title: The cohesin release factor WAPL restricts chromatin loop extension [ESS]

city: Utrecht

first: Robin H.

last: van der Weide

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: The spatial organization of chromosomes influences many nuclear processes including gene expression. The ring-shaped cohesin complex shapes the 3D genome by looping together convergent CTCF sites along chromosomes. We show here with high-resolution Hi-C analysis that chromatin loop size can be increased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL alsoincreased, and that cohesin’s DNA release factor WAPL restricts the degree of this extension. WAPL also prevents looping between incorrectly oriented CTCF sites. Through haploid genetics we find that WAPL deficiency bypasses the need for cohesin’s DNA loader SCC4 and we reveal that SCC4 promotes the extension of chromatin loops. We provide functional evidence in support of the model that chromatin loops are processively enlarged by the extrusion of DNA from cohesin rings. We conclude that the balanced activity of SCC4 and WAPL enables cohesin to correctly structure chromosomes to ensure proper transcriptional control.

overall_design: Genes required for viability of three independent ∆WAPL cell lines were profiled as previously described in detail (Blomen et al., 2015). In short, gene trap retrovirus was produced in HEK293T cells by transfection of the packaging plasmids Gag-pol, VSVg, and pAdvantage in addition to the previously described gene trap plasmid (Jae et al., 2013).

first: Robin

first: Vincent

last: Blomen


title: The cohesin release factor WAPL restricts chromatin loop extension [4C]

status: Public on May 03 2017

country: Netherlands

overall_design: 4C was performed in WT and WaplKO HAP1 with biological replicate.

middle: H

first: Elzo

last: de Wit


title: Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling

city: los angeles

first: Danyang

last: Gong

state: CA

address: 650 Charles Young Dr. So.

department: pharmacology

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

platform_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design: Refer to individual Series


title: Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling (mRNA)

summary: Virus-like vesicles (VLVs) are membrane derived cellular vesicles that resemble native envelope viruses in organization and conformation, but lack viral capsid and/or genome. During productive virus infection, both infectious virions and non-infectious VLVs are produced and released into the extracellular space. VLVs have been shown to play a role in intercellular communication and in facilitating virus infection. The study of VLVs in the context of gammaherpesvirus infection has been largely restricted due to the technical difficulty of separating VLVs and virions. Here we report a strategy for using a KSHV mutant deficient in capsid assembly to isolate VLVs during infection. Using Mass Spectrometry analysis, we identified that VLVs contain viral glycoproteins required for cellular entry, and tegument proteins involved in regulating lytic replication. Functional analysis showed that VLVs could activate the RTA promoter, the lytic switch for KSHV, and further induce KSHV lytic gene expression from latency. We used RNA sequencing to do a genome-wide analysis of cellular responses triggered by VLVs, and revealed that PRDM1, a master regulator in cell differentiation, was up-regulated. Our data shows that VLVs play an important role in promoting KSHV lytic replication by inducing PRDM1 expression which activates the RTA promoter. Our study significantly extends our current understanding of VLVs.

overall_design: 1. Analyze KSHV lytic gene expression profile induced by VLV. 2. Globally analyze cellular response induced by VLV.


title: The cohesin release factor WAPL restricts chromatin loop extension. [RNA-Seq]

summary: The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can be increased, and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin’s DNA release factor WAPL restricts the degree of this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.

overall_design: RNAseq was performed in control, ΔWAPL 3.3, ΔWAPL 1.14, ΔSCC4 and ΔWAPL/ΔSCC4 cells in triplicate.


title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [ChIP-seq]

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restricted expression, and single nucleotide polymorphisms (SNPs) within SP140 associate with Crohn’s disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unknown.
Results:  Individuals carrying CD-associated SNPs within SP140 had defective SP140 mRNA splicing, diminished SP140 protein, and severely suppressed innate immune signatures that stratified them from other CD patients.
Conclusion: SP140 is a critical orchestrator of macrophage identity, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by suppressed innate immunity.

overall_design: ChIP-seq for SP140 in human macrophages stimulated with LPS for 4 hours versus 0h controls. A and b denote technical replicates.

first: Stuti

last: Mehta

first: Lorena

last: Pantano

middle: J

first: Kate

middle: L

last: Jeffrey


title: The cohesin release factor WAPL restricts chromatin loop extension. [ChIP-Seq]

overall_design: ChIPseq for CTCF and SMC1 was performed in control, ΔWAPL HAP1 , ΔSCC4 and ΔWAPL/ΔSCC4cells.


title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [ATAC-Seq]

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

summary:
Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restricted expression, and single nucleotide polymorphisms (SNPs) within SP140 associate with Crohn’s disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unknown.
Results: Individuals carrying CD-associated SNPs within SP140 had defective SP140 mRNA splicing, diminished SP140 protein, and severely suppressed innate immune signatures that stratified them from other CD patients.
Conclusion: SP140 is a critical orchestrator of macrophage identity, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by suppressed innate immunity.

overall_design: ATAC-seq in human macrophages stimulated with IFNg for 24h, and LPS stimulation for 4 hours: siRNA mediated knockdown of SP140 versus controls.

first: Shanna

last: Sui


title: Cell fixation and preservation for droplet-based single cell transcriptomics

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary:
Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells, in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. Another challenge are rare cells that need to be collected over several days, or samples prepared at different times or locations.
Results: Here, we used chemical fixation to overcome these problems. Methanol fixation allowed us to stabilize and preserve dissociated cells for weeks. By using mixtures of fixed human and mouse cells, we showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression from live and fixed samples correlated well with bulk mRNA-seq data. We then applied methanol fixation to transcriptionally profile primary single cells from dissociated complex tissues. Low RNA content cells from Drosophila embryos, as well as mouse hindbrain and cerebellum cells sorted by FACS, were successfully analysed after fixation, storage and single-cell droplet RNA-seq. We were able to identify diverse cell populations, including neuronal subtypes.  As an additional resource, we provide 'dropbead', an R package for exploratory data analysis, visualization and filtering of Drop-seq data.
Conclusions: We expect that the availability of a simple cell fixation method will open up many new opportunities in diverse biological contexts to analyse transcriptional dynamics at single cell resolution.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Mixtures of human and mouse cells, either live or fixed, or fixed and stored for several weeks were used for droplet-based single cell mRNA transcriptome profiling. The methods were also successfully applied to primary cells isolated from Drosophila embryos and newborn mouse hindbrain/cerebellum.

first: Jonathan

last: Alles

first: Samantha

middle: D

last: Praktiknjo

first: Christine

last: Kocks

first: Nikolaus

last: Rajewsky


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Mm]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

type: Methylation profiling by high throughput sequencing

summary: In the developing retina, as in many other regions of the central nervous system, multipotent neural progenitor cells undergo unidirectional changes to produce differentiated cells in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinal development in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell type–specific differentiation programs. We identified developmental stage–specific superenhancers and showed that the majority of epigenetic changes during murine retinal development are conserved in the human retina. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed the same integrated epigenetic analysis of murine and human retinoblastomas and iPSCs derived from murine rod photoreceptors.  The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from a neurogenic to a terminal pattern of cell division and murine retinoblastomas initiate earlier in development than human tumors. The epigenome of retinoblastomas was far more similar to that of normal retina than was the epigenome of retinal-derived iPSCs but we were able to identify retinal specific epigenetic memory. Together, these data provide an in depth view of the dynamic epigenome during neurogenesis and how that relates to developmental tumors and epigenetic memory in iPSCs produced from neurons.

overall_design: Examination of 8 different histone modifications and 3 transcription factors, transcriptome, DNA methylation in 23 cell types

first: Issam

last: Aldiri

first: Lu

last: Wang

first: Xiang

last: Chen

first: Daniel

last: Hiler

first: Lyra

last: Griffiths

first: Marc

last: Valentine

first: Abbas

last: Shirinifard

first: Marie-Elizabeth

last: Barabas

first: Jiakun

last: Zhang

first: Dianna

last: Johnson

first: Sharon

last: Frase

first: John

last: Easton

first: Jinghui

first: Elaine

middle: R

last: Mardis

first: Richard

middle: K

last: Wilson

first: James

last: Downing

first: Michael

middle: A

last: Dyer


title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-seq]

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

institute: Harvard Chan School of Public Health

overall_design:
RNA-seq of 8 samples of peripheral blood derived mononuclear cells from CD patients having T/T or C/C genotype for rs6716753 SNP, with and without LPS treatment. 4 samples from healthy individuals with and without LPS treatment. RNA-seq of human macrophages (total 8 samples from 2 independent donors) stimulated with IFNg for 24h, and LPS (100ng/mL) for 4 hours: siRNA mediated knockdown of SP140 versus controls.

RNA-seq of human macrophages (total 8 samples from 2 independent donors) stimulated with IFNg for 24h, and LPS (100ng/mL) for 4 hours for each condition: siRNA mediated knockdown of SP140 versus controls.

first: Stuti

last: Mehta

first: Shanna

last: Sui

first: Kate

last: Jeffrey


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [ChIP-Seq_Hs]

first: Beisi

last: Xu

first: Issam

last: Aldiri

first: Lu

last: Wang

first: Xiang

last: Chen

first: Daniel

last: Hiler

first: Lyra


title: Directed differentiation of human embryonic stem cells to corneal endothelial cell-like cells: A transcriptomic analysis

status: Public on May 07 2017

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

summary: The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. Human embryonic stem cells (hESCs) hold the promise of providing an abundant donor source for generating CEC cells for cell replacement therapies. Here we demonstrate that CEC-like cells can be efficiently derived from human ESCs. In addition, we performed global gene expression profiling of stem-cell-derived CEC cells, incorporating with adult CEC cells, fetal CEC cells and other human tissue type data. Our data indicate that hESC-derived CEC-like cells closely resemble human fetal CEC cells.

overall_design:
We analyzed a total of 44 samples.
6 samples were sequenced by our group. High-throughput RNA-seq data from human ES cell-derived CEC-like cells samples (n=4) and cultured adult CEC samples (n=2) using Illumina HiSeq 2000.
38 samples are publicly available in GEO.
The entire set of processed data is linked below as supplementary file 44_samples_RPKM.txt.

first: Songtao

last: Yuan

first: Ganlu

last: Hu

first: Qinglu

last: Song

first: Guoping

last: Fan


title: Genome-wide detection of STAT3 binding sites in human Th17 cells

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

summary: STAT3 is a major transcription factor driving the polarization of Th17 cells in response to IL-6, TGF-β and IL1-β. STAT3 is phosphorylated and forms a homodimer and translocates into the nucleus. There STAT3 binds to specific DNA sequences, regulating the transcription of its target genes. Here we have analyzed on a genome wide level the STAT3 binding sites, after 0.5h and 4h of  IL-6, TGF-β and IL1-β induction, in naive human CD4+ T cells.

overall_design: Altogether 2 samples from 1 biological replicate were analyzed.

first: Subhash

last: Tripathi

first: Riitta

last: Lahesmaa


title: Condensin plays a role in both interphase nuclei and premature chromosome condensation

city: Melbourne

first: Tao

last: Zhang

state: Vic

address: Flemington Road, Parkville

department: Chromosome Research

country: Australia

institute: Murdoch childrens research institute

summary:
Purpose: to identify how condensin I removal affects gene expression globally.
Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation.
Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated.
Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase.

overall_design: Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.

first: Damien

last: Hudson

first: Ji

last: Kim


title: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis

first: Kate

last: Jeffrey

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: MicroRNA-28 replacement for non-Hodgkin lymphoma therapy

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: Our studies identify the role of mIR-28 in germinal center response and its therapeutic potential for the treatment of non-Hodgkin lymphomas

overall_design: The effect of miR-28 expression in the transcriptome was analyzed in Ramos Burkitt B cells by RNASeq.

first: Nahikari

last: Bartolomé-Izquierdo

first: Virginia

middle: G

last: de Yébenes

first: Angel

middle: F

last: Álvarez-Prado

first: Sonia

middle: M

last: Mur

first: Juan

last: Lopez del Olmo

first: Sergio

last: Roa

first: Jesus

last: Vazquez

first: Almudena

last: Ramiro


title: Gene expression profiling of the octuple jazQ mycT mutant shows that the MYC transcription factors control expression of many genes mis-regulated in jazQ, and also identifies some MYC-indepedent expression changes

status: Public on May 02 2017

city: East Lansing

first: Gregg

last: Howe

state: MI

address: 612 Wilson Rd

department: Plant Research Laboratory

institute: Michigan State University

summary: The quintuple jaz mutant jazQ and the triple myc mutant mycT affect plant defense and growth. We used RNA-sequencing to query the transcriptomes of jazQ and mycT, as well as the combined jazQ mycT octuple mutatant, and examined how these mutations alter the expression of genes mis-regulated in jazQ. The data highlight how jasmonate signaling pathways are largely governed by MYC transcription factors, but also highlight some MYC-independent expression patterns.

overall_design:
Analysis of Col-0 (wildtype), jazQ, mycT, and jazQ mycT (four genotypes), with three biological replicates per genotype - 12 total samples.

This series contains the re-use of 6 samples from GSE79012 (Col-0 and jazQ).

first: Ian

middle: T

last: Major

first: Marcelo

last: Campos


title: The cohesin release factor WAPL restricts chromatin loop extension [DamID]

first: Robin H.

last: van der Weide

overall_design: DamID was performed as described (Peric-Hupkes et al., 2010).

first: Robin

first: J

middle: O

last: Yáñez-Cuna


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Hs]

first: Beisi

last: Xu

first: Issam

last: Aldiri

first: Lu

last: Wang

first: Xiang

last: Chen

first: Daniel

last: Hiler

first: Lyra

last: Griffiths

first: Marc

last: Valentine

first: Abbas

last: Shirinifard

first: Marie-Elizabeth

last: Barabas

first: Jiakun

last: Zhang

first: Dianna

last: Johnson

first: Sharon

last: Frase

first: John

last: Easton

first: Jinghui

first: Elaine

last: Mardis

first: Richard

last: Wilson

first: James

last: Downing

first: Michael

last: Dyer


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in PB- and PB-Gbx2-transfected 46C mouse embryonic stem cells

city: Hefei

first: Manman

address: No 111, Jiu Long Road

country: China

institute: anhui university

summary: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in 46C mouse embryonic stem cells overexpressing PB-Gbx2 or PB empty vector at gene expression level. Results provide important information of the response of up-regulating Gbx2, such as specific mechano-responsive genes, up- or down-regulated genes that were mainly enriched in signaling pathways regulating pluripotency of stem cells

overall_design: Total RNA obtained from Gbx2-overexpressed 46C ESCs compared to empty vector-transfected control 46C ESCs. Cells were cultured in serum medium supplemented with LIF.

first: Shoudong

last: Ye


title: Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling (microRNA)

first: Danyang

last: Gong

overall_design: Analyze microRNA in KSHV VLVs


title: small RNA-seq of Ler. WT and Ler; 35S-HA-RICE1 D52A transgenic plant

city: College Station

first: Xiuren

state: TX

address: Biochemistry/Biophysics Bldg, Suite 103, 2128 TAMU, 300 Olsen Blvd

institute: Texas A&M University

summary: We examined global miRNA profiles of 3-weeks old 35S-HA-RICE1 D52A transgeneic plants compared to Ler wild-type using illumina sequencing. We conclude that, in general, both miRNA and miRNA* expression levels are downregulated in catalytically-defective RICE1 transgenic plants compared to Ler wild type.

overall_design: miRNA profiles of 3-week-old Ler wild-type and 35S-HA-RICE1 D52A transgeneic plants were generated in triplicate by illumina sequencing

first: Zhonghui


title: High-throughput and site-specific identification of 2'-O methylation sites using Ribose Oxidation sequencing (RibOxi-Seq)

city: Farmington

first: Gordon

middle: G.

last: Carmichael

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

summary: We report our newly developed method for high-throughput sequencing of 2'-O methylation sites using positive signal and site specific approach. The pilot experiment using MiSeq generated ~2.5 million reads per sample. The 2'-O methylation site identification produced a promising distribution pattern matching known sites. For accurate and sensitive base call, >10 million reads are required per sample as evidenced in the NextSeq experiment.

overall_design: Total RNA extracted are aliquoted either as control or oxidized samples. The control RNAs are digested and subjected to custom small RNA sequencing library preparation, while the oxidized group has additional steps after digestion to oxidize RNA ends to selectively enrich fragments with 2'-O methylated terminal base for subsequent library preparation.

first: Yinzhou

last: Zhu

first: Stephan

middle: P

last: Pirnie


title: Poly(A)-ClickSeq resolves CF25-mediated alternative poly-adenylation, HeLa

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary: Poly(A)-ClickSeq is a new methodology for the sequencing of the 3'UTR/poly(A) tail junction of RNA. We analysed both wild-type and CF25Im knock-down HeLa cells in culture using Poly(A)-ClickSeq to find the distribution of poly(A) sites in these samples and determine the role of CF25Im in poly(A) site selection (alternative poly-adenylation, APA).

overall_design: RNA was extracted from HeLa cells with or without CF25Im Knock-down, each in triplicates, and sequenced using Poly(A)-ClickSeq and sequencing once on a HiSeq and once on a MiSeq

first: Andrew

last: Routh

first: Eric

last: Wagner

first: Ping

last: Ji


title: Small RNA profiles of three different mycovirus-infected Aspergillus fumigatus isolates, created using Illumina high definition adapters

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

summary: Small RNA libraries of three different mycovirus-infected A. fumigatus isolates were constructed by using Illumina high definition adapters. sRNAomes were analysed and  putative virus-derived small RNAs were identified.

overall_design: Analysis of small RNA profiles of three different mycovirus-infected A. fumigatus isolates

first: Selin

last: Özkan

last: Xu

first: Tamas

last: Dalmay

first: Robert

last: Coutts


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Hs]

first: Beisi

first: Issam

last: Aldiri

first: Lu

last: Wang

first: Xiang

last: Chen

first: Daniel

last: Hiler

first: Lyra

last: Griffiths

first: Marc

last: Valentine

first: Abbas

last: Shirinifard

first: Marie-Elizabeth

last: Barabas

first: Jiakun

last: Zhang

first: Dianna

last: Johnson

first: Sharon

last: Frase

first: John

last: Easton

first: Jinghui

first: Elaine

last: Mardis

first: Richard

last: Wilson

first: James

first: Michael


title: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [ChIP-Seq_Mm]

first: Beisi

last: Xu

first: Issam

last: Downing

last: Dyer


title: Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [Stickleback]

city: Durham

last: Rawls

state: North Carolina

address: Duke University 213 Research Drive, Box 3580 DUMC CARL Building 327

institute: Duke University

summary: We profiled genome-wide accesssible chromatin data and RNA-seq from four species (zebrafish, stickleback, mouse, and human) to identify commonly regulated genes and regulatory metods in intestinal epithelial cells (IECs).  We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals.  Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species.  Finally, we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay.

overall_design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in stickleback

first: Colin

last: Lickwar

first: J

last: Camp

first: Matthew

last: Weiser

first: David

last: Kingsley

first: Terrence

middle: S

last: Furey

first: Shehzad

middle: Z

last: Sheikh


title: Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [zebrafish]

overall_design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in zebrafish


title: Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination

city: Madison

first: Marisa

last: Otegui

state: WI

address: 1525 Linden Dr.

department: Botany

institute: University of Wisconsin-Madison

summary: The cereal endosperm consists of starchy endosperm (ST) cells, which accumulate storage proteins and starch, the peripheral aleurone (AL) cells, which mobilize these storage compounds during germination, and transfer cells in contact with the maternal vascular tissues, and the embryo-surrounding region. We conducted RNA-sequencing and analyzed transcript profiles of AL and ST tissues at 18 and 22 days after pollination (DAP), when storage compounds such as proteins, starch, triacylglycerols, specialized metabolites, and minerals are actively synthesized in the maize endosperm. We combined published RNA-seq datasets from other kernel tissues at different developmental stages to analyze gene expression connected to synthesis and accumulation of storage compounds and metabolites. Using weighted correlation network analysis (WGCNA), we identified gene modules associated with metabolic pathways related to nutritional properties of the maize endosperm. We also provide information of novel marker genes specifically expressed in AL and ST, at either early or late developmental stages. This study is important for understanding maize endosperm development and for developing strategies to improve nutritional quality of maize kernels.

overall_design: We examined B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination,respectively. We collected 2 biological replicates for each tissue sample for RNA-sequencing.

first: Francisca

middle: C

last: Reyes

first: Kengo

last: Morohashi

first: Xinxin

last: Ding

first: Xiaoguo

first: Erich

last: Grotewold


title: A comparative study of endoderm differentiation in humans and chimpanzees

city: Chicago

first: Lauren

middle: Elizabeth

last: Blake

state: Illinois

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: There is substantial interest in the genetic regulatory framework that is established in early human development, and in the evolutionary forces that shaped early developmental processes in humans. Progress in these areas has been slow because it is difficult to obtain relevant biological samples. Recent technological developments in the generation and differentiation of inducible pluripotent stem cells (iPSCs) provide the ability to develop in vitro models of early human and non-human primates developmental stages. We have previously established matched iPSC panels from humans and chimpanzees. Using these panels, we comparatively characterized gene regulatory changes through a four-day timecourse differentiation of iPSCs (day 1) into primary streak (day 2), endoderm progenitors (day 3), and definitive endoderm (day 4). As might be expected, we found that differentiation stage (in effect, cell type) is the major driver of variation in gene expression levels in our study, followed by species. We then identified thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we considered gene-specific dynamic regulatory trajectories throughout the timecourse, we found that 75% of genes, including nearly all known endoderm developmental markers, have conserved trajectories in the two species. Interestingly, we observed a marked reduction of both intra- and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of variation in endoderm progenitors. The reduction in variation in gene expression levels at a specific developmental stage, paired with the high degree of conservation of temporal expression across species, is consistent with the dynamics of developmental canalization. Overall, we conclude that endoderm development in iPSC-based models are highly conserved and canalized between humans and our closest evolutionary relative.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: We used a panel of 6 human and 4 chimpanzee iPSC lines previously derived and characterized in the Gilad lab. We differentiated the iPSCs into definitive endoderm, a process that was completed over 3 days, and included replicates of cell lines over the differentiation process.  We harvested RNA from iPSCs (day 0) prior to differentiation and subsequently every 24 hours to capture intermediate populations corresponding to primitive streak (day 1), endoderm progenitors (day 2), and definitive endoderm (day 3). Overall, we collected a total of 32 human samples and 32 chimpanzee samples. We assessed used RNA sequencing to estimate gene expression levels in all samples. There are a total of 64 samples (6 human cell lines + 2 technical replicates at 4 time points; 4 chimpanzee cell lines x 2 technical replicates at 4 time points.)

middle: E

first: Samantha

last: Thomas

first: John

last: Blischak

first: Chiaowen

last: Hsiao

first: Claudia

last: Chavarria

first: Marsha

last: Myrthil

first: Yoav

last: Gilad

first: Bryan

last: Pavlovic


title: Single cell RNA-sequencing of day 15 cells derived from the directed differentiation of human iPSCs towards lung epithelium

city: South San Francisco

first: Ian

last: Driver

state: California

address: 486 Cabot Road

department: Bioinformatics

institute: Gordian Biotechnology

summary: It has been postulated that during human fetal development all cells of the lung epithelium derive from an embryonic endodermal NKX2-1+ precursor, however, this hypothesis has not been formally tested due to an inability to purify or track this theorized cell for detailed characterization. Progress has been made in deriving lung epithelial cells from human induced pluripotent stem cells (iPSCs). However, little is known about the heterogeneity or genetic programs of the cells generated using these lung differentiation protocols. We engineered and differentiated NKX2-1GFP reporter iPSCs in vitro, recapitulating the major developmental milestones of lung development, to generate and isolate human primordial lung progenitors (day 15 of differentiation) that expresses NKX2-1 but are initially devoid of markers of differentiated lung lineages. To further characterize the cells generated in the lung directed differentiation protocol we performed single cell RNA-seq analysis of cells on day 15 of lung directed differentiation. We analyzed sorted NKX2-1GFP+ cells for the iPSC line C17 and cells from the iPSC line BU3.

overall_design: We sorted C17NKX2-1GFP+ and BU3 cells on day 15 of the lung directed differentiation and loaded into separate Fluidigm C1 integrated fluidics circuits (IFCs).  Lysis, conversion polyA+RNA into full length cDNA and amplification of cDNA was performed using the Fluidigm C1 according to the manufacturer’s protocol. After sequencing on an Illumina Hiseq2500 80 single cell transcriptional profiles from BU3 and 65 from ips17 cell line were compared after filtering and normalization.

first: Finn

last: Hawkins

first: Darrell

last: Kotton


title: Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

last: Rawls

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

sample_organism:
Danio rerio
Homo sapiens
Gasterosteus aculeatus

overall_design:
Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in four species (zebrafish, stickleback, mouse, and human)
Refer to individual Series

Please note that the mouse data was from previously published data from GSE57919.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Human Pluripotent Stem Cell-Derived Endocardial-like And Primary Cardiac Endothelial Cell Transcriptomes

city: West Lafayette

first: Xiaoping

last: Bao

state: Indiana

address: 480 Stadium Mall Drive

department: Chemical Engineering

institute: Purdue University

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for different cell lineage formation from human pluripotent stem cells (hPSCs). We report here the application of RNA-sequencing technology for transcriptome profile of human primary cardiac microvascular endothelial cells and hPSC-derived endocardial endothelial cells, and compare to those of other cell lineages including hPSCs, mesoderm, cardiomcyotyes as well as mouse cardiac microvascular and endocardial endothelial cells. Six cardiac endothelial cell samples from two different hPSC lines and one donor were performed in IIIumina HiSeq2500. The resulting sequence reads (about 20 million reads per sample) were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data confirmed the stable expression of key endocardial endothelial cell markers including CDH5, vWF, PECAM1, NFATC1 and NPR3, and the gene set enrichment analysis (GSEA) showed enrichment in angiogenesis and vasculature development. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to endocardial function. This study represents the first detailed analysis of endocardial-like endothelial cell transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying the differentiation of hPSCs into endocardium.

overall_design: Endothelial transcriptome profiles of human primary cardiac microvascular endothelial cells and hPSC-derived endocardium were generated by RNA-seq technology using IIIumina HiSeq2500

first: Sean

last: Palecek


title: Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (RNA-seq AML development)

city: Montreal

first: Magalie

last: Celton

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: IRIC

summary: Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. Stepwise RNA-seq data from this model shows that in the context of AML driven by the MLL-AF9 (MA9) oncogene, the genetic background of the donor does not have a detectable effect. Comparison of these model leukemias from multiple single donors to AML patient samples containing MA9 translocations revealed conserved gene expression patterns not previously highlighted in this genetic sub-type. We further demonstrate that the expression of one of these genes, RET, is essential both in vivo and in vitro growth of MA9 AMLs .

overall_design: study of transcriptome during the development of MLL-AF9 AML


title: Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets [RNA-Seq_normal]

overall_design: Transcriptome of normal cells (CD34+)  from different donors


title: Small RNA profiles of mycovirus-free and mycovirus-infected Aspergillus fumigatus isolates, created using ScriptMiner adapters

first: Irina

last: Mohorianu

summary: Small RNA libraries of 4 different mycovirus-infected and -free isogenic lines of A. fumigatus were constructed using Scriptminer adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified.

overall_design: Analysis of small RNA profiles of 4 different mycovirus-infected A. fumigatus isolates

first: Selin

last: Özkan

first: Ping

last: Xu

first: Tamas

last: Dalmay

first: Robert

middle: H

last: Coutts


title: Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets [RNA-Seq_AML]

overall_design: Transcriptome of several AML cell lines


title: Regions of very low H3K27me3 partition the Drosophila genome into topological domains [HiC-seq]

city: Cambridge

first: Rob

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

summary: We have investigated boundaries of topologically associated domains (TADs) in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the TSSs of the housekeeping genes than with the H3K27me3 domain boundaries. We suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

overall_design: Analysis of 3D chromatin organization using Hi-C with DpnII in Drosophila Kc167 cells.

first: Jose

last: Magbanua

first: Bettina

last: Fischer


title: Regions of very low H3K27me3 partition the Drosophila genome into topological domains

type: Genome binding/occupancy profiling by genome tiling array

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

We have investigated boundaries of topologically associated domains (TADs) in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the TSSs of the housekeeping genes than with the H3K27me3 domain boundaries. We suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

overall_design: Refer to individual Series

first: Sherif

last: El-Sharnouby


title: Sperm cells are passive cargo of the pollen tube in plant fertilization

status: Public on May 01 2017

city: Bei Jing

first: huang

last: jiaying

address: Yiheyuan Road

department: School of life science

institute: Peking University

summary: Sperm cells of seed plants have lost their motility and are transported by the vegetative pollen tube cell for fertilization. The extent to which sperm cells regulate their own transportation is a long-standing debate. By using the novel Arabidopsis double mutant drop1 drop2, we demonstrate here that sperm cells are only passive cargo and that the vegetative tube cell as a vehicle controls the entire journey.

overall_design: the semi-in-vivo pollen tubes of wild type (WT) and drop mutant using single-cell RNA sequencing

first: Jun

last: Zhang

first: Qingpei

last: Huang

first: Sheng

last: Zhong


title: ZNF516 Is a Potent Suppressor of the EGFR Oncogene through Chromatin Targeting of the CtBP/LSD1/CoREST Complex

city: China

first: Xinhua

last: Liu

state: State...

address: 300070, Qixiangtai rd, Tianjin

institute: Tianjin Medical University

summary: In this study, we report that ZNF516 functions as a transcription repressor. We showed that ZNF516 is physically associated with the CtBP/LSD1/CoREST corepressor complex and transcriptionally represses the expression of a collection of genes including EGFR that are critically involved in cell proliferation and motility. We demonstrated that the ZNF516 inhibits the proliferation and invasive potential of breast cancer cells in vitro and suppresses breast cancer growth and metastasis in vivo. We explored the clinical significance of the ZNF516-CtBP/LSD1/CoREST-EGFR axis in breast carcinomas.

overall_design: Target genes of ZNF516 in MCF-7 cells.

first: Lifang

last: Li

first: Lin

last: He

first: Jianguo

last: Yang

first: Fei

last: Pei

first: Wanjin

first: Shumeng

first: Zhe

last: Chen

first: Guojia

last: Xie

first: Bosen

first: Xia

last: Ting

first: Zihan

first: Tong

last: Jin

first: Xujun

first: Wenting

first: Shuai

last: Yuan

first: Ziran

first: Chongyang

last: Wu

first: Yu

first: Xiaohan

last: Yi

first: Jing

last: Liang

first: Yongfeng

last: Shang

first: Luyang

last: Sun


title: Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

summary: DNA methylation is a conserved epigenetic mark important for genome integrity, development and environmental responses in plants and mammals.  Active DNA demethylation in plants is initiated by a family of 5mC DNA glycosylases/lyases (i.e. DNA demethylases). The role of DNA demethylases in transposon regulation, pathogen responses, and gene imprinting and other developmental processes have been studied extensively in the model plant Arabidopsis thaliana. Recent studies suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlROS1/SlDML1/2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes include not only hundreds of ripening induced genes but also many ripening repressed genes. Our results show that SlROS1 is critical for tomato fruit ripening, and suggest that active DNA demethylation is required for both the activation of ripening induced genes and inhibition of ripening repressed genes.

overall_design:
MethylC-Seq: 6 samples examined, wild type (WT) 25dpa (day after anthesis), WT 46dpa, and WT 60dpa, sldml2-1 25dpa , sldml2-1 46dpa (two replicates), sldml2-2 60dpa (2 replicates);
mRNA-Seq: 3 samples examined, WT 25dpa, WT 46dpa and sldml2-1 46dpa (2 replicates)

first: Kai

last: Tang

first: Yihai

last: Wang

first: Zhaobo

last: Lang


title: RNA-seq analysis of WT and SCL28-OX in the Arabidopsis thaliana root tip

city: Seoul

first: Jeong-eun

last: Choe

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

summary: Genome-wide transcriptome analysis to identify downstream genes that are transcriptionally regulated by SCL28 (At1g63100)

overall_design: mRNA samples were prepared from the root tips of 5 d-old WT and SCL28-OX seedlings which were grown in a growth room at 22 ℃ under a constant light condition.

first: Jun

last: Lim


title: Mapping the human DC lineage through the integration of high dimensional techniques

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Dendritic cells (DC) are professional antigen-presenting cells that orchestrate immune responses. The human DC population comprises two main functionally-specialized lineages, whose origins and differentiation pathways remain incompletely defined. Here we combine two high-dimensional technologies — single-cell mRNA sequencing and Cytometry by Time-of-Flight (CyTOF), to identify human blood CD123+CD33+CD45RA+ DC precursors (pre-DC). Pre-DC share surface markers with plasmacytoid DC (pDC) but have distinct functional properties that were previously attributed to pDC. Tracing the differentiation of DC from the bone marrow to the peripheral blood revealed that the pre-DC compartment contains distinct lineage-committed sub-populations including one early uncommitted CD123high pre-DC subset and two CD45RA+CD123low lineage-committed subsets exhibiting functional differences. The discovery of multiple committed pre-DC populations opens promising new avenues for the therapeutic exploitation of DC subset-specific targeting.

overall_design: Single cell mRNA sequencing was used to investigate the transcriptomic relationships within the dendritic cell precursors within the peripheral blood.

first: Peter

last: See

first: Charles-Antoine

last: Dutetre

first: Jinmiao

first: Florent

last: Ginhoux


title: Genome-wide analysis of transcription factor binding sites during somatic cell reprogramming

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

summary: We report that Zic3 and Esrrb synergistically enhance the reprogramming efficiency when transduced with Oct4, Sox2 and Klf4 (OSK) into murine fibroblasts. By ChIP-seq analysis, we reveal that Zic3 recruits Esrrb to its own binding sites, some of which are proximal to glycolysis-related genes, thereby cooperatively upregulating these genes to activate glycolytic metabolism, and that Esrrb binds to genes related to mitochondrial oxidative phosphorylation. Therefore, our study suggests that Zic3 and Esrrb activate pluripotency gene network by regulating the balance of metabolic pathways.

overall_design: Examination of binding of 2 different transcription factors in 4 different conditions

first: Masamitsu

last: Sone


title: Generation of pure GABAergic neurons by transcription factor programming

city: Stanford

first: Samuele

last: Marro

address: 256 Campus Drive

institute: Stanford University

summary: We performed RNA sequencing (RNA-seq) of two independent human Ascl1, Dlx2 and Myt1l-iN cell cultures

overall_design: The human induced neurons were co-cultured with mouse glia for 4 weeks and the whole transcriptome was analyzed

last: Yang

first: Marius

last: Wernig


title: The metabolic regulator mTORC1 controls terminal myeloid differentiation

city: Boston

first: Pui

last: Lee

address: 60 Fenwood Rd.

institute: Brigham and Womens Hospital

summary: Monocytes are derived from hematopoietic stem cells through a series of intermediate progenitor stages, but the factors that regulate this process are incompletely defined. Using a Ccr2/Cx3cr1 dual-reporter system to model murine monocyte ontogeny, we conducted a small molecule screen that identified an essential role of mechanistic target of rapamycin complex 1 (mTORC1) in the development of monocytes and other myeloid cells.

overall_design: Examination of gene expression in 1) Granulocyte-Monocyte Progenitors from Raptor KO mice, Tsc2 KO mice and controls; and 2) DR-ER-Hoxb8 cells differentiated in the presence of DMSO, rapamycin or SL0101-01

middle: Y

last: Nigrovic


title: TWEAK mediates inflammation in experimental atopic dermatitis and psoriasis

first: Suzanne

last: Szak

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Atopic dermatitis and psoriasis are driven by alternate type 2 and type 17 immune responses, but some proteins might be critical to both diseases. We show that a deficiency of the TNF superfamily molecule TWEAK (TNFSF12) in mice results in defective maintenance of atopic dermatitis-specific Th2 and psoriasis-specific Th17 cells in the skin, and impaired expression of disease-characteristic chemokines and cytokines, such as CCL17 and TSLP in atopic dermatitis, and CCL20 and IL-19 in psoriasis. The TWEAK receptor, Fn14, is upregulated in keratinocytes and dermal fibroblasts, and TWEAK induces these cytokines and chemokines alone and in synergy with the signature T helper cytokines of either disease, IL-13 and IL-17. Furthermore, subcutaneous injection of recombinant TWEAK into naïve mice induces cutaneous inflammation with histological and molecular signs of both diseases. TWEAK is therefore a critical contributor to skin inflammation and a possible therapeutic target in atopic dermatitis and psoriasis.

overall_design: Eight- to 12-week old male mice were used. TWEAK-deficient animals were bred in house on the C57BL/6 background, and Fn14-deficient animals on a BALB/c.  Atopic Dermatitis-like disease was induced by epicutaneous treatment with HDM extract (10 μg/mouse and treatment) and SEB (500 ng/mouse and treatment) given in 2 cycles on days 1 and 4, and 14 and 17, on the shaved and tape-stripped back skin over a 23 day period.

first: Daniel

last: Sidler

first: Ping

last: Wu

first: Rana

last: Herro

first: Meike

last: Claus

first: Dennis

last: Wolf

first: Yuko

last: Kawakami

first: Toshiaki

first: Linda

last: Burkly

first: Michael

last: Croft


title: Brown adipose tissue macrophages control tissue innervation and homeostatic energy expenditure

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Tissue resident macrophages provide a systemic innate immune defense network and critically contribute to establishment and maintenance of tissue homeostasis. Here we used constitutive and inducible mutagenesis to delete the nuclear transcription regulator methyl-CpG binding protein 2 (MeCP2) in defined tissue macrophages. Animals lacking the Rett syndrome-associated gene in macrophages did not show signs of neurodevelopmental disorder, but surprisingly displayed altered body composition and spontaneous obesity. This phenotype involved neither hyper-phagia, primary hyper-insulinemia nor inflammation, but rather could be linked to impaired brown adipose tissue (BAT) function. Specifically, mutagenesis of a BAT-resident CX3CR1+ macrophage subpopulation compromised homeostatic, though not acute cold-induced thermogenesis. Mechanistically, steady state BAT malfunction of pre-obese mice harboring mutant macrophages was associated with decreased sympathetic innervation and lower local norepinephrine titers, resulting in reduced adipocyte expression of the thermogenic factors UCP1 and DIO2. Mutant macrophages were found to over-express PlexinA4, which might contribute to the phenotype by repulsion of Sema6A-expressing sympathetic axons. Collectively, we report a previously unappreciated homeostatic role of macrophages in the control of tissue innervation, disruption of which in BAT results in metabolic imbalance.

overall_design: BAT macrophages taken from CX3CR1-cre, CX3CR1-CreER:tomato and CX3CR1-CreER:mecp2:ribo-tag for gene profiling in steady state

first: Yochai

first: Sigalit

last: Boura-Halfon


title: Transcriptome of choroid endothelial cells from P5 and P30 mice.

city: Madrid

first: Ignacio

last: Benedicto

address: Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary:
Purpose: The outer blood-retina barrier is established through the coordinated terminal maturation of the retinal pigment epithelium (RPE), fenestrated choroid endothelial cells (ECs) and Bruch’s membrane, a highly organized basement membrane that lies between both cell types. Here we study the contribution of choroid ECs to this process by comparing their gene expression profile before (P5) and after (P30) the critical postnatal period when mice acquire mature visual function.
Methods: ECs from P5 and P30 mice were labeled in vivo by retro-orbital injection of fluorescently-labeled anti-VE-Cadherin. After 10 minutes, mice were euthanized, eyeballs were enucleated and the anterior segment was discarded. After removal of the neural retina, RPE/choroid was mechanically dissected from the sclera and digested. ECs were isolated by flow cytometry and processed immediately for RNA extraction.
Results: Transcriptome analyses show that whereas P5 choroid EC transcriptome is preferentially enriched in cell cycle- and chromosome-related transcripts, reflecting an immature phenotype, the transcriptome of adult (P30) choroid ECs is enriched in genes encoding proteins involved in ‘biological adhesion’, including a variety of extracellular matrix (ECM)-related genes.
Conclusion: these results strongly suggest that mature choroid ECs actively participate in extracellular matrix assembly and regulation.

overall_design: Transcriptome of choroid ECs isolated from P5 and P30 mice (3 independent isolations, 7 animals per isolation) was determined using the Illumina HiSeq2000 platform. Upon quality control using FastQC, raw reads were aligned to the mouse genome (mm9) using TopHat with default parameters. CuffLinks with GC and upper quartile normalization was then used to calculate normalized expression levels.

first: Guillermo

middle: L

last: Lehmann

last: Ginsberg

middle: J

last: Nolan

first: Rohan

last: Bareja

first: Olivier

last: Elemento

first: Shahin

last: Rafii

first: Enrique

last: Rodriguez-Boulan


city: Denver

first: Anthony

last: Gerber

state: CO

address: 1400 Jackson St

department: Medicine

institute: National Jewish Health

summary: We previously demonstrated that the transcription factor, KLF15, is a glucocorticoid-regulated gene that represses primary human airway smooth muscle (ASM) proliferation. Here, we show that KLF15 also represses ASM hypertrophy. To uncover the mechanistic basis for these effects, we integrated transcriptome data from KLF15 over-expression with genome-wide analysis of RNA Polymerase II (RNAPII) and glucocorticoid receptor (GR) occupancy (i.e. ChIP-seq). This led us to identify PLCD1 as both a KLF15-regulated gene and a repressor of ASM hypertrophy.

overall_design: Genome-wide transcriptional targets of KLF15 in human airway smooth muscle cells were determined by RNA-seq in cells transduced with a KLF15-expressing adenovirus (Ad-KLF15) compared to a control adenovirus (Ad-GFP).

first: Sarah

middle: K

last: Sasse

first: Vineela

last: Kadiyala

first: Thomas

last: Danhorn

first: Reynold

middle: A

last: Panettieri Jr

first: Tzu

last: Phang

middle: N


title: Acquired resistance mechanisms to capmatinib, a MET inhibitor in MET-amplified non-small cell lung cancer cells

first: Seulki

last: Kim

address: 101, Daehak-ro

institute: Seoul National University Cancer Research Institute

summary:
Purpose: MET is a receptor tyrosine kinase (RTK) that has been considered a druggable target in non-small cell lung cancer (NSCLC). To understand the mechanisms of resistance to MET-TKIs and establish therapeutic strategies, we developed an in vitro model using capmatinib-resistant cell lines (EBC-CR1, CR2, and CR3) derived from the MET-amplified NSCLC cell line EBC-1.
Methods: We established capmatinib-resistant NSCLC cell lines from the MET-amplified NSCLC cell line EBC-1 and identified alternative signaling pathways using 3’mRNA sequencing and human phospho-RTK arrays. Copy number alterations were evaluated by quantitative PCR and cell proliferation assay; activation of RTKs and downstream effectors were compared between the parental cell line EBC-1 and the EBC-CR1, -CR2, and -CR3 resistant cell lines.
Results: We found that epidermal growth factor (EGFR) mRNA expression and protein activation were increased in EBC-CR1–3 cells compared to EBC-1 cells. EBC-CR1 cells showed EGFR-dependent growth and sensitivity to afatinib, an irreversible EGFR TKI. EBC-CR2 cells, which overexpressed the EGFR-MET heterodimer, responded dramatically to the combination of capmatinib and the phosphoinositide-3 kinase catalytic subunit α (PIK3CA) inhibitor afatinib. In addition, EBC-CR3 cells, which had activated EGFR along with amplified PIK3CA, were sensitive to the combination of afatinib and the PI3Kα inhibitor.
Conclusions: Our in vitro studies suggested that activation of EGFR signaling and/or genetic alteration of downstream effectors like PIK3CA were alternative resistance mechanisms used by capmatinib-resistant NSCLC cell lines. In addition, combined treatments with MET, EGFR, and PI3Kα inhibitors may be an effective therapeutic strategy in MET-TKI-resistant NSCLC patients.

overall_design: RNA-Seq analysis of  capmatinib-resistant cell lines (EBC-CR1, CR2, and CR3) derived from the MET-amplified NSCLC cell line EBC-1.


title: Cancer-cell intrinsic gene expression signatures minimise the confounding effects of intratumoural heterogeneity in colorectal cancer patient classification.

city: Belfast

first: Philip

last: Dunne

address: Lisburn Road

institute: Queens University Belfast

summary: Stromal-derived intratumoural heterogeneity (ITH) has been shown to undermine molecular stratification of patients into appropriate prognostic/predictive subgroups. Using several clinically relevant colorectal cancer (CRC) gene expression signatures, we assessed the susceptibility of these signatures to the confounding effects of ITH using gene expression microarray data obtained from multiple tumour regions of a cohort of 24 patients, including central tumour, the tumour invasive front and lymph node metastasis.

overall_design: Transcriptional profiles generated from matched central tumour, invasive front and lymph node regions from 24 colorectal cancer patients.

middle: D


title: Multifunctional glial support by Semper cells in the Drosophila retina

city: Detroit

first: Tiffany

last: Cook

address: 540 E. Canfield Avenue

department: Molecular Medicine and Genetics

institute: Wayne State University

summary: Using cell-restricted transcriptome analysis, here we show that Drosophila ommatidial cone (or Semper) cells are enriched for conserved glial regulators and effectors, including many characteristic of vertebrate retinal glia: Müller glia and astrocytes.

overall_design: RNA-seq based analysis of Drosophila retinal cone cells (3 developmental stages) and photoreceptors.  1 sample per cell type - 4 total libraries sequenced.

first: Mark

last: Charlton-Perkins

first: Elke

last: Buschbeck

first: Edward

last: Sendler


title: Global gene expression in P. pastoris during mitotic and meiotic growth, with and without meiotic regulator Ndt80

city: San Francisco

first: Isabel

last: Nocedal

state: CA

institute: UCSF

summary: The purpose of this experiment was to identify the genes with increased expression during sporulation in wild-type P. pastoris, and during sporulation in cells with Ndt80 deleted.  Cells were grown unti log-phase in YPD or in sporulation media (0.5% sodium acetate, 1% potassium chloride, 1% glucose, 2% agar plates ) for 30 hours.  Each experiment was repeated three times and sequenced on an Illumina HiSeq 4000

overall_design: P. pastoris WT meiotic expression vs. WT mitotic expression and Ndt80 del meiotic expression vs. WT meiotic expression, with three technical replicates for each.


title: Identification of target genes of TAZ in the prostate cancer cells

city: Shanghai

first: Chen-Ying

last: Liu

address: 1665 Kong Jiang Road

institute: Xinhua Hospital, Shanghai Jiao Tong University

summary: We found that the transcriptinal co-activator TAZ is a basal cell marker for the prostate epithelium which is lost in the prostate cancer tissues and re-expression of TAZ in the prostate cancers may be a indicator of malignancy. TAZ promotes cell migraiton, EMT and metastasis in the prostate cancers. To elucidate the underlying mechanism, we performed the RNA-seq analysis of TAZ knockdown DU145 cells using two independent TAZ shRNA and pLKO control cells.

overall_design: Two TAZ knockdown DU145 cells using two independent TAZ shRNA and two pLKO control DU145 cells were used for RNA-seq.

first: Wanjin

last: Hong


title: Expression profiling of Glycine max seed maturation by high throughput sequencing

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

summary: A transcriptome analysis of soybean seeds harvested at different developing stages (between stage 7.1 and stage 9) was carried out to understand the molecular events occuring during the acquisition of seed longevity during maturation.

overall_design: RNAseq from developing Glycine max seeds from stage 7.1 (mid-seedfilling) to final maturation

first: Juliana

last: Pereira Lima

first: Olivier

last: Leprince

first: Edvaldo

last: Aparecido Amaral da Silva


title: ChIP-Seq of constitutively expressed Ndt80A-Myc and Ndt80B-Myc in S. stipitis

summary: The purpose of this experiment was to identify the genes bound by the two Ndt80 paralogs in S. stipitis when constitutively expressed. Both paralogs were tagged with c-myc, the native Ndt80 promoter was replaced with the E. gossypii Tef1 promoter and the protein was immunoprecipitated with a c-myc antibody.  Cells were grown unti log-phase in YPD.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 2500.

overall_design: S. stipitis Ndt80A-myc vs. untagged control, and Ndt80B-myc vs. untagged control, with two technical replicates for each


title: Acetyl CoA metabolism by ACSS2 regulates neuronal histone acetylation and hippocampal memory [RNA-seq In Vitro]

city: Philadelphia

first: Shelley

middle: L.

last: Berger

state: Pennsylvania

address: 3400 CIVIC CENTER BLVD

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Metabolic production of acetyl-CoA has been linked to histone acetylation and gene regulation, however the mechanisms are largely unknown. We show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) is a critical and direct regulator of histone acetylation in neurons and of mammalian spatial object memory. We observe increased nuclear ACSS2 in differentiating neurons in vitro. Genome-wide, ACSS2 binding corresponds with increased histone acetylation and gene expression of key neuronal genes. These data indicate that ACSS2 functions as a chromatin-bound co-activator to increase local concentrations of acetyl-CoA and to locally promote histone acetylation for transcription of neuron-specific genes. Remarkably, in vivo attenuation of hippocampal ACSS2 expression in adult mice impairs long-term spatial memory, a cognitive process reliant on histone acetylation. ACSS2 reduction in hippocampus also leads to a defect in upregulation of key neuronal genes involved in memory, and these hippocampal genes are pre-bound by ACSS2. These results reveal a unique connection between cellular metabolism, gene regulation, and neural plasticity, establishing a link between generation of acetyl-CoA “on-site” at chromatin of critical neuronal genes.

overall_design: Includes two replicates of RNA-seq from differentiated CAD neurons with or without ACSS2 inhibitor (four samples total)

first: Philipp

last: Mews

first: Greg

last: Donahue

first: Adam

middle: M

last: Drake

first: Vincent

last: Luczak

first: Ted

last: Abel


title: Acetyl CoA metabolism by ACSS2 regulates neuronal histone acetylation and hippocampal memory [in vivo ChIP-seq]

overall_design:
Includes one sample each of ACSS2 and H3K9ac chIP-seq using material from mouse hippocampus, with input and whole histone subunit H3 included as a sonication control.
Please note that the input and H3 was used as a control for peak calling and track representation for ACSS2 and H3K9ac, respectively.


title: Acetyl CoA metabolism by ACSS2 regulates neuronal histone acetylation and hippocampal memory [RNA-seq In Vivo]

overall_design: Includes two replicates of RNA-seq from WT or ACSS2 knockdown mice (hippocampus) with or without SOR (spatial object recognition) training; thus, eight samples total.


title: Gene expression profile of human multiple myeloma cell line MM.1S after knockdown of KDM6B

first: Hiroto

last: Ohguchi

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Recent studies have delineated cancer type-specific roles of histone 3 lysine 27 (H3K27) demethylase KDM6B/JMJD3 depending on its H3K27 demethylase activity. Here we show that KDM6B is expressed in multiple myeloma (MM); and that shRNA-mediated knockdown and CRISPR-mediated knockout of KDM6B abrogate MM cell growth and survival. TNFα or bone marrow stromal cell culture supernatants induce KDM6B, which is blocked by IKKβ inhibitor MLN120B, suggesting KDM6B is regulated by NF-κB signaling in MM cells. RNA-sequencing and subsequent ChIP-qPCR analyses reveal that KDM6B is recruited to the loci of genes encoding components of MAPK signaling pathway including ELK1 and FOS, and upregulates these genes expression without affecting H3K27 methylation level. Overexpression of catalytically-inactive KDM6B activates expression of MAPK pathway-related genes, confirming its function independent of demethylase activity. We further demonstrate that downstream targets of KDM6B, ELK1 and FOS, confer MM cell growth. Our study therefore delineates KDM6B function that links NF-κB and MAPK signaling pathway mediating MM cell growth and survival, and validates KDM6B as a novel therapeutic target in MM.

overall_design: Human multiple myeloma cell line MM.1S was transduced with either shRNA against KDM6B or luciferase (control) in triplicate. A total of 6 RNA samples (3 KDM6B knockdown and 3 control) were used for RNA-sequencing analysis.

first: Kenneth

last: Anderson


title: ChIP-Seq of constitutively expressed Ndt80-Myc in P. pastoris

summary: The purpose of this experiment was to identify the genes bound by Ndt80 in P. pastoris when constitutively expressed. Ndt80 was tagged with c-myc, the native Ndt80 promoter was replaced with the E. gossypii Tef1 promoter and the protein was immunoprecipitated with a c-myc antibody.  Cells were grown unti log-phase in YPD.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 2500.

overall_design: P. pastoris Ndt80-myc vs. untagged control, with two technical replicates for each


title: ChIP-Seq of constitutively expressed Ndt80-Myc in K. lactis

summary: The purpose of this experiment was to identify the genes bound by Ndt80 in K. lactis when constitutively expressed. Ndt80 was tagged with c-myc, the native Ndt80 promoter was replaced with the K. lactis Gal1 promoter and the protein was immunoprecipitated with a c-myc antibody.  Cells were grown overnight in SRaffinose until log-phase, then in SRaffinose + 1.7% Galactose for 5 hours.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 4000.

overall_design: K.lactis Ndt80-myc vs. untagged control, with two technical replicates for each


title: ChIP-Seq of constitutively expressed Ndt80-Myc in S. cerevisiae

summary: The purpose of this experiment was to identify the genes bound by Ndt80 in S. cerevisiae when constitutively expressed, for the native Ndt80 as well as a heterologous Ndt80 from Pichia pastoris. For the ChIPs on the native Ndt80s, Ndt80 was tagged with c-myc; for the heterologous ChIP P. pastoris Ndt80 was integrated into the S. cerevisiae genome and tagged with c-myc.  In both cases, the native Ndt80 promoter was also replaced with an A. gossypii Gal1 promoter and the protein was immunoprecipitated with a c-myc antibody.  Cells were grown overnight in SRaffinose until log-phase, then in SRaffinose + 1.7% Galactose for 5 hours.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 4000.

overall_design: S. cerevisiae Ndt80-myc vs. untagged control and heterologous P. pastoris Ndt80-myc in S. cerevisiae vs. untagged control, with two technical replicates for each


title: N6-methyladenosine dynamics during early vertebrate embryogenesis

city: Oslo

first: Håvard

last: Aanes

address: Sognsvannsveien 20

department: Dept of microbiology

country: Norway

institute: Oslo University Hospital

summary: Early vertebrate embryogenesis is characterized by extensive post-transcriptional regulation during the maternal-to-zygotic transition. The N6-methyladenosine (m6A) modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability, translation efficiency and effect on miR-430 degradation kinetics. Notably, we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. After zygotic genome activation m6A is associated with improved stability and dampens the effect of miR-430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms, for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development.

overall_design: Examination of m6A in four different developmental stages


title: Amino Acid Transporter Slc38a5 Mediates Glucagon Receptor Inhibition-Induced Pancreatic α-Cell Hyperplasia in Mice

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: Glucagon supports glucose homeostasis by stimulating hepatic gluconeogenesis, in part by promoting the uptake and conversion of amino acids into gluconeogenic precursors.  Genetic disruption or pharmacologic inhibition of glucagon signaling results in elevated plasma amino acids, and compensatory glucagon hypersecretion involving expansion of pancreatic α-cell mass. Regulation of pancreatic α- and β-cell growth has drawn a lot of attention because of potential therapeutic implications. Recent findings indicate that hyperaminoacidemia triggers pancreatic α-cell proliferation via an mTOR-dependent pathway. We confirm and extend these findings by demonstrating that glucagon pathway blockade selectively increases expression of the sodium-coupled neutral amino acid transporter Slc38a5 in a subset of highly proliferative α-cells, and that Slc38a5 is critical for the pancreatic response to glucagon pathway blockade; most notably, mice deficient in Slc38a5 exhibit markedly decreased α-cell hyperplasia to glucagon pathway blockade-induced hyperaminoacidemia. These results show that Slc38a5 is a key component of the feedback circuit between glucagon receptor signaling in the liver and amino acid-dependent regulation of pancreatic α-cell mass in mice.

overall_design: Examination of the transcriptomes of pancreatic islets of mice treated with GCGR-antibody and an isotype control antibody.

first: Jinrang

last: Kim

first: Jesper

last: Gromada


title: Integrative epigenomic analysis in MLL-AF9 acute myeloid leukemia (AML) and B-acute lymphoblastic leukemia (B-ALL)

city: Montreal

first: Magalie

last: Celton

address: 2950, Chemin de Polytechnique

institute: IRIC

summary: Next generation DNA sequencing of acute myeloid leukemia (AML) patient samples has revealed novel recurrent mutations while at the same time highlighting the genetic heterogeneity of the disease. These observations suggest that an extraordinarily large number of combinations of mutations can contribute to leukemogenesis. In order to address the question of the contribution of patient genetic background to AML we have developed a model system to generate multiple human leukemias in a single donor’s genetic background. Stepwise RNA-seq data from this model shows that in the context of AML driven by the MLL-AF9 (MA9) oncogene, the genetic background of the donor does not have a detectable effect. Comparison of these model leukemias from multiple single donors to AML patient samples containing MA9 translocations revealed conserved gene expression patterns not previously highlighted in this genetic sub-type. We further demonstrate that the expression of one of these genes, RET, is essential both in vivo and in vitro growth of MA9 AMLs .

overall_design: study of methylome during the development of MLL-AF9 AML


title: CmrA, a novel transcription regulator involved in the multidrug resistance of Pseudomonas aeruginosa

city: Besançon

first: Catherine

last: Llanes

state: Doubs

address: 19 rue Ambroise Paré

department: UFR Sciences médicales et pharmaceutiques

institute: Université de Bourgonge Franche-Comté

summary:
Purpose: Recently we have characterize 43 clinical isolates of Pseudomonas aeruginosa overproducing the efflux pump MexEF-OprN. About 45% of these strains did not display mutations in any of the regulators known to control mexEF-oprN expression. Here we identified a novel regulator of the efflux operon mexEF-oprN that we named CmrA by characterizing in vitro selected mutants from the strain PA14.
Methods: MexEF-OprN overproducing spontaneous mutants were selected in vitro using the reference strain PA14 in presence of chloramphenicol. Selected mutants (PJ mutants) were characterized using different criteria such as antibiotic susceptibility and production of virulence traits. Gene expression was evaluated by RT-qPCR. Whole genome sequencing of selected mutants (PJ mutants) was performed using IonTorrent technology. Knock-out mutants were constructed by overlapping PCR and homologous recombination. Finally, a transcriptomic analysis by RNAseq was performed to identify the genes depending on CmrA.
Results: Characterization of the 4 selected PJ mutants showed that these strains have resistance and virulence profiles slightly differentent from those typically observed in MexEF-OprN overproducing strains (mexS- NfxC strains). The cmrA+ strains (here called NfxC2) showed moderate resistance to MexEF-OprN antibiotic substrates (ciprofloxacin, chloramphenicol and trimethoprim from 8- to 32-fold compared to PA14) and showed a less compromised capacity to produce some virulence traits (rhamnolipids, elastase, biofilm and pyocyanin) as well as the swarming motility. Whole genome sequencing of PJ mutants led to the identification of SNPs in the gene PA14_38040 (PA14_RS15465 after 2015 genome annotation uptdate). The gene PA14_RS15465 codes for an unknown transcriptional activator and was named cmrA for chlormaphenicol resistance activator. Aminoacid substitutions in CmrA found in PJ mutants were shown to constantly activate this regulator. Further characterization by gene inactivation showed that cmrA is responsible for the activation of the expression of the mexEF-oprN operon in PJ mutants. The locus cmrA was characterized and the complete sequence, including regulatory sequeces, was submitted to GenBank (accession number KX274690).  Further analysis showed that the CmrA-activating pathway was dependent on mexS and mexT, both genes are known to affect mexEF-oprN expression. Finally, the transcriptomic analysis of the PJ01 mutant (compared to PA14 and to PJ01∆mexT) revealed that CmrA significally activate the expression of 11 genes most of them coding for enzymes involved in redox regulation.
Conclusions: The discovery of cmrA opens the posibility to give an explanation to those clinical strains overproducing the efflux pump MexEF-OprN for unknown reasons. Our data shows that this regulator can activate the efflux pump in a way that the strain is capable to tolerate the antibiotics substrates of the pump and to mantain its capacity to produce some virulence traits. CmrA seems to have a role in the activation of regulatory pathways involved in redox homeostasis as shown by the transcriptomic analysis. The fact that the MexEF-OprN pump is activated at the same time that a redox system let us think that this pump could be related to intracellular detoxification of molecules altering the intracellular homeostasis as it has been previously proposed. We are currently analyzing the transcriptome of CmrA to describe the whole activation pathway of this regulator.

overall_design: Analysis of 3 samples of total RNA from Pseudomonas aeruginosa strains (PA14, PJ01 and PJ01ΔmexT). Each sample was analyzed in triplicate. The PA14 strain was used as the reference in order to identify the CmrA-dependent genes

first: Paulo

last: Juarez

first: Patrick

last: Plésiat

first: Katy

last: Jeannot


title: Systematic identification and characterization of long non-coding RNAs in zebrafish through RNA-Seq

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

summary: We sequenced mRNA from embryonic heart of zebrafish larvae 4 days post fertilization, adult heart of 6-month-old WIK fish, and adult muscle of adult fish consisting of both fast-twitch and slow-twitch fibers.

overall_design: Examination of mRNA and long noncoding RNA levels in embryonic heart, adult heart, and adult muscle tissues

first: Xiaolei

last: Xu


title: Genome-wide effect of STING-mediated activation in T cells

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

summary: Using wild type mice and mice deficient for STING, we compared genome-wide expression of RNA in response to STING activation with DMXAA

overall_design: To look for the role of STING-mediated pathway in activation of T cells, we activated naïve T cells with DMXAA, a synthetic agonist of STING, together with activation of TCR. To define a STING-specific effect, STING-deficient animals were used as a control. We isolated naïve T cells from peripheral lymph nodes, negatively selected them using magnetic beads coated with antibodies, and activated cells for 4 hours in specified conditions. Next, we isolated RNA and made library using TruSeq kit (Illumina) for the library construction.One replica of each sample is provided

first: Bridget

last: Larkin


title: Human Adult Sorted Live Cell Erythroblasts transduced with Sigma shRNA Clone TRCN0000162889 targeting SLC25A39 with puromycin selection RNAseq.

city: Bethesda

first: Jeffery

last: Miller

address: 10 Center Drive Room 9N311

department: NIDDK

institute: NIH

summary: Erythroblasts cultured from mobilized CD34+ cells from six healthy adult human donors were used to generate an erythroblast transcriptome transduced with Sigma shRNA Clone TRCN0000162889 targeting SLC25A39 gene. Cellular maturation was maintained including enucleation.  On culture day 14 total RNA was isolated (see PMID: 23798711 for details). These RNA-Seq profiles were generated after flow cytometric sorting (live cell gating of culture Day 14 erythroblasts according to forward and side scatter). Preliminary screening data demonstrated a robust increase in fetal hemoglobin that may be due to off-target effects from this shRNA clone. See Series GSE94147 for Empty Vector Control dataset.

overall_design:
Human CD34+ cells from health donor transduced with lentivirus expressing Sigma shRNA Clone TRCN0000162889 to knockdown SLC25A39 gene expression in serum free culture.  RNA extracted from sorted live cell gate on Day 14 using Qiagen miRNeasy Mini Kit.  1ug of RNA was used for library construction and Ribo depletion with globin subtraction.
Acknowledgement: We would like to thank Gerard Bouffard and the National Human Genome Research Institute for their expertise and assistance with RNA-seq.

first: Y

middle: T

last: Lee

first: Colleen

last: Byrnes


title: Induction of DlaT-Specific Th17 Cell Differentiation by Intestinal P. UF1 Bacterium

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

department: Pathology

institute: University of Florida

summary:
Summary: Incidence of necrotizing enterocolitis (NEC), which remains a leading and intractable cause of mortality in preterm infants, is attenuated by feeding human breast milk (HBM). We report that this diminution correlates with alterations in the gut microbiota, particularly enrichment of Propionibacterium species. Transfaunation of microbiota from HBM-fed preterm infants, or a Propionibacterium strain, P. UF1, cultured therefrom, to mice conferred protection against pathogens and correlated with profoundly increased intestinal Th17 cells, sustained regulatory T cells (Tregs), and reduced pathogen-induced inflammation. Th17 cell differentiation was dependent on dihydrolipoamide acetyltransferase (DlaT) of the bacterial surface layer. Binding of P. UF1 with its cognate receptor, SIGNR1, resulted in the activation of intestinal phagocytes. Importantly, P. UF1 significantly mitigated induced NEC in neonatal mice. Together, these results mechanistically elucidate the protective effects of HBM and P. UF1-induced immunoregulation that safeguard against proinflammatory diseases, including NEC.
Purpose: The goal of this study is to discover differentially epxressing genes between wild-type P. UF1 and DdlaT P. UF1 bacteria to reveal the critical role of DlaT in P. UF1 metabolism and potentially link it with P. UF1-induced protective immunity in the mice
Methods: Total RNA was extracted from P. UF1 and ΔdlaT P. UF1 strains cultured in MRS medium. The ScriptSeq Complete Gold Kit was used for rRNA depletion and the cDNA library generation. Subsequently, cDNA libraries were evaluated, pooled and sequenced on the Illumina MiSeq machine, which generates 7-8 million paired-end reads (~75nt) per sample. The sequence reads first underwent data preprocessing and quality evaluation including trimming off the low quality ends of reads. Rockhopper was used to map sequence reads to annotated P. UF1 genome, normalize the counts values by upper quartile normalization and perform differential expression analysis using NB statistical model
Results and conclusion: Data demonstrated that deletion of dlaT in P. UF1 resulted in significant activation of genes involved in the glycolytic pathway and significant changes in metabolic pathways, potentially influencing DC and T cell regulatory responses. However, these induced metabolic alterations are not critical for antigen-dependent Th17 response accordingly.

overall_design: mRNA profiles of wild-type and DdlaT P. UF1 bacteria were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Yong

last: Ge

first: Mansour

last: Mohamadzadeh


title: Mfd alters global transcription patterns in undamaged Escherichia coli cells

city: Research Triangle Park

first: Rachel

last: Krasich

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

summary: We uncovered evidence for an expanded role of transcription-coupled repair factor Mfd in Escherichia coli. In mfd knockout cells, expression of 75 genes was significantly increased while that of 18 genes was diminished. GO term analysis revealed that the affected genes were disproportionately from certain functional groups. RNA levels in the knockout deviated from wild type beginning at transcription start sites, arguing against premature termination as the cause. RNA-seq analysis in cells overexpressing Mfd revealed dramatic deviation of gene expression in the chromosome terminus region. Taken together, our data support a novel role for Mfd in transcription regulation.

overall_design: Examination of E coli mfd knockdown and Mfd-overexpressing cells compared to wildtype E. coli controls

first: Kenneth

last: Kreuzer


title: Next generation sequencing analysis of soy glyceollins and 17-β estradiol: Effects on transcript abundance in the female mouse brain

city: Louisville

first: Cynthia

last: Corbitt

state: Kentucky

address: 139 Life Sciences Building, University of Louisville

department: Department of Biology

institute: University of Louisville

summary: Purpose: The goal of this study was to compare and contrast the next generation sequencing data to data obtained from a whole brain microarray study

overall_design: Examination of the effects of Glyceollin alone, 17β Estradiol alone or in combination on gene expression in the adult female mouse brain

first: Sanaya

middle: F

last: Bamji

first: Eric

last: Rouchka

first: Yan

first: Xiaohong

last: Li

first: Teheodore

last: Kalbflesich


title: ChIP-Seq of constitutively expressed Ndt80A-Myc and constitutively and endogenously expressed Ndt80B-Myc in C. albicans

first: Isabel

last: Nocedal

summary: The purpose of this experiment was to identify the genes bound by the two Ndt80 paralogs in C. albicans when constitutively expressed, and for Ndt80B when endogenously expressed. Both paralogs were tagged with c-myc, and the protein was immunoprecipitated with a c-myc antibody.  For constitutive expression, each native Ndt80 promoter was replaced by the C. albicans Tdh3 promoter.  Cells were grown unti log-phase in YPD.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 2500.

overall_design: C. albicans constitutively expressed Ndt80A-myc vs. untagged control, Ndt80B-myc vs. untagged control, and endogenous Ndt80B-myc vs. untagged control, with two technical replicates for each


title: ChIP-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages

first: Haiqing

last: Zhao

address: 3400 N Charles St

department: Biology

institute: Johns Hopkins University

summary: Lamins, the major components of the nuclear lamina, have diverse functions in many cellular processes. Despite broad expression, lamins have been implicated in cell type-specific roles in development, aging and disease by regulating gene expression. Yet, due to the lack of in depth lineage-specific functional studies, it remains unclear whether or how lamins regulate cell type-specific functions. Using targeted knockout of lamin B1 in the olfactory sensory neuron lineage, we show that lamin B1 is not required for early stages of olfactory sensory neuron differentiation but is needed for formation of mature neurons that properly respond to odor stimulation. Lamin B1 mutant cells exhibited decreased expression of genes involved in mature neuron function, increased expression of genes atypical of the olfactory lineage and clustered nuclear pore distribution. These results demonstrate that the universally expressed lamin B1 regulates cell type-specific gene expression and terminal differentiation.

overall_design: Samples were generated from sorted regenerated olfactory epithelium cells lacking Lamin B1 (Lmnb1) and control (heterozygous cells). Each sample was collected from one mouse. Data are from two experimental samples, one control and one mutant, each split and probed for H3K4me3 and H3K9me3 separately. Treatment, sample preparation, sequencing, animal sex, age, and parents are the same for mutant and control.

first: Crystal

last: Gigante

first: Zhaobin

last: Zheng

first: Yixian


title: Regulation of small RNAs and corresponding targets in Nod factors-induced Phaseolus vulgaris root hair cells

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM

summary: A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.

overall_design: Small RNA sequencing from Nod factor-induced Phaseolus vulgaris root hairs

first: Formey

last: Damien

first: Jose

last: Martin Rodriguez

first: Alfonso

last: Leija

first: Olivia

middle: S

last: Estrada

first: Luis

last: Cárdenas

first: Georgina

last: Hernández


title: Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (Leukemia Cell Bank)

first: Magalie

last: Celton

overall_design: Transcriptome of MLL-AF9 AML pediatric patients


title: ChIP-Seq of Ndt80-Myc in S. cerevisiae during meiosis and sporulation

institute: UCSF

summary: The purpose of this experiment was to identify the genes bound by Ndt80 in S. cerevisiae during meiosis and sporulation.  Ndt80 was tagged with c-myc and the protein was immunoprecipitated with a c-myc antibody.  Cells were grown in liquid YPA (2% Peptone, 2% Potassium Acetate, 1% Yeast Extract) at room temperature for 22 hours.  Each experiment was repeated twice and sequenced on an Illumina HiSeq 4000.

overall_design: S. cerevisiae Ndt80-myc vs. untagged control with two technical replicates for each


title: RNA-seq of Lmnb1-/- and Lmnb1+/- olfactory lineages

overall_design: Transcriptome profiles were generated from sorted regenerated olfactory epithelium cells lacking Lamin B1 (Lmnb1) and control (heterozygous cells). Each sample is collected from one mouse. Data are from two experimental groups (G1,G2), each containing a control and a mutant sample. Different groups differ in treatment, parents, age and sex. Within a group, treatment, sample preparation, sequencing, animal sex, age, and parents are the same.


title: Pseudotemporal ordering of single cells reveals metabolic control of postnatal beta cell proliferation

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Maintenance of blood glucose homeostasis depends on appropriate pancreatic beta cell mass, which is established during early postnatal life through expansion of beta cell numbers. Postnatally, the proliferative capacity of beta cells declines rapidly but the cell extrinsic cues and intracellular signals that cause this decline remain unknown. Here we generated single-cell RNA-seq data of beta cells from multiple postnatal time points and ordered cells based on transcriptional similarity along a linear trajectory. This analysis increased the resolution of transcriptome dynamics during postnatal beta cell development and revealed decreasing mRNA levels of a network of transcription factors, mitochondrial genes and regulators of amino acid metabolism. Through experimental validation we show that these transcription factors and metabolic pathways drive neonatal beta cell proliferation and mass expansion, suggesting a causal role for their regulation in the postnatal decline of beta growth.

overall_design: Single-cell transcriptomes of sorted beta cells from mIns1-H2B-mCherry mice at five different time points, encompassing the period between birth and post-weaning.

first: Chun

last: Zeng


title: Differential expression analysis of Far2 knock-out and wild-type Mus musculus kidney RNA-seq data.

city: Bar Harbor

first: Yuka

last: Takemon

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

summary: We identified the gene Far2, encoding the fatty acyl-coA reductase 2, to be associated with mesangial matrix expansion (MME) in the mouse (PMID: 24009241). In order to verify this association we obtained the C57BL/6N-Far2tm2a(KOMP)Wtsi/2J (JR#018805) strain from The Jackson Laboratory's KOMP2 program and compared this strain to it's control strain (C57BL/6N) for several renal characteristics. At 6 months of age the knockout mice have a significantly better kidney function (measured as glomerular filtration rate) but the MME is at a comparable level. However, as MME increases in the control strain at 12 months of age, MME does not increase in the knockout until 18 months of age. In order to explore changes at the gene expression level, we compared RNA sequence reads from 6-month old kidneys. Our analysis showed a decrease of RNA expression for several tubular damage markers (NGAL, KIM-1) and an increase in several genes in the fatty acid metabolism pathway.

overall_design: This study consists of 3 biological replicates of the C57BL/6N-Far2tm2a(KOMP)Wtsi/2J and 3 biological replicates of C57BL/6N, which are compared to each other

first: Ron

last: Korstanje