selumetinib resistance driven by KRASG13D amplification is not reversible. In these cells ERK1/2 reactivation does not inhibit proliferation but drives a ZEB1-dependent epithelial-to-mesenchymal transition that increases cell motility and promotes resistance to traditional chemotherapy agents arguing strongly against the use of ‘drug holidays’ in cases of KRASG13D amplification.

overall_design: Cells were treated with either selumetinib or DMSO and treated for 4,16,or 48 hours before being harvested and assayed

first: Matthew

last: Sale

first: Kathryn

last: Balmanno

first: Jayeta

last: Saxena

first: Eiko

last: Ozono

middle: E

last: McIntyre

first: Katarzyna

last: Wojdyla

last: Gilley

first: Anna

last: Woroniuk

first: Karen

middle: D

last: Howarth

first: Gareth

last: Hughes

first: Jonathan

last: Dry

first: Mark

last: Arends

first: David

last: Oxley

first: Susan

last: Ashton

last: Adams

first: Julio

last: Saez-Rodriguez

first: Paul

last: Smith

last: Cook


title: Genome-wide maps of chromatin state in neural stem/progenitor cells (NSC) from mouse neonatal forebrain [ChIA-PET]

first: Federico

last: Zambelli

summary: We report the application of single-molecule-based DNA sequencing technology for high-throughput profiling of long-range chromatin interactions in Sox2-deleted and wild type NSC, by improved ChIA-PET procedure (in situ ChIA-PET) with antiRNApolII antibodies. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide maps of inter-molecular ligated DNA representing long-range interactions in chromatin.

overall_design: Analysis of RNApolII-mediated long-range interactions in chromatin of Sox2-deleted and wild type neural stem/progenitor cells (NSC) cultured from neonatal mouse brains.

first: Chee-Hong

last: Wong

last: Favaro

first: Harianto

last: Tjong

first: Miriam

last: Pagin

first: Yanfen

last: Zhu


title: Widespread Alterations in Translation Elongation in the Brain of Fmr1 Knock-Out Mice

status: Public on Mar 10 2019

city: New York

first: Peter

last: Sims

address: 3960 Broadway

department: Systems Biology

institute: Columbia University

summary: FMRP is a polysome-associated RNA-binding protein encoded by Fmr1 and lost in Fragile X syndrome. Increasing evidence suggests that FMRP regulates both translation initiation and elongation, but the gene-specificity of these effects is unclear. To elucidate the effects of FMRP loss on translation, we used ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of Fmr1 knock-out mice. We found a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP, and an increase for terminal oligo-pyrimidine (TOP) motif-containing genes canonically controlled by mTOR-4EBP-eIF4E signaling. Amino acid motif- and gene-level analyses both showed a widespread reduction of translational pausing in Fmr1 knock-out mice. Our findings are consistent with a model of FMRP-mediated regulation of both translation initiation through eIF4E and elongation that is disrupted in Fragile X syndrome.

overall_design: Examination of genome-wide translational state in Fmr1-deficient and wild-type mouse cortex via next-generation sequencing-based profiling of transcription and translation

first: Sohani

last: Sharma

first: Jordan

last: Metz

first: Hongyu

last: Li

first: Benjamin

last: Hobson

first: Nicholas

last: Hornstein

last: Sulzer

first: Guomei

last: Tang

middle: A


title: H3K4ox-Mediated Chromatin Condensation Protects Breast Cancer Cells from the DNA Damage Repair Machinery

status: Public on Mar 06 2019

city: Barcelona

first: Sandra

last: Peiró

address: Aiguader 88

department: Programa de Recerca en Càncer

country: Spain

institute: IMIM-Hospital del Mar

summary: Using an H3K4ox-specific antibody, we determined that the H3K4ox modification is enriched in triple-negative breast cancer (TNBC) cells compared with luminal breast cancer subtypes—correlating with high LOXL2 levels— and, importantly, is found primarily in heterochromatin.

overall_design: a) H3K4ox ChIP-seq in MDA-MB-231 cells; b) ATACseq in MDA-MB-231 infected with shRNA against LOXL2; and c) RNA seq in MDA-MB-231 infected with shRNA against LOXL2

first: JP

last: Cebrià-Costa

first: A

last: Gonzalez

first: L

last: Pascual-Reguant

last: Iturbide

first: J

last: Querol

first: G

last: Serra

first: D

last: Andreu

first: C

last: Bernadó

last: Arribas

last: García de Herreros

first: S


title: MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing

status: Public on Mar 05 2019

city: Bandar Sunway

first: Lian Yih

last: Pong

state: Selangor

address: Jalan Lagoon Selatan

department: Jeffrey Cheah School of Medicine and Health Sciences

country: Malaysia

institute: University Monash Malaysia

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background. Dengue caused by dengue virus (DENV) serotypes -1 to -4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood.
Methods. Using a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expression of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection.
Results. A total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were accessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection.
Conclusion. This study provides the first insight into the global miRNA expressions of mouse livers in response to DENV-1 infection in vivo and the possible roles of miRNAs in modulating the adaptive immune responses during DENV-1 infection.

overall_design: miRNA profiles of livers from three DENV-1-infected mice and from three uninfected mice were generated by deep sequencing using Illumina MiSeq Benchtop Sequencer.

first: Lian

first: Sinikka

last: Parkkinen

first: Amreeta

last: Dhanoa

first: Han

last: Gan

first: Indeevari Abisheka

middle: C

last: Wickremesinghe

first: Sharifah

last: Syed Hassan


title: Hi-C from THP-1 (ENCSR748LQF)

status: Public on Mar 03 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
in situ MboI Hi-C

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptome (RNA-Seq) analysis of Atlantic cod (Gadus morhua) precision cut liver slices (PCLS) exposed to benzo[a]pyrene (BaP) and ethynylestradiol (EE2)

city: Bergen

first: Fekadu

last: Yadetie

address: Thormøhlensgt. 53A/B

department: Biology

country: Norway

institute: University of Bergen

summary:
Purpose: The objective of this study is to use Atlantic cod (Gadus morhua) PCLS culture and RNA-seq analysis to map gene expression responses to BaP and EE2 exposure in Atlantic cod.
Methods: A total of 8 (3 females and 5 males) juvenile cod (G. morhua) (average body weight 498 g) were used for PCLS (n = 6-8 per group). PCLS preparation and chemical exposure in the culture was performed as previously described (Eide et al., 2014). Cod liver slices were cultured in 24-well plates in the growth medium containing DMSO vehicle (CAS No: 67-68-5), BaP (CAS No: 50-32-8) (10 or 1000 nm), EE2 (CAS No: 57-63-6) (10 or 1000 nm) or BaP and EE2 mixture (10 or 1000 nm each). After 48 hors of culture, the slices were collected and snap frozen in liquid nitrogen and stored at -80 °C for RNA extraction.
Results: In total, we had 47 high-quality samples, which were aligned to the published CDS of Atlantic cod (ftp://ftp.ensembl.org/pub/release-90/fasta/gadus_morhua/cds/Gadus_morhua.gad) using HISAT2 v2.1.0 (Kim et al., 2015). Counts were generated from the alignments using SAMtools v1.4.1 (Li et al., 2009). Differential expression analysis was performed using edgeR v3.18.1 (McCarthy et al., 2012) between control group and each treated group using paired test, after removing the genes with all-zero counts across all samples of the two compared groups. Differentially expressed genes were defined by p-value < 0.05 after adjustment using the Benjamini-Hochberg multiple testing correction. Several genes were differentially expressed in the BaP and EE2 and mixture treatment groups compared to the group. Hierarchical clustering showed that signature expression profile of top differentially expressed genes in response to the single treatment was distinctly maintained also in the equimolar binary mixtures.
Conclusions: Combining high-throughput RNA-seq analysis and PCLS culture in Atlantic cod, we have shown that BaP and EE2 differentially regulated many genes in the AHR and ER pathways. The results show that omics data can be generated using an efficient PCLS in vitro culture system.

overall_design: The seven treatment groups are DMSO (vehicle control), 10nM BaP, 1uM BaP, 10nM EE2, 1uM EE2, 10nM Mix (BaP + EE2, 10nM each) and 1uM Mix (BaP + EE2, 1uM each). Each treatment group consists of PCLS RNA samples prepared from 6-8 fish (n = 6-8 per group). A total of 47 samples were sequenced. For each sample, 50 million 75 bp paired-end reads were generated.

first: Xiaokang

last: Zhang

first: Eileen

last: Hanna

first: Libe

last: Aranguren

first: Nello

last: Blaser

first: Inge

last: Jonassen

first: Anders

last: Goksøyr

first: Odd

last: Karlsen


title: Establishing a preclinical model of squamous lung cancer to investigate of novel chemopreventive approaches in high risk individuals with bronchial premalignant lesion

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Lung cancer is the leading cause of cancer mortality due to limited diagnosis and interception of disease at its earliest curable stages. We have identified transcriptional alterations in epithelial and immune pathways in human lung squamous premalignant lesions (PMLs).  To investigate the molecular alterations identified and test prevention strategies pre-clinical models are required. The carcinogen induced N-nitroso-tris-chloroethylurea (NTCU) mouse model of lung squamous cell carcinoma (LUSC) is a promising model that develops histologically comparable lung PMLs to those that precede LUSC development in humans; however, the associated molecular alterations and immune environment driving PML and LUSC development in this model have not been well characterized.

overall_design: To characterize the NTCU model we chose to examine the lesions that developed in 2 strains of mice, SWR/J and A/J, which are sensitive to developing LUSC, as not all mouse strains develop disease with treatment of NTCU. Additionally, we selected mice treated with varying total doses of NTCU ranging from 14-50 umol, where treatments with 40 or 80 mmol/L of NTCU were topically administered for 14-25 weeks.  The range of doses allowed for the isolation of RNA from a range of lesions across both strains. We additionally included normal airway from mice treated with vehicle control (acetone).

first: Sarah

last: Mazzilli

first: Jennifer

last: Beane

first: Avrum

last: Spira


title: Hi-C from THP-1 (ENCSR669GJD)


title: Loss of RNA-binding protein Sfpq causes long-gene transcriptopathy in skeletal muscle and severe muscle mass reduction with metabolic myopathy (Primary culture, mRNA-seq)

status: Public on Mar 18 2019

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: Growing evidences are suggesting that extra-long genes in mammals are vulnerable for full-gene length transcription and dysregulation of long genes is a mechanism underlying human genetic disorders. Skeletal muscle expresses Dystrophin which is 2.26 Mbp in length; however, how long-distance transcription is achieved is totally unknown. We had discovered RNA-binding protein SFPQ preferentially binds to long pre-mRNAs and specifically regulates the cluster of neuronal genes > 100 kbp. Here we investigated the roles of SFPQ for long gene expression, target specificities, and also physiological functions in skeletal muscle. Loss of Sfpq selectively downregulated genes >100 kbp including Dystrophin and caused progressive muscle mass reduction and metabolic myopathy characterized by glycogen accumulation and decreased abundance of mitochondrial oxidative phosphorylation complexes. Functional clustering analysis identified metabolic pathway related genes as the targets of SFPQ. These findings indicate target gene specificities and tissue-specific physiological functions of SFPQ in skeletal muscle.

overall_design: We analyzed polyA-tailed RNA profiles including transcribing RNAs in primary myoblasts obtained from skeletal muscles of 1-month-old SfpqSM-KO (n=3) and control (n=3) mice under differentiated condition using Ion-proton.

first: Motoyasu

last: Hosokawa

first: Akihide

last: Takeuchi

last: Iida

first: Masatoshi

last: Hagiwara


title: Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq]

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: In this study, we investigated the role of tranfer RNA genes (tDNAs) in genome organization and nuclear function by generating a chromosome lacking all its tDNAs. Our analyses of this tDNA-less chromosome show that loss of these genes affects nucleosome postioning, SMC protein binding, centromere clustering, long range chromosome folding and epigenetic silencing.

overall_design: We compared the binding of Scc2 which loads cohesins and condensins on yeast chromosomes in wild type and tDNA-less chromosome III strains by ChIP Seq.

first: Omar

last: Hamdani

first: Namrita

last: Dhillon

first: Tsung-Han

middle: S

last: Hsieh

first: Takahiro

last: Fujita

first: Josefina

last: Ocampo

first: Jacob

last: Kirkland

first: Tetsuya

last: Kobayashi

first: Brandon

last: Friedman

first: Derek

last: Fulton

first: Kenneth

last: Wu

first: Masaya

last: Oki

first: Kerry

last: Bloom

first: David

last: Clark

first: Oliver

last: Rando

first: Rohinton

last: Kamakaka


title: Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-seq]

overall_design: We compared the transcriptome in wild type and tDNA-less chromosome III strains by RNA Seq.


title: Identification of nucleic acids that supports protein renaturation

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

institute: Barts & The London School of Medicine & Dentistry

summary: Many proteins require RNA to remain soluble in cell and tissue lysate. Here we used RNA- and DNA- immunoprecipitation to identify what types of nucleic acids are associated with these proteins after in vitro renaturation.

overall_design:
RNAse-aggregated proteins were renatured with pre-fragmented genomic DNA or total RNA. After removal of insoluble (re-aggregated) proteins, the soluble fraction was subjected to immunoprecipitation or membrane capture. Each IP was done twice on different material and include IP with IgG or GFP antibodies as controls for the RNA and the DNA, respectively. Membrane capture were performed twice on biological replicates but only once for the negative control.
RNA-seq on RNA-immunoprecipitated with antibodies to Abeta, neurofilament heavy chain and Tau in lysate from human neurons. Two biological replicates of each IP were analysed, except for Abeta, where only one sample were available. Significantly associated transcripts were identified by comparing read densities in IP-samples to read densities in samples immunoprecipitated with non-specific IgG antibodies.

first: Johan

last: Aarum

first: Claudia

middle: P

last: Cabrera

first: Tania

last: Jones

first: Shiron

last: Rajendran

first: Gavin

last: Giovannoni

first: Michael

last: Barnes

first: Andrea

last: Malaspina


title: Transfer RNA Genes Affect Chromosome Architecture and Function

first: Razvan

last: Chereji

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

overall_design: Refer to individual Series


title: Ground state of pluripotency cannot be maintained in mouse embryonic stem cells upon prolonged inhibition of GSK3

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

institute: Centre for genomic regulation (CRG)

summary: We compare gene expression changes in mESCs culture in serum/LIF or 2i/LIF which favour the ground state pluripotency. Published RNASeq data where compared with newly generated data set in order to indentify transciptional signatures associated with pluripotency of mouse ES cells

overall_design: Examination of dynamic gene expression in mouse ES cells culture in convetional media (serum/LIF) and in 2i/LIF which favour the gorund state pluripotency

first: Elisa

last: Pedone

first: Lucia

last: Marucci

first: Maria

last: Cosma


title: Expansion of bacteriophages during disease worsens intestinal inflammation and colitis

status: Public on Mar 01 2019

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Purified phage was used to prevent tumor growth in a mouse model of bacteria aggravated-colorectal cancer. Composite E. coli phage or vehicle control was added to the drinking water of specific pathogen free (SPF) APCmin mice and animals were colonized with E.coli NC101. APCmin mice displayed no overall difference in the number of tumors that formed within the small intestine, however colonization with E. coli NC101 accelerated the growth of tumors resulting in a significant increase in large tumor formation. Importantly, bacteriophage treatment of AIEC colonized APCmin animals significantly reduced E. coli colonization.

overall_design: 4 week old APCmin heterozygous mice were given a cocktail of 3 E. coli phage in drinking water for 4 weeks, then challenged with E. coli NC101 via oral gavage biweekly for 2 weeks. Mice were then maintained on drinking water containing phage mixture for 2 months.

first: Lasha

last: Gogokhia

first: Zac

last: Stephens


title: Expression data from feathers of the black/red morphs of the Gouldian finches

city: Sheffield

first: Kang-Wook

last: Kim

address: Western Bank

department: Animal and Plant Sciences

institute: The University of Sheffield

summary:
Regenerating feathers of the Gouldian finches were collected from heads of moulting individuals from an Australian captive population.
Affymetrix microarrays were used to examine gene expression differences between black and red morphs.

overall_design: Gene expression in regenerating feathers of black (n=3) and red (n=3) individuals were measured on Affymetrix microarrays and compared.

first: Simon

last: Griffith

first: Terry

last: Burke


title: Single cell RNA sequencing of primary-isolated erythroid progenitors [BFUEs_Set2]

first: Hojun

last: Li

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: Single cell RNA sequencing of freshly isolated mouse burst forming unit-erythroid (BFU-E).

overall_design: One 96 well plate with 24 BFU-E.

first: Inma

last: Barrasa


title: Disruption of the exocyst induces podocyte loss and dysfunction

status: Public on Mar 02 2019

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President street

department: Medicine

institute: Medical University of South Carolina

summary: In this study we plan to compare the profiles of control sample (cultured podocytes) with the Exoc5 knock down in cutured podocytes to examine the differentially expressed genes.

overall_design: We hope to identify the genes that are downregulated on knocking down Exoc5 in cultured human podocytes cells


title: HLA Class II analysis of human pancreatic beta cells

city: Worcester

first: Alan

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: We interrogated the transcriptome from bulk-sorted T1D donor β-cells as compared to non-diabetic donors. We found β-cells also expressed mRNA for HLA Class II and Class II antigen presentation pathway components, but not a macrophage marker.

overall_design: Beta cells from 12 non-diabetic donors were compared to beta cells from 4 type I diabetic donors

first: David

last: Blodgett

first: Sambra

last: Redick

first: Alper

last: Kucukural

first: Manuel

last: GGarber

first: Alvin

last: Powers

last: Harlan


title: RNA-sequencing WT vs SOCS3 knockout Glioblastoma stem-cells

city: Toronto

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

summary: Glioblastoma stem cells were infected with lentivirus expressing a non-targeting (gRNA-LacZ) or SOCS3 targeting gRNA to assess the function of SOCS3 in the stem cell compartment of Glioblastoma

overall_design: Three biological replicates each of gRNA-LacZ and gRNA-SOCS3 GSCs (G510NS line)

first: Stephane

last: Angers


title: Comparison of methylome data generated with HiSeq X Ten and NovaSeq

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

institute: The University of Tokyo

type: Methylation profiling by high throughput sequencing

summary: To compare the difference of sequencing platform, a sequencing library was served for sequencing on HiSeq X Ten and NovaSeq 6000.

overall_design: Whole-genome bisulfite sequencing library was prepared with tPBAT protocol, then the library was served for sequencing on HiSeq X Ten and NovaSeq 6000.


title: Effect of miR-92a-3p and/or miR-489-3p inhibition on aorta endothelium of Apoe-/-;5/6Nx

city: Nashville

first: Kasey

last: Vickers

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University

summary: The role of endothelial miR-92a-3p and miR-489-3p in CKD-associated atherosclerosis was examined by mRNA expression analysis in Apoe-/- mice with 5/6 nephrectomy treated with locked-nucleic acid (LNA) inhibitors complexed with high-density lipoprotein (HDL).

overall_design: RNA sequencing of aortic endothelial cell total RNA from Apoe-/- (B6.129P2-Apoetm1Unc/J) with 5/6 nephrectomy for 7 weeks and one week after treatment with saline, HDL, HDL + LNA92a, HDL + LNA489, or HDL + LNA92a + LNA489. Surgery was performed on 9 week old female mice maintained on regular chow diet. The mice recieved a single retro-orbital treatment 7 weeks post surgery and were sacrificed 1 week post treatment. The aortic endothelium was sheared to collect total RNA, which was sequenced with 4 biological replicates per group.

first: Carrie

middle: B

last: Wiese


title: Single cell RNA sequencing of primary-isolated erythroid progenitors [BFUE, CFUE, intermediates]

city: Cambridge

summary: Single cell RNA sequencing of freshly isolated mouse burst forming unit-erythroid (BFU-E) , colony forming unit-erythroid (CFU-E), and intermediate stages of erythroid development cells.

overall_design: One 96 well plate with 24 BFU-E, 24 CFU-E, 24 cells with 25-35% expression of CD71/CD24, and 24 cells with 50-60% expression of CD71/CD24.


title: Single cell RNA sequencing of primary-isolated erythroid progenitors [daughter cells]

summary: Single cell mouse BFU-E  (burst forming unit-erythroid ) were FACS-deposited into individual wells of a 96-well plate containing PCM either with or without 100 nM dexamethasone. After 16hrs cells from wells that contained a single pair of daughter cells were separated and each individual daughter cell transcriptome was obtained by single cell RNA-seq.

overall_design: 13 daughter cells pairs untreated and 13 pairs treated with 100 nM dexamethasone.


title: Single cell RNA sequencing of primary-isolated erythroid progenitors [BFUE & CFUE]

summary: single cell RNA sequencing of freshly isolated mouse burst forming unit-erythroid (BFU-E) and colony forming unit-erythroid (CFU-E).

overall_design: one 96 well plate with BFUEs plus one 96 well plate with CFUEs


title: Single cell RNA sequencing of primary-isolated erythroid progenitors


title: Mesenchymal stem cells shift mitochondrial dynamics and enhance oxidative phosphorylation in recipient cells

city: Calgary

first: Christopher

last: Newell

address: 2500 University Dr NW

institute: University of Calgary

summary:
Mesenchymal stem cells (MSC) are the most commonly used cells in tissue engineering and regenerative medicine. MSC can promote host tissue repair through several different mechanisms including donor cell engraftment, release of cell signaling factors and the transfer of healthy organelles to the host. In the present study, we examine the specific impacts of MSC on mitochondrial morphology and function in host tissues. Employing in vitro cell culture of inherited mitochondrial disease and an in vivo animal experimental model of low-grade inflammation (high fat feeding), we show human-derived MSC to alter mitochondrial function. MSC co-culture of skin fibroblasts from mitochondrial disease patients rescued aberrant mitochondrial morphology from a fission state to a more fused appearance indicating an effect of MSC co-culture on host cell mitochondrial network formation. In vivo experiments confirmed mitochondrial abundance and mitochondrial oxygen consumption rates were elevated in host tissues following MSC treatment. Furthermore, microarray profiling identified 226 genes with differential expression in the liver of animals treated with MSC, with cellular signaling and actin cytoskeleton regulation as key upregulated processes. Collectively, our data indicate that MSC therapy rescues impaired mitochondrial morphology, enhances host metabolic capacity and induces widespread host gene shifting. These results highlight the potential of MSC to modulate mitochondria in both inherited and pathological disease states.
To examine the effect of MSC therapy on global gene expression and cell signaling pathways, microarray gene expression analysis was performed on liver tissues.

overall_design: Mice were fed a high-fat diet for 20 weeks and injected with either MSCs (HFM group) or saline as controls (HFS group) before being sacrificed 24 hours following injection and liver tissue harvested for microarray analysis. Expression profiling was performed using 5 μg of total RNA extracted from frozen liver tissue from animals in both groups (n = 7 per group due to damage of one sample per group in transit). Biotinylated cRNA was synthesized from cDNA and fragmentation as detailed in the manufacturer's protocol for GeneChip Mouse Gene 1.0 ST microarrays (Affymetrix; Santa Clara, CA).

first: Jane

last: Shearer

first: Dustin

last: Hittel


title: A chromatin modulator sustains self-renewal and enables differentiation of postnatal neural stem cells

city: Birmingham

first: Kushani

last: Shah

state: AL

address: 1825 University Blvd.

department: Biochemistry & Molecular Genetics

institute: University of Alabbama at Birmingham

summary: It remains largely unclear if efficient H3K4 methylation, an epigenetic modification associated with gene activation, regulates fate determination of the postnatal neural stem cells (NSCs). By inactivating the Dpy30 subunit of the major mammalian H3K4 methyltransferase complexes in specific regions of mouse brain, we demonstrate a crucial role of efficient H3K4 methylation in maintaining both the self-renewal and differentiation capacity of postnatal NSCs. Loss Dpy30 disrupts the development of dentate gyrus and subventricular zone, the major regions for postnatal NSC activities. Dpy30 is indispensable for sustaining the self-renewal of NSCs in a cell-intrinsic manner. Dpy30 also enables the differentiation of mouse and human neural progenitor cells to neuronal and glial lineages. Dpy30 directly regulates H3K4 methylation and the induction of several genes critical in neurogenesis. These findings link a prominent epigenetic mechanism of gene expression to the fundamental properties of NSCs, and may have implications in neurodevelopmental disorders.

overall_design: Samples 1-6 are RNA-seq from Dentate Gyrus (DG) and samples 7-12 are RNA-seq from Subventricular zone (SVZ) from mice of control and KO genotypes.

first: Gwendalyn

last: King

first: Hao

last: Jiang


title: The bZIP mutant CEBPB(V285A) has sequence specific DNA binding propensities similar to CREB1

city: Bethesda

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

institute: NIH/NCI


title: The expression profile of lung sqaumous cell carcinoma (SCC) and adenosquamous carcninoma (ASC) of CCSPiCreLkb1f/fPtenf/f mice

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

summary: Lung cancer, majorly divided into non-small cell lung cancer (80-85%) and small cell lung cancer (15-20%), is the leading cause of cancer death in USA. Squamous Cell Carcinoma (SCC) is one of major subtypes of non-small cell lung cancer. Although genomic analysis of tumors from SSC patients have identified frequently mutated genes in these tumors, it’s still largely unknown which genes determine SCC development. Now we found that ablation of Lkb1 and Pten could induce SCC and ASC around 3 months of age.  Therefore, transcriptome analysis of lung SCC and ASC of CCSPiCreLkb1f/f mice will help us understand how Lkb1 and Pten regulate the development of lung SCC and ASC.

overall_design: We compare gene expression levels in mouse lungs and tumors in the following groups. Specifically, 3-month-old wild type mouse (Lkb1f/fPtenf/f) lungs will be collected as the control group, and SCC of 3-month-old CCSPiCreLkb1f/fPtenf/f mice will be collected as the tumor groups.

first: Francesco

last: DeMayo


title: The bZIP mutant CEBPB(V285A) has DNA binding propensities similar to CREB1 [CEBPMut_5mC_5hmC]

summary: The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. The X-ray structure of CREB1 binding the half site GTCA identifies an alanine in the DNA binding region interacting with the methyl group of T, structurally analogous to the methyl group of methylated C. This alanine is replaced with a valine in CEBPB. To explore the contribution of this amino acid to binding with methylated cytosine of the GCAA half-site, we made the reciprocal mutants CEBPB(V285A) and CREB1(A297V) and used protein binding microarrays (PBM) to examine binding to four types of double-stranded DNA (dsDNA): 1) DNA with cytosine in both strands (DNA(C|C)), 2) DNA with 5-methylcytosine (M) in one strand and cytosine in the second strand (DNA(M|C)), 3) DNA with 5-hydroxymethylcytosine (H) in one strand and cytosine in the second strand (DNA(H|C)), and 4) DNA with both cytosines in all CG dinucleotides contain- ing 5mC (DNA(5mCG)). When binding to DNA(C|C), CEBPB (V285A) preferentially binds the CRE consensus motif (TGACGTCA), similar to CREB1. The reciprocal mutant, CREB1(A297V) binds DNA with some similarity to CEBPB with strongest binding to the methylated PAR site 8-mer TTACGTAA. These data demonstrate that V285 residue inhibits CEBPB binding to methylated cytosine of the GCAA half-site.

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of CEBPB, CREB1, and the two mutants CEBPB(V285A) and CREB1(A297V).  Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines.  We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine.  Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.


title: Single cell RNA sequencing of primary-isolated erythroid progenitors [Days 1-3]

first: Hojun

last: Li

summary: single cell RNA sequencing of freshly isolated mouse BFU-E  (burst forming unit-erythroid ) cells cultured for 1, 2, or 3 days with and without 100nM dexamethasone

overall_design: six 96 well plates

first: Inma

last: Barrasa


title: The bZIP mutant CEBPB(V285A) has sequence specific DNA binding propensities similar to CREB1 [CEBPMut_5mCG]

summary: The bZIP homodimers CEBPB and CREB1 bind DNA containing methylated cytosines differently. CREB1 binds stronger to the C/EBP half-site GCAA when the cytosine is methylated. For CEBPB, methylation of the same cytosine does not affect DNA binding. The X-ray structure of CREB1 binding the half site GTCA identifies an alanine in the DNA binding region interacting with the methyl group of T, structurally analogous to the methyl group of methylated C. This alanine is replaced with a valine in CEBPB. To explore the contribution of this amino acid to binding with methylated cytosine of the GCAA half-site, we made the reciprocal mutants CEBPB(V285A) and CREB1(A297V) and used protein binding microarrays (PBM) to examine binding to four types of double-stranded DNA (dsDNA): 1) DNA with cytosine in both strands (DNA(C|C)), 2) DNA with 5-methylcytosine (M) in one strand and cytosine in the second strand (DNA(M|C)), 3) DNA with 5-hydroxymethylcytosine (H) in one strand and cytosine in the second strand (DNA(H|C)), and 4) DNA with both cytosines in all CG dinucleotides containing 5mC (DNA(5mCG)). When binding to DNA(C|C), CEBPB (V285A) preferentially binds the CRE consensus motif (TGACGTCA), similar to CREB1. The reciprocal mutant, CREB1(A297V) binds DNA with some similarity to CEBPB with strongest binding to the methylated PAR site 8-mer TTACGTAA. These data demonstrate that V285 residue inhibits CEBPB binding to methylated cytosine of the GCAA half-site.

overall_design: Protein binding microarray (PBM) experiments were performed for the DNA binding domain of CEBPB, CREB1, and the two mutants CEBPB(V285A) and CREB1(A297V).   Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded and methylated or unmethylated 44K Agilent microarrays, containing a DeBruijn sequence design, in order to determine their sequence preferences. Details of the methylated PBM protocol are described in Mann et al., Genome Research, 2013


title: The Role of JNK1/2 in Mouse Lung Squamous Cell Carcinoma (SCC) Development

summary: Lung cancer is the leading cause of cancer death in USA. Squamous Cell Carcinoma (SCC) is one of the subtypes of lung cancer. It is still largely unknown which genes or pathways regulate lung SCC development. Recently, we found JNK1/2 pathway was inhibited in mouse lung SCC induced by double ablation of Pten and Lkb1 in mouse lung epithelial cells.  Now we aim to identify a genome-wide molecular signature of JNK1/2 signaling in mouse squamous cell carcinoma cells and determine pathways that transduce JNK1/2 signaling.

overall_design: We will compare gene expression levels in mouse SCC cells in gRNA -Control group and gRNA-Jnk1/2 group.


title: Transcriptomic screen to identify genes regulated by IP3R in Drosophila third-instar larval nervous system

city: Bangalore

first: Gaiti

last: Hasan

address: GKVK Campus,

country: India

institute: NCBS, TIFR

summary: Organisms need to co-ordinate growth with development particularly in the context of nutrient availability. Thus, multiple ways have evolved to survive extrinsic nutrient deprivation during development. In the holometabolous insect Drosophila, growth occurs during larval development.  Larvae are therefore critically dependent on nutritional inputs for pupariation. Post critical weight however, they pupariate even when starved. How nutrient availability is coupled to the internal metabolic state for the decision to pupariate in not well understood and needs better understanding. Wild type larvae, when subjected to nutrient deprivation as mid-third instar larvae, pupariate and also emerge as adults, even though smaller than normally fed ones (Jayakumar et al., 2016; Megha and Hasan, 2017).  A recent study (Jayakumar et al., 2016) identified a neuronal circuit that enables wild-type larvae to survive protein deprivation and pupariate. IP3R function in a subset of glutamatergic neurons is a crucial part of the circuit. However, the cellular role of IP3R in these neurons is not understood.  In Drosophila neurons, the IP3R causes and facilitates store-operated calcium entry (Chakraborty et al., 2016; Venkiteswaran and Hasan, 2009). Thus it is likely, that the IP3R also regulates expression of genes that regulate this phenomenon. In this study, we have compared the gene expression profiles of control and itpr knockdown larval brains to identify genes that act downstream of the IP3R to regulate pupariation under nutrition stress.

overall_design: mRNA sequencing from three biological relicates of control and two biological replicates of IP3R knockdown third instar larval brains

first: Shlesha

last: Richhariya


title: RIP-Seq of EBNA1 from EBV in HEK293T cells

city: Sherbrooke

first: Bisaillon

last: Martin

state: Québec

address: 3201, rue Jean-Mignault

department: Biochimie

institute: Université de Sherbrooke

summary: RIP-Seq of the viral protein EBNA1-HA-FLAG from EBV in HEK293T cells

overall_design: RIP-Seq of the viral protein EBNA1-HA-FLAG from EBV was carried in HEK293T cells and in control HEK293T cells using anti-HA beads

first: S

last: Boudreault

first: M

last: Bisaillon

last: Scott


title: The Role of Lkb1 in Mouse Lung Squamous Cell Carcinoma (SCC) Development

summary: Lung cancer, majorly divided into non-small cell lung cancer (80-85%) and small cell lung cancer (15-20%), is the leading cause of cancer death in USA. Squamous Cell Carcinoma (SCC) is one of major subtypes of non-small cell lung cancer. Although genomic analysis of tumors from SSC patients have identified frequently mutated genes in these tumors, it’s still largely unknown which genes determine SCC development. Now we found that ablation of alone Lkb1 could induce SCC around 12 months of age.  Therefore, transcriptome analysis of lung SCC of CCSPiCreLkb1f/f mice will help us understand how Lkb1 regulates the development of lung SCC.

overall_design: We compare gene expression levels in mouse lungs and tumors in the following groups. Specifically, 13-month-old wild type mouse (Lkb1f/f) lungs will be collected as the control group, and SCC of 13-month-old CCSPiCreLkb1f/f mice will be collected as the tumor groups.


title: Preclinical model of obesity and ER-positive breast cancer

city: Oklahoma City

first: Elizabeth

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

summary: Here, we developed a mouse model of diet induced obesity that is graft competent.  In this model, we grew an ER-positive breast cancer patient derived tumor.  Following ovariectomy and estrogen deprivation therapy, tumors continued to grow in obese but not lean mice.  RNAsequencing analysis was performed on tumors from estrogen-supplemented lean mice, and from lean and obese mice after estrogen deprivation.  This analysis identified fibroblast growth factor receptor signaling as a potential driver of tumor progression in the context of obesity.

overall_design: LFLS E2 N=4; LFLS EWD N=4; HFHS EWD N=4, HFHS E2 N=3

first: Paul

last: MacLean

first: Austin

last: Gillen


title: Whole transcriptome RNA sequencing of E16.5 Six2TGC and Six2TGC;miR-17~92fl/fl nephron progenitors

city: Pittsburgh

first: Jacqueline

last: Ho

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: Children's Hospital of Pittsburgh

summary: The goal of this study is to identify dysregulated mRNAs and lncRNAs in nephron progenitors as a consequence of a loss of miR-17~92 post-transcriptional regulation

overall_design: Nephron progenitors were FACS sorted from E16.5 Six2TGC (Control) and Six2TGC;miR-17~92fl/fl (Mutant) kidneys based on the GFP driven by the Six2 locus. A total of 3 replicates per genotype were used for the whole transcriptome RNA sequencing. Each replicate consists of nephron progenitors pooled from 4 embryos, resulting in 12 samples per genotype assayed in this manner.

first: Y

last: Phua

first: J


title: Hippo Deficiency Leads to Cardiac Dysfunction with Cardiomyocyte De-differentiation

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

summary: The Hippo pathway regulates organ size by modulating cell proliferation and apoptosis. It is activated by myocardial stress and contributes to myocardial injury by promoting cardiomyocyte apoptosis. We investigated the role of the endogenous Hippo pathway in the stressed heart, using cardiac-specific WW45 knockout mice (WW45 cKO). Unexpectedly, chronic suppression of the Hippo pathway exacerbated the progression of heart failure induced by pressure overload (PO), despite reducing apoptosis and promoting cardiomyocyte proliferation. WW45 downregulation induced upregulation of YAP and TEF-1 target genes, including oncostatin M (OSM), and fetal-type genes involved in de-differentiation, as well as myofibrillar disorganization and dysfunction in cardiomyocytes. OSM upregulation further upregulated YAP/TEF-1, thereby potentiating de-differentiation. Suppression of any component of the amplification loop, namely YAP, TEF-1, or OSM, inhibited the effect of Hippo downregulation. Thus, cardiomyocytes under stress risk apoptotic death by activating the Hippo pathway in order to maintain differentiation and contraction against hemodynamic overload.

overall_design: Cardiac mRNA profiles of 3-months old control (flox/flox) and cardiac specific WW45 knockout (flox/flox-alpha-MHC-CRE) mice were generated. 1 CT and 1 WW45 cKO mice were at baseline conditions, whereas 1 CT and 1 WW45 cKO were subjected to 4 weeks of transverse aortic constriction (TAC).

first: Ji Yeon

first: Bin

last: Tian

first: Sebastiano

last: Sciarretta

first: Junichi

last: Sadoshima


title: Analysis of gene expression in primary human foreskin keratinocytes +/- HPV16 E7 or PTPN14 knockout

status: Public on Feb 28 2019

city: Philadelphia

last: White

address: 3610 Hamilton Walk, 203C Johnson Pavilion, Mail Code 6114

department: Otorhinolaryngology

institute: University of Pennsylvania

summary: This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV16 E7 or several HPV16 E7 variants.  We also generated and conducted RNA-seq on primary human foreskin keratinocytes that were CRISPR-Cas9 edited with nontargeting sgRNA or sgRNA targeting PTPN14.

overall_design: mRNA profiles in primary HFK were generated for the following samples (# of replicates): empty vector (3), HPV16 E7 (3), HPV16 E7 ∆21-24 (also known as ∆DLYC) (2), Cas9 + nontargeting sgRNA (2), Cas9 + sgRNA targeting PTPN14 (2).  Retroviral vectors are MSCV-IP N-HA empty or MSCV-P C-FlagHA for E7 expression.  CRISPR-Cas9 vectors are LentiCRISPR v2 with sgRNA sequences from Brunello sgRNA library (Doench et al (2016) Nature biotechnology 34, 184-191.)


title: Differential expression of  miRNA  in stage-specific prostate cancer

city: Cleveland

first: Shiv

middle: Shankar

last: Verma

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

summary: Dysregulation of microRNAs (miRNAs) can majorly contribute to prostate cancer tumor development, progression, and are differentially expressed in normal and cancer tissues. Glass-based chip assay was designed for prostate cancer cell lines; from early disease stage to advance and to castration resistance prostate cancer (CRPC). We have used glass based chip microarray assay (miRNA-microarray); and our attempt identified that the expression of miR-301 was upregulated at early stage and miR- 146/146b showed increased in expression during the advanced stage of prostate cancer. While the expression of miR-205 and miR-221 was consistently downregulated across all the disease stage; from early to advanced and also during the CRPC stage. Also, we have identified some disease-specific/signature miRNAs for e.g. miR-204 which was differentially expressed only during early stage of prostate cancer and miR-520 was during CRPC stage.

overall_design: The expression of  non coding RNA (miRNA) of normal prostate cell line and prostate cancer cell lines (AR positive and AR negative) were analyzed

first: Sanjay

last: Gupta


title: Defining transcription factor networks that govers SCC growth [RNA-Seq]

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

summary: Differential gene expression analysis were performed between Pitx1 silenced SCC cells and controls in two independent SCC lines

overall_design: Compared control and Pitx1 deficient cells to define gene sets control by Pitx1 in SCCs.

first: Sastre-Perona

last: Ana

first: Schober

last: Markus


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CRC_ATAC]

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Lineage tracing provides unprecedented insights into the fate of individual cells and their progeny in complex organisms. While effective genetic approaches have been developed in vitro and in animal models, these cannot be used to interrogate human physiology in vivo. Instead, naturally occurring somatic mutations have been utilized to infer clonality and lineal relationships between cells in human tissues, but current approaches are limited by high error rates and scale, and provide little information about the state or function of the cells. Here, we show how somatic mutations in mitochondrial DNA (mtDNA) can be tracked by current single cell RNA-Seq (scRNA-Seq) or single cell ATAC-Seq (scATAC-Seq) for simultaneous analysis of single cell lineage and state. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their use as clonal markers to infer lineal relationships. We trace the lineage of human cells by somatic mtDNA mutations in a native context both in vitro and in vivo, and relate it to expression profiles and chromatin accessibility. Our approach should allow lineage tracing at a 100- to 1,000-fold greater scale than with single cell whole genome sequencing, while providing information on cell state, opening the way to chart detailed cell lineage and fate maps in human health and disease.

overall_design: Primary cells from a patient with colorectal adenocarcinoma were sorted based on EPCAM+ surface marker expression and forwarded to a combination of 1) ATAC-seq and single cell RNA-seq. ATAC-seq from the tumor plus two adjacent healthy tissue samples are shown here.

first: Leif

last: Ludwig


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CRC_scRNA]

overall_design: Primary cells from a patient with colorectal adenocarcinoma were sorted based on EPCAM+ surface marker expression and forwarded to a combination of 1) ATAC-seq and single cell RNA-seq. The single-cell RNA-seq data are listed here.


title: Genome-wide mapping of Lef1 occupancy in conventional CD4+ T cells

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Determine genome-wide binding locations by Lef1 in conventional CD4+ T cells

overall_design: WT C57BL/6 mice at 8-10 weeks old were used to sort purify for conventional CD4+ (GFP-CD25-) cells from the spleen, and the cells were used in ChIP-Seq analysis.

first: Hai-Hui

last: Xue


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_barcoding_ATAC]

overall_design: A population of 25 transfected TF1 cells were expanded and forwarded to a combination of 1) ATAC-seq and single cell RNA-seq. The bulk ATAC-seq sample is listed here. Meta data includes heteroplasmic variant information for both the bulk and sum of single cells.


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_barcoding_scRNA]

overall_design: A population of 25 transfected TF1 cells were expanded and forwarded to a combination of 1) ATAC-seq and single cell RNA-seq. The single-cell RNA-seq data are listed here. Meta data includes heteroplasmic variant information per cell as well as the group assigned based on the lentiviral barcoding


title: Single cell RNA-sequencing of 75-day old human H1 and H9 embryonic stem cell-derived cerebral organoids

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

institute: University of Cambridge

summary: The scRNA-seq analysis of 75 day old human cerebral organoids grown at the air-liquid interface (ALI-COs) reveals six well-defined major clusters. Cell-type and maturity markers define a (1) distinct population of deep layer subcortical projection neurons, (2) upper layer intracortical (callosal) projection neurons and intermediate progenitors, (3) ventricular and subventricular zone radial glial cells, (4) more mature upper and deep layer neurons, (5) interneurons and (6) actively dividing cells with intermediate progenitor and radial glia markers. In addition, the gene expression profile of these clusters corresponds with their expected functional characteristics appropriate to their maturity. Altogether, our data reflect a full repertoire of cortical neuronal and progenitor identities corresponding with the stages of cortical development in age-matched fetal brains.

overall_design: Single cell RNA-sequencing data was generated using the 10X Genomics Chromium Single Cell 3' Chip and workflow.

first: George

last: Gibbons

first: Stefano

last: Giandomenico

first: Marco

last: Galardini

first: Pedro

last: Beltrao

first: Madeline

last: Lancaster

first: Andras

last: Lakatos


title: Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (Hi-C)

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

summary: Mechanisms by which the mammalian gametes encode epigenetic information that can be transmitted to the progeny are relatively unknown. We find that many sperm promoters in mouse sperm are occupied by phosphorylated forms of RNA polymerase II and the Mediator complex. Analysis of ATAC-seq data suggest that the same promoters are occupied by components of the transcription complex in GV and MII oocytes and preimplantation embryos. Furthermore, distal ATAC-seq sites containing transcription factor motifs are conserved in monkeys and humans. ChIP-seq analyses confirm that transcription factors, including FoxA1 and the androgen and estrogen receptors, occupy distal enhancers. These sites and their interactions with promoters in the gametes are maintained in the early embryo. Additionally, sperm- or oocyte-specific interactions mediated by CTCF/cohesin are only present in the paternal or maternal chromosome, respectively in the zygote and 2-cell stages. These interactions converge in both chromosomes by the 8-cell stage. These results suggest that the mammalian gametes contain a large repertoire of transcription factors that organize a complex pattern of 3D interactions and can be transmitted to the zygote after fertilization.

overall_design: Analysis of transcription factors in sperm by Hi-C

first: Yoon

middle: H

first: Hannah

last: Gold

first: Isaac

last: Kremsky

first: M

last: Rowley

first: Brianna

last: Bixler

first: Kanchana

last: Punyawai

first: Anthony

middle: W

last: Chan

first: Victor

last: Corces


title: Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

city: Boston

first: Hongjae

last: Sunwoo

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School, HHMI

summary: During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/ Polycomb spreading, silencing, and changes in chromosome architecture.

overall_design:
Xist CHART-seq, H3K27me3 ChIP-seq, H2AK119ub ChIP-seq in WT, Xist RepB, EED KO, RING1A/B KO MEF cells.
RNA-seq in WT MEF, Xist RepB mutant MEF, WT ES and two RepB mutant ES cells.
in situ HiC in WT MEF, Xist RepB mutant MEF, WT ES, and RepB mutant ES cells

first: D

last: Colognori

first: H

first: A

last: Kriz

first: C

last: Wang

first: J

middle: T

last: Lee


title: Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ATAC-seq)

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: Analysis of transcription factors in sperm, GV-stage oocytes, and MII-stage oocytes by ATAC-seq

middle: J


title: Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ChIP-seq)

overall_design: Analysis of transcription factors in sperm by ChIP-seq


title: Computational detection and experimental validation of segmental duplications and associated copy number variants in river buffalo (Bubalus bubalis)

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

type: Genome variation profiling by genome tiling array

summary: Duplicated sequences are the important source of gene innovation and structural variation within mammalian genomes. Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). Aligning to the UMD3.1 cattle genome, we estimated 44.6 Mb (~1.73% of cattle genome) segmental duplications in the autosomes and X chromosome using the sequencing reads of Olimpia (the sequenced water buffalo). 70.3% (70/101) duplications were experimentally validated using the fluorescent in situ hybridization. We also detected a total of 1344 CNV regions across 14 additional water buffalos as well as Olimpia, amounting to 59.8Mb of variable sequence or 2.2% of the cattle genome. The CNV regions overlap 1245 genes and are significantly enriched for specific biological functions such as immune response, oxygen transport, sensory system and signalling transduction. Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffalos as test samples and Olimpia as the reference. Using a linear regression model, significant and high Pearson correlations (r = 0.781) were observed between the digital aCGH values and aCGH probe log2 ratios. We further designed Quantitative PCR assays to confirm CNV regions within or near annotated genes and found 74.2% agreement with our CNV predictions.

overall_design: Whole genome high-denstiy CGH arrays manufactured by Agilent containing ~974,016 oligonucleotide probes were designed and fabricated on a single slide to provide an evenly distributed coverage on cattle UMD3.1 with an average interval of ~3.1 kb between probes. The reference animal chosen was Olimpia, an Italian Mediterranean river buffalo.

first: Shuli


title: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [ATAC-Seq]

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

summary: We performed ATAC-seq  on WT, BAF60c KO, and BAF170 KO CPs and CMs in 2-5 biological replicates follwing Corces et al., 2017 paper.

overall_design: ATACSeq was performed for each samples with 50, 000 viable cells, libraries were sequenced with NEB nextSeq system using high throuput V2 150 cycle kit.

first: Swetansu

last: Hota


title: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq II]

summary: We performed differential mRNA analysis in WT and BRG1 KO cells during  cardiac precursor and cardiomyocytes stages of directed differention of mouse ES cells to cardiac myocytes. We show that BRG1 activity is  higher in  cardiac precursor cells and severely reduced in cardiac myocytes

overall_design: 12 samples, triplicates


title: Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo

first: Yoonhee

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

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [ChIP-Seq]

summary: Genome-wide occupancy analysis of BRG1 during cardiac precursor and crdiomyocyte stages of differentiation in WT and cells lacking BAF60c or BAF170

overall_design: BRG1 ChIPSeq was performed in cardiac precursor and cardiomyoctes in  wild type cells and cells lacking BAF60c or BAF170 proteins


title: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CC100_scATAC]

first: Caleb

last: Lareau

summary:
Lineage tracing provides unprecedented insights into the fate of individual cells and their progeny in complex organisms. While effective genetic approaches have been developed in vitro and in animal models, these cannot be used to interrogate human physiology in vivo. Instead, naturally occurring somatic mutations have been utilized to infer clonality and lineal relationships between cells in human tissues, but current approaches are limited by high error rates and scale, and provide little information about the state or function of the cells. Here, we show how somatic mutations in mitochondrial DNA (mtDNA) can be tracked by current single cell RNA-Seq (scRNA-Seq) or single cell ATAC-Seq (scATAC-Seq) for simultaneous analysis of single cell lineage and state. We leverage somatic mtDNA mutations as natural genetic barcodes and demonstrate their use as clonal markers to infer lineal relationships. We trace the lineage of human cells by somatic mtDNA mutations in a native context both in vitro and in vivo, and relate it to expression profiles and chromatin accessibility. Our approach should allow lineage tracing at a 100- to 1,000-fold greater scale than with single cell whole genome sequencing, while providing information on cell state, opening the way to chart detailed cell lineage and fate maps in human health and disease.
A variety of experimental designs using cells derived from both in vitro and in vivo to determine the efficacy of using mtDNA mutations in human clonal tracing.

overall_design: A population of 30 primary hematopoietic cells were expanded and forwarded to a combination of ATAC-seq and single cell ATAC-seq. single cell ATAC-seq samples are listed here.

first: Leif

last: Ludwig


title: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq III]

summary: We compared differential gene expression between WT and BAF60c KO  and between WT and BAF170 KO cardiac precursors and cardiomyocytes

overall_design: 18 samples


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CC100_ATAC]

overall_design: A population of 30 primary hematopoietic cells were expanded and forwarded to a combination of 1) ATAC-seq and single cell ATAC-seq OR 2) ATAC-seq and scRNA-seq. Both bulk ATAC-seq samples are listed here. Meta data includes heteroplasmic variant information for both the bulk and sum of single cells


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [Colonies_ATAC]

overall_design: Primary hematopoietic colonies were processed with bulk ATAC-seq


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_scMito]

overall_design: Individually sorted cells from clonally derived TF1 clones (C9, D6, and G10) were processed with single cell Mito-seq


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [CC100_scRNA]

overall_design: A population of 30 primary hematopoietic cells were expanded and forwarded to a combination of ATAC-seq and single cell RNA-seq. single cell RNA-seq samples are listed here.


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_scATAC]

overall_design: Clonally derived TF1 clones (C9, D6, and G10) were processed with single cell ATAC-seq using the Fluidigm C1 machine


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_scRNA]

overall_design: Individually sorted cells from clonally derived TF1 clones  (C9, D6, and G10) were processed with single cell RNA-seq (Smart-seq2)


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [Colonies_scRNA]

overall_design: Single cells from clonally derived hematopoietic colonies were processed with single cell RNA-seq (Smart-seq2)


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_RNA]

overall_design: Cells from 3 separate TF1 clones (C9, D6, and G10) were processed with bulk RNA-seq (Smart-seq2)


title: Human lineage tracing enabled by mitochondrial mutations and single cell genomics [TF1_clones_ATAC]

overall_design: TF1 (sub-)clones were clonally derived by single cell sorting in an iterative manner and expanded before processing each clone with bulk ATAC-seq. Sample names reflect the clonal lineage order


title: Fetal ovary expression profile

status: Public on Feb 27 2019

first: Svetlana

last: Yatsenko

address: 300 Halket St

institute: University of Pittsburgh

summary: We sequenced RNA extracted from a 21-weeks gestation human ovary, at the time when dynamic developmental changes occur in human ovarian development and include primordial follicle formation. We examined genes comprised by copy number variants in fertile and POI women for their expression level in ovarian tissue.

overall_design: analysis of genes expreesion in fetal ovaries

first: Yatsenko

last: Svetlana

first: Rajkovic

last: Aleksandar


title: GATA3 enhances the neurogenic potential of primary human astrocytes after traumatic injury [exp2]

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

summary: Astrocytes are an abundant cell type in the vertebrate central nervous system and can act as neural stem cells in specialized niches where they constitutively generate new neurons. Outside the stem cell niches, however, these glial cells are not neurogenic. Although injuries in the mammalian central nervous system lead to profound proliferation of reactive astrocytes (RAs), which cluster at the lesion site to form a gliotic scar, neurogenesis does not take place. Therefore, a plausible regenerative therapeutic option is to coax the RAs to form neurons as an endogenous reservoir for repair. However, little is known on the mechanisms by which regenerative neurogenesis can be induced in mammalian RAs. In zebrafish, Gata acts as a regenerative factor that induces the plasticity of glial cells after injury. However, the effects of GATA in human astrocytes are not known. Therefore, in this report, we investigated how overexpression of GATA in primary fetal human astrocytes would affect the neurogenic potential before and after injury, and determined the transcriptional regulation exerted by GATA using next-generation sequencing. We found that GATA expression in primary human astrocyte cultures is not induced after scratch injury. Lentivirus-mediated overexpression of GATA significantly increased the number of SOX- expressing neural progenitors and altered the expression levels of genes related to cell proliferation and neurogenesis. Our results suggest that GATA is sufficient for enhancing the neurogenic potential of primary human astrocytes  after injury.

overall_design: GFP or GATA3 tansduced primary human astrocytes were cultured in 3D StarPEG-Heparin hydrogels, stab lesions were created and RNA was isolated.

first: Hilal

last: Celikkaya

first: Mehmet

middle: I

last: Cosacak


title: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [HCC1599_HiChIP]

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

summary:
Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells.
Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states.
Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes.
Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells.

overall_design: ChIP-seq, RNA-seq and HiChIP in Notch-on, -off, -recovery conditions in TNBC and MCL cell lines to profile Notch transcriptional complex binding, histone modification, Notch target genes and contact between regulatory elements.

first: Yeqiao

last: Zhou

first: Jelena

last: Petrovic

first: Robert

last: Faryabi


title: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [Rec-1_HiChIP]

overall_design: ChIP-seq, RNA-seq and SMC1 HiChIP in Notch-on, -off, -recovery conditions in TNBC and MCL cell lines to profile Notch transcriptional complex binding, histone modification, Notch target genes and contact between regulatory elements.


title: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_HiChIP]


title: Rapid recapitulation of non-alcoholic steatohepatitis upon loss of HCF-1 function in mouse hepatocytes [ChIP-seq]

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

summary: Background and Aims: Host-cell factor 1 (HCF-1), encoded by the ubiquitously expressed X linked gene Hcfc1, is an epigenetic co-regulator important for mouse development and cell proliferation, including during liver regeneration. Here, we examine the role of HCF-1 in adult tissue physiology using, as model, the resting mouse liver. Methods: We used a hepatocyte-specific inducible Hcfc1 knock-out allele (called Hcfc1hepKO), to induce HCF-1 loss in hepatocytes of hemizygous Hcfc1 hepKO/Y males by four days. In heterozygous Hcfc1hepKO/+ females, owing to random X-chromosome inactivation, upon Hcfc1hepKO allele induction, a 50/50 mix of HCF-1 positive and negative hepatocyte clusters is engineered. Results: The livers with Hcfc1hepKO/Y hepatocytes displayed a 21 24-day terminal non-alcoholic fatty liver (NAFL) followed by non-alcoholic steatohepatitis (NASH) disease progression typical of severe NAFL disease (NAFLD). In contrast, in livers with heterozygous Hcfc1hepKO/+ hepatocytes, HCF-1-positive hepatocytes replaced HCF-1-negative hepatocytes and revealed only mild-NAFL development. Loss of HCF-1 led to loss of PGC1 alpha protein levels, probably owing to its destabilization, and deregulation of gene expression particularly of genes involved in mitochondrial structure and function, likely explaining the severe Hcfc1hepKO/Y liver pathology. Interestingly, although HCF-1 binds to over 5000 transcriptional start sites in the resting liver, expression of only a minor subset of the associated genes was affected by HCF-1 loss. Conclusion: HCF-1 is essential for proper liver physiology likely playing both transcriptional and non-transcriptional roles. These genetically-engineered loss-of-HCF-1 mice represent models for the study of NASH and NAFLD resolution.

overall_design: Mouse liver from Male KO were subjected to HCF1 ChIP and then sequenced at day zero and day four after Tamoxifen injection. Both samples have their corresponding Input data.

first: Shilpi

last: Minocha

first: Viviane

last: Praz

first: Dominic

last: Villeneuve

first: Catherine

last: Moret

first: Maykel

last: Lopes

first: Danièle

last: Pinatel

first: Winship

last: Herr


title: Rapid recapitulation of non-alcoholic steatohepatitis upon loss of HCF-1 function in mouse hepatocytes

overall_design: Refer to individual Series


title: Rapid recapitulation of non-alcoholic steatohepatitis upon loss of HCF-1 function in mouse hepatocytes [RNA-seq]

summary: Background and Aims: Host-cell factor 1 (HCF-1), encoded by the ubiquitously expressed X linked gene Hcfc1, is an epigenetic co-regulator important for mouse development and cell proliferation, including during liver regeneration. Here, we examine the role of HCF-1 in adult tissue physiology using, as model, the resting mouse liver. Methods: We used a hepatocyte-specific inducible Hcfc1 knock-out allele (called Hcfc1hepKO), to induce HCF-1 loss in hepatocytes of hemizygous Hcfc1 hepKO/Y males by four days. In heterozygous Hcfc1hepKO/+ females, owing to random X-chromosome inactivation, upon Hcfc1hepKO allele induction, a 50/50 mix of HCF-1 positive and negative hepatocyte clusters is engineered. Results: The livers with Hcfc1hepKO/Y hepatocytes displayed a 21–24-day terminal non-alcoholic fatty liver (NAFL) followed by non-alcoholic steatohepatitis (NASH) disease progression typical of severe NAFL disease (NAFLD). In contrast, in livers with heterozygous Hcfc1hepKO/+ hepatocytes, HCF-1-positive hepatocytes replaced HCF-1-negative hepatocytes and revealed only mild-NAFL development. Loss of HCF-1 led to loss of PGC1 alpha protein levels, probably owing to its destabilization, and deregulation of gene expression particularly of genes involved in mitochondrial structure and function, likely explaining the severe Hcfc1hepKO/Y liver pathology. Interestingly, although HCF-1 binds to over 5000 transcriptional start sites in the resting liver, expression of only a minor subset of the associated genes was affected by HCF-1 loss. Conclusion: HCF-1 is essential for proper liver physiology likely playing both transcriptional and non-transcriptional roles. These genetically-engineered loss-of-HCF-1 mice represent models for the study of NASH and NAFLD resolution.

overall_design: Mouse liver samples from male WT, male KO, and female heterorygotes were collected from day zero to day 14 after Tamoxifen injection. Replicates were generated for all male samples from day zero to day nine, and for male KO at day 14 as well. The total number of samples sequenced is 63.


title: GBM microglia

city: St Louis

first: Winnie

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

summary: High grade glioma in mice and human have been shown to be greatly impacted by the infiltration of macrophages in the tumor, but it is unknown whether the populations of macrophages in the tumors may have different roles in the tumor. Flow sorting and high throughput RNA-seq was employed to examine the two main populations of macrophages in the high grade mouse glioma, denoted by the high or low surface expression of CD45, and they were compared to the resident population of microglia in normal brain tissues that express low levels of CD45.

overall_design: Ntv-a;Ink4a-Arf-/-;Gli-luc macrophages from mice were flow sorted. Upregulated genes of glioma associated microglia were verified and further examined.

first: Jason

last: Walker

first: Todd

last: Wylie

first: Vincent

last: Magrini

first: Malachi

last: Griffith

first: Obi

middle: L

first: Elaine

middle: R

last: Mardis

first: David

last: Gutmann

first: Jasreet

last: Hundal


title: miR-19 protects heart from myocardium infarction

status: Public on Feb 26 2019

city: Hangzhou

first: Jinghai

last: Chen

address: 268 Kai-Xuan Road, North Central Building 540

department: Institute of Translational Medicine

institute: Zhejiang University

summary: The adult heart has been considered as an organ with limited regenerating capability due to mature cardiomyocytes exit the cell cycle and stop proliferating. It has been reported that miR-17-92 cluster plays a key role in cardiomyocyte proliferation. According to the seed sequence, miR-17-92 cluster includes miR-18, miR-19, miR-20 and miR-92 families. Here, we show that intra-cardiac injection of miR-19 mimic into adult mouse hearts protects heart from myocardial infarction injury with reduced apoptosis, enhanced cardiomyocyte proliferation and cardiac regeneration. We performed the RNA-seq profiling in both injection of control mimic and miR-19 mimic post myocardial infarction. The transcriptome analysis indicates that genes related to immune response and cardiac remodeling were repressed by miR-19 in infarcted hearts.

overall_design: Examine expression of mRNAs in control mimic and miR-19 mimic injected hearts after myocardium infarction

first: Da-zhi

last: Wang


title: GATA3 enhances the neurogenic potential of primary human astrocytes after traumatic injury [exp1]

first: Caghan

last: Kizil

overall_design: GFP or GATA3 tansduced human primary astrocytes 2D culture were scratched and RNA isolation done

first: Hilal

last: Celikkaya

first: Mehmet

last: Cosacak


title: ONECUT2 Drives Neuroendocrine Prostate Cancer Through Hypoxia Signaling

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: To determine the underlying mechanism of ONECUT2 in prostate cancer hypoxia, we conducted a series of RNA-Seq and ChIP-Seq experiments in LNCaP and PC3 cells under normoxia and hypoxia conditions. We did RNA-Seq in LNCaP cells with or without OC2 overexpression and in PC3 cells with or without OC2 knockdown. We used anti-Flag antibody to perform the ChIP-Seq experiment in PC3 cells with Flag and OC2 fusion protein overexpression. We also performed HIF1A ChIP-Seq in AR-negative prostate cancer cell line PC3 under hypoxia condition with or without ONECUT2 or SMAD3 siRNA knockdown. SMAD3 and HIF2A ChIP-Seq were conducted in PC3 cells under hypoxia condition. To confirm the interactions between transcription factors, we also performed ChIP-reChIP-seq. We did the primary ChIP experiment using anti-SMAD3 antibody and then we subjected the ChIPed chromatin by the primary ChIP to reChIP experiments using anti-HIF1A or anti-HIF2A antibody. The reChIPed DNA was submitted to next generation sequencing.

overall_design: Profiling transcription factor binding and gene expression related with OC2 function in hypoxia response of prostate cancer

first: Housheng

last: He


title: Transcriptome profile of ATP7B KO cells and WT cells treated with Copper (Cu) to study Autophagy as a pro-survival mechanism in Wilson disease

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

summary: To understand whether hepatic cells use autophagy to defend against Cu toxicity in WD, we employed ATP7B knockout (ATP7B-KO) HepG2 cell line, by  Quant-seq experiments. Transcriptome analysis of the of ATP7B KO cells and WT cells treated with Copper (Cu) compared with untreated cells.

overall_design: total RNA was extracted from ATP7B KO cells and WT cells treated with Copper (Cu); RNA extracted from untreated cells was used as control.

first: R

last: De Cegli

last: Polishchuk


title: Genome organization of dengue and Zika viruses

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Dengue and Zika are closely related members of the Flaviviridae family of positive, single-stranded RNA viruses and are of global clinical importance.  These viruses utilize an 11kb RNA genome for translation and replication, and much remains to be learnt about how the entire genome folds to enable virus function. Here, we performed high throughput RNA secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains within their virus particles. We identified structures that are associated with translation pausing, and are evolutionary conserved by integrating synonymous mutation rates into our analysis.  Genome-wide interaction mapping revealed alternative structures, as well as extensive long-range RNA interactions – including the known circularization signals– within the virus particles.  Many of these long-range interactions are conserved across the viruses and/or clustered into “hubs” that are shown to be functionally important. This comprehensive structural resource of dengue and Zika viruses reveals that viral genome organization is much more complex than previously appreciated and deepens our understanding of the molecular basis for viral pathogenesis.

sample_organism:
Homo sapiens
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
Zika virus

overall_design: Local RNA structure probing and long-range RNA interactome mapping in 4 dengue serotypes and 4 Zika strains

first: Adelene

last: Sim

first: Xin

middle: N

last: Lim

first: Wy

last: Ng

first: Tanu

last: Chawla

first: Jong

last: Aw

first: Yang

last: Shen

first: Kum-Loong

last: Boon

first: Ming

last: Choy

first: Andreas

last: Wilm

first: Paola

middle: F

last: de Sessions

first: Martin

last: Hibberd

first: Niranjan

last: Nagarajan

first: Eng

middle: E

last: Ooi

first: Peter

last: Bond

first: October

middle: M

last: Sessions

first: Yue

last: Wan


title: Comparative transcriptome analysis of a novel obligate Methylomonas sp. DH-1 reveals key differences in the transcriptional responses in C1 and secondary metabolite pathways during growth on methane and methanol

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

summary: We integrated genomic and transcriptomic analysis of a newly isolated obligate Methylomonas sp. DH-1 grown on methane and methanol. Comparative transcriptomic analysis between methane and methanol as a sole carbon source revealed different transcriptional responses of Methylomonas sp. DH-1, especially in C1 assimilation, the secondary metabolites pathways and the oxidative stress related genes

overall_design: Examination of the differental expression genes when cultured Methylomonas sp. DH-1 in two different carbon sources methane and methanol

first: Anh

middle: D

last: Nguyen

first: Eun-Yeol

last: Lee


title: Transcriptome analysis of TP53-R248L overexpressed 19NS patient-derived glioblastoma cells

first: Seok Won

last: Ham

address: Anam-ro 145

department: College of Life Sciences & Biotechnology

institute: Korea University

summary: This study demonstrates the role of TP53 gain-of-function (GOF) mutation on glioblastoma progression. However, little is known about the transcriptional alteration upon TP53 GOF mutation. In this study, we found that TP53 GOF mutation (R248L mutation) promotes the enrichment of multiple gene signatures related to inflammation and chemotaxis. Particularly, through in vitro and in vivo approaches, we verified that TP53 GOF mutation enhances NFKB signaling which in turn up-regulates CCL2 and TNFA. Taken together, these results suggest the function of TP53 GOF mutation driving aggressiveness of malignant brain tumor.

overall_design: A patient-derived glioblastoma cell line 19NS was transfected with pLL CMV puro (19NS-control) or pLL CMV TP53-R248L puro (19NS-TP53-R248L). The 3 biological replicates of RNA extracts in these cells was used for transcriptome analysis.

first: Hyunggee