title: Heterogeneous DNA methylation changes in acute myeloid leukemia associate with cancer-specific gene expression signatures and disruption of the hematopoietic regulatory network

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

summary: DNA methylation is known as a stable epigenetic mark that is linked to gene silencing in cancer. Specific sets of DNA methylation changes have been linked to cancer subgroups. Here we generated genome-wide DNA methylation profiles of acute myeloid leukemia (AML) patient samples. A subset of genomic regions showed extensive hypervariation among AML patients. As such, none of the identified differentially methylated regions (DMRs) as compared to normal heamatopoietic precursor cells were common to all AML cases. Gain of methylation is restricted to regions that in human ES cells are marked with both H3K27me3 and H3K4me3 (bivalent marks). These regions are associated with lowly expressed and silent genes in healthy progenitors. Expression changes associated with aberrant methylation occurred infrequently, but revealed a small and highly specific subset of DMRs associated with myeloid function and cancer-specific pathways.  Furthermore, loss of DNA methylation in AML specifically targeted a small number modules in heamatopoietic regulatory networks, in a mutually exclusive manner. Our data emphasize the variation in DNA methylation patterns between different AML cases, but shows that among these changes, a core set of changes drives cancer-essential alterations in gene expression and regulation.

overall_design: To investigate DNA methylation in acute myeloid leukemia (AML) in a genome-wide unbiased fashion, we applied MethylCap-seq. This method involves capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation Illumina sequencing of eluted DNA.

first: Arie

first: Femke

last: Simmer

first: Anita

last: Kaan

first: Lucia

last: Altucci

first: Hendrik

last: Stunnenberg


title: Gene expression profiling of melanoma cell lines by RNASeq

status: Public on Apr 30 2018

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

country: USA

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: Panel of 53 melanoma cell lines were gene expression profiled by RNA-Seq for molecular classification

overall_design: mRNA profiles of 53 melanoma cell lines

first: Lidia

last: Robert

first: Deborah

middle: J

last: Wong

first: Mohammed

middle: S

last: Atefi

first: Antoni

last: Ribas

first: Thomas

middle: G

last: Graeber


title: Expression data for sweet orange fruits in different development stages

city: Changsha

first: Lu

last: Xiaopeng

address: 1 Nongda Rad.

country: China

institute: Hunan Agricultural University

summary: Citrate is demonstrated to be an indispensable secondary metabolite in citrus fruit. Citrus citrate content is affected by accumulation, degradation, usage, transport and storage. The detail mechanisms of citrate accumulation are complicated in citrus fruit and there are other regulating pathways that have yet to be discovered. In this study, we utilized genomic expression investigation to gain a deep insight into the citrate-accumulation-related biological processes in sweet orange.

overall_design: Transcriptome examination of four samples at different developing stages in two sweet orange cultivars.

first: Xie

last: Shenxi


title: Transcriptome profile of Dictyostelium cell during ER-stress

status: Public on Apr 28 2018

city: Cd de Mexico

first: Roberto

last: Coria

state: Cd de Mexico

address: Apartado Postal 70-600

department: Molecular Genetics

country: Mexico

institute: Instituto Fisiologia Celular

summary: The Unfolded Protein Response (UPR) is an adaptive pathway that restores cellular homeostasis after endoplasmic reticulum (ER) stress caused by an impairment of its protein folding capacity. The ER-resident kinase/ribonuclease Ire1 is the only UPR sensor that has been conserved during evolution from yeast to mammals; in these organisms, Ire1 transmits information from the ER to the nucleus trough the non-conventional splicing of Hac1 (yeast)/Xbp1 (metazoans) mRNA. We described the Dictyostelium discoideum ER-stress response and characterized its single bonafide Ire1 orthologue, IreA. We found that tunicamycin (TN) triggers a gene-expression program that increases the protein folding capacity of the ER and that alleviates ER protein load. Further, IreA resulted essential not only for cell-survival after TN-induced ER-stress, but also to accomplish about nearly 40% of the transcriptional changes induced upon a TN treatment. In addition, we described that autophagy is activated in Dictyostelium cells after a TN treatment and that autophagy-defective mutants exhibited increased sensitivity to this drug. The response of Dictyostelium cells to ER-stress involves the combined activation of an IreA-dependent gene expression program and the autophagy pathway.

overall_design: Poly A RNA profile of wild-type (WT) and ireA- mutant Dictyostelium cells treated and non-treated with tunicamycin (TN) were generated by deep sequencing, in duplicate, using illumina MiSeq. The assembly of the data was performed using TopHat and Cufflinks software. Onthology enrichment analysis were performed with PANTHER and DAVID web tools

first: Eunice

last: Dominguez-Martin

first: Gerardo

last: Coello

first: Laura

last: Ongay-Larios

last: Kawasaki

first: Olivie

last: r Vincent

first: Ricardo

last: Escalante


title: Evolved Repression Overcomes Enhancer Robustness

city: Ashburn

first: Ella

last: Preger-Ben Noon

state: VA

address: 19700 Helix Drive

institute: HHMI Janelia Research Campus

summary: Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same transcription factor, and it is not clear how robust enhancers can evolve loss of expression through point mutations. Here, we report the high-resolution functional dissection of a robust enhancer of the shavenbaby gene that has contributed to morphological evolution. We found that robustness is encoded by many binding sites for the transcriptional activator Arrowhead and that, during evolution, some of these activator sites were lost, weakening enhancer activity. Complete silencing of enhancer function, however, required evolution of a binding site for the spatially restricted potent repressor Abrupt. These findings illustrate that recruitment of repressor binding sites can overcome enhancer robustness and may minimize pleiotropic consequences of enhancer evolution. Recruitment of repression may be a general mode of evolution to break robust regulatory linkages.

overall_design: 8 samples are analyzed: background GFP- and target GFP+ cells from four independent sortings.

first: Fred

middle: P

last: Davis

first: David

middle: L

last: Stern


title: Analysis of LPS-stimulated WT and Tnip2[D310N] bone marrow-derived macrophages

status: Public on May 01 2018

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

country: United Kingdom

institute: University College London

summary: This experiment was conducted to analyse the effect of mutating the ubiquitin binding function [D310N] of ABIN2 (Tnip2) on the LPS-induced expression of mRNAs in bone marrow-derived macrophages.

overall_design: WT and Tnip2[D310N] BMDMs, LPS (100ng/ml), n=3/genotype, Unstimulated, 30mins, 60mins, 120mins, 240mins and 360mins. 36 samples in total, Single end, 75bp

first: Steven

middle: C

first: Stamatia

last: Papoutsopoulou

first: Michael

last: Pattison

first: Probir

last: Chakravarty


title: Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)

status: Public on Apr 27 2018

city: Bethesda

first: Jeffrey

middle: Allen

last: Farrell

state: MD

address: 6 Center Drive (6A/1A06)

department: Division of Developmental Biology

institute: National Institute of Child Health and Human Development

summary: Wild-type zebrafish embryos were mechanically dissociated and profiled using Drop-seq

overall_design: Drop-seq was performed on 28 groups of 20-40 visually staged, mechanically dissociated embryos. Samples were combined and sequenced in batches DS2-DS5.

middle: A

first: Yiqun

last: Wang


title: Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

summary:
During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Drop-seq analysis of wild-type embryos (38,731 cells, 12 timepoints, 28 samples total, 20-40 embryos per sample), SMART-seq2 analysis of wild-type and MZoep mutant embryos (52 wild-type and 364 MZoep cells from 50% epiboly stage), and 10X single-cell sequencing analysis of WT and MZoep mutant embryos (3,000 WT and 2,200 MZoep cells from 6-somites stage).


title: Single-cell RNAseq (SMART-seq2) of wild-type (TLAB) and MZoep (tz57) zebrafish embryos at 50% epiboly stage

summary: SMART-seq2 was performed on single cells isolated from visually staged zebrafish embryos.

overall_design: Samples were all sequenced in one batch. Some were generated with a 5' UMI-tagged method, and others are full-length SMART-seq2.


title: Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype

status: Public on Apr 26 2018

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

summary:
Purpose: A proof of concept study examining the disease modelling capabilities of patient iPSC derived kidney organoids.
Methods: A proband was diagnosed by genome sequencing with compound heterozygous IFT140 mutations. A one-step reprogramming/gene-editing protocol of proband fibroblasts was used to derive both uncorrected patient and isogenic gene-corrected induced pluripotent stem cells (iPSC) which were differentiated to kidney organoids. Organoids were examined by immunofluorescence. Additionally, epithelial cells magnetically sorted from whole kidney organoids underwent transcriptional profiling and spheroid culture.
Results: Differential expression analysis of organoid epithelial cell fractions demonstrated apicobasal polarity, cell-cell junction and dynein motor assembly downregulation in patient organoids. Defective ciliary morphology and spheroid culture were rescued in gene corrected organoids.
Conclusions: This study validates patient iPSC-derived kidney organoids as a novel, faithful and patient-specific model to further the study of inherited renal disease in regenerated, human, in vitro tissue.

overall_design: RNA-seq of three replicates each of uncorrected (IFT140 compound heterozygous) and gene-corrected (IFT140 heterozygous) the epithelial cells isolated from patient iPSC derived kidney organoids.

first: Thomas

last: Forbes


title: Metabolic and Transcriptional Alterations in the Early Stages of Cardiac Fuel Switch Hint at Novel mTOR-mediated Regulation of Hypertrophy [RNA-seq]

city: Chapel Hill

first: Jonathan

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

summary:
1. Background- Long-chain acyl-CoA synthetases (ACSL) catalyze the conversion of long-chain fatty acids (FA) to fatty acyl-CoAs.  Cardiac-specific ACSL1 knockout results in a shift towards glycolysis that promotes mTORC1-mediated ventricular hypertrophy.  We used unbiased metabolomics and gene expression analyses to examine the early effects of genetic inactivation of FA oxidation on cardiac metabolism and function.
2. Methods and Results- Compared to WT hearts, global cardiac transcriptional analysis revealed differential expression of 245 genes in Acsl1H-/- hearts 2 weeks after Acsl1 ablation.  Comparison of the 2- and 10-week transcriptional responses uncovered 139 genes whose expression was uniquely changed upon short-term cardiac inactivation of ACSL1.  In particular, partial ACSL1 ablation led to the distinct upregulation of fibrosis genes, a phenomenon not observed after complete ACSL1 knockout.  Metabolomic analysis identified 65 metabolites altered in hearts displaying partially reduced ACSL activity, whereas rapamycin treatment normalized the cardiac metabolomic fingerprint.  Chronic mTOR inhibition via rapamycin treatment revealed novel mTORC1 targets involved in fibrosis, amino acid catabolism, and mitochondrial transport and metabolism.
3. Conclusions- Short-term cardiac-specific ACSL1 inactivation (Acsl1H-/-) resulted in metabolic and transcriptional derangements distinct from those observed upon complete ACSL1 knockout, leading to the identification of novel mTORC1 targets that regulate cardiac hypertrophy development, and suggesting heart-specific mTOR signaling that occurs during the early stages of substrate switching.  Moreover, the rate of increased glucose use correlated negatively with hypertrophy development, strongly suggesting that hearts do not become hypertrophied if they can compensate or switch faster from FA to glucose use.

overall_design: 2x2 factorial desigend experiment, temporal changes in cadiac gene expression after silencing Acsl1 expression in the heart (Acsl1H-/- vs Acsl1flox/flox)  with or without treatment with rapamycin. Biological replicates: 5 per condition.

first: Rosalind

last: Coleman


title: PDGFRa+gp38+ mesenchymal cells in the peripheral tissues support terminal differentiation of ILC2 originated from fetal liver progenitor cells.

city: Yokohama City

first: Kazuyo

last: Moro

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Integrated Medical Science

country: Japan

institute: Riken Yokohama

summary: Group 2 innate lymphoid cells (ILC2) are tissue-resident innate lymphocytes that are derived from common lymphoid progenitor (CLP). While specific progenitors and transcription factors essential for ILC2 differentiation have been well studied, external factors that regulate the commitment from CLP to ILC lineage, site that promote ILC2 terminal differentiation, and stromal cells that provide optimal microenvironment for ILC2 specific development are not fully understood. we demonstrated that the three key external factors such as concentration of IL-7 and the strength and duration of Notch signaling conditionally determined the fate of CLP toward T cell, B cell, or ILC lineages, which seems to be an important process from CLP to CHILP differentiation in the fetal liver. Furthermore, we identified ILC progenitors lacking the developmental potential to become T or B cells, and KLRG1- immature ILC2 that require STAT5 for functional maturation in the mesentery. We also identified PDGFRa+gp38+ mesenchymal cells in the mesentery that support ILC2 differentiation from ILC progenitors but not from CLP. Finally, single-cell RNA-sequencing (scRNA-seq) analysis of mesenteric cells demonstrated that PDGFRa+gp38+ cells are heterogeneous populations. Collectively, our result suggested that early differentiation of ILC2 occurs in the primary lymphoid organ with regulation of environmental factors, and final differentiation occurs in the peripheral tissues once after CHILP migrate into the periphery.

overall_design: Duplicate samples (mouse 1 and mouse 2) were processed for single cell-based RNA sequencing with Illumina HiSeq 2500 with 50 paired-end reads, using barcorded RNA library.

first: Satoshi

last: Koga


title: Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants [RNA-Seq]

status: Public on Apr 29 2018

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Aging is a time-dependent biological phenomenon governed by complex networks of regulatory components and their transitions over lifetime. Yet, there have been limited efforts to pin down age-associated networks and map their dynamic characteristics onto aging phenotypes. Here, we built time-course genetic regulatory networks of NAM/ATAF/CUC (NAC) transcription factors during the course of leaf aging in Arabidopsis, using causal regulatory relationships among NACs identified from mutants of 49 aging-associated NACs. These temporal networks revealed a regulatory inversion from activating to repressive regulatory modes at a pre-senescent stage. The inversion was governed by three hub NACs, and their mutants conferred earlier aging with altered expression of reactive oxygen species and salicylic acid response genes. Overexpression of the hub NACs delayed the regulatory inversion, rendering delayed age-dependent cell death. We conclude that the regulatory inversion in NAC networks at a pre-senescent stage directs when age-dependent cell death should proceed in plants.

overall_design: We measured mRNA expression level of anac017, anac082 and anac090 knockout mutants and WT (n=3 for each) at 18 days of leaf age

first: Hyo-Jung

last: Kim

first: Jingil

first: Jung-Ju

first: Sung-Hyun

last: Hong

first: Jeongsik

first: Jinhee

first: Hye-Ryun

last: Woo

first: Pyung-Ok

last: Lim

first: Daehee

last: Hwang

first: Hong-Gil

last: Nam


title: Self-recognition of an inducible host lncRNA by RIG-I feedback restricts innate immune response

city: Beijing

first: Minghong

last: Jiang

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences

summary: In this study, we employed a combination of UV-RIP-seq, PacBio-seq and iCLIP-seq technologies to identify long non-coding RNA associated with cytoplasmic RIG-I protein in mouse macrophages cells.

overall_design: Two UV-RIP were performed using anti-Flag antibody in RAW264.7 cells stably expressing Flag-tagged RIG-I with or without vesicular stomatitis virus (VSV) infection for 12 hr, then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing. One RIP was performed using anti-RIG-I antibody in RAW264.7 cells with VSV infection for 12 hr, then co-purified RNAs were sequenced using PacBio’s SMRT long-read sequencing strategy. Total RNA from mouse peritoneal macrophages was analyzed using PacBio sequencing. iCLIP was performed using anti-RIG-I antibody in RAW264.7 cells upon VSV infection for 12 hr and then made Illumina HiSeq2500 SE50 Sequencing.

first: Shikun

last: Zhang

first: Zongheng

last: Yang

first: Hongyu

last: Lin

first: Jun

last: Zhu

first: Lun

last: Liu

first: Wendie

first: Shuo

first: Wei

first: Yuanwu

last: Ma

first: Lianfeng

first: Xuetao

last: Cao


title: The basic helix-loop-helix transcription factor SHARP1 is an oncogenic driver in MLL-AF6 Acute Myelogenous Leukemia

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute Myeloid Leukemia (AML) with MLL gene rearrangements demonstrate unique gene expression profiles driven by MLL-fusion proteins. Here, we identify the circadian clock transcription factor SHARP1 as a novel oncogenic target in MLL-AF6 AML, which has the worst prognosis among all subtypes of MLL rearranged AMLs. SHARP1 is expressed solely in MLL-AF6 AML, and its expression is regulated directly by MLL-AF6 / DOT1L. Suppression of SHARP1 induces robust apoptosis of human MLL-AF6 AML cells. Genetic deletion in mice delays the development of leukemia and attenuated leukemia-initiating potential, while sparing normal hematopoiesis. Mechanistically, SHARP1 binds to transcriptionally active chromatin across the genome and activates genes critical for cell survival as well as key oncogenic targets of MLL-AF6. Our findings demonstrate the unique oncogenic role for SHARP1 in MLL-AF6 AML.

overall_design:
ChIP-seq and RNA-seq using ML-2 cells.
ChIP-seq using SHI1 cells.

first: Akihiko

last: Numata

first: Hui

last: Kwok

first: Akira

last: Kawasaki

first: Henry

first: Touati

last: Benoukraf

first: Jon

last: Kerry

first: Erica

last: Ballabio

first: Marta

last: Tapia

first: Deepak

last: Bararia

first: Qi-Ling

last: Zhou

middle: Q

first: Aniruddha

last: Deshpande

first: Robert

last: Welner

first: Ruud

last: Delwel

first: Reshma

last: Taneja

first: Thomas

last: Milne

first: Daniel

last: Tenen


title: Sox9 positive periosteal cells in repair of adult long bone fractures

status: Public on Apr 25 2018

first: Andrew

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: The phases of fracture healing have been well characterized. However, the exact source and genetic profile of the skeletal progenitors that participate in bone repair is somewhat unclear. Sox9 expression in skeletal elements precedes bone and cartilage formation and a Sox9+ cell type is retained in the adult periosteum. We hypothesized that Sox9+ periosteal cells are multipotent skeletal progenitors normally participating in fracture repair. To test this hypothesis we used tamoxifen (TM)-mediated lineage tracing of Sox9+ cells in Sox9CreErt2:Td-Tomato mice. TM injection indelibly labels Sox9+ cells and all their descendants with the fluorescent reporter protein Td-Tomato. Intact mouse femora were harvested 2 weeks after TM injection and analyzed by histology and immunostaining and RNA sequencing, to evaluate the skeletal distribution and gene expression profile of Td-Tomato positive cells in the adult femur. To assess the role of these cells in fracture repair, mice underwent a closed mid-diaphyseal femoral fracture and their hind limbs were harvested at 3, 9 or 56 days post-fracture to assess the contribution of Sox9+ and Td-tomato+ cells in the fracture healing process. In the intact adult mouse femur, Td-Tomato-labelled cells were observed in articular and growth plate cartilage where Sox9 is known to be expressed, but also in the primary spongiosa, periosteum, and endosteum. RNA sequencing and subsequent analysis showed that Td-Tomato positive periosteal cells were enriched in Sox9 transcripts, and transcripts for various osteogenic and chondrocyte specific genes. In a femoral fracture model, we showed that pre-labeled Td-Tomato positive descendent cells were mobilized during the fracture repair process, expanding and migrating towards the fracture site 3 days post-fracture. Here, Td-Tomato positive cells differentiate into chondrocytes and osteoblasts in the soft and hard callus, respectively, 9 days post-fracture. By 2 months post-fracture, descendants of the original Sox9 labelled cell population were prevalent in the cortex and periosteum, and amongst the differentiated osteocyte population embedded within the cortical bone. Thus, a Sox9+ progenitor population resides in the adult periosteum. Fate tracing shows that these cells likely play a substantial role in repair of the fractured femur giving rise to chondrocytes, osteoblasts and mature cortical osteocytes. To our knowledge this is the first report of this Sox9+ cell population in the periosteum of the adult long bone. Taken together with developmental studies on skeletal formation, our data suggest that Sox9+ osteochondroprogenitors play a continuous role in skeletal formation throughout life.

overall_design: Double heterozygous mice, carrying one allele of Sox9CreErt2 driver and one allele of Td-Tomato reporter, were generated by crossing heterozygous Sox9CreErt2 (Sox9tm1(cre/ERT2)Haak) with homozygous Td-Tomato (Gt(ROSA)26Sortm14(CAG-tdTomato)Hze) mice. The mice received 3 intraperitoneal injections of 100µL tamoxifen (TM) solution (20 mg/mL diluted in corn oil), at 48-hour intervals. Intact mouse femora were harvested 2 weeks after the last tamoxifen injection and analyzed with RNA sequencing to determine the gene expression profile of periosteal cells of the femur. Femoral diaphyses were digested in a liberase solution (100ug/mL in PBS) for 2 hours in a fast shaking rocker at 37 oC, 100 rpm to obtain diaphyseal periosteum cells. Digested cells were filtered and single cell suspensions were subjected to FACS sorting to collect Td-Tomato positive and negative cells. About 10,000 Td-Tomato positive cells and 10,000 Td-Tomato negative control cells were isolated after two collections from 18 femora (9 mice). Total RNA was extracted from each cell population separately with Qiagen RNAasy micro kit with DNaseI digestion according to the manufacturer’s instructions. Duplicated experimental RNA sequencing libraries were made with a SMARTer Universal Low Input RNA Kit and 75 nucleotide paired-end sequencing performed on an Illumina Nextseq 500 sequencer in USC’s Epigenomics Core facility. Sequence reads were mapped by the Star aligner and quantified within the Partek Genomics Suite software (http://www.partek.com) to identify differentially expressed genes. The resulting gene list was uploaded to DAVID GO analysis tool (https://david.ncifcrf.gov/) to extract the enriched gene ontology terms of TdTomato positive periosteal cells.

first: Xinjun

last: He

first: Sofia

last: Bougioukli

first: Brandon

last: Ortega

first: Eric

last: Arevalo

first: Jay

middle: R

last: Lieberman


title: Regulatory inversion in NAC networks steers the timing of age-dependent cell death in plants

first: Ji-Hwan

last: Park

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Comparative Transcriptomes Analysis for different Yarrowia lipolytica strains synthesizing different levels of β-carotene as end products.

city: Tianjin

first: man

last: wang

address: yaguan road

institute: Tianjin University

summary:
Purpose: According to comparative transcriptomes data, the differentially expressed genes within these selected Y. lipolytica strains can be digged out and further analyzed, seeking potential targets that were tuned drastically and might improve β-carotene production when modified.
Methods: mRNA profiles of three Y. lipolytica strains ctrl, Y5_2, Y5_3 (each named as Yl_5_1, Yl_5_2, Yl_5_3 in related manuscript) were generated in triplicate using illumina. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample. The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data. The read counts for each gene in the genome were summarized as processed data.
Results: In all strain samples, the transcriptome data for all 6145 genes throughout genome were detected. The results showed that the expression levels of nearly half of the total genes were tuned to a higher or a lower value.
Conclusions: There were 2848 differentially expressed genes between strain ctrl and Y5-2 and this number was 2889 for ctrl vs. Y5_3. The GO and KEGG enrichment of these differentially expressed genes would be further operated for exploring drastically regulated functions and pathways.

overall_design: The transcirptomes of different Yarrowia lipolytica strains were sequenced by Illumina, giving both unchanged genes and differentially expressed genes that would affect β-carotene production.

first: Duo

last: Liu

first: Wang

last: Man

first: Yingjin

last: Yuan


title: Fosl1 transdifferentiate embryonic stem cells to differentiated trophoblast stem cells (RNA-seq)

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: During mammalian embryonic development, the first lineage commitment event gives rise to two distinct cell populations: the trophectoderm (TE) and the inner cell mass (ICM). The TE consists of outer cells of the blastocyst and ultimately forms the placenta while the ICM gives rise to all the embryonic tissues. Numerous transcription factors (TFs) guiding ICM differentiation into different embryonic tissues have been characterized. However, only a few TFs that are required for TE specification and differentiation have been identified, and much less is understood as to how these TFs interact with other TFs or with their chromosomal targets in order to drive cell fate towards TE lineage. Understanding trophectoderm development is crucial because cells in this lineage are required for proper embryo implantation in the uterus. Defects in this lineage can cause early failure of pregnancy as well as other pregnancy related disorders such as preeclampsia and intrauterine growth restriction (IUGR). Here, we characterize the function of one of TE-specific TF, Fosl1, which was previously suggested as having some role in placental development. We utilized mouse embryonic stem (ES) cells (derived from ICM) and showed that ectopic expression of Fosl1 can transdifferentiate ES cells to differentiated TS cells (trophoblast giant-like cells). We show that Fosl1 does so by directly binding and activating TE specific genes and genes associated with epithelial-mesenchymal transition (EMT). Using mouse trophoblast stem (TS) cells, we also establish that Fosl1 is required for specification of TS cells to trophoblast giant cells (TGCs) subtype. Therefore, we postulate that Fosl1 is a key regulator of TS cell differentiation.

overall_design: RNA-seq assays were performed using BirA-expressing ES cell lines- expressing BirA only or BirA and biotin-tagged Fosl1.

first: Kim

last: Jonghwan


title: Smoking induced expression of the GPR15 gene indicates its potential role in chronic inflammatory pathologies

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

institute: Murdoch University

summary: The aim of present study was to study the changes in peripheral blood gene expression profile induced by smoking. RNA was extracted from the PBMCs of 48 persons with detailed smoking history (24 were non-smokers, 16 were current smokers and 8 were ex-smokers). Gene expression profile was evaluated with the RNA sequencing and results were analyzed separately in males (24) and females (24). In male smokers, 13 genes were statistically significantly (FDR < 0.1) differentially expressed. In female smoker, 5 genes were differentially expressed with the FDR<0.1. Most of the differentially expressed genes were different between male and female smokers. However, GPR15, expression was changed in male and female smokers compared to non-smokers. Further analysis on the methylation of the genes GPR15 identified significant hypomethylation in smokers compared to non-smokers. GPR15 is the chemo-attractant receptor that regulates T-cell migration and immunity. Up-regulation of GPR15 could explain to some extend the health hazards of smoking for chronic inflammatory diseases

first: Gea

last: Kõks

first: Andres

last: Metspalu

first: Mari-Liis

last: Uudelepp

first: Maia

last: Limbach

first: Pärt

last: Peterson


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [Hi-C]

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne

summary: We hypothesized that entry into senescence of different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant high mobility group (HMG) B1 and B2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries.

overall_design: Hi-C was generated in HUVEC (D1-D3), IMR90 (I10, I79) and MSC (D) using HindIII restriction digestion and HMGB2 knockdown HUVEC (NTC, siHMGB2)

first: Argyris

last: Papantonis

first: Anne

last: Zirkel


title: The transcriptome comparison data between Saccharomyces cerevisiae cells in xylose consumption phase after glucose depleted in glucose-xylose co-fermentation and when xylose was the sole carbon source.

city: Qingdao

first: Yu

last: Shen

state: Shandong

address: binhai road 72

department: Microbiology and Biotechnology Institute

institute: Shandong University

summary: The xylose fermentation rate during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage) was much lower than that when xylose was the sole carbon source (defined as X stage). BSGX001 and XH7 are two engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between GX stage and X stage of  BSGX001 and XH7, respectively.

overall_design: Samples were taken from the cells in X stage and GX stage respectively. Each strain under each condition had duplicates. Then RNAseq-technology was employed to generate the transcriptome data.

first: Shan

last: Wei


title: Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [bulk RNA-Seq]

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. Using bulk chromatin accessibility profiles to scaffold our single-cell data analysis, we constructed an epigenomic landscape of human hematopoiesis and characterized epigenomic heterogeneity within phenotypically sorted populations to find epigenomic lineage-bias toward different developmental branches in multipotent stem cell states. We identify and isolate sub-populations within classically-defined granulocyte-macrophage progenitors (GMPs) and use ATAC-seq and RNA-seq to confirm that GMPs are epigenomically and transcriptomically heterogeneous. Furthermore, we identified transcription factors and cis-regulatory elements linked to changes in chromatin accessibility within cellular populations and across a continuous myeloid developmental trajectory, and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements. Overall, this work provides a template for exploration of complex regulatory dynamics in primary human tissues at the ultimate level of granular specificity – the single cell.

overall_design: Profiles of bulk RNA profiles, assayed using RNA-seq, across sorted cell types from CD34+ bone marrow.


title: Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [bulk ATAC-Seq]

overall_design: Profiles of bulk epigenomes, assayed using ATAC-seq, across sorted cell types from CD34+ bone marrow.


title: The dTAG system for immediate and target-specific protein degradation

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: The dissection of complex biological systems requires target-specific control of protein function or abundance. Genetic perturbations have markedly advanced science but are variably limited by off-target effects, multi-component complexity and irreversibility. Most limiting to the study of fast biology is the requisite delay from modulation to experimental measurement. To enable the immediate and selective control of single protein abundance, we created a chemical biology system that leverages the potency of cell-permeable heterobifunctional degraders. The dTAG system pairs a novel allele-specific degrader of FKBP12F36V with expression of FKBP12F36V in-frame with a target protein of interest. By transgene expression or CRISPR-mediated locus-specific knock-in, we exemplify a generalizable strategy to study the immediate consequent biology of protein loss. Using dTAG, we observe an unexpected superior anti-proliferative effect of BET bromodomain inhibition and degradation over selective BRD4 degradation, characterize immediate effects of KRASG12V loss on proteomic signaling, and demonstrate rapid degradation in vivo. This technology platform is expected to confer high kinetic resolution to biological investigation and provide early target validation in the context of drug discovery.

overall_design: We performed two ERCC spike-in normalized RNA-sequencing experiments to quantify transcriptional changes upon dTAG-13 treatment. In the first experiment (see datasets identified as associated with 'Control-related experiment'), we profiled control NIH/3T3 cells treated with DMSO, dTAG-13, ortho-AP1867, AP1867, Thalidomide, dBET6, and dTAG-47 for four hours. In the second experiment (see datasets identified as associated with 'KRAS-related experiment'), we profiled NIH/3T3 cells expressing FKBP12F36V-KRASG12V treated with DMSO, dTAG-13 for four and eight hours to induce KRASG12V degradation, or Trametinib (GSK112021) for four and eight hours to inhibit MEK as well as control NIH/3T3 cells with treated with DMSO. All samples were prepared in biological triplicate.

first: Behnam

last: Nabet

first: Michael

last: Erb

first: Matthew

last: Lawlor

middle: E


title: MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing

city: Stanford

first: Johan

last: Jeong

address: Rm.G2035, 265 Campus Dr.

department: Pathology

institute: Stanford University

type: Genome variation profiling by high throughput sequencing

summary: Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks.  However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development.  Here we utilized TALENs to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells.  Selected cytokine combinations enabled monoclonal outgrowth and immortalization of initially rare translocated cells, which were distinguished by elevated MLL target gene expression, high surface CD9 expression, and increased colony forming ability.  Subsequent transplantation into immune-compromised mice induced myeloid leukemias within 48 weeks, whose pathologic and molecular features extensively overlap with de novo patient MLL-rearranged leukemias.  No evidence of secondary pathogenic mutations was revealed by targeted exome sequencing and whole genome RNA-seq analyses, suggesting the genetic sufficiency of t(9;11) translocation for leukemia development from human HSPCs.  Thus, genome editing enables modeling of human acute MLL-rearranged leukemia in vivo reflecting the genetic simplicity of this disease and provides an experimental platform for biological and disease modeling applications.

overall_design:
For RNA-sequencing, RNA was purified from xenografted leukemic mouse bone marrow and cultured cells using Trizol (Invitrogen) followed by RNeasy kit (Qiagen) as manufacturer’s instructions, and sample quality was evaluated using Agilent RNA 6000 nano chip and Agilent 2100 Bioanalyzer (Agilent, St. Laurent, QC, Canada).  More than 2mg of total RNA per sample was submitted for RNA-sequening.
For targeted exome sequencing, genomic DNA was extracted from cultured cells and mouse bone marrow cells using the DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany) and analyzed using the TruSight myeloid sequencing panel targeting 54 frequently mutated genes in blood cancers (Illumina, CA, USA).  Paired-end sequencing runs were performed on a MiSeq (Illumina) with reagent kit v3 according to manufacturer’s instructions.  Paired sequences obtained from each sample were mapped to human genome reference GRCh37/hg19.  Variant calls were annotated by Variant Effect Predictor (VEP).

first: Corina

last: Schneidawind

last: Cleary


title: Topological demarcation by HMGB2 is disrupted early upon senescence entry and induces CTCF clustering across cell types [RNA-seq]

overall_design: Gene expression profiles generated by sequencing total (ribodepleted) RNA from HUVEC (D1-D3), polyA-selected or nascent (factory) RNA from IMR90 (I10 and I79), polyA-selected RNA from MSC (donors A-D), or polyA-selected RNA from control (NTC) and HMGB2-knockdown (HMGB2-KD) HUVEC.


title: ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease [ChIP-seq]

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary: Here we show that estrogen-related receptor γ (ERRγ) is an essential transcriptional coordinator of both renal mitochondrial and reabsorptive functions.  ERRγ is highly and specifically expressed in the RECs, and its expression correlates with kidney function in humans.  We generated REC-ERRγ KO mice which developed severe renal mitochondrial and reabsorptive dysfunction and fluid-filled cysts.  Transcriptome and cistrome analysis revealed that ERRγ directly regulates mitochondrial metabolism and renal reabsorption.  ChIP-reChIP-Seq studies further suggest that ERRγ employs a distinct mechanism to regulate renal reabsorption genes through functional cooperation with hepatic nuclear factor 1 beta (HNF1β), mutations of which cause strikingly similar renal dysfunction and cysts in humans and animals.  Together these findings reveal a novel role for ERRγ in simultaneously coordinating a transcriptional program for renal energy production via mitochondria and energy consumption to perform reabsorptive functions required for normal kidney function

overall_design: Identification of ERRg, HNF1b, and ERRg-HNF1b cobound sites in C57Bl6/J mouse kidneys

first: Liming

last: Pei


title: HCMV Latently infected Kasumi-3 transcription analysis.

status: Public on Apr 24 2018

city: Cleveland

first: Eain

middle: Anthony

last: Murphy

state: OH

institute: Cleveland Clinic Foundation

summary:
HCMV latnecy within hematopoetic precursor cells was evaluated by infecting cells and establishing latency using a recombinant virus that allows for labeing of RNA species only in the context of a viral infection thereby allowing purification of these transcripts from mock infected cells.
We used microarrays to detail the global programme of gene expression to identify changes in host transcription during HCMV latency.

overall_design: Kasumi-3 cells were either mock infected or infected with HCMV TB40e expressing T. gondii UPRT and IE2-2a-eGFP,  Cells were sorted 96hpi to remove lytically replicating cells.  Remaining cells were either uninfected or latenlty infected Kasumi-3 cells.  This population was treated with 4-thoi uracil allowing incorporation of the label into the UPRT expressing cells only.  After 6 hrs of labeling, RNA was isolated and used in a Biotin switch assay to purify labeled RNA from pre-existing RNA and RNA from uninfected cells.  In parallel, mock infected cells were labeled with 4-thio Uradine adn used as a negative control.  RNA transcription was monitored by affymetric array hybridization.


title: A B-ARR-mediated cytokinin transcriptional network directs hormone-cross regulation and shoot development

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: While the biosynthesis, degradation, and signaling pathways for the essential plant hormone cytokinin have been extensively studied, the direct transcriptional targets of B-type ARRs, the key TFs essential for cytokinin action have not been defined. We epitope tagged four B-ARRs (1, 10, 12, and 14) using recombineering techniques and profiled TF binding sites using chromatin immunoprecipitation sequencing (ChIP-seq). The resulting cytokinin transcriptional response network allowed construction of the first cytokinin TF network, identification of numerous direct downstream targets along with the B-ARR-6BA motif and elucidation of one mechanism of activation of WUSCHEL, which requires a high concentration of cytokinin in shoot apical meristem for TF binding.

overall_design: we present the profiles of in vivo DNA binding sites for the genetically redundant type-B ARABIDOPSIS RESONSE REGULATORS (B-ARRs): ARR1, ARR10, and ARR12 along with ARR14 using recombineering YFP tagged lines and subsequent chromatin immunoprecipitation sequencing (ChIP-seq) analysis. The expression and genomic protein localization of B-ARRs overlap extensively, demonstrating numerous common targets among the B-ARRs. The negative regulators of cytokinin signaling, the type-A ARRs (A-ARRs), are the top ranked targets of B-ARRs. These findings confirm an immediate negative B-ARR-driven feedback loop in cytokinin signaling. Constructing a cytokinin primary response transcriptional network revealed a recurring theme involving extensive cross-regulation both within the components of the cytokinin pathway and with other plant hormone response pathways.

first: Mingtang

last: Xie

first: Hongyu

last: Chen

first: Ryan

last: O'Neil

first: Carol

last: Huang


title: Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis

first: Yusheng

last: Zhao

address: Yuanmingyuan Road #2, Haidian District

institute: China agricultural university

type: Methylation profiling by high throughput sequencing

summary: Epigenetic markers such as histone acetylation and DNA methylation determine chromatin organization. In eukaryotic cells, metabolites from organelles or the cytosol affect epigenetic modifications. However, the relationships between metabolites and epigenetic modifications are not well understood in plants. We found that peroxisomal acyl-CoA oxidase 4 (ACX4), an enzyme in the fatty acid β-oxidation pathway, is required for suppressing the silencing of some endogenous loci as well as Pro35S:NPTII in the ProRD29A:LUC/C24 transgenic line. The acx4 mutation reduces nuclear histone acetylation and increases DNA methylation at the NOS terminator of Pro35S:NPTII, and at some endogenous genomic loci, which are also targeted by the demethylation enzyme REPRESSOR OF SILENCING 1 (ROS1). Furthermore, mutations in multifunctional protein 2 (MFP2) and 3-ketoacyl-CoA thiolase-2 (KAT2/PED1/PKT3), two enzymes in the last two steps of the β-oxidation pathway, lead to similar patterns of DNA hypermethylation as in acx4. Thus, metabolites from fatty acid β-oxidation in peroxisomes are closely linked to nuclear epigenetic modifications, which may affect diverse cellular processes in plants.

overall_design:
Examine DNA methylation,and RNA expression changes by whole-genome bisulfite sequencing; RNA sequencing in A. thaliana wild type and acx4,Col-0,ros1-4,acx4-1,mfp2-2,kat2-3 mutants
Examine histone acetylation changes by whole-genome sequencing;  H3K9Ac-, H3K14Ac-, H3K18Ac-, H3K23Ac-ChIP-seq in A. thaliana wild type and acx4 mutant.

first: Lishuan

last: Wang

first: Chunlei

first: Xinye

last: Liu

first: Jinkui

last: Cheng

first: Shaofang

last: Li

first: Jian-Kang

last: Zhu

first: Zhizhong

last: Gong


title: LIN-41 RIP-Seq

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: FLAG-GFP tagged LIN-41 was immunoprecipitated using FLAG dynabeads (Sigma) from lysates of young adult C.elegans. After washing steps, bound fraction (IP) was eluted from beads and associated RNAs were isolated by using the Pico pure RNA isloation kit (Invitrogen)

overall_design: RNA isolated from Input and IP fractions were sequenced for two biological replicates to identify RNAs specifically enriched in IP fraction

first: Pooja

last: Kumari


title: RNA-sequencing in immortalized human mammary epithelial cells

city: Philadelphia

first: Peter

last: Choi

state: PA

address: 3501 Civic Center Blvd, CTRB 4400

department: Pathology and Laboratory Medicine

institute: The Children's Hospital of Philadelphia

summary: The epithelial-to-mesenchymal transition (EMT) contributes to tumor heterogeneity and has been implicated in tumor initiation and metastasis. To systematically identify genes involved in EMT, we performed a genome-scale expression screen in human mammary epithelial cells and found a striking enrichment in RNA splicing factors. In particular, the RNA-binding proteins QKI and RBFOX1 were necessary and sufficient to promote EMT and stem-like states. Among the transcripts cooperatively regulated by both factors, we found that alternative splicing of the actin-binding protein FLNB plays an essential role in the regulation of EMT. The skipping of FLNB exon 30 and the elevated expression of QKI were strongly associated with EMT gene signatures in both basal B subtype breast cancer cell lines and basal-like breast cancer patient samples. These observations demonstrate that alternative splicing regulated by QKI and RBFOX1 plays an active role in promoting EMT in basal-like breast cancers.

overall_design: RNA-sequencing libraries were generated from immortalized human mammary epithelial cells (HME) overexpressing negative control proteins EGFP or HcRed, or candidate ORFs QKI, RBFOX1 or SNAI1. For each ORF, two to three replicates were sequenced.

first: Ji

first: William

last: Hahn


title: Epigenomic conservation of transposable element silencing [ChIP-seq]

first: Michelle

last: Ward

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Transposable elements (TEs) comprise a substantial proportion of primate genomes. Because of the potential deleterious effects of TEs during development, TEs are targeted for silencing by sequence-specific KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, acquire mutations to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. To investigate the short-term evolution of TE silencing, we profiled the genome-wide distribution of H3K9me3 in both human and chimpanzee induced pluripotent stem cells. We performed chromatin immunoprecipitation followed by high-throughput sequencing for H3K9me3, as well as total RNA sequencing in ten human and seven chimpanzee individuals. H3K9me3 enrichment was quantified in 141,642 regions determined to be orthologous between the two species. These H3K9me3-enriched regions were overlaid on a compiled set of 4 million orthologous TEs that can be mapped in both species.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: We collected H3K9me3 and Input ChIP-seq data from 10 human and 7 chimpanzee iPSC lines.


title: Expression Profiling of Cisplatin Resistant SKOV3 Cell Lines vs. Wild Type SKOV3 Cell Lines

city: Washington

first: Wenge

state: DC

address: 800 22nd Street NW, , Science & Engineering Hall 8480

department: School of Medicine and Health Sciences

institute: George Washington University

summary: Ovarian cancer SKOV3 cells were studied to profile the expression of wild type (WT, Cisplatin Susceptible) cells and Cisplatin Resistant (CR) cells. The goal was to gain insights or to build hypotheses into the mechanisms of Cisplatin resistance in this cell-based model.

overall_design: The study included two experimental groups, SKOV3 wild-type cells and SKOV3 Cisplatin resistant cells.  Each group had two biological replicate samples.

first: Wei

last: Zhou

last: Sun

last: Zheng


title: Hox Abdominal-B Genes in the Developing Kidney

city: Cincinnati

first: Keri

middle: Anne

last: Drake

state: Ohio

address: 3333 Burnet Avenue

department: Nephrology

institute: Cincinnati Children's Hospital Medical Center

summary: The Hox complex consists of 39 genes arranged in 4 clusters of flanking genes and 13 paralogous groups in mammals. To assess the functional redundancy of Hox abdominal-B genes during renal development, we used a modified recombineering strategy to simultaneous introduce frameshift mutations into the Hox9, Hox10, and Hox11 flanking genes of the HoxA, HoxC, and HoxD paralogous groups. We performed RNA seq on whole kidneys at E18.5 in triplicates for representative genotypes including: wild type; Hoxa9,10,11-/- HoxC9,10,11+/-, Hoxa9,10,11+/- HoxC9,10,11-/-, Hoxa9,10,11-/- HoxC9,10,11-/-. Our results suggest that the loss of Hox function results in a partial metanephric to mesonephric transformation, with tubules co-expressing markers of both proximal tubules and collecting ducts, as well as markers of mesonephric-derived epididymis tubules.

overall_design: mRNA profiles were generated by performing RNA-seq on whole kidneys at E18.5 in triplicates for Hox mutant genotypes including: 1) wild type; 2) Hoxa9,10,11-/- HoxC9,10,11+/-, 3) Hoxa9,10,11+/- HoxC9,10,11-/-, and 4) Hoxa9,10,11-/- HoxC9,10,11-/- by deep sequencing using Illumina Hi-Seq 2500

first: Steven

last: Potter


title: ERRγ coordinates a transcriptional program of mitochondrial and renal reabsorptive functions implicated in kidney disease

first: Grant

last: Barish

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

overall_design: Refer to individual Series


title: Sequential expression profile  of cortical neuron differentiation from human induced pluripotent stem cells (iPSCs) by RNA-Seq

city: Evanston

first: Jubao

last: Duan

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: We aim to profile the dynamic changes of gene expression dynamics during cortical neuron differentiation from human iPSCs. We used RNA-seq to map open chromatins in iPSCs, neural stem cells (NSCs) at day 33 and day 41.

overall_design: We assembled gene expression profiles in iPSCs derived from fibroblasts (GM01835), and iPSC-differentiated cortical neural stem cells (NSCs) at day 33 and day 41 of neural induction (designated as iN-d33 for simplicity), and neurons at day 41 (iN-d41). At each stage (iPSC, iN-d33 or iN-d41), we included two cell culture replicates. We mapped the raw FASTA file against human g1000 transcriptome and counted the RPKM value of each gene using R-based scripts.

first: Siwei

last: Zhang

first: Winton

last: Moy

first: Hanwen


title: Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance (RNA-Seq)

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: BACKGROUND: Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. To determine the dynamics of these molecular changes, we obtained high throughput omics data weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. RESULTS: An unsupervised algorithm, CoGAPS, was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically. CONCLUSIONS: Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize resistance. These genes include FGFR1, which was associated with EGFR inhibitor resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. Our findings provide a relevant towards better understanding of the time course progression of changes resulting in acquired resistance to targeted therapies. This is an important contribution to the development of alternative treatment strategies that would introduce new drugs before the resistant phenotype develops.

overall_design: RNA isolation and sequencing were performed for 23 samples including 2 replicates of parental SCC25 cetuximab sensitive cell line, generations of SCC25 cell lines treated with either cetuximab or PBS over weeks (each week of treatment labeled C1 to C11), and a set of 11 stable cetuximab resistant clones derived from SCC25. Sequencing was performed at the Johns Hopkins Medical Institutions (JHMI) Deep Sequencing & Microarray Core Facility. Total RNA was isolated from a total of 1x106 cells using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. The RNA concentration was determined by the spectrophotometer Nanodrop (Thermo Fisher Scientific, Waltham, MA) and quality was assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) system. An RNA Integrity Number (RIN) of 7.0 was considered as the minimum to be used in the subsequent steps for RNAseq. Library preparation was performed using the TrueSeq Stranded Total RNAseq Poly A1 Gold Kit (Illumina, San Diego, CA), according to manufacturer’s recommendations, followed by mRNA enrichment using poly(A) enrichment for ribosomal RNA (rRNA) removal. Sequencing was performed using the HiSeq platform (Illumina) for 2X100bp sequencing. Reads were aligned to hg19 with MapSplice16 and gene expression counts were quantified with RSEM17. Gene counts were upper-quartile normalized and log transformed for analysis following the RSEM v2 pipeline used to normalize TCGA RNA-seq data.

first: Christine

middle: H

last: Chung


title: RNA-seq analysis of murine gastric tissue from Lats1/2-knockout mice

status: Public on Apr 23 2018

city: Daejeon

first: Wonyoung

address: 291 Daehak-ro

institute: KAIST

summary: YAP and TAZ play oncogenic roles in various organs, but the role of YAP/TAZ activation in gastric cancer in vivo has been understudied. We investigated whether and how YAP/TAZ initiates gastric tumorigenesis in vivo and its significance in human gastric cancer. We studied Lats1fl/fl;Lats2fl/fl;Lgr5-CreER mice, which have activated YAP/TAZ in pyloric stem cells. Gastric tissues were collected and analyzed by histopathology and immunostaining. To scrutinize the molecular mechanisms, we performed RNA sequencing in gastric tissue samples. Tissue microarray and public transcriptome data were analyzed to investigate the importance of YAP/TAZ in human gastric cancer.

overall_design: Gastric pyloric tissue of Lats1fl/fl;Lats2fl/fl;Lgr5-CreER, or Lats1fl/fl;Lats2fl/fl mice that were 8 weeks after tamoxifen injection were collected in duplicates. RNAs were sequenced with Illumina NextSeq 500.

first: Dae-Sik

last: Lim


title: YAP/TAZ initiates gastric tumorigenesis via upregulation of MYC

type: Non-coding RNA profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: high-throughput transciptome study for rhesus macaque

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

summary: In this study, we successfully identified the causal gene underlying the phenotype of extreme high insulin level in a founder population of rhesus macaque. To further reveal the molecular mechanism, especially the effect of mutated gene on transcriptome profile, we performed paired-end, strand-specific, polyA-postive RNA-Seq in two tissues (fat and muscle) of both case and control monkeys.

overall_design: This submission represents several rhesus samples for fat and muscle tissue RNA-seq

first: Chuan-Yun

last: Li


title: Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

first: Aaron

middle: F

last: Straight

state: CA

address: 279 Campus Drive, B409A

department: Biochemistry

summary: RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

overall_design: Proximity-ligation and sequencing mapping of RNA-to-DNA contacts

first: Jason

last: Bell

first: David

last: Jukam

first: Nicole

last: Teran

first: Viviana

middle: I

last: Risca

first: Owen

middle: K

last: Smith

first: Whitney

last: Johnson

first: Jan

last: Skotheim

first: William

middle: J

last: Greenleaf


title: Long ncRNA Landscape in the Ileum of Treatment Naïve Early Onset Crohn Disease

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

summary:
Objective: Long non-coding RNAs (lncRNA) regulate gene transcription and diverse cellular functions. We previously defined a novel core inflammatory and metabolic ileal gene signature in treatment naïve pediatric Crohn Disease (CD), however, genome-wide characterization of lncRNA expression was lacking. We now extend our analyses to define a more comprehensive view that includes lncRNA.
Design: Using RNAseq, we performed a systematic profiling of lncRNAs and protein-coding genes expression in 177 ileal biopsies. Co-expression analysis was used to identify functions and tissue-specific expression. RT-PCR was used to test lncRNAs regulation by IL-1β in Caco-2 enterocytes model.
Results: We characterize a widespread dysregulation of 459 lncRNA in the ileum of treatment naïve pediatric CD patients. Unsupervised and supervised classifications using the 459 lncRNA showed comparable patients’ grouping as the 2160 dysregulated protein-coding genes, linking lncRNA to CD pathogenesis. Co-expression and functional annotation enrichment analyses across several tissues and cell types showed that the up-regulated LINC01272 is associated with a myeloid pro-inflammatory signature while the down-regulated HNF4A-AS1 exhibits association with an epithelial metabolic signature. We further validated expression and regulation of prioritized lncRNA upon IL-1β exposure in differentiated Caco-2 cells. Finally, we identified significant correlations between LINC01272 and HNF4A-AS1 expression and more severe mucosal injury.
Conclusion: We define differentially expressed lncRNA in the ileum of treatment naive pediatric CD. We show lncRNA utility to correctly classify disease or healthy states and demonstrate their regulation in response to an inflammatory signal. These lncRNA, after mechanistic exploration, may serve as potential new targets for RNA-based interventions.

overall_design: Using RNAseq, we performed a systematic profiling of lncRNAs and protein-coding genes expression in 21 days differentiated caco-2 cells

first: Y

last: Haberman

first: M

last: BenShoshan

first: P

last: Dexheimer

first: T

last: Klein

first: S

last: Halparin

first: B

last: Weiss

middle: D

last: Walters

first: R

middle: N

last: Baldassano

first: J

last: Noe

last: Markowitz

last: Rosh

middle: B

last: Heyman

first: A

middle: M

last: Griffiths

first: W

middle: V

last: Crandall

first: D

last: Mack

middle: S

last: Baker

last: Kellermayer

last: Patel

last: Otley

last: Steiner

last: Gulati

middle: L

last: Guthery

first: N

last: LeLeiko

last: Moulton

last: Kirschner

last: Snapper

last: Oliva-Hemker

last: Cohen

last: Keljo

last: Ziring

last: Aronow

last: Anikster

last: Hyams

last: Kugathasan

first: L

last: Denson


title: Long non-coding and coding RNAs characterization in Peripheral Blood Mononuclear Cells and Spinal Cord from Amyotrophic Lateral Sclerosis patients

status: Public on Apr 22 2018

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Alteration in RNA metabolism, concerning both coding and long non-coding RNAs (lncRNAs), may play an important role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we performed RNA-seq analysis to investigate, in Peripheral Blood Mononuclear Cells (PBMC) and spinal cord tissues, the regulation of non-coding and coding RNAs in Sporadic ALS patients (SALS), ALS mutated (FUS, TARDBP and SOD1) patients and matched controls. A total of 293 differentially expressed (DE) lncRNAs were found in SALS patients, as instead a limited amount of lncRNAs was found deregulated in mutated patients. Out of 87 mRNAs detected as differentially expressed in SALS patients, the 10 most differentially expressed were down-regulated and associated to transcription regulation, immunity and apoptosis pathways. 2 Taken together our data highlighted the importance, for the understanding of ALS disease, of extending the knowledge on transcriptome molecular alterations and on the significance in the disease of the classes of regulatory lncRNAs. Our data brought the light on the importance of lncRNAs and mRNAs regulation in central and peripheral systems, offering starting points for new investigations about pathogenic mechanism involved in ALS disease.

overall_design: 11 SALS sporadic patients (sla0109sals, sla0110sals, sla0210sals, sla0514sals, sla1213sals, sla1812sals, sla2014sals, sla2311sals, sla2311sals, sla2411sals, sla2710sals, sla3311sals), two FUS mutated (sla0315fus, N3912FUS), two TARDBP mutated (sla1814tardbp, sla0507tardbp), two SOD1 mutated (N17809SOD1, sla0515) were analysed with respect three healthy donors (c2, c775, c89) to detect differential expression at the level lof long-non-coding genes.

first: Stella

last: Gagliardi

first: Susanna

last: Zucca

first: Cecilia

last: Pandini

first: Luca

last: Diamanti

first: Matteo

last: Bordoni

first: Daisy

last: Sparviero

first: Maddalena

last: Arigoni

first: Martina

last: Olivero

first: Orietta

last: Pansarasa

first: Mauro

last: Ceroni

first: Cristina

last: Cereda


title: RNA-Sequencing of 2,4-D treated Brachypodium distachyon roots containing NLS

city: Conway

first: Arijit

last: Mukherjee

state: AR

address: 201 Donaghey Avenue, UCA

department: Biology

institute: University of Central Arkansas

summary: In this study we treated Brachypodium distachyon roots with synthetic auxin, 2,4-D, to induce nodule-like structures (NLS) and performed RNA-seq to assess transcriptome changes during NLS formation.

overall_design: Three biological replicates per treatment; total RNA was isolated individually from each replicate.

first: Megan

last: Bowman


title: Characterization of DCL4 missense alleles provides novel insights into its ability to process distinct classes of dsRNA substrates

city: Strasbourg

first: Patrice

last: Dunoyer

state: Alsace

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

summary: In the model plant Arabidopsis thaliana, four Dicer-like proteins (DCL1-4) mediate the production of various classes of small RNAs (sRNAs). Among these four proteins, DCL4 is by far the most versatile RNaseIII-like enzyme and previously identified dcl4 missense alleles were shown to uncouple the production of the various classes of DCL4-dependent sRNAs. Yet, little is known about the molecular mechanism pertaining this uncoupled production. Here, by studying the subcellular localization, interactome and binding to the sRNA precursors of three distinct dcl4 missense alleles, we simultaneously highlight the absolute requirement of its helicase domain for efficient production of all DCL4-dependent sRNAs, and identify an important determinant of DCL4 versatility within its PAZ domain that is mandatory for efficient processing of intramolecular foldback dsRNA precursors but dispensable for the production of siRNAs from RDR-dependent dsRNA susbtrates. This study not only provides novel insights into DCL4 mode of action in plants but also delineates interesting tools to further study the complexity of plant RNA silencing pathways.

overall_design: RNA library of immunoprecipitated RNA from Col-0 (WT), pDCL4-DCL4-6:FHA/dcl4-2 and pDCL4-DCL4-8:FHA/dcl4-2  Arabidopsis flowers or seedlings were generated by deep sequencing, using Illumina HiSeq 2500 v4.

first: Thomas

last: Montavon

first: Yerim

last: Kwon

first: Aude

last: Zimmermann

first: Philippe

last: Hammann

first: Timothée

last: Vincent

first: Valérie

last: Cognat

first: Bergdoll

last: Marc

first: Fabrice

last: Michel


title: miRNA-seq analysis of YAP5SA overexpressed gastric epithelial cells

first: Wonyoung

last: Choi

summary: To investigate whether YAP upregulates MYC via miRNA repression, we sequenced miRNAs from gastric epithelial cells (HFE-145) either expressed with vector or YAP-5SA.

overall_design: Duplicates of HFE-145 cells either expressing vector or YAP-5SA were analyzed.

first: Dae-Sik

last: Lim


title: Electrophilic stress induced by dimethyl itaconate regulates IkB-zeta-mediated inflammatory responses

status: Public on Apr 21 2018

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Interplay between metabolic state of the cell and its ability to undergo immunological activation has been recently recognized as a treasure chest of novel fundamental regulatory principles. Itaconate, and its membrane permeable derivative dimethyl itaconate (DI) were recently shown to selectively inhibit subset of cytokines during macrophage activation (e.g. Il1b, il6, Il12b but not TNF), yet the precise mechanism of this effect remained unclear. We find that selectivity of DI action stems from the inhibitory effects of electrophilic stress exerted by DI on IkB-zeta protein translation, leading to selective control of the secondary wave of Nfkb-signaling. Mechanistically, DI leads to glutathione depletion and subsequent activation of both Nrf2-dependent and Nrf2-independent stress responses. We find that IkB-zeta regulation is carried out in Nrf2-independent manner, and identify Atf3 as a key mediator of DI effects on IkB-zeta/IL6. This inhibitory effect is conserved across species and cell types, as evident from inhibition of IkB-zeta production in activating human monocytes and IL-17A stimulated keratinocytes of both human and mice. Finally, DI administration in vivo ameliorated IL17/IkB-zeta-driven skin pathology in the mouse model of psoriasis, highlighting therapeutic potential of this regulatory pathway.

overall_design: Bone marrow-derived macrophages (BMDMs) from WT and Nrf2–/– mice were derived in 7 days in MCSF supplemented complete RPMI. Some samples cells were stimulated with 250 uM DimethylItaconate(DI) for 12 hours prior to collection for RNA-seq.

first: Monika

last: Bambouskova

first: Vicky

last: Lampropoulou

first: Alexey

last: Sergushichev


title: Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning

city: Urbana

first: Erik

last: Procko

address: 601 S Goodwin Ave

institute: University of Illinois

summary: Chemokine receptors CXCR4 and CCR5 regulate white blood cell trafficking, and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine directed evolution of CXCR4 and CCR5 libraries comprising nearly all ~7,000 single amino acid substitutions with deep sequencing to define sequence-fitness landscapes for surface expression and ligand interactions. Functional interaction sites are mapped based on conservation; for example, extracellular residues are conserved for binding HIV-1-blocking antibodies, as expected. Chemokine CXCL12 interacts with residues extending asymmetrically into the CXCR4 ligand-binding cavity, and distal mutations within allosteric and G protein coupling sites are identified that enhance chemokine binding. CCR5 residues conserved for gp120 interactions partially overlap with the chemokine-binding site, and gp120 binding is increased by acidic substitutions in the CCR5 N-terminus and extracellular loops. Furthermore, general features are apparent from sequence patterns, including membrane regions that are intolerant to polar mutations, and deleterious cysteine substitutions within extracellular loops.

overall_design: Single-site saturation mutagenesis libraries were constructed of human CXCR4 and CCR5, and expressed in human Expi293F cells (a HEK293 derivative). Cells were evolved by FACS for surface expression and binding to protein ligands. Frequencies of variants in the sorted population (measured from RNA transcripts) were compared to frequencies in the DNA libraries to calculate log(base2) enrichment ratios for all amino acid substitutions.  All evolution experiments were in duplicate.

first: Jeremiah

last: Heredia


title: Prerequisite Barcoding of Cell-Type-Rpecific Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [RNA-seq]

city: La jolla

first: Hong

last: Kim

address: 9500 Gilman Dr.

institute: University of California, Sand diego

summary: While cell-type-restricted enhancers are initially detected following cooperative binding of positionally-determined DNA binding transcription factors during determination/differentiation, it remains unknown whether there are preceding events in embryonic stem cells (ESCs) that are functionally important to activate cell-type-restricted enhancer networks. Here, using murine macrophages as a model, we report that, while largely devoid of characteristic enhancer marks (H3K4me1, H3K4me2, H3K27Ac, H3K27me3 and p300) in ESCs, macrophage enhancers are activated as transcription units mainly by the binding of a single, at most two, ESC transcription factors. This provides “premarking” of these enhancers, as is also observed for other cell types. In contrast, ESC-active enhancers are cooperatively bound by multiple ESC transcription factors, including Esrrb, Nanog, Oct4 and Sox2 (ENOS). Interestingly, the strength of this signature in ESCs is functionally important for subsequent robust cell-restricted enhancer activation during macrophage differentiation events, as independently demonstrated by analysis of multiple ENOS motif–deleted macrophage-restricted enhancers. The ENOS-determined location of hydroxymethylation of the enhancers in ESCs could serve as a potential molecular memory for subsequent enhancer activation in the mature macrophage. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily “barcoded” by binding of a single ESC transcription factor in ESCs, with the strength of their binding dictating enhancer activation in mature cells.

overall_design: RNA-seq experiment was designed to understand transcription regulation in ESCs, the mutant ESC clones of Tlr1 locus generated by CRISPR/Cas9 and macrophage. The mutant clones (mutant #10, mutant #14) were deletion of 8bp Esrrb motif in Tlr1 enhancers, and no deletion in WT


title: The role of AR associated protein and lncRNA in androgen signaling

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed RNA sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Long term androgen deprivation (LTAD) to explore the differences of androgen signaling in prostate cancer progression. We analyzed the role of PSF, CTBP1-AS and COBLL1 which we identified as regulators of androgen signaling.

overall_design: RNA sequence analysis of androgen-regulated genes in two prostate cancer cells


title: TLR4 deficiency reduces inflammatory signaling by reprogramming macrophage lipid metabolism

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

institute: Garvan Institute of Medical Research

summary: Chronic inflammation is a hallmark of obesity and is linked to the development of numerous diseases. The activation of toll-like receptor 4 (TLR4) by long-chain saturated fatty acids (lcSFAs) is an important process in understanding how obesity initiates inflammation. While experimental evidence supports an important role for TLR4 in obesity-induced inflammation in vivo, via a mechanism thought to involve direct binding to and activation of TLR4 by lcSFAs, several lines of evidence argue against lcSFAs being direct TLR4 agonists. Using multiple orthogonal approaches, we herein provide evidence that while loss-of-function models confirm that TLR4 does, indeed, regulate lcSFA-induced inflammation, TLR4 is not a receptor for lcSFAs. Rather, we show that TLR4-dependent priming alters gene expression, lipid metabolic pathways, and membrane lipid composition, which are necessary for lcSFA-induced inflammation. These results reconcile previous discordant observations and challenge the prevailing view of TLR4's role in initiating obesity-induced inflammation.

overall_design: Comparison of BMDM from WT and Tlr4-/- mice that were either untreated, collected after 6h of pre-treatment in media containing 5% FBS and 2% BSA, or were pre-treated in media containing Poly(I:C).

first: Mark

last: Febbraio

first: Graeme

last: Lancaster


title: Single cell transcriptomics reveal an essential role for Hippo signaling in cell state transitions during cardiac fibroblast development

city: Houston

first: Yang

last: Xiao

state: Texas

address: One Baylor Plaza,  Room 509E, Baylor College of Medicine, Department of Molecular Physiology

institute: Baylor College of Medicine

summary: We use single cell RNA-sequencing (Drop-seq) to profile cardiac cells (excluded atria) from control (Wt1 CreERT2/+; Rosa26mTmG/+) and epicardial-deficient Lats1/2 kinase embryonic hearts (Wt1 CreERT2/+; Lats1/2 F/F; Rosa26mTmG/+) at E13.5 and E14.5.  Each experimental group includes cells sampled from four embryonic hearts.

overall_design: Drop-seq of e13.4 and e14.5 Control and Wt1-CreER; Lats1/2 fl/fl cardiac tissue.

first: Xiao

last: Yang

first: Matthew

middle: C

last: Hill

first: James

last: Martin


title: Altered Neocortical Gene Expression, Brain Overgrowth and Functional Over-Connectivity in Chd8 Haploinsufficient Mice

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

institute: King's College London

summary: Truncating CHD8 mutations are amongst the highest confidence risk factors for autism spectrum disorders (ASD) identified to date. Here, we report that Chd8 heterozygous mice display increased brain size, motor delay, hypertelorism, pronounced hypoactivity, and anomalous responses to social stimuli. Whereas gene expression in the neocortex is only mildly affected at mid gestation, over 600 genes are differentially expressed in the early postnatal neocortex. Genes involved in cell adhesion and axon guidance are particularly prominent amongst the downregulated transcripts. Resting-state functional MRI identified increased synchronized activity in corticohippocampal and auditory-parietal networks in Chd8 heterozygous mutant mice, implicating altered connectivity as a potential mechanism underlying the behavioral phenotypes. Together, these data suggest that altered brain growth and diminished expression of important neurodevelopmental genes that regulate long-range brain wiring are followed by distinctive anomalies in functional brain connectivity in Chd8 +/− mice. Human imaging studies have reported altered functional connectivity in ASD patients, with long-range under-connectivity seemingly more frequent. Our data suggest that CHD8 haploinsufficiency represents a specific subtype of ASD where neuropsychiatric symptoms are underpinned by long-range over-connectivity.

overall_design: RNA was isolated from microdissected cortices at E12.5 (both hemispheres) and P5 (one hemisphere and DNase-treated using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer?s instructions (n = 3 per experimental group). cDNA was end-repaired, adaptor-ligated, and A-tailed. Samples were sequenced over 2 lanes of the Illumina HiSEq 4000 platform.

first: Philipp

last: Suetterlin

first: Shaun

last: Hurley

first: Conor

last: Mohan

first: Kimberley

last: Riegman

first: Marco

last: Pagani

first: Angela

last: Caruso

first: Jacob

last: Ellegood

first: Alberto

last: Galbusera

first: Ivan

last: Crespo-Enriquez

first: Caterina

last: Michetti

first: Yohan

last: Yee

first: Robert

last: Ellingford

first: Olivier

last: Brock

first: Alessio

last: Delogu

first: Philippa

last: Francis-West

first: Jason

middle: P

last: Lerch

first: Maria

last: Scattoni

first: Alessandro

last: Gozzi

first: Cathy

last: Fernandes


title: Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere sequestration

city: Geneva

first: Lukas

last: Hafner

state: Geneva

address: 30 quai Ernest-Ansermet

department: Molecular Biology

institute: University of Geneva

summary: The budding yeast telomere binding protein Rif1 (Rap1-interacting factor 1) plays an evolutionarily conserved role in the control of DNA replication timing, which operates through an interaction with the PP1 phosphatase. Rif1-PP1 has been proposed to inhibit origin firing by reversing the phosphorylation of key targets involved in replication initiation. However, it is not yet known if Rif1 binds directly to the replication origins that it controls. Here we show that in unperturbed yeast cells Rif1 primarily regulates late-replicating telomere-proximal origins. Using Chromatin Endogenous Cleavage (ChEC)-seq, we find that Rif1 is robustly detected at many late-replicating origins that we identify as targets of its inhibitory action. Abrogation of Rif1 telomere binding, through mutation of its Rap1 binding module, leads to increased Rif1 binding and late origin inhibition elsewhere in the genome. Our results support a model whereby Rif1 inhibits replication initiation by binding directly at origins, most of which are near telomeres, where Rif1 is concentrated through its interaction with telomere-bound Rap1 protein.

overall_design: DNA replication timing was studied using leading strand polymerase Chromatin Immunoprecipitation seq (ChIP-seq) in cells released from an alpha factor block (G1 block) at different timepoints and quantitative sequencing of asynchronous FACS sorted S-phase cells (sort-seq). Protein binding of Rif1 was evaluated by Chromatin endonuclease cleavage seq (ChEC-seq)

first: Aleksandra

last: Lezaja

first: Laure

last: Lemmens

first: Maksym

last: Shyian

first: Benjamin

last: Albert

first: Cindy

last: Follonier

first: Jose

last: Nunes

first: Massimo

last: Lopes

first: David

last: Shore

first: Stefano

last: Mattarocci

first: Xu

last: Zhang


title: mitoCPR  - a surveillance pathway that protects mitochondria in response to mitochondrial import stress

status: Public on Apr 20 2018

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Mitochondrial functions are essential for cell viability and rely on protein import into the organelle. Various disease and stress conditions can lead to mitochondrial import defects. We find that inhibition of mitochondrial import in budding yeast activates a surveillance mechanism, mitoCPR, that is aimed at ameliorating mitochondrial import and protecting mitochondria during import stress. mitoCPR induces expression of Cis1 which associates with the mitochondrial translocase to reduce the accumulation of mitochondrial precursor proteins at the organelle surface. Clearance of precursor proteins depends on the Cis1 interacting AAA+ ATPase Msp1 and the proteasome suggesting that Cis1 facilitates degradation of un-imported proteins at the mitochondrial surface.

overall_design: Five replicates of Empty Vector controls, six replicates of PSD1 overexpressors, six replicates of  PSD1 overexpressors harboring a PDR3 deletion and five replicates of V5-PSD1 overexpressors.

first: Hilla

last: Weidberg

first: Angelika

last: Amon


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [MeDIP-Seq]

first: Hong

last: Kim

overall_design: MeDIP experiments were designed to study epigenetic signature in ESC


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [ATAC-Seq]

overall_design: ATAC experiments were designed to understand the chromatin openness in ESC and macrophage


title: Functional co-operativity of long-noncoding RNAs at the neuroblastoma susceptibility locus 6p22.3 controls disease progression via USP36-CHD7-SOX9 gene regulatory axis.

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

summary: We report 6p22 locus lncRNAs, which were identified as differentially expressed between high and non-high risk neuroblastoma  tumors using RNA sequencing. we identified CASC15-003 and CASC15-004 lncRNAs act as prognostic biomarker in neuroblastoma.

overall_design: Functional characterization for CASC15-003 and CASC15-004 lncRNAs was done using knockdown strategies followed by RNA-seq

first: Chandrasekhar

last: Kanduri

first: Tanmoy

last: Mondal

first: Prasanna

last: Juvvana

middle: T

last: Kosalai


title: RNA Sequencing of adult high grade glioblastoma tumors

city: New York

first: Richard

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU School of Medicine

summary: RNA extracted from fresh frozen adult high grade glioblastomas were sequenced for transcriptomic analysis.

overall_design: Fresh frozen glioblastoma human primary tumor samples (24 IDH WT glioblastomas, Age: Min = 29, Max = 84, median = 65; 12 Male, 12 Female)

first: Matija

last: Snuderl

first: Kivanc

last: Birsoy


title: RNA-seq analysis of alternative splicing between two Arabidopsis accessions and its inheritance in hybrid

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: To uncover the possible regulatory mechanism in regulatory alternative splicing in plants evolution, we used RNA-seq to compare the transcriptomes in Arabidopsis ecotypes Col and C24. We found different class of AS types have different regulatory mechanisms in Arabidopsis and divergence of alternative splicing in different class is varied in evolution. Sequence variation analysis had found evolution divergent AS events significantly altered their sequences compared to conserved events and the variation is AS class specific.

overall_design: RNA-seq analysis of alternative splicing in the shoots of 14 day old seedlings of two Arabidopsis(Col and C24) and their reciprocal hybrids (Col x C24 and C24 x Col).

first: Mei

last: Yang

first: Guangming

last: He

first: Xingwang

last: Deng


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [4C-Seq]

overall_design: 4C-Seq experiments were designed to examine the physycal interaction between premarked putative macrophage enhancer and cognate promoter


title: Comparative transcriptome of Neurospora crassa strains

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We utilised high-throughput genomic approache to investigate transcriptional changes in two Neurospora strains (74A [wild-type] and mutant Δmus-52), under different phosphate availability conditions to evaluate the effects of mus-52 deletion in gene transcriptional modulation, and thus, infer its influence regarding metabolic response to changing extracellular levels of inorganic phosphate (Pi).
Methods: All N. crassa strains were maintained on Vogel’s minimal medium, pH 5.8, at 30°C. Conidia from each strain were germinated for 5 h at 30°C in an orbital shaker (200 rpm), in low-Pi (10µM) and high-Pi (10mM) media. Total RNA was isolated from both strains and a total of 4 cDNA libraries were sequenced, with their respective biological triplicates corresponding to the paired libraries, using an Illumina HiSeq2000 sequencer, to generate 100 bp paired-end reads. FastQC software was used to visualize the library quality before and after trimming. For quality and sequence filtering, a Phred score lower than 20 was employed to remove sequencing bases from the read ends. Filtered reads were mapped onto the N. crassa genome using Bowtie2 software. The reads count values were obtained and used to calculate the expression variation of the transcripts from different conditions, considering the statistical significance of the differential gene expression. qRT–PCR validation was performed using SYBR Green assays.
Results: extracellular Pi availability influenced the expression of genes involved in several biological functions. The main affected gene groups were those associated with integral components of the membrane, such as transport, regulation, and cell signalling pathways, as well as genes involved with the nucleolus and protein synthesis. The absence of mus-52 affected global gene transcription in all conditions tested, highlighting the expression of some specific gene groups, such as transcription factors, kinase proteins, circadian clock-related genes, oxi-reduction balance, phosphate pathways, and general metabolism.
Conclusions: The consequences of N. crassa mus-52 disruption to the cell may be deeper than the obvious phenotypic aspect. It may affect canonical and non-canonical pathways, leading to alternative adaptive processes, altering the perception and response to the environmental changes.

overall_design: Transcriptional profile of N. crassa strains using RNA-sequencing technique to evaluate the effects of mus-52 deletion in gene transcriptional modulation, and thus, infer its influence regarding metabolic response to changing extracellular levels of inorganic phosphate.

first: Maíra

last: Martins

first: Eriston

last: Gomes

middle: R

first: Wellington

last: Pedersoli

first: Nilce

last: Martinez-Rossi

first: Antonio

last: Rossi


title: Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [Pro-cap]

first: Hong

last: Kim

overall_design: Pro-cap experiment was designed to understand transcription unit in ESC and macrophage.


title: Gene expression profiling study by RNA-seq for identifying gene signatures associated with castration-refractory prostate cancer (CRPC) development.

city: Daejeon

first: Seon-Kyu

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to identify gene signature associated with castration-refractory prostate cancer (CRPC) development. We carried out RNA-seq based transcriptome profiling using 45 prostate samples with various disease progression steps such as benign prostate hyperplasia (BPH), primary cancer of prostate (CaP), advanced CaP and CRPC. Via various statistical analyses, we identified significant gene set associated with each progression step and observed that AR was the only gene feature associated with all progression steps, indicating that AR is the crucial mediator of and has a diverse activity across the CaP progressions. Among the samples in this data set, there are 4 pairs of advanced CaP and CRPC samples, in which each pair was obtained from the same patient. Using these paired samples, we also determined differentially expressed genes between advanced CaP and CRPC, and performed comparative analysis of significant gene lists in matched sample pairs and in unpaired remained samples. By assessing expression difference between advanced CaP and CRPC groups, 309 and 182 genes were statistically significant in paired and unpaired samples, respectively (P < 0.001). When these two gene lists were compared, a total of 15 genes were common and applied to a number of downstream experimental assays.

overall_design: RNA-seq data of 45 CRPC samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).

first: Jeong-Hwan

first: Seon-Young

first: Seok-Joong

last: Yun

first: Wun-Jae


title: A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection [Berry_London]

status: Public on Apr 19 2018

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases.

overall_design:
We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.

All samples in this series were re-analyzed from GSE19444. There are links on each sample page to the original sample.

first: Raman

last: Verma

first: Christine

last: Graham

first: Jo

last: Lee

first: Tran

last: Trang

first: Matthew

last: Richardson

first: Patrick

last: Lecine

first: Philippe

last: Leissner

last: Berry

first: Robert

last: Wilkinson

first: Karine

last: Kaiser

first: Marc

last: Rodrigue

first: Gerrit

last: Woltmann

first: Pranabashis

last: Haldar

first: Anne

last: O'Garra


title: Differentially Expressed Genes upon Knockdown of ZRANB1 or EZH2 in LM2 Cells

status: Public on Apr 18 2018

first: Li

last: Ma

state: TX

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

summary: EZH2, the catalytic component of the Polycomb repressive complex 2 (PRC2), silences gene transcription by methylating histone H3 at lysine 27. Recently we identified ZRANB1 as the EZH2 deubiquitinase. ZRANB1 binds, deubiquitinates, and stabilizes EZH2. To determine whether ZRANB1 is a functional regulator of EZH2, we performed RNA-Seq analysis to compare the effect of ZRANB1 knockdown or EZH2 knockdown on global gene expression.

overall_design: mRNA profiles of control, ZRANB1 knockown, or EZH2 knockdown LM2 cells were generated from triplicate samples using RNA-Seq

first: Peijing

last: Zhang

first: Zhenna

last: Xiao

first: Mutian

first: Minjung

first: Jia

last: Li

first: Yun

last: Huang

first: Deqiang

last: Sun