title: Time-series analysis of transcription factor knockdown in Drosophila S2R+ cells using RNA-Seq.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

summary: To understand how RNAi depletion of transcription factors impact the Drosophila transcriptome, we performed selective knockdown of 46 transcription factors in Drosophila S2R+ cell line.  We treated cells with long double strand RNAs by bathing for 1 to 3 days.  We purified polyA+ RNA and prepared strand-specific RNA-Seq libraries.  We quantitatively measured transcriptomic responses using a time series analysis.

overall_design: We depleted a total of 46 different transcription factors in S2R+ cells.  In each well of a 96 well plate, we targeted a single transcription factor for knockdown using a single double stranded RNA reagent.  Except for two transcription factors that we have used on only one reagent (alphaCOP and Trf), a total of two different double strand RNAs reagents were used per transcription factor.  We had six different control wells in our plates: two wells targeting the E. coli LacZ gene, one well targeting GFP, one well targeting thread (= Death-associated inhibitor of apoptosis 1. Flybase ID:  FBgn0260635) gene -- which gave us a visual information of knockdown by causing cell death, and two wells where we didn’t treat any double strand RNA.  Total number of these samples and controls are 96.  We prepared three of such plates, and incubated for 24, 48, and 72 hours.  From the cells, we isolated polyA+ RNA to prepare strand-specific RNA-Seq libraries.  We performed RNA-Seq based on Illumina-platform to have read lengths of 76 base pairs, in single-ends.

first: H

last: Lee

first: M

last: Buckner

first: Q

last: Gilly

first: Y

last: Hu

first: S

last: Mohr

first: N

last: Perrimon

first: B


title: Environmental Enrichment Induces Pericyte and IgA-Dependent Wound Repair and Lifespan Extension in a Colon Tumor Model [Microbiome]

status: Public on Apr 26 2017

city: Salt Lake City

first: Melinda

middle: L.

last: Angus-Hill

state: UT

address: 2000 Circle of Hope

department: Medicine

institute: University of Utah

summary: Environmental enrichment (EE) replicates mind-body therapy by providing complex housing to laboratory animals to improve their activity levels, behavior and social interactions. Using a Tcf4Het/+ ApcMin/+-mediated model of colon tumorigenesis, we found that EE vastly improved the survival of tumor-bearing animals, with differential effect on tumor load in male compared to female animals. Analysis of Tcf4Het/+ ApcMin/+ males showed drastically reduced expression of circulating inflammatory cytokines and induced nuclear hormone receptor signaling, both of which are common in the wound repair process. Interestingly, EE provoked tumor wound repair resolution through revascularization, plasma cell recruitment and IgA secretion, replacement of glandular tumor structures with pericytes in a process reminiscent of scarring, and normalization of microbiota. These EE-dependent changes likely underlie the profound improvement in survival of colon-tumor-bearing Tcf4Het/+ ApcMin/+ males. Our studies highlight the exciting promise of EE in the design of future therapeutic strategies for colon cancer patients.

overall_design: Bacterial Genomic DNA isolated from Stool collected from male mice with 4 different genotypes (WT, ApcMin, Tcf4Het, Tcf4Het ApcMin) and two different housing conditions (Non-enriched, NE; Environmentally Enriched, EE).

middle: L


title: Changes in miRNA in the lung and blood after whole thorax irradiation in rats: biomarkers for radiation-induced injuries

status: Public on Apr 25 2017

city: Milwaukee

first: Meetha

last: Medhora

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Radiation oncology

institute: Medical College of Wisconsin

type: Non-coding RNA profiling by high throughput sequencing

summary: We used a rat model of whole thorax x-ray irradiation to profile the microRNA (miRNA) in lung and blood up to 4 weeks after radiation. Small RNA from normal and irradiated Wistar rat lungs and blood were analyzed by next-generation sequencing and the changes by radiation were identified by deRNA-seq at 1, 2, 3 and 4 weeks after irradiation.  The average total reads/library was 2,703,137 with a mean of 88% mapping to the rat genome.  Detailed profiles of 100 of the most abundant miRNA in rat blood and lung are described.

overall_design: Profile of miRNA in Wistar rat lungs and blood with and without radiation from 1 to 4 week after radiation were generated by next generation sequencing. Each group contains three rats.

first: Feng

last: Gao

first: Pengyuan

last: Liu

first: Jayashree

last: Narayanan

first: Meiying

last: Yang

last: Fish

first: Yong

first: Mingyu

last: Liang

first: Elizabeth

middle: R

last: Jacobs


title: Differential gene expression following exposure to rivals in male Drosophila melanogaster.

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: We used RNAseq to detect differential gene expression in Drosophila melanogaster males exposed to rival males or not for a period of 2, 26 or 50h. Dahomey wild type males were raised at a density of 100 larvae per vial on SYA medium. Upon eclosion, males were stored 10 per vial and then at 1d old placed in individual vials for 5days. Rival wild type males were then introduced to the focal males for 2, 26 or 50h. The focal males were then snap frozen in liquid nitrogen. Prior to RNA extraction, males were separated into abdomen and Head+Thorax body parts. RNA was extracted (MiRVana kit) from pools of n = 40 male body parts and sent for RNA sequencing (Illumina HiSeq, 50 cycles, non directional, 4 samples per lane). We then followed a set of careful QC procedures and analysed the data for differential gene expression due to the presence or absence of rival males over time. Differential expression of transcrits was validated by using qRT-PCR on the same biological samples.

overall_design: We analysed 2 treatments (rivals / no rivals) x 3 time points (2h, 26h or 50h) x 3 biological replicates x 2 body parts (Head+Thorax, Abdomen) = 36 samples. Samples are coded as: timepoint (2, 26, 50), treatment (E = no rival, R = Rival), body part (H = Head+Thora,; A = Abdomen), replicate (1,2,3).

first: Amanda

last: Bretman

first: Damian

last: Smith

first: Emily

last: Fowler

first: Tamas

last: Dalmay

first: Tracey

last: Chapman


title: The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana [RNA-Seq]

status: Public on Apr 24 2017

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Gene bodies of vertebrates and flowering plants are occupied by histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. The profiles of enrichments in DNA methylation and H3.3 over gene bodies are correlated and both depend similarly on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. We engineered H3.3 knockdown in Arabidopsis and observed transcription reduction that predominantly affected genes responsive to environmental cues. When H3.3 levels were reduced, gene bodies showed a loss of DNA methylation correlated with transcription levels. To study the origin of changes in DNA methylation profiles when H3.3 levels are reduced, we examined genome wide distributions of several histone H3 marks, H2A.Z, linker histone H1 and nucleosome densities. We observed that in absence of H3.3, H1 distribution increased in gene bodies. This depends on levels of gene transcription. We propose that H3.3 prevents recruitment of H1, which in turn promotes chromatin folding and antagonizes access to DNA methyltransferases responsible for gene body methylation. Thus, gene body methylation is likely shaped by H3.3 dynamics in relation with transcriptional activity.

overall_design: Examination of transcription in WT and H3.3 knock down samples by RNA-Seq

first: Heike

last: Wollmann

first: Ramesh

last: Yelagandula


title: RNA sequencing of erythroid and granulomonocytic colonies differentiated from transduced bone marrow CD34+ cells expressing U2AF1 S34F mutation, U2AF1 wild-type or empty vector control

first: Stephen

last: Taylor

institute: CBRG

summary: Mutations of the splicing factor U2AF1 are frequent in the myeloid malignancy myelodysplastic syndromes (MDS) and in other cancers. Patients with MDS suffer from peripheral blood cytopenias, including anemia, and increasing bone marrow blasts. We investigated the impact of the common U2AF1 S34F mutation on cellular function and mRNA splicing in the main cell lineages affected in MDS. We demonstrated that U2AF1 S34F expression in human hematopoietic progenitors impairs erythroid differentiation, and skews granulomonocytic differentiation towards granulocytes. RNA-sequencing of erythroid and granulomonocytic colonies revealed that U2AF1 S34F induced a higher number of cassette exon splicing events in granulomonocytic than erythroid cells, and altered mRNA splicing of many transcripts (expressed in both cell types) in a lineage-specific manner. The introduction of isoform changes identified in the target genes H2AFY and STRAP into hematopoietic progenitors recapitulated phenotypes associated with U2AF1 S34F expression in erythroid and/or granulomonocytic cells, suggesting a causal link. Importantly, we provided evidence showing that isoform modulation of the U2AF1 S34F target genes H2AFY and STRAP rescues the erythroid differentiation defect in U2AF1 S34F MDS cells, raising the possibility of using splicing modulators therapeutically. These data have critical implications for understanding MDS phenotypic heterogeneity, and for the development of new targeted therapies.

overall_design: RNA sequencing was performed to identify the aberrant splicing events associated with U2AF1 S34F mutation (n=3) compared to U2AF1 wild-type (n=3) and empty vector control (n=3) in BFU-E and CFU-G/M colonies respectively.

first: Bon

middle: H

last: Yip


title: The histone H3 variant H3.3 regulates gene body DNA methylation [BiSulfite-seq]

type: Methylation profiling by high throughput sequencing

summary: Gene bodies of vertebrates and flowering plants are occupied by histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. The profiles of enrichments in DNA methylation and H3.3 over gene bodies are correlated and both depend similarly on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. We engineered H3.3 knockdown in Arabidopsis and observed transcription reduction that predominantly affected genes responsive to environmental cues. When H3.3 levels were reduced, gene bodies showed a loss of DNA methylation correlated with transcription levels. To study the origin of changes in DNA methylation profiles when H3.3 levels are reduced, we examined genome wide distributions of several histone H3 marks, H2A.Z, linker histone H1 and nucleosome densities. We observed that in absence of H3.3, H1 distribution increased in gene bodies. This depends on levels of gene transcription.We propose that H3.3 prevents recruitment of H1, which in turn promotes chromatin folding and antagonizes access to DNA methyltransferases responsible for gene body methylation. Thus, gene body methylation is likely shaped by H3.3 dynamics in relation with transcriptional activity.

overall_design: one wild type, two H33 knockdown samples

first: Frederic

last: Berger

first: Tetsuji

last: Kakutani


title: Gene expression profiles of distinct mesenchymal cell populations in Peyer's patches

city: Stanford

first: Kazuki

last: Nagashima

state: CA

address: 290 Jane Stanford Way, Room W117 Fischbach Lab

department: Bioengineering

institute: Stanford University

summary: The purpose of this experiment is to characterize Peyer's patch-resident distinct mesenchymal stromal cells, including marginal reticular cells (MRCs) and M cell-inducer (MCi) cells.

overall_design: Mesenchymal cells were sorted from Peyer's patches of wild-type mice using flow cytometry (n=5).

first: Hiroshi

last: Takayanagi


title: ATAC sequencing of K-562 cells

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We analysed the global effect of c-Myb knockdown and rescue with ectopically expressed WT c-Myb and c-Myb D152V on chromatin accessibility by ATAC-seq

overall_design: Cells were tranfected with siRNA for 24 hours and  50 000 cells were harvested for ATAC. Three individual experiments were performed. Libraries were prepared and 40-bp paired-end reads were obtained using an Illumina Nextseq 500 sequencer

first: Odd

middle: S

last: Gabrielsen

middle: M

first: Roza

middle: B

last: Lemma


title: The histone H3 variant H3.3 regulates gene body DNA methylation

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

overall_design: Refer to individual Series


title: Genes upregulated in old Candida glabrata

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Comparison of young and old Candida glabrata cells reveals regulation of genes involved in cell wall remodeling, sterol biogenesis, stress pathways

overall_design: Transcriptome of 0-2 generation-old (young) Candida glabrata cells of strain BG2 were compared to 12-14 generation-old (old) Candida glabrata cells of strain BG2

first: Tejas

last: Bouklas

middle: C

last: Fries


title: Transcriptional analysis of the adaptation of Ustilago maydis to grow under nitrogen fixation conditions

city: Hermosillo

first: Miguel

middle: Angel

last: Hernandez

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas No. 46

department: Coordinación de Tecnología de Alimentos de Origen Vegetal

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo

summary: In this study we show the transcriptional analysis after shifting the Ustilago maydis from media with ammonium as a nitrogen source to media lacking ammonium. From these, 49 genes were up-regulated and 41 were down-regulated. The functional description and gene ontology terms associated to the diferentially expressed genes revealed that various key pathways were represented, including, secondary metabolism, the metabolism of nitrogen, amino acid, fatty acid and amino sugar, among others, suggesting that the interplay of U. maydis with its N2 fixing bacterial endosymbiont is a flexible process that may be active during the adaptation to the fungus to the different nitrogen sources, and possibly during its pathogenic style of life.

overall_design:
The strain of U. maydis used in this study was FB2. The strain, was maintained at -70 ºC, recovered in complete medium and then grown in liquid minimum medium (MM) at 28 ºC. U. maydis cells were inoculated to MM with (NH4)NO3 as nitrogen source (+N), and in the same basal medium without (NH4)NO3 (-N), and incubated under shaking conditions at 28 ºC for 24 h.
To identify the differentially expressed genes of U. maydis cells growing fixation conditions, we prepared two RNA-Seq libraries from three biological replicates pooled of yeast-like cells of U. maydis FB2 strain grown with an added nitrogen source (+N), or without an added nitrogen source (-N) obtained at the end of the log phase (24h). The RNA-seq libraries were sequenced by Illumina HiSeq200 using the paired-end protocol (Illumina Inc. San Diego, CA, USA).

first: José

middle: A

last: Sánchez-Arreguin

last: Hernández-Oñate

first: Claudia

middle: G

last: León-Ramirez

last: Ruiz-Herrera


title: Molecular codes for cell type specification in Brn3 Retinal Ganglion Cells

first: Matthew

middle: J

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Visual information is conveyed from the eye to the brain by distinct types of Retinal Ganglion Cells  (RGCs). It is largely unknown how RGCs acquire their defining morphological and physiological features  and connect to upstream and downstream synaptic partners. The three Brn3/Pou4f transcription factors  (TFs) participate in the combinatorial code for RGC type specification but their exact molecular roles are  still unclear. We use deep sequencing to define (i) transcriptomes of Brn3a and/or Brn3b positive RGCs,  (ii) Brn3a and/or Brn3b dependent RGC transcripts and (iii) transcriptomes of retinorecipient areas of the  brain at developmental stages relevant for axon guidance, dendrite formation and synaptogenesis. We reveal  a combinatorial code of transcription factors, adhesion molecules and determinants of neuronal morphology  that are differentially expressed in specific RGC populations and selectively regulated by Brn3a and/or  Brn3b. This comprehensive molecular code provides a basis for understanding neuronal cell type  specification in RGCs.

overall_design: For retinal ganglion cells (RGCs) alkaline phosphatase (AP) positive and negative cells from Brn3aAP/WT, Brn3aAP/KO, Brn3bAP/WT, and Brn3bAP/KO from dissociated mouse retina at embryonic day 15 and post-natal day 3 were isolated by magnetic beads coupled to anti-AP mouse monoclonal antibodies. Lateral geniculate nucleus (LGN), superior colliculus (SC) and pretectal area (PTA) retinorecipient nuclei from wild type post-natal day 3 mice were visualized by anterograde tracing, microdissected, and processed for RNA isolation. Total RNA was extracted by Qiagen RNeasy using on-column DNase treatment (Qiagen) and analyzed by 2100 Bioanalyzer (Agilent Technologies Genomics). High quality of total RNA (RIN: >8.0) was subjected to sequencing library construction using 20 ng of total RNA as input. Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each RGC library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases. Brain samples were paired-end sequenced to 125 bases on an Illumina HiSeq2500. Fastq files were generated from reads passing chastity filter.

first: Szilard

last: Sajgo

first: Miruna

last: Ghinia

first: Friedrich

last: Kretschmer

first: Katherine

last: Chuang

first: Suja

last: Hiriyanna

first: Zhijian

last: Wu

first: Octavian

last: Popescu

first: Tudor

last: Badea


title: Transgenerational transmission of environmental information in C. elegans

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: RNA sequencing of N2 worms. Heterochromatic repetitive DNA transmits environmentally-acquired information for up-to fourteen generations in C. elegans

overall_design: RNA sequencing of N2 worms grown at 25 degrees, worms propagated for 3 generations at 20 degrees after temperature shift from 25 degrees, and worms grown at a reference temperature of 20 degrees. This series includes RNA sequencing of set25 mutant worms grown at a reference temperature of 20 degrees.

first: Adam

last: Klosin

first: Cristina

last: Hidalgo

first: Tanya

last: Vavouri

first: Ben

last: Lehner


title: Transcriptional profiles of CD8+ T cells from peripheral blood of melanoma patients before and after anti-PD1 therapy

status: Public on Apr 23 2017

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: RNA-Seq analysis was used to study the profile of CD8 t cells from melanoma patients before and after treatment to understand if we can detect transcriptional changes in peripheral blood

first: Alexander

last: Huang

last: Wherry

first: Josephine

last: Giles


title: Fam60a defines a embryonic stem cell specific Sin3a/Hdac complex.

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary:
ChIP coupled with NGS identifies genome-wide binding sites of a  ES cells specific Sin3a/Hdac complex.
The aim of these experiments is to study the role of Fam60a in the Sin3a/Hdac complex. ChIP-Seq experiments reveal that Fam60a is required to maintain high levels of Sin3a binding on target genes in mESCs. Depletion of Fam60a causes a drop of Sin3a binding to target sites. Underlining the function of Fam60a in mES cells, ChIP-seq analysis of Sin3a and Fam60a in mouse fibroblasts reveal strikingly low global binding level of Sin3a to its target genes while Fam60a is absent at these sites.

overall_design: ChIP-Seq of Sin3a and Fam60a in E14 mESCs and NIH3T3. ChIP-Seq of Sin3a following shRNA-mediated knockdown of Fam60a in mESCs.

first: Gundula

last: Streubel

first: Sriganesh

last: Jammula

first: Adrian

middle: P

last: Bracken


title: Interferon regulated genes in mouse intestine after irradiation and prophylactic Rig-I activation

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: As RIG-I activation induces potent IFN-I responses,we analyzed the role of IFN-I in intestinal tissue protection and prevention of GVHD. We performed RNA sequencing with tissue samples from SI of WT mice that received TBI -/+ previous 3pRNA treatment and  -/+ antibody-mediated blockade of IFNAR. Application of 3pRNA before TBI resulted in a significant increase of IFN-inducible genes in the SI as compared to solely irradiated mice. Blockade of IFNAR signaling abrogated 3pRNA-mediated up-regulation of IFN-induced genes, demonstrating that RIG-I-induced gene-regulation depends on IFN-I.

overall_design: Balb/c mice were solely irradiated (9Gy) (n=3), pretreated with Rig-I agonist 3pRNA prior (d-1) to irradiation (n=3) or pre-treated with 3pRNA (d-1) + anti-IFNaR1 blocking antibody (d-2) prior to irradiation (n=3). RNA from small intestines was isolated 12h after irradiation and used for RNA sequencing.

first: Julius

last: Fischer

first: Gabriel

last: Eisenkolb

first: Marcel

last: van den Brink

first: Hendrik

last: Poeck


title: Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates [fCLIP-seq]

city: Seoul

first: Kyowon

last: Jeong

address: 1 Gwanak-ro

country: South Korea

institute: Seoul National University

summary: MicroRNA (miRNA) maturation is initiated by DROSHA, a double-stranded RNA (dsRNA)-specific RNase III enzyme. By cleaving primary miRNAs (pri-miRNAs) at specific positions, DROSHA serves as a main determinant of miRNA sequences and a highly selective gate-keeper for the canonical miRNA pathway. However, the sites of DROSHA-mediated processing have not been annotated on a genomic scale, and it remains unclear to what extent DROSHA functions outside the miRNA pathway. Here we establish a protocol termed ‘formaldehyde crosslinking and immunoprecipitation followed by sequencing (fCLIP-seq)’ that allows identification of DROSHA cleavage sites at single nucleotide resolution. fCLIP identifies numerous cleavage sites that do not match the ends of annotated mature miRNAs, particularly at the 3′ termini, suggesting widespread end modifications during miRNA maturation such as trimming and tailing. fCLIP also finds many pri-miRNAs undergoing alternative processing, yielding multiple miRNA isoforms. Moreover, we discover dozens of novel substrates that are bound and cleaved by DROSHA. These substrates are processed less efficiently than canonical pri-miRNAs, and produce only minute amounts of small RNAs. Depletion of DROSHA results in an increase of the hairpin-containing transcripts. Thus, the hairpins may serve mainly as cis-elements for DROSHA-mediated gene regulation rather than as miRNA genes. fCLIP-seq not only accurately maps the cleavage sites of DROSHA and suggests noncanonical functions of DROSHA, but also could be a general tool for investigating interactions between dsRNA binding proteins and structured RNAs.

overall_design: fCLIP-seq of total RNA in HEK293T and HeLa cell lines (2 replicates per each cell line)

first: Baekgyu

last: Kim

first: V

middle: N


title: Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates [RNA-seq]

overall_design: RNA-seq of total RNA in siRNA-transfected HEK293T cells (3 replicates)


title: C. neoformans gene expression by SIR2 deletion in strains H99 and RC2 subjected to glucose starvation

first: Jinsheng

last: Yu

summary: Analysis of raw data demonstrated regulation of genes involved in transmembrane transport, transcription and translation; molecular functions that included transporter activity; and cellular components that included the cell membrane, ribosome, nucleolus, and mitochondria

overall_design: Cryptococcus neoformans strains H99 and RC2 and respective SIR2 mutant were grown in rich media (2% glucose) or calorie restricted media (0.05% glucose) for 16h and total RNA was isolated for RNAseq

first: Tejas

last: Bouklas

first: Bettina

last: Fries


title: Genome-wide mapping of DROSHA cleavage sites on primary microRNAs and novel substrates


title: Methyl-seq and ChIP-seq analyses of TSPAN8-high and TSPAN8-low subpopulations of ID4-EGFP+ undifferentiated spermatogonia

city: San Antonio

first: Brian

middle: P.

last: Hermann

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

summary: P6 ID4-EGFP+ undifferentiated spermatogonia stained robustly (high) or weakly (low) for TSPAN8 were isolated by FACS.

overall_design: Pooled independent sorts of each population were used for reduced-representation methyl-seq or ChIP-seq for three histone modifications (H3K4me3, H3K27Ac and H3K27me3).

first: Kazadi

last: Mutoji

first: Keren

last: Cheng

first: John

last: McCarrey


title: Lysine-specific demethylase 1 metastasis of androgen-independent PCa cells [ChIP-seq]

city: Freiburg

first: Anett

last: Ketscher

state: BW

address: Breisacher Str. 66

department: Urology

country: Germany

institute: University Freiburg

summary:
The aim of this study is to identify the LSD1 target genes in metastatic androgen independent prostate cancer
Lysine-specific demethylase 1 (LSD1) was shown to control gene expression and cell proliferation of androgen-dependent prostate cancer (PCa) cells, whereas the role of LSD1 in androgen-independent metastatic prostate cancer remains elusive. Here, we show that depletion of LSD1 leads to increased migration and invasion of androgen-independent PCa cells. Transcriptome and cistrome analyses reveal that LSD1 regulates expression of lysophosphatidic acid receptor 6 (LPAR6) and cytoskeletal genes including the focal adhesion adaptor protein paxillin (PXN). Enhanced LPAR6 signalling upon LSD1 depletion promotes migration with concomitant phosphorylation of PXN. In mice LPAR6 overexpression enhances, whereas knockdown of LPAR6 abolishes metastasis of androgen-independent PCa cells. Taken together, we uncover a novel mechanism of how LSD1 controls metastasis and identify LPAR6 as a promising therapeutic target to treat metastatic prostate cancer.

overall_design: LSD1 binding profile in prostate cancer cell

first: Eric

last: Metzger

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: Lysine-specific demethylase 1 metastasis of androgen-independent PCa cells [RNA-seq]

overall_design: Transcriptional profiling of LSD1 KO prostate cancer cell


title: Lysine-specific demethylase 1 metastasis of androgen-independent PCa cells


title: Analysis of canonical A-to-I RNA editing in Drosophila using ICE-seq

city: Irvine

first: Eddie

last: Park

address: 2300 Biological Sciences 3

department: DevCell

institute: UCI

summary: The predominant form of RNA editing in animals is the enzymatic conversion of adenosine to inosine that is sequenced in cDNA as guanine.  While RNA editing should be identifiable from RNA-seq data alone, genomic SNPs as well as sequencing and mapping errors result in a high false-positive rate. We used Inosine Chemical Erasing (ICE) with deep sequencing (ICE-seq) in order to validate A-to-I RNA editing genome-wide without the need for the sequencing of the underlying genomic DNA. We called RNA editing events in the head transcriptome of the reference strain of Drosophila melanogaster and six resequenced strains of Drosophila yakuba using the Illumina HiSeq and NextSeq platforms. We compared RNA editing sites reported in other studies and measured the level of conservation between D. melanogaster and D. yakuba. We found that while some of the best-studied editing sites in D. melanogaster are also edited in D. yakuba, we also detect a significant amount of species-specific editing in genes with different Gene Ontology enrichments, which suggests that the biological function of RNA editing in the two Drosophila species is diverging.

sample_organism:
Drosophila melanogaster
Drosophila yakuba

overall_design: ICE-seq and RNA-seq pairs were generated for 6 strains of Drosophila yakuba and two replicates of Drosophila melanogaster. Two additional RNA-seq libraries were generated on the HiSeq and NextSeq.

first: Rebekah

last: Rogers

first: Peter

last: Andolfatto

first: Kevin

last: Thornton

first: Ali

last: Mortazavi


title: A549 cell transcriptome responses to infection with H7N9 influenza virus

status: Public on Apr 22 2017

city: Shanghai

first: Pei

last: Hao

state: Shanghai

address: No.320 Yueyang Road

department: Bioinformatics Platform

country: China

institute: Institut Pasteur of Shanghai

summary: mRNA-Seq analysis was used to profile the cellular transcriptome of A549 cells at multiple time points in response to infection with influenza H7N9.

overall_design: A549 cells were infected with H7N9(A/Anhui/1/2013 ) at MOI of 1 for 1.5h, 3h and 7h. The mRNA was derived from the total RNA using poly-T oligo-attached magnetic beads. Then the mRNA was fragmented and converted into cDNA. The adapters were ligated to the cDNA and then the fragments were amplified by PCR. Paired-end sequencing (101 × 2) was performed using a Hiseq-2000 (Illumina). Each condition of the samples was sequenced in duplicate.

first: Wu

last: Zhong


title: TET2 protects the genome from mutagenicity through interacting with MSH6

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

summary: Ten eleven translocation 2 (TET2) is a member of dioxygenases that catalyze the multi-step 5-methylcytosine oxidation. Loss-of-function TET2 mutations frequently occur in various types of hematological malignancies; however, the underlying mechanism remains poorly understood. Here, we show that Tet2-/- mice develop spontaneous myeloid, T- and B-cell malignancies. Exome sequencing of Tet2-/- tumors reveals acquisition of numerous mutations. The mutational frequency in Tet2-/- tumors is significantly greater at loci containing Tet2-dependent active demethylation sites. In addition, the analyses of TET2-interacting protein unveil the association between TET2 and MutS Homolog 6 (MSH6). TET2-depleted cells display elevated spontaneous mutational frequencies and increased microsatellite instability, characteristics of mismatch repair deficient cells. Furthermore, myelodysplastic syndrome (MDS) patients with mutant TET2 have significantly higher mutational events than patients with wild-type TET2. Our findings reveal genomic hypermutability driven by the loss of TET2 as a novel contributing mechanism for TET2 loss-mediated pathogenesis of diverse hematological malignancies.

overall_design: Given the role of Tet proteins in 5mC oxidation, we employed a previously established chemical labeling and affinity purification method coupled with high-throughput sequencing (hMe-Seal) to profile the genome-wide distribution of 5hmC. Furthremore, we used an established MEL cell line to perform ChIP-seq to identify the Tet2-binding sites across the genome.

first: Mingjiang

last: Xu


title: A high temperature RNA-seq dataset for studies of gene expression variation in the MAGIC line resource of Arabidopsis thaliana

city: Salt Lake City

first: Richard

last: Clark

state: Utah

institute: University of Utah

summary: To understand expression phenotypes in Arabidopsis thaliana at high temperature, a set of the Multiparent Advanced Generation Inter-Cross (MAGIC) recombinant inbred lines were grown under long day conditions (16 hours light: 8 hours dark) at 20˚C and then shifted to 30˚C for 48 hours. RNA was collected at the 4th true leaf stage, and RNA-seq data was generated using the Illumina method. The MAGIC lines included are largely a subset of lines for which comparable RNA-seq data was collected at a constant 20˚C (allowing the same genotypes to be compared at 20˚C and after the high temperature shift at approximately the same developmental stage and under otherwise the same growth conditions). The read data for the analogous low temperature study can be found under GEO submission GSE94107.

overall_design: In total 103 RNA-seq samples from different inbred lines from the Multiparent Advance Generation InterCross (MAGIC) population in the reference plant, Arabidopsis thaliana, were generated. For each sample, RNA was collected from the aerial shoot from 20 seedlings at the 4th true leaf stage (after a temperature shift from 20˚C to 30˚C), and Illumina mRNA-seq libraries were constructed (a single library was constructed with each line; that is, each MAGIC line is represented by one biological replicate). Using these libraries, which were non-stranded, paired-end 100 bp RNA-seq Illumina reads were generated for each sample, and used to quantify gene expresison in each MAGIC line. The resulting expression phenotypes are suitable for describing the impacts of segregating genetic variation on the control of gene expression.

last: Mott

first: Gunnar

last: Raetsch

first: Andre

last: Kahles

first: Josh

last: Steffen

first: Edward

last: Osborne

first: Robert

last: Greenhalgh


title: RNA-sequencing of human skeletal myocytes from healthy, obese, and type 2 diabetic subjects

city: Gothenburg

first: Leif

last: Väremo

address: Kemivägen 10

department: Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). Obesity is tightly associated with T2D, making it challenging to isolate specific effects attributed to the disease alone. By using an in vitro myocyte model system we were able to isolate the inherent properties retained in myocytes originating from donor muscle precursor cells, without being confounded by varying extracellular factors present in the in vivo environment of the donor. We generated and characterized transcriptional profiles of myocytes from 24 human subjects, using a factorial design with two levels each of the factors T2D (healthy or diseased) and obesity (non-obese or obese), and determined the influence of each specific factor on genome-wide transcription. We identified a striking similarity of the transcriptional profiles associated independently with T2D or obesity. Obesity thus presents an inherent phenotype in skeletal myocytes, similar to that induced by T2D. Through bioinformatics analysis we found a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating the observed transcriptional signatures. Functional characterization of the expression profiles revealed dysregulated myogenesis and down-regulated muscle function in connection with T2D and obesity, as well as up-regulation of genes involved in inflammation and the extracellular matrix. Further on, we identified a metabolite subnetwork involved in sphingolipid metabolism and affected by transcriptional up-regulation in T2D. Collectively, these findings pinpoint transcriptional changes that are hard-wired in skeletal myocytes in connection with both obesity and T2D.

overall_design: Isolated skeletal muscle precursor cells from 24 males and females (6 normal glucose tolerant, 6 obese, 6 type 2 diabetic, and 6 obese and type 2 diabetic) were differentiated in vitro and stimulated with insulin. RNA from fully differentiated myotubes sampled at 0, 0.5, 1, and 2 hours after insulin stimulation was quantified using RNA-seq (96 samples in total). The 6 base-line (0h) samples from normal glucose tolerant individuals are available under the submission GSE63887, the remaining 90 samples are contained in this submission.

first: Tora

middle: I

last: Henriksen

first: Camilla

last: Scheele

first: Christa

last: Broholm

first: Maria

last: Pedersen

first: Mathias

last: Uhlén

first: Bente

last: Klarlund Pedersen

first: Jens

last: Nielsen


title: Salmonella Cascade assembles on both cis- and -trans encoded CRISPR RNAs

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: CRISPR/Cas loci commonly encode both proteins and small guide RNAs (crRNAs) to assemble ribonucleoproteins particles (RNPs) that confer a sequence-based, adaptive immunity against viruses and plasmids in prokaryotes. However, it has not been established whether this conserved synteny of RNA and protein genes is needed for the efficient RNP production in vivo. We show that the pathogenic bacterium Salmonella Typhimurium harbours two physically unlinked loci, CRISPR01 and CRISPR02, both of which produce mature crRNAs, although CRISPR02 lacks the protein genes for the type I-specific Cascade complex. Utilizing these coexisting complete and orphan CRISPR loci, we provide the first in vivo evidence for a crRNA-dependent assembly of Cascade. Strikingly, the full RNP assembles identically on crRNAs from either CRISPR cassette, i.e. regardless of their expression in cis or trans. Deep sequencing of Cas-bound transcripts identifies crRNAs derived from both loci as the sole bona fide targets of Cascade, although individual Cas proteins may interact with other cellular RNAs outside of the Cascade context. Altogether, our data demonstrate that CRISPR RNAs, independently of their origin, serve as the organizing centre of Cascade in vivo and are the main reason-to-be for its protein components in Salmonella.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: RNA-seq approach for RNA samples from cultures of Salmonella enterica serovar Typhimurium strain SL1344 Cas-protein CoIPs, harvested at mid-log. Salmonella expressing 3×FLAG-tagged Cas proteins were grown in LB at 37°C until OD600 of 0.5. For each strain cells equivalent to an OD600 of 50 were collected in parallel and subjected to Cas coIP and control coIP as described in (35).For each sample two cDNA libraries from total RNA were prepared to enriche for transcripts  5’OH : one library is generated from untreated RNA, whereas the other is treated with polynucleotide kinase (PNK).

first: Nadja

last: Heidrich

first: Alexandre

last: Smirnov

first: Yanjie

last: Chao

last: Reinhart

first: Jörg

last: Vogel


title: A global view of RNA-protein interactions reveals novel root hair cell fate regulators

status: Public on Apr 21 2017

first: Shawn

last: Foley

address: 433 S. University Ave

summary: The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites. Using these sequences, we identify two RBPs that regulate hair cell development. Specifically, we find that SERRATE functions in a microRNA-dependent manner to inhibit hair cell fate, while also terminating hair growth in differentiated hair cells independent of microRNAs. Additionally, we show that GLYCINE-RICH PROTEIN 8 alleviates phosphate starvation stress while promoting hair cell fate. In total, this global analysis reveals novel post-transcriptional regulators of plant root epidermal cell fate.

overall_design: Protein interaction profile sequencing (PIP-seq) in the nuclei of Arabidopsis thaliana root hair or nonhair cells.  These are crosslinked with formaldehyde and treated with two RNases (ssRNase and dsRNase) with two replicates

middle: W

first: Brian

middle: D

last: Gregory


title: Single-cell profiling of tumor infiltrating T cells and macrophages [RNA-Seq]

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary: Effective therapies for non-small cell lung cancer (NSCLC) remain challenging despite an increasingly comprehensive understanding of somatically altered oncogenic pathways. It is now clear that therapeutic agents with potential to impact the tumor immune microenvironment potentiate immune-orchestrated therapeutic benefit. Herein we evaluated the immunoregulatory properties of histone deacetylase (HDAC) and bromodomain inhibitors, two classes of drugs that modulate the epigenome, with a focus on key cell subsets that are engaged in an immune response. By evaluating human peripheral blood and NSCLC tumors, we show that the selective HDAC6 inhibitor ricolinostat promotes phenotypic changes that support enhanced T cell activation and improved function of antigen presenting cells. The bromodomain inhibitor JQ1 attenuated CD4+Foxp3+ T regulatory cell suppressive function and synergized with ricolinostat to facilitate immune-mediated tumor growth arrest, leading to prolonged survival of mice with lung adenocarcinomas. Collectively, our findings highlight the immunomodulatory effects of two epigenetic modifiers that, together, promote T cell-mediated anti-tumor immunity and demonstrate their therapeutic potential for treatment of NSCLC.

overall_design: Single-cell comparison of vehicle (control) and HDAC inhibitor (ricolinostat)-treated tumor infiltrating T cells and macrophages

first: Dennis

middle: O

last: Adeegbe


title: The histone H3 variant H3.3 regulates gene body DNA methylation [ChIP-seq]

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Gene bodies of vertebrates and flowering plants are occupied by histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. The profiles of enrichments in DNA methylation and H3.3 over gene bodies are correlated and both depend similarly on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. We engineered H3.3 knockdown in Arabidopsis and observed transcription reduction that predominantly affected genes responsive to environmental cues. When H3.3 levels were reduced, gene bodies showed a loss of DNA methylation correlated with transcription levels. To study the origin of changes in DNA methylation profiles when H3.3 levels are reduced, we examined genome wide distributions of several histone H3 marks, H2A.Z, linker histone H1 and nucleosome densities. We observed that in absence of H3.3, H1 distribution increased in gene bodies. This depends on levels of gene transcription. We propose that H3.3 prevents recruitment of H1, which in turn promotes chromatin folding and antagonizes access to DNA methyltransferases responsible for gene body methylation. Thus, gene body methylation is likely shaped by H3.3 dynamics in relation with transcriptional activity.

overall_design: Examination of 2 different histone modifications and 3 histones in WT and H3.3 knock down samples in replicates.

first: Heike

last: Wollmann

first: Ramesh

last: Yelagandula


title: Genome-wide characterization of mammalian promoters with distal enhancer functions

city: Marseille

first: Salvatore

last: Spicuglia

state: PACA

address: 163, Avenue de Luminy

department: TAGC U1090

country: France

institute: INSERM

summary: Gene expression in mammals is precisely regulated by combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might play enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene-promoters. Extensive CRISPR/Cas9 genomic manipulation demonstrated their involvement in cis-regulation of distal gene expression in their natural loci. Our results have important implications for the understanding of complex gene regulation in normal development and disease.

overall_design: CapStarr-seq analysis of DnaseI regions in K562 and HeLa cell lines (2 replicates) and in the plasmid library before transfection (Input).

first: Lan

middle: M

last: Dao

first: Ariel

last: Galindo-Albarran

first: Jaime

last: Castro

first: Charbel

last: Souadi

first: Guillaume

last: Charbonnier

first: Aurélien

last: Griffon

first: Laurent

last: Vanhille

first: Charlotte

last: Soler

first: Tharshana

last: Stephen

first: Eric

first: Alejandra

last: Medina

first: Jacques

last: van Helden

first: Denis

last: Puthier

first: David

last: Martin

first: Jaafar

last: Alomairi

first: Magali

last: Torres

first: Nicolas

last: Fernandez


title: miR-219 Cooperates with miR-338 in Myelination and Promotes Myelin Repair in the CNS

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: microRNAs (miRNAs) have been implicated in oligodendrogenesis and demyelinating diseases; however, identification of individual miRNAs responsible has remained elusive. Through targeted mutagenesis, we find that miR-219 is required for proper oligodendrocyte differentiation and myelination in vivo. Deletion of miR-338 together with miR-219 further exacerbates hypomyelination phenotypes. Temporally specific ablation reveals a critical role for miR-219 in oligodendrocyte remyelination after demyelination, while overexpression of miR-219 promotes precocious oligodendrocyte maturation and myelin regeneration. Accordingly, administration of miR-219 mimics to lysolecithin-induced demyelinating lesions in the murine spinal cord and brain enhances myelin restoration. Through integrating analyses of transcriptome profiling and biotin-affinity miRNA pull-down, we identify a set of stage-specific targets of miR-219, including Etv5 and Lingo1, as oligodendrocyte differentiation inhibitors. Inhibiting Etv5 and Lingo1 leads to a partial rescue of differentiation defects observed in miR-219-mutant OLs in vitro. Together, our findings identify context-specific miRNA-regulated checkpoints that control CNS myelinogenesis and myelin repair.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: 4 RNA-Seq samples from P12 optic nerves of Ctrl and miR-219 dCKO mice (duplicates, Ctrl and dCKO); 4 RNA-Seq samples from rat OPC with Ctrl or miR-219 mimic transduction (duplicates, Ctrl and miR-219 mimic); 4 RNA-Seq samples from rat iOL with Ctrl or miR-219 mimic transduction (duplicates, Ctrl and miR-219 mimic); and 2 RNA-Seq samples of biotin-miR-219 pull down from rat OPC (ctrl and miR-219 pull down).

first: Haibo

last: Wang

first: Yaqi

last: Deng


title: A computational systems approach for identification of synergistic specification genes facilitates lineage conversion to prostate tissue

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary: We report that a computational systems approach can identify cell type specification genes that act synergistically, and demonstrate its application for reprogramming of fibroblasts to prostate tissue. We have employed three such master regulators (FOXA1, NKX3.1, and androgen receptor, AR) in a primed conversion strategy to generate prostate tissue from mouse fibroblasts, involving expression of pluripotency factors, tissue recombination with embryonic urogenital mesenchyme, and renal grafting.

overall_design: RNA-sequencing profiles of prostate tissues and fibroblasts were generated and compared to RNA-sequencing profiles of induced prostate tissue in tissue recombinants.

first: Flaminia

last: Talos

first: Michael

last: Shen


title: Perturbation-response genes reveal signaling footprints in cancer gene expression

status: Public on Apr 20 2017

first: Florian

last: Uhlitz

department: Computational Oncology

summary: Aberrant cell signaling can cause cancer and other diseases and is a focal point of drug research. A common approach is to infer signaling activity of pathways from gene expression. However, mapping gene expression to pathway components disregards the effect of post-translational modifications, and downstream signatures represent very specific experimental conditions. Here we present PROGENy, a method that overcomes both limitations by leveraging a large compendium of publicly available perturbation experiments to yield a common core of Pathway RespOnsive GENes. Unlike existing methods, PROGENy can (i) recover the effect of known driver mutations, (ii) provide or improve strong markers for drug indications, and (iii) distinguish between oncogenic and tumor suppressor pathways for patient survival. Collectively, these results show that PROGENy accurately infers pathway activity from gene expression.

overall_design: HEK293∆RAF1:ER cells were treated with different stimuli (4OHT, Ly29002, TNFa, TGF1b, IFNg) for different periods of time (1h, 4h).

last: Schubert

first: Bertram

last: Klinger

first: Martina

last: Klünemann

first: Anja

last: Sieber

first: Sascha

last: Sauer

first: Mathew

last: Garnett

first: Nils

last: Blüthgen

first: Julio

last: Saez-Rodriguez


title: RNAseq profiling of AMCase-expressing lung epithelial cells

city: San Francisco

first: Steven

last: Van Dyken

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: We have generated novel reporter mice (“ChiaRed”) to study the role of the acidic mammalian chitinase (AMCase) in lung homeostasis and in response to immune challenge.

overall_design: Lung epithelial cells from wild-type mice (WT; n=3) and AMCase-expressing ChiaRed+ cells were isolated from the lungs of homozygous (CC; n=2) and heterozygous (C+; n=3) ChiaRed mice to compare differentially expressed transcripts by RNA-Seq analysis in these cells.

last: Locksley


title: Single-cell sequencing of individual murine aortal smooth muscle cells (C57BL/6)

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: Smooth muscle-specific EGFP reporter mice (Myh11-CreERT2pos;dTom/EGFP-reporter) were sacrificed and perfused with PBS. The aorta including common carotid arteries was dissected, minced, and enzymatically digested for 90-120 minutes while shaking at 37°C in a digestion mix containing collagenase II (2 mg/ml; Worthington), elastase-I (0.04 mg/ml; Sigma), and DNase1 (5 U/ml; New England Biolabs). Cell suspensions were serially filtered through 70µm and 40µm cell strainers followed by washing twice with PBS. Aortic smooth muscle cells were sorted on a JSAN cell sorter (Bay Biosciences, Japan) based on their EGFP expression.Single-cell transcriptome analysis was performed on a C1 Autoprep station (Fluidigm) using 5-10µm mRNA Arrays and standard protocols. 15.000 events sorted on a JSAN swift  sorter were suspended in 10 µl resuspension buffer (PBS + 0.5% bovine serum albumin + 2nM EDTA, sterile filtered) and further diluted (6:4) in suspension buffer. 3µl were loaded to the C1 Array while remaining cells (~10.000) were used for total RNA isolation using µRNeasy micro kit (Qiagen) combined with on-column DNase digest (Qiagen). RNA was quantified by Qubit HS RNA Assay (Thermo Fisher) and used for tube control. Pre-amplification and cDNA synthesis were done with Smarter ultra-low RNA Kit (Clontech) without changes to the standard protocol. cDNA obtained from C1 system was quantified using PicoGreen assay (Thermo Fisher) and diluted to 0.1–0.3 ng/μl. Picking of positive cDNA samples and library preparation were done with NGS Express pipetting robot (Perkin Elmer) using custom made protocols. Barcoded and amplified libraries were pooled in groups of 16 libraries for final SRRI-bead based cleanup and quantified by Qubit HS dsDNA Assay (Thermo Fisher) and BioAnalyzer 2100 HS DNA Assay (Agilent). Sequencing was performed on Nextseq500 Sequencer (Illumina) using v2 chemistry and High Output Flow Cell with 75bp single end protocol. Raw data files were trimmed using Reaper with a quality cutoff of 53 (length 20 bp, prefix 50 bp) and a minimum clean read length of 50 bp. Reads were then mapped to the genome (mm10) using STAR. FeatureCounts was used to assign reads to genes from the Gencode vM6 annotation. Genes with less than 50 counts across all cells were discarded prior to normalization. The knn.error.models function from SCDE59 was used to construct cell-specific error models by evaluating the gene counts for a observed cell vs. the expected gene counts from the k most similar cells. The parameter k was chosen to resemble roughly three subpopulations. Estimated fragments per million mapped reads (FPM, in log scale) were then obtained using the scde.expression.magnitude function.

overall_design: Analysis of 82 individual murine aortal smooth muscle cells (C57BL/6)

first: Harmandeep

last: Kaur

first: Stefan

last: Günther

first: Jens

last: Preussner

first: Nina

last: Wettschureck


title: NGS analysis of WT and snf2∆ transcriptomes

city: Los Angeles

first: Stephen

last: Douglass

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Despite its streamlined genome, there are important examples of regulated RNA splicing in Saccharomyces cerevisiae. One of the most striking is the regulated splicing of meiotic transcripts, part of the dramatic reprogramming of gene expression upon meiotic onset. Here we show a crucial role for the chromatin remodeler Snf2, part of the Swi/Snf complex in meiotic regulation of splicing. We find that the complex affects meiotic splicing in several ways. First, meiosis-specific expression of the splicing activator Mer1 is Swi/Snf dependent, involves precise timing of acetylation of histone H3K9 at the MER1 locus, and changes in the acetylation state of Snf2. Additionally, Swi/Snf abundance regulates meiosis-specific downregulation of ribosomal protein encoding RNAs, leading to the redistribution of spliceosomes from this abundant class of intron-containing RNAs to meiotic transcripts. This regulation is achieved by rapid downregulation of the Snf2 protein. Taken together these data reveal that the Swi/Snf complex coordinates a cascade of events to direct the regulated splicing of meiotic genes, establishing it as a master regulator of meiotic splicing in S. cerevisiae.

overall_design: Sequencing of rRNA depleted transcriptomes in 4 different S. cereviseae strains

first: Srivats

last: Venkataramanan

first: Anoop

last: Galivanche

first: Tracy

last: Johnson


title: Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties

city: NEW YORK

first: NADEJDA

last: TSANKOVA

state: NEW YORK

address: 1425 MADISON AVENUE 9TH FLOOR

department: PATHOLOGY

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

summary: Characterization of non-neoplastic and malignant human stem cell populations in their native state can provide new insights into gliomagenesis. Here we developed a purification strategy to directly isolate EGFR+/– populations from human germinal matrix (GM) and adult subventricular zone autopsy tissues, and from de-novo glioblastoma (GBM) resections, enriching for cells capable of binding EGF ligand (LBEGFR+), and uniquely compared their functional and molecular properties. LBEGFR+ populations in both GM and GBM encompassed all sphere-forming cells and displayed proliferative stem cell properties in vitro. In xenografts, LBEGFR+ GBM cells showed robust tumor initiation and progression to high-grade, infiltrative gliomas. Whole transcriptome sequencing analysis confirmed enrichment of proliferative pathways in both developing and neoplastic freshly isolated EGFR+ populations, and identified both unique and shared sets of genes. The ability to prospectively isolate stem cell populations using native ligand-binding ability opens new doors into understanding both normal human progenitors and tumor cell biology.

overall_design: We performed full transcriptome sequencing by RNA-seq on freshly isolated EGFR+ and EGFR– populations from human brain germinal matrix (GM, n=3) and from human glioblastoma (GBM, n=3) resections. Three biological replicates were sequenced for each group: GM EGFR+, GM EGFR–, GBM EGFR+, and GBM EGFR–. Sequencing was performed on Illumina HiSeq 2500 (125bp pair-end sequencing, 38-50mil paired-end reads/sample).

first: Nadejda

last: Tsankova

first: Jessica

last: Tome-Garcia

first: Elena

last: Zaslavsky

first: German

last: Nudelman

first: Rut

last: Tejero

first: Raymund

middle: L

last: Yong

first: Robert

last: Sebra

first: Huaien

last: Wang

first: Mary

last: Fowkes

first: Margret

last: Magid

first: Martin

last: Walsh

first: Violeta

last: Silva-Vargas

first: Roland

middle: H

last: Friedel

first: Fiona

last: Doetsch


title: Genes regulated by RANK in the epithelium of Peyer's patches

city: Stanford

first: Kazuki

last: Nagashima

state: CA

address: 290 Jane Stanford Way, Room W117 Fischbach Lab

department: Bioengineering

institute: Stanford University

summary: The purpose of this experiment is to identify the molecules which are regulated by epithelial RANK in Peyer's patches.

overall_design: Epithelial mRNA profiles of Peyer's patches from Vil1-Cre RANK flox/Delta (cKO) mice and RANK flox/Delta (control) mice were generated (n=4).

first: Shinichiro

last: Sawa

first: Josef

last: Penniger

first: Hiroshi

last: Takayanagi


title: DDX54 regulates transcriptome dynamics during DNA damage response [RNA-seq2]

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

summary: The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of posttranscriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing irradiation (IR). Interestingly, more than 260 proteins including many nucleolar proteins showed increased binding to poly(A) RNA in IR-exposed cells. The functional analysis of DDX54, a candidate genotoxic stress responsive RNA helicase, revealed that this protein is an immediate-to-early DDR regulator required for the splicing efficacy of its target IR-induced pre-mRNAs. Upon IR exposure, DDX54 acts by increased interaction with a well defined class of pre-mRNAs which harbor introns with weak acceptor splice sites, as well as by protein-protein contacts within components of U2 snRNP and spliceosomal B complex, resulting in lower intron retention and higher processing rates of its target transcripts. Since DDX54 promotes survival after exposure to IR its expression and/or mutation rate may impact DDR-related pathologies. Our work indicates the relevance of many uncharacterized RBPs potentially involved in the DDR.

overall_design: Gene expression profiling of MCF-7 cells upon DDX54 knockdown exposed to ionizing radiation

first: Milek

last: Miha

first: Landthaler

last: Markus


title: DDX54 regulates transcriptome dynamics during DNA damage response [PAR-CLIP]

overall_design: Identification of wild-type and mutant DDX54 binding sites in untreated and DNA-damage induced condition


title: DDX54 regulates transcriptome dynamics during DNA damage response

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

overall_design: Refer to individual Series


title: Discrimination of Stem Cell Status after Subjecting Cynomolgus Monkey Pluripotent Stem Cells to Naive Conversion

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: Experimental animal models have played an indispensable role in the development of human induced pluripotent stem cell (iPSC) research. The, derivation of high-quality (so-called “true Naive state”) iPSCs of non-human primates enhances their application and safety for human regenerative medicine. Although several attempts have been made to convert human and non-human primate PSCs into a truly Naive state, it is unclear which evaluation methods can discriminate them as being truly Naive. Here we derived Naive-like Cynomolgus monkey (Cm) (Macaca fascicularis) embryonic stem cells (ESCs) and iPSCs, and evaluated their potential as a highly accurate indicator of the properties of Naive-like human ESC/iPS cells. Several characteristics of Naive-like Cm ESCs including colony morphology, teratoma-forming ability, leukaemia inhibitory factor dependency, and mitochondrial respiration were confirmed. Next, we generated Cm iPSCs and converted them to a Naive-like state. When these were subjected to in vitro differentiation, some exhibited heterogeneity and showed resistance to differentiation. The difficulty of achieving chimeric contribution to mouse or rabbit embryos suggested incomplete Naive conversion. Actually, transcriptomic comparison of PSCs with early Cm embryos elucidated the partial achievement of Naive conversion. This study offers valuable pointers for deriving true Naive PSCs while avoiding irrelevant or misleading evidence of Naive-like features.

overall_design: RNAseq analysis of cynomolgus monkey ESCs/iPSCs cultured in Primed, Naive-like and Differentiated conditions using SC3-seq technology.

first: Arata

last: Honda

first: Tomonori

last: Nakamura

first: Yoshihiro

last: Kawano

first: Haurna

last: Izu

first: Narantsog

last: Choijookhuu

first: Kimiko

last: Honsho

first: Ysuhiro

last: Takashima

first: Ikuhiro

last: Okamoto

first: Michiko

last: Hirose

first: Tadashi

last: Sankai

first: Yoshitaka

last: Hishikawa

first: Atsuo

last: Ogura

first: Mitinori

last: Saitou

first: Takuya

last: Yamamoto


title: DDX54 regulates transcriptome dynamics during DNA damage response [4SU-seq]

first: Markus

last: Landthaler

overall_design: Primary and mature transcript profiling of MCF-7 cells exposed to ionizing radiation using 4SU-seq

first: Milek

last: Miha


title: FTO regulates adult neurogenesis through modulating the dynamics of N6-methyladenosine

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

summary: Fat mass and obesity-associated gene (FTO) is a member of the Fe (II) and oxoglutarate-dependent AlkB oxygenase family, and has been linked to obesity and intellectual disability. However, the role of FTO in neurodevelopment and neurogenesis remains largely unknown. Here, we show that FTO is expressed in adult neural stem cells (aNSCs) and neurons, and displays dynamic expression during postnatal neurodevelopment. The loss of FTO leads to the decreased brain size and body weight. We found that FTO deficiency could reduce the proliferation and neuronal differentiation of aNSCs in vivo, which leads to the impaired learning and memory. Given the role of FTO as a demethylase of N6-methyladenosine (m6A), we further performed the genome-wide m6A profiling and observed the dynamic m6A modification during postnatal neurodevelopment. The loss of FTO could lead to the altered m6A modifications on the mRNAs of several key components of BDNF pathway. These results together suggest that FTO play important roles in neurogenesis and learning and memory.

overall_design: Gene expression analyses were performed on mRNA samples isolated from the hippocampi of adult Fto knockout mice (8-12 weeks old) and age/gender-matched wild-type C57BL/6 mice. N6-methyladenosine (m6A) epitranscriptome profiling was performed on mRNA samples isolated from the hippocampi of 2-week-old and 6-week-old male wild-type C57BL/6 mice.

first: Peng

last: Jin


title: Gene expression in neonatal NKT cells and lymphoma samples from mice with high E protein levels

city: Durham

first: Yuan

last: Zhuang

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University


title: Bulk RNA-sequencing of murine atrioventricular nodes

first: Matthias

last: Nahrendorf

state: MA

address: 185 Cambridge St.

department: Center for Systems Biology

institute: Massachusetts General Hospital

summary: Tissue-resident macrophages abound in the distal atrioventricular (AV) node of the heart, electrically couple to conducting cardiomyocytes via Connexin (Cx) 43-containing gap junctions and are implicated in normal and aberrant cardiac conduction. Moreover, conditional deletion of Cx43 in macrophages (tamoxifen-inducible Cx3cr1 Cx43-/- mice) delays AV conduction and acute depletion of macrophages in Cd11bDTR mice induces progressive AV block.

overall_design: Comparison of microdissected AV nodes from control, Cx3cr1 Cx43-/- and macrophage-depleted Cd11bDTR mice, three biological replicates each.

first: Maarten

last: Hulsmans

first: Andrej

last: Savol


title: Total RNA-seq of HeLa cells upon conventional or improved RNA extraction

city: Sapporo

first: Tetsuro

state: Hokkaido

address: Kita-15-jo Nishi-7-chome, Kita-Ku

department: Institute for Genetic Medicine

institute: Hokkaido University

summary: We devised a novel improved RNA extraction method, and performed total RNA-seq to determine the effect of improved RNA extraction.

overall_design:
Examination of total RNAs that were derived from the same cell/TRI Reagent solution, split into two and extracted by either a conventional or improved RNA extraction method.
Hokkaido System Science, Co.

first: Takeshi

last: Chujo


title: Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

summary: Here, we define the landscape and dynamics of active regulatory DNA in cutaneous T cell lymphoma (CTCL) by Assay of Transposase-Accessible Chromatin (ATAC-seq). Analysis of 111 human CTCL and control samples revealed extensive chromatin signatures that distinguished leukemic vs. non-leukemic (host) CD4+ T cells in CTCL patients, vs. CD4+ T cells in healthy donors. We identify three dominant patterns of transcription factor (TF) activation that drive leukemia regulomes, as well as TF deactivations that alter host T cells in CTCL patients. Clinical response to histone deacetylase inhibitors (HDACi) is strongly associated with a concurrent gain in chromatin accessibility. HDACi causes distinct chromatin responses in leukemic and host CD4+ T cells, reprogramming host T cells toward normalcy. These results provide a foundational framework to study personal regulomes in human cancer and epigenetic therapy.

overall_design:
We examined chromatin structure using ATAC-seq in purified human CD4+ T cells in 30 samples from 10 health donors and 81 samples from 14 patiets with cutaneous T cell leukemia (CTCL), treated with HDACi anti-cancer drugs, such as Vorinostat and Romidepsin. Each donor provided cells per time point via a single standard 5 ml blood draw, and CD4+ T cells were isolated applying RosetteSep Human CD4+ T Cell Enrichment Cocktail (Experimental Procedures). Because CTCL is typically characterized by a dominant CD4+ T cell clone bearing an unique T cell receptor, we purified CTCL leukemic cells from patients (defined by CD4+, CD26-, and T cell receptor V-beta clone+) vs. host CD4+ T-cell (defined by CD4+, CD26-, V-beta clone-) from the same patients by fluorescence activated cell sorting (FACS). Leukemic, host and bulk T cells were obtained from 10 out of 15 patients who had detectable V-beta clone, and only bulk T cells were obtained for the remaining 5 patients without detectable V-beta clone. Although number and proportion of leukemic and host cells varies depending on the stage and drug response of each individual, especially at a later stage of drug treatment, we were able to obtain at least 50,000 CD4+ T cells per sample.

Please note that the indicated 'Day' (in the sample title)  for Normal donors means when the blood was drew. For example “Normal_Donor1_Day38_Rep2” means this sample was drew on day 38. Day for Patients means days after the first drug treatment. For example “BulkCTCL_Patient1366_Romi_Day28” means this is a Bulk cell sample from Patient 1366, who was treated with Romidepsin, and the blood was drew on Day 28 according to the first day of treatment, and on that day, the patient was also treated with the same drug.

first: Lisa

middle: C

last: Zaba

first: Paul

last: Giresi

first: Rui

last: Li

first: Randall

last: Armstrong

first: Willian

last: Greenleaf

first: Youn

last: Kim

first: Howard

middle: Y

last: Chang


title: DDX54 regulates transcriptome dynamics during DNA damage response [RNA-seq1]

first: Markus

last: Landthaler

overall_design: Gene expression profiling of MCF-7 cells exposed to 4SU, UV and ionizing radiation

first: Milek

first: Landthaler

last: Markus


city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

summary: Sequencing of ponatinib-resistant LC-2/ad derivatives (PR1 and PR2) and parental LC-2/ad cells was performed in order to determine mechanisms of acquired resistance in the PR1 and PR2 cell lines. NRAS p.Q61K mutation identified in PR1 cells. Upregulation of wild-type EGFR signaling identified in PR2 cells.

overall_design: Sequencing of ponatinib-resistant LC-2/ad derivatives (PR1 and PR2) and parental LC-2/ad cells was performed.

first: Sarah

middle: K

last: Nelson Taylor

first: Anh

middle: T

last: Le

first: Minjae

last: Yoo

first: Aik-Choon

first: Robert

last: Doebele


title: Transcriptional dependencies in diffuse intrinsic pontine glioma

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

summary: Diffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor with limited therapeutic options. The majority of cases of DIPG exhibit a mutation in histone 3 (H3K27M) that results in oncogenic transcriptional aberrancies. We show here that DIPG is vulnerable to transcriptional disruption using either bromodomain inhibition or CDK7 blockade. We observe that targeting oncogenic transcription through either of these methods synergizes with HDAC inhibition and that DIPG cells resistant to HDAC inhibitor therapy retain sensitivity to CDK7 blockade. Furthermore, identification of super-enhancers in DIPG provides insights toward the cell of origin, highlighting oligodendroglial lineage genes, and reveals unexpected mechanisms mediating tumor viability and invasion, including potassium channel function and EPH-ephrin signaling. The findings presented here demonstrate transcriptional vulnerabilities of DIPG and elucidate previously unknown mechanisms of DIPG pathobiology.

overall_design: RNA-seq and ChIP-seq was performed in patient-derived DIPG cell cultures in two replicates. Libraries were sequenced on Illumina NextSeq or HiSeq, 1x75 for RNA-seq and 2x75 for ChIP-seq.

first: Surya

last: Nagaraja


title: Gene expression in neonatal NKT cells and lymphoma samples from mice with high E protein levels [RNA-Seq]

first: Yuan

last: Zhuang

summary: Inhibitor of DNA binding proteins (ID), including Id1-4, are transcriptional regulators involved in promoting cell proliferation and survival in various cell types. Although upregulation of Id proteins have been widely reported to be associated with a broad spectrum of tumors, recent studies have identified that Id3 also plays a tumor suppressor role in the development of Burkitt’s lymphoma in humans and Hepatosplenic T cell lymphomas in mice. However, there is a lack of evidence to suggest the tumor suppressor roles for other Id genes, particularly Id2, which is highly expressed in many T lymphocytes. In this study we report that Id2 plays a tumor suppressive role in collaboration with Id3 in developing T cells in mice. We found that there was rapid lymphoma development in Id2f/fId3f/fLckCre mice caused by unchecked neonatal expansion of invariant Natural Killer T (iNKT) cells and a unique subset of innate-like, CD1d-independent T cells. These tumors also gave rise to lymphomas in Rag-deficient mice, reaffirming the inherent tumorigenic potential of these cells. Microarray analysis revealed a significantly modified program in expanding iNKT cells that ultimately contributed to tumorigenesis. Similar pathways in CD1dTet- tumors were verified by RNASeq. We found chromosome instability and significant upregulation of several different signaling pathways, including pathways for multiple chemokines, cytokines and their receptors, in these tumors. While Id proteins are being considered as potential therapeutic targets in some cancer models, our results highlight the possibility of aggravated tumorigenesis upon suppression of Id2 and Id3.

overall_design: Pre-malignant iNKT (TCRβ+CD1dTet+) cells were sorted from three 20 day old L-DKO mice. Lymphoma cells (T cells that are CD1dTet+ or CD1dTet-) were sorted from tissues of 18-37 week old L-DKO mice. Total RNA was extracted, and paired-end libraries were prepared and sequenced using Illumina Hi-Seq 4000

first: Jia

first: Sumedha

last: Roy

first: Young-Mi

first: Shibo

first: Baojun

last: Zhang

first: Cassandra

last: Love

first: Anupama

last: Reddy

first: Deepthi

last: Rajagopalan

first: Sandeep

last: Dave

first: Anna

last: Diehl


title: Transcriptional profiles of Drosophila melanogaster testes and seminal vesicles/testes terminal epithelium.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Testes and testes terminal epithelium/seminal vesicles were dissected and separated from 4-5 day old Oregon-R-modENCODE Drosophila melanogaster males.  RNA-sequencing was then performed on these two distinct biological structures.

overall_design: Testes and testes terminal epithelium/seminal vesicles were dissected and separated from 4-5 day old Oregon-R-modENCODE Drosophila melanogaster males on two consecutive days resulting in two biological replicates.  Total RNA was immediately extracted and used to prepare poly-A RNA-seq libraries.  Single-end 50 bp sequencing was performed on all four samples and mapped to the Flybase Drosophila melanogaster release 6.06 genome.

first: Leif

last: Benner

first: Tim

last: Karr


title: Gene expression changes in the absence of the carbon catabolite repressor, CreA.

status: Public on Apr 19 2017

city: Hanover

first: Robert

last: Cramer

state: NH

address: 74 College St

department: Microbiology&Immunology

institute: Geisel School of Medicine at Dartmouth College

summary: This experiment was designed to test the change in gene expression in the absence of the transcription factor, CreA. Two media conditions were tested to determine the role of this  transcription factor in repressing (glucose) and derepressing (ethanol) carbon sources.

overall_design: RNA was extracted from a creA-null mutant and the parental wild type strain (CEA10) under two media conditions (glucose, ethanol).

first: Sarah

last: Beattie


title: Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients

city: Copenhagen

first: Kristoffer

last: Vitting-Seerup

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

summary: Purpose: To identify transcriptional changes by RNA-seq in tumor samples, before bevacizumab combination treatment and after bevacizumab combination treatment in both responding and non-responding recurrent glioblastoma patients

overall_design:
Three comparison analyses were further performed: 1.) Paired analysis of pre- and post-treated samples from responding patients; 2.) Comparison of pre-treated samples of responders vs. non-responders; 3.) Paired analysis of pre- and post-treated samples from non-responding patients
The sample 'characteristics: batch' represents a combination of the RNA-extraction date and the library-preparation date for each sample.

first: T

last: Urup

first: U

last: Lassen


title: Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis (RNA-Seq).

city: Vari

first: George

last: Kollias

address: 34 Fleming Street

department: Institute of Immunology/Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/National and Kapodistrian University of Athens

summary: We used deep sequencing to probe the transcriptome, the methylome and the chromatin landscape of cultured mouse arthritogenic SFs at three stages of disease, as well as SFs stimulated with human TNF. We performed bioinformatics analyses at the gene, pathway and network levels, compared mouse and human data, and validated selected genes in both species.

overall_design: RNA, DNA methylation and H3K4me3 profiles of SFs from Tg197 and WT mice at the ages of  3 (Early),8 (Established) and 11 (Late) weeks old were generated by deep sequencing, in triplicates, using Illumina HiSeq2000 platform.

first: Panagiotis

last: Chouvardas

first: Evangelos

last: Ntougkos

first: Fani

last: Roumelioti

first: Caroline

last: Ospelt

first: Mojka

last: Frank-Bertoncelj

first: Andrew

last: Filer

first: Christopher

last: Buckley

first: Steffen

last: Gay

first: Christoforos

last: Nikolaou


title: Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis (MethylCap-Seq).


title: Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis


title: Transcriptomics of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. Sequencing chemistry v2 or v4 (Illumina) was used.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of gene expressive levels in siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues

first: Xin

last: Yang

first: Yun-Gui

first: Baofa


title: Single-base resolution methylome of 5-Methylcytosine in human and mouse transcriptome

summary: mRNAs of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement. mRNAs were fragmented to ~200 nt and treated by Sodium bisulfite solution (pH 5.1) containing Hydroquinone. Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2500 (Illumina) in pair-end mode, creating reads with a length of 125 bp. Sequencing chemistry v4 (Illumina) was used and every sample was sequenced at one lane.

overall_design: Explore the single-base resolution methylome of 5-Methylcytosine in mammalian transcriptome


title: Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

summary: Piwi in a complex with Piwi-interacting RNAs (piRNAs) triggers transcriptional silencing of Transposable Elements (TEs) in Drosophila ovaries, thus ensuring genome stability. To do this, Piwi must scan the nascent transcripts of genes and TEs for complementarity to piRNAs. The mechanism of this scanning is currently unknown. Here we report the DamID-seq mapping of multiple Piwi-interacting chromosomal domains in somatic cells of Drosophila ovaries. These domains significantly overlap with genomic regions tethered to Nuclear Pore Complexes (NPCs). Accordingly, Piwi was coimmunoprecipitated with the component of NPCs Elys and with the Xmas-2 subunit of RNA transcription and export complex, known to interact with NPCs. However, only a small Piwi fraction has transient access to DNA at nuclear pores. Importantly, although 36%of protein-coding genes overlap with Piwi-interacting domains and RNA-immunoprecipitation results demonstrate promiscuous Piwi binding to numerous genic and TE nuclear transcripts, according to available data Piwi does not silence these genes, likely due to the absence of perfect base-pairing between piRNAs and their transcripts.

overall_design:
DamID-seq: Ovaries from transgenic flies, expressing Dam or Dam-Piwi constructs in ovarian somatic cells, were collected for quantification of genome-wide methylation levels via next-generation sequencing.
RIP-seq: RIP-seq with anti-Piwi antibodies in OSC Drosophila cell line, treated or untreated with Actinomycin D.

first: Artem

last: Ilyin

first: Semen

last: Doronin

first: Oxana

last: Olenkina

first: Elena

last: Mikhaleva

first: Evgeny

last: Yakushev

first: Yuri

last: Abramov

first: Stepan

last: Belyakin

first: Anton

last: Ivankin

first: Alexey

last: Pindyurin

first: Vladimir

last: Gvozdev

first: Mikhail

last: Klenov

last: Shevelyov


title: Methylated DNA Immunoprecipitation Sequencing of WT and βRapKO mice

city: Shanghai

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Purpose: DNA methylation has been proposed to drive functional maturation of pancreatic beta cells. To evaluate the possibility that altered methylation is involved in mTORC1-dependent beta cell maturation.

overall_design: DNA immunoprecipitation sequencing (MeDIP-seq) was carried out on islets isolated from 8-week-old βRapKO and WT mice.

first: Qidi

last: Wang


title: Single-cell RNA-sequencing of murine atrioventricular node macrophages

city: Boston

first: Matthias

last: Nahrendorf

summary: Tissue-resident macrophages abound in the distal atrioventricular (AV) node of the heart, electrically couple to conducting cardiomyocytes via Connexin (Cx) 43-containing gap junctions and are implicated in normal and aberrant cardiac conduction.

overall_design: Comparison of 76 single-cell transcriptomes from murine AV node macrophages.

first: Maarten

last: Hulsmans

first: Andrej

last: Savol


title: Genomic responses of mouse synovial fibroblasts during TNF-driven arthritogenesis greatly mimic those of human rheumatoid arthritis (H3K4me3-Seq).

first: George

last: Kollias

first: Panagiotis

last: Chouvardas

first: Evangelos

last: Ntougkos

first: Fani

last: Roumelioti

first: Caroline

last: Ospelt

first: Mojka

last: Frank-Bertoncelj

first: Andrew

last: Filer

first: Christopher

last: Buckley

first: Steffen

last: Gay

first: Christoforos

last: Nikolaou


title: Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish (pericytes)

status: Public on Apr 18 2017

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Analyse gene expression in brain pericytes

overall_design: Adult zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate, with 6 brains used per samples.

first: Neil

last: Bower

first: Benjamin

last: Hogan


title: 5-methylcytosine promotes mRNA export

first: Bao-Fa

last: Sun

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

overall_design: Refer to individual Series


title: Mural lymphatic endothelial cells regulate meningeal angiogenesis in the zebrafish

summary: Analyse gene expression in mural lymphatic endothelial cells (muLECs)

overall_design: Adult zebrafish brains were dissociated using Liberase and lyve1 Dsred postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate, with 6 brains used per samples.


title: mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.

summary: 48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta  egfp postive cells FAC sorted into Trizol LS.  RNA was extracted and amplified before sequencing.  Samples were prepared in triplicate, with 6 brains used per samples.

overall_design: wild type vs mutant

first: Katrzyna

last: Koltowska


title: Epigenetic identity in AML is mostly dependent on disruption of non-promoter regulatory elements and reveals potentially antagonistic effects of mutations in epigenetic modifiers [human]

city: New York

first: Jacob

middle: Lowell

last: Glass

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Aberrant DNA methylation of gene promoters is a hallmark of AML. To define how cytosine methylation is redistributed in AML more precisely we performed base-pair resolution methylome sequencing in 119 patients. We find that leukemic DNA methylation patterning is tightly linked to somatic mutations and primarily driven by regulatory elements outside of promoters and by CpG shores as opposed to CpG islands. Active enhancers displayed much stronger focal differential methylation than promoters and were generally aberrantly hypomethylated except in IDH2 mutant and CEBPA silenced AMLs. AMLs with dominant hypermethylation feature greater epigenetic disruption of promoters. Those with dominant hypomethylation, such as DNMT3A mutated AMLs, display greater disruption of distal and intronic regions. IDH mutant AMLs manifest profound hypermethylation whereas DNMT3A mutant AMLs manifest profound hypomethylation of a different set of CpGs.  In striking contrast, AMLs with co-occurring IDH1 and DNMT3A mutations exhibited epigenetic antagonism in which most CpGs affected by either mutation alone were no longer affected in the double mutant cases.  These patients featured a unique gene expression profile featuring deregulated expression of RAS pathway that was not linked to DNA methylation.

overall_design: Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) was performed on 119 AML samples, which are a subset of those profiled using HELP in PMC3008568.

first: Duane

last: Hassane

first: Roberto

last: Avelino

first: Francine

middle: E

last: Garrett-Bakelman

first: Mame

last: Fall

first: Alicia

last: Alonso

first: Peter

middle: J

last: Valk

first: Ruud

last: Delwel

first: Ari

last: Melnick

first: Maria

last: Figueroa


title: Transcriptomic profile of the Beauveria bassiana infection to the Galleria mellonella

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. Genome-wide insight into the infection of the fungi is critical for genetic improvement of fungal insecticides but has been poorly explored. We constructed three transcriptomes of Beauveria bassiana at 24, 48 and 72 hours post treatment of infection (BbI) and of control (Bbc).

overall_design: 1,Beauveria bassiana groewn on PDA medium. 2,Beauveria bassiana at 24 hours post treatment of infection. 3, Beauveria bassiana at 48 hours post treatment of infection. 4, Beauveria bassiana at 72 hours post treatment of infection

first: Yu-long

first: An-hui

last: Chen


title: Next Generation Sequencing Facilitates Differential Expression Analysis of miRNA Expression In the Whole Blood Samples Obtained From Prostate Cancer Patients vs. Controls

city: Richmond

first: Zendra

last: Zehner

state: VA

address: 1101 E Marshall St

department: Department of Biochemistry

institute: Virginia Commonwealth University

summary: Research conducted using the novel approach of Next Generation Sequencing to determine the differentially expressed microRNAs in whole blood samples from prostate cancer patients.

overall_design: The whole blood miRNA  samples from both controls and patients were sequences and a differential expressional analysis was conducted to identify possible biomarkers to distinguish patients from controls.

first: Rhonda

last: Daniel

first: Qianni

last: Wu

first: Gene

last: Clark


title: EpCAM controls morphogenetic programs during zebrafish pronephros development

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

institute: University Freiburg Medical Center

summary: Epithelial cell adhesion molecule EpCAM is a transmembrane glycoprotein that is dynamically expressed in human and murine renal epithelia during development. The levels of EpCAM in the renal epithelium are upregulated both during regeneration after ischemia/reperfusion injury and in renal-derived carcinomas. The role of EpCAM in early kidney development, however, has remained unclear. To identify potential programs and signaling pathways that are controlled by EpCAM during pronephros development, we developed a method to study the transcriptomes of specific pronephric segments. Combining laser capture microdissection (LCM) with RNA sequencing (RNA-seq), we generated genome-wide transcriptional profiles of the distal late tubules of wild type and EpCAM-deficient embryos.

overall_design: RNA-seq of LCM-dissected pronephric cells from EpCAM-deficient and control zebrafish embryos

first: Sebastian

last: Kuechlin

first: Maximilan

last: Schoels

first: Krasimir

last: Slanchev

first: Silke

last: Lassmann

first: Gerd

last: Walz

middle: A


title: Tn-seq experiment with sub-inhibitory concentrations of WhiB7-specific antibiotics in Mycobacterium smegmatis

city: Vancouver

first: Charles

last: Thompson

state: British Columbia

address: 2350 Health Sciences Mal

department: Microbiology and Immunology

institute: University of British Columbia

summary: A pool of ~55,000 transposon mutants was exposed to sub-MIC antibiotics to monitor for conditionally essential genes under all selections with the hypothesis the genes would be positive regulators of WhiB7

overall_design: Tn-seq of Mycobacterium smegmatis untreated or treated with one of the following antibiotics: Roxithromycin, Chloramphenicol, or Tetracycline.

first: Jan

last: Burian


title: Epithelial-Mesenchymal Micro-Niches Govern Stem Cell Lineage Choices (ATAC-seq)

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Adult tissue stem cells (SCs) reside in niches, which through intercellular contacts and signaling, influence SC behavior. Once activated, SCs typically give rise to short-lived transit-amplifying cells (TACs), which then progress to differentiate into their lineages. Here, using single cell RNA-sequencing, we unearth unexpected heterogeneity among SCs and TACs of hair follicles. We trace the roots of this heterogeneity to micro-niches along epithelial-mesenchymal interfaces, where progenitors display molecular signatures reflective of spatially distinct local signals and intercellular interactions. Using lineage-tracing, temporal single cell analyses and chromatin landscaping, we show that SC plasticity becomes restricted in a sequentially and spatially choreographed program, culminating in seven spatially arranged uni-lineage progenitors within TACs of mature follicles. By compartmentalizing SCs into micro-niches, tissues gain precise control over morphogenesis and regeneration: Some progenitors specify lineages immediately; others retain potency, preserving self-renewing features established early while progressively restricting lineages as they experience dynamic changes in microenvironment.

overall_design: Mouse bulge hair follicle stem cell and hair germ cells at telogen stage were FACS-purified and analyzed by ATAC-seq

first: Elaine

last: Fuchs


title: E. coli evolution to alternating substrate conditions

city: La Jolla

first: Troy

last: Sandberg

address: 9500 Gilman Dr

institute: UCSD

summary: Escherichia coli was evolved under growth conditions in which the carbon substrate alternated between glucose and either glycerol, xylose, or acetate with every tube of growth. Controls were also evolved to each substrate individually, without switching.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Expression profiling of wild-type and evolved strains grown on M9 minimal medium with either glucose, glycerol, xylose, or acetate as the sole carbon source.


title: MCF7 breast cancer cell response to estradiol

city: Nijmegen

first: H.

middle: G.

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

country: Netherlands

institute: Radboud University

summary: The experiment was designed to uncover the response to estradiol (E2) in MCF7 breast cancer cells.  The first step was to create a reference sample in a ligand free environment.  For that, the cells were placed into estradiol free media for 3 days,  which reduced the binding between ER-alpha and E2. The cells were then ready to be re-exposed to E2.  Following the introduction of E2, the resultant changes were tracked by multiple ChIP-seq experiments.  The experiments were performed at 0, 5, 10, 20, 40, 80, 160, 320, 640 and 1280 minutes after the stimulation.  Each ChIP-seq experiment was carried out with a different antibody to measure genome-wide changes in  genomic occupancy of their specific protein targets. Specifically, the studied protein factors and  histone modifications were: ER-alpha, H3K4me3, and H2AZ.  Other previously published data from the same set  of experiments are available for Pol-II ChIP-Seq and RNA-Seq (GEO accession GSE62789 and GSE44800).

overall_design: ChIP-seq using 3 different antibodies at 10 different times after estradiol treatment of MCF7 cells

first: Tomasz

last: Dzida

first: Mudassar

last: Iqbal

first: Iryna

last: Charapitsa

first: Filomena

last: Matarese

first: Hendrik

middle: G

first: George

last: Reid

first: Antti

last: Honkela

first: Magnus

last: Rattray


title: Transdifferentiation as a mechanism of treatment resistance in a mouse model of castration-resistant prostate cancer

city: Newark

first: Antonina

last: Mitrofanova

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

summary:
Analysis of transcriptome of prostate tissue from the anterior lobe or tumor from 9, 12, 13, 14, and 16 months old mouse
Prostate tissue or tumor from 9 month old Nkx3.1CreERT2/+ mice, 14 month old Nkx3.1CreERT2/+;Ptenflox/flox mice (intact, treated with vehicle), 16 month old Nkx3.1CreERT2/+;Ptenflox/flox mice (castrated, treated with vehicle or abiraterone), 12 month old Nkx3.1CreERT2/+;Ptenflox/flox;P53flox/flox mice(intact, treated with vehicle), 13 month old Nkx3.1CreERT2/+;Ptenflox/flox;P53flox/flox mice (castrated, treated with vehicle or abiraterone) was harvested, and snap frozen for subsequent molecular analysis

overall_design: Total RNA obtained from prostate tissues or tumors. Prostate tissues or tumors were harvested and processed for RNA isolation and transcriptome analysis using the MagMAX RNA isolation kit (Ambion).

first: Min

last: Zou

first: Nicolas

last: Floch

first: Cory

last: Abate-Shen


title: Epithelial-Mesenchymal Micro-Niches Govern Stem Cell Lineage Choices (bulk RNA-Seq)

overall_design: Mouse hair follicle stem cell, outer root sheath (ORS), basal hair bulb cells, suprabasl hair bulb cells in Anagen-VI were FACS-purified for RNA-seq.


title: Cooperative regulatory functions of miR858 and MYB83 in transcriptome reprogramming during cyst nematode parasitism of Arabidopsis

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

summary: RNA-seq analysis was conducted to identify differentially expressed genes in miR858 and MYB83 overexpression lines compared to the wild-type Col-0 plants.

overall_design: mRNA profiles of two weeks old Arabidopsis root of Col-0 (wild type), miR858 resistant MYB83 overexpression line and miR858 overexpression line were generated by deep sequencing, in triplicate using HiSeq 2500 system.

first: Tarek

last: Hewezi