title: RNA-SEQ of wheat Jing411

status: Public on Aug 07 2019

city: Baoding

first: KE

last: XU

state: Hebei

institute: Hebei agricultural university

summary: Exposure to cold conditions is a major abiotic stress affecting crop growth and productivity. Elucidation of genetic mechanisms underlying response to low temperature is needed. To assess the relationship between the genes and the cold tolerance of wheat, transcriptomics analyses were performed to study changes in gene  profiles of cultivar Jing 411 after cold acclimation and freezing treatment. The wheat cultivar Jing 411 was subjected to transcriptome sequencing. The RNA was sequenced on a HiSeq 2500 platform, and the generated data were analyzed using TopHat v2.0.

overall_design: Four treatment (cold acclimation:LTA, unacclimation:NTG, acclimation and freezing:LTAF and unacclimation and freezing: NTGF) and each treatment for three biological replicates

first: Yong

last: Zhao

first: Ke

last: Xu


title: Cancer-related gene expression analysis after treatment of prostate cancer cells with exercise-conditioned serum from advanced-stage prostate cancer patients after a 12-week WB-EMS training

status: Public on Aug 08 2019

city: Erlangen

first: Yurdagül

last: Zopf

address: Ulmenweg 18

department: Medicine 1

country: Germany

institute: University Clinic Erlangen

summary: We treated the prostate tumor cell line LNCaP with serum from prostate cancer patients that participated in a 12-week physical exercise and nutrional study. Exercise was conducted in form of whole-body electromyostimulation (WB-EMS). All patients from the control and the intervention group received nutritional counseling to achieve high-protein dietary intake (please refer to Schink, Herrmann et al, 2018; PMID: 30208857). Serum from all patients was taken at study entry and at the end of the intervention in week 12. Additionally, human primary skeletal muscle cells were treated with electric pulse stimulation to simulate in vitro exercise. EPS-conditioned medium was then also used to incubate prostate tumor cells. Treatment with either study patient serum or conditioned myotube medium was done for 24 h and for 72 h. Total RNA was isolated and cancer-related gene expression was analyzed using Nanostring technology.

overall_design: In the study presented here, we analyzed the cancer-related gene expression profile of LNCaP cells after the incubation with serum pools from 8 WB-EMS or 6 control patients; also, EPS-conditioned myotube medium (pool from 3 independent stimulations) was used.

first: Raphaela

last: Schwappacher


title: Expression data from Knockdown of ILF3 in DLD1 cell line

city: 广州

first: Kai

last: Li

state: 广东

address: 员村二横路26号

department: Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease

country: China

institute: Sun Yat-sen University

summary:
Colorectal cancer malignant progression depends on the aberrant oncogenic expressions. During tumorigenesis, the oncogeneic genes mutation or expression, following specific sets of genes are up-regulated or down-regulated. Some of them, for instance, control metabolism reprogramming to promote tumor growth and maliganant progression.
We used microarrays to detail the global programme of gene expression regulated by ILF3, which is overexpressed in colorectal cancer.

overall_design: Colorectal cancer cell line DLD1 with ILF3 high expression was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression profiles regulated by ILF3 in Colorectal cancer cell. To that end, we transfected DLD1 cells with scramble RNA (NC, negative control) and sh-ILF3 (shRNA-31).

first: Mong-Hong

last: Lee


title: Neural progenitor cells mediated by histone variant H2A.Z.2 regulate microglia development in the embryonic brain

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study are to compare the different transcripts between H2A.Z.2 knockout in NPCs and WT E16.5 cerebral brain tissue.

overall_design: Methods:  Total RNA was extracted from E16.5 cortical tissue of H2A.Z.2 cKO and WT mice.Then RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Significantly differentially expressed genes were identified when we compared Normalized Reads Count between groups with p < 0.05 and |Log2FoldChange| > 1.

first: Zhongqiu


title: Analysis of globle gene expression changes observed in fibroblasts isolated via explant outgrowth and 45-minute differential binding

city: Philadelphia

first: Michael

last: Beers

state: PA

address: 3450 Hamilton Walk

country: USA

institute: University of Pennsylvania

summary: Fibroblasts are a ubiquitous cell type that are found in many tissue types and are associated  with a variety of diseases including most fibrotic disorders.  We isolated fibroblast cells using explant outgrowth methodologies and compare the genomic signature of these cells to cells isolated using 45-minute differential binding.

overall_design: 14 total pulmonary fibroblast samples were used in this study. These fibroblasts were isolated from 4 lungs with end-stage idiopathic pulmonary fibrosis and 3 normal donors  lungs (controls) designated brain dead, non-diseased but not suitable for transplantation.  8 IPF samples included 4 isolated via explant outgrowth and 4 isolated via 45 minute differential binding .  Three normal samples included 3 isolated via explant outgrowth and 3 isolated via 45 minute differential binding.  RNA extraction was carried out using Qiagen RNeasy Kit.  Experimental/control samples were amplified amino-allylated RNA labeled with Cy5 and Stratagene Reference RNA was amplified and amino-allylated and labeled with Cy3.  One round of amplification was carried out using Ambion MessageAmp II kit with amino-allylated UTP according to the protocol of the Duke University Institute for Genome Sciences and Policy.  Amplification and amino-allylation of the Stratagene Reference RNA and Hybridization of Reference with all samples were carried out by the Duke Institute for Genomic Sciences and Policy.

first: Rebecca

middle: T

last: Beuschel

first: Jorge

middle: F

last: Davilla

first: Sarah

middle: N

last: Bui

first: Edwinia

last: Battle

first: Merte

last: Lemma

first: Luis

middle: R

last: Rodriguez

first: Steven

middle: D

last: Nathan

first: Geraldine

middle: M

last: Grant


title: Colorectal cancer cell lines with SETDB1 depletion [RNA-seq]

city: Daejeon

first: Soobeom

state: Daejeon

address: E16, 709, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We performed RNA sequencing analysis of three colorectal cancer cell lines (Caco2, HCT116, SW480) with SETDB1 knockdown. Samples were obtained after flow cytometry sorting according to KRT20 expression level.

overall_design: Examination of three colorectal cancer cell lines upon SETDB1 downregulation

first: Kwang-Hyun

last: Cho


title: Colorectal cancer cell lines basal expression [microarray]

summary: We performed microarray analysis of four colorectal cancer cell lines (Caco2, HCT116, SW480, and SW620).


title: PNET animal model: new insights (II)

city: Chicago

first: Yingtao

last: Bi

state: IL

address: 750 North Lake shore drive

institute: Northwestern University

summary: We studied our CNS-PNET animal model to get new insights on the onset of tumor formation

overall_design: RNA-seq of tumors from CNS-PNET animal model

first: Sergey

last: Malchenko


title: Locally renewing resident synovial macrophages provide a protective barrier for the joint [scRNA-seq]

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

summary: Macrophages (MΦs) are considered to contribute to chronic inflammatory diseases such as rheumatoid arthritis 1. However, both the exact origin and role of MΦs during inflammatory joint disease remain unclear. Here, we used multiple fate-mapping approaches in conjunction with 3D-light-sheet fluorescence microscopy and single cell RNA sequencing to perform a comprehensive spatiotemporal analysis of the composition, origin and differentiation of MΦ subsets within the healthy and inflamed joint and subsequently studied their roles during arthritis. This approach revealed dynamic membrane-like structures consisting of a distinct population of CX3CR1+ tissue-resident MΦs that formed an internal immunological barrier at the synovial lining and physically secluded the joint. Barrier-forming MΦs displayed features otherwise typical of epithelial cells, and maintained their numbers through a pool of locally proliferating CX3CR1- mononuclear cells embedded into the synovial tissue. Unlike recruited monocyte-derived MΦs, which actively contributed to joint inflammation, such epithelial-like CX3CR1+ lining MΦs restricted the inflammatory reaction by providing a tight junction-mediated shield for intra-articular structures. Our data thus reveal an unexpected functional diversification among synovial MΦs and have important implications for the general role of MΦs in health and disease

overall_design: mRNA profiles of sorted CD45+ CD11b+ mononuclear cells of synovial tissue of mice at steady state and day 1, day 2 and day 5 post arthritogenic K/BxN serum transfer serum transfer were generated by single cell sequencing using Illumina HiSeq 2500 sequencer.

first: Gerhard

last: Kroenke

first: Stephan

last: Culemann

first: Anika

last: Klingberg

first: Arif

middle: B

last: Ekici


title: The luh-4 mutant has a differential transcriptional program in response to Al stress

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

summary: To investigate how LUH regulates Al binding to cell-wall and thus inhibition of root growth under Al stress, a transcriptional analysis through RNAseq was performed by comparing the luh-4 mutant and WT plants in the presence or absence of Al. In WT plants, 316 and 336 genes, respectively, were up- and down-regulated at least 2-fold, while in luh-4, 239 and 305 genes, respectively, were up- and down-regulated at least 2-fold by Al stress. By comparison with WT seedlings, we found that 103 and 38 genes, respectively, were up- and down-regulated at least 2-fold in the non-stressed luh-4 mutant, while 77 and 33 genes, respectively, were up- and down-regulated at least 2-fold in Al-subjected luh-4 roots.

overall_design: Total RNA obtained from control (non-treated roots) and Al-exposed roots. Six day old plants were treated with and without Al treatment for 4 h, then total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN), and then Illumina sequencing was performed.

first: Xiaoyu

last: Geng

first: Zhaojun

last: Ding


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

city: Aoba-ku Seiryo

first: Tetsuya

last: Akiyama

state: Sendai Miyagi

department: Neurology

country: Japan

institute: Tohoku university

summary:
Transcriptome analysis of partially degraded and fragmented RNA samples from hiPSCs-derived MNs with Venus or Fos-B + Venus expression by lentivirus infection
Fos-B could had a function on axon branching with hiPSCs-derived MNs. However, the grobal profiling under Fos-B expression was not fully elucidated. Thus, we constructed Venus or Fos-B + Venus expression lentivirus and subsequently infected those virus to hiPSCs-derived MNs. Increasing number of axon branching was detected with Fos-B expression MNs, and we demonstrated the pathological confirmation of true exon level expression profiling approach with Fos-B expressed MNs.

overall_design: We analyzed hiPSCs-derived MNs with Venus or Fos-B + Venus expressing lentivirus infection each from 3 baches using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Naoki

last: Suzuki

first: Masashi

last: Aoki


title: RNA 5-methylcytosine facilitates maternal-to-zygotic transition through preventing maternal RNA decay

first: Bao-Fa

last: Sun

address: Da-Tun Road

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

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: m5C profiles in zebrafish embryo sample.

summary: Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 μl nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Examination of m5C levels in zebrafish embryo.

first: Ying

first: Wenlan

first: Xiao

last: Han

first: Baofa

first: Yuigui


title: Analysis of in vivo (MOG/CFA) activated 2D2 T cells  in presence or absence of NIK

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center Mainz

summary: Goal of this study was to compare transcriptional changes of in vivo (MOG/CFA) activated 2D2 T cells in the absence or presence of NIK

overall_design: Mixed BMCs consisting 50% of CD90.1hom 2D2NIKflfl BM and 50% of CD90.1/2+ 2D2NIK∆T BM were immunized with MOG/CFA and cells from dLN were sorted four days later for live Vβ11+CD4+CD90.1+ (2D2 NIKflfl) or Vβ11+CD4+CD90.1+CD90.2+ (2D2 NIK∆T) cells. RNA was isolated from cells and mRNA profiles were generated by deep sequencing using Illumina MiSeq.

first: Sonja

last: Lacher

first: Matthias

last: Klein


title: Transcriptomics analysis of gene expression in wide type, ybx1 MO, pabpc1a MO zebrafish embryo sample.

summary: The maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic-driven programing. However, how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) in zebrafish early embryos, we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box-binding protein 1 (Ybx1) prefers to recognizing m5C-modified mRNAs through p-p interaction with a key residue Trp45 in its cold shock domain (CSD), which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation-regulated maternal mRNA stability during zebrafish MZT, highlighting the critical role of m5C mRNA methylation in early development.

overall_design:
Examination of [1] gene expressive levels in wide type and ybx1 MO zebrafish embryo [2] gene expressive levels in pabpc1a MO zebrafish embryo [3] mRNA lifetime in wide type zebrafish embryo.

Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol Reagent (Ambion). mRNA was extracted with using Dynabeads mRNA Purification Kit (Ambion) and subjected to TURBO DNase (Invitrogen) treatment at 37C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

Synchronously developing embryos were treated with 0.2 ng of Pol II inhibition alpha-amanitin (Sigma) at one-cell stage and were collected at indicated time points. 100 embryos were collected for each time point in duplicates. The total RNA was extracted by Trizol (Invitrogen) and used for RNA-Seq. An equal amount of external RNA control consortium (ERCC) RNA spike-in control (Thermo Fisher) was added to the total RNA samples as internal controls. The RNA was subjected to ribosomal RNA depletion with Ribo-Zero rRNA Removal Kit (Illumina) followed by library construction using NEB Next® Ultra? RNA library Prep Kit (NEB). RNA stability profiling was generated from two biological replicates.


title: Translatome and transcriptome analysis of resting B and T cells from mice

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

country: India

institute: National Institute of Immunology

summary: We isolated ex vivo resting state B and T lymphocytes from B6 mouse spleen using magnetic separation (Miltenyi). After 2 hours of rest in RPMI mediaum, these cells were either used to isolate total RNA for RNAseq library preparation or treated with cycloheximide and proceeded with RNase digestion and library preparation for ribosome profiling (Riboseq).

overall_design: RNAseq and Riboseq for resting state total B and T cells.

first: G

middle: A

first: Gagan

last: Dev


title: Genome wide SMC1A-mediated chromatin looping changes (HiChIP) in TAE684-sensitive, resistant, resistant shBORIS and resistant shGFP Kelly cells.

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed SMC1A-mediated HiChIP analysis in sensitive, resistant, resistant shBORIS and resistant shGFP Kelly cells.

overall_design: SMC1A HiChIP data from sensitive, resistant, resistant shBORIS and resistant shGFP Kelly cells were generated by deep sequencing using Illumina HiSeq 2500.

first: David

last: Debruyne

first: Rani

last: George


title: Ybx1 binding sites and Ybx1-binding m5C sites in zebrafish embryo sample.

overall_design:
Examination of Ybx1 binding sites, and Ybx1-binding m5C sites in zebrafish embryo.

RIP-seq: Briefly, 500 zebrafish embryos at shield stage (4 hpf) were resuspended with 2 ml lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 0.4 U/Î¼l RNasin) by rotating at 4Â°C for 30 min and centrifuged at 15,000 g for 15 min. The supernatant was collected and pre-cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre-cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti-Ybx1 antibody (prepared by AbMax, China) and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. After washing with1 ml ice-cold NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 0.4U/Âµl RNasin) for eight times and once with 1ml ice-cold 1Ã— PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA , 0.2% SDS), the beads was treated in 200 ul PK buffer containing 20 ul proteinase K (Roche, 0311582001) for 1 h at 55Â°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 (pH4.3~4.7) and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase (Invitrogen, AM2238).

iCLIP-seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 (Stratalinker 2400, Stratagene), lysed and subjected to mild fragmentation. Crosslinked RNA-protein complexes were immunoprecipated using polyclonal Ybx1 antibody (Abmax) and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA-Seq kit (Takara). All the libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 150 bp.

RNA-RIP-BisSeq: Briefly, 500 zebrafish embryos at shield stage (4 hpf) were resuspended with 2 ml lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 0.4 U/Î¼l RNasin) by rotating at 4Â°C for 30 min and centrifuged at 15,000 g for 15 min. The supernatant was collected and pre-cleared with protein A Dynabeads by rotation at 4Â°C for 1 h. 50 Î¼l pre-cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti-Ybx1 antibody (prepared by AbMax, China) and 30 Î¼l Protein A Dynabeads for 4 h at 4Â°C or overnight. After washing with1 ml ice-cold NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 0.4U/Âµl RNasin) for eight times and once with 1ml ice-cold 1Ã— PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA , 0.2% SDS), the beads was treated in 200 ul PK buffer containing 20 ul proteinase K (Roche, 0311582001) for 1 h at 55Â°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 (pH4.3~4.7) and ethanol precipitation. The purified mRNA was used for RNA-BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 (Dhfr mRNA serves as methylation conversion control) was fragmented to ~100-nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent (Ambion), then stopped by 10× RNA stop solution (Ambion), and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution (pH 5.1), which is a 100:1 mixture of 40% sodium bisulfite (Sigma) and 600 µM hydroquinone (Sigma) and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns (PALL Corporation) with centrifugation. After washed with nuclease-free water and centrifuged for five times, the RNA was finally disolved in 75 ?l nuclease-free water and then desulfonated by incubation with an equal volume of 1 M Tris-HCl (pH 9.0) at 75 °C for 1 h. After ethanol precipitation, the RNA was resuspended in 11 µl of RNase-free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase (Invitrogen) and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.


title: Effects of olfactory-specific Bcl11b overexpression on gene expression in the main olfactory epithelium of neonatal mice.

city: Yokohama

first: Junji

last: Hirota

state: Kanagawa

address: 4259-B63, Nagatsuta-cho

department: Center for Biological Resources and Informatics

institute: Tokyo Institute of Technology

summary: Individual olfactory sensory neurons (OSNs) express a single odorant receptor (OR) gene from the class I or class II repertoire in mice. The mechanisms that regulate the binary fate specification of OSNs remain unknown. Here we show that the transcription factor Bcl11b, which is expressed in class II OSNs determines the OR class to be expressed in OSNs. Genetic studies provide evidence that class I is a default-fate and Bcl11b permits a class II fate by suppressing a class I-OR enhancer. These findings reveal a unique transcriptional mechanism that serves as a binary switch to select the OR class and is crucial to both the anatomical and functional organization of olfactory system.

overall_design: The mRNA profiles in the main olfactory epithelium (MOE) of neonatal Control and Bcl11b-overexpressing Tg mice were generated by deep sequencing, using an Illumina MiSeq sequencer

first: Takayuki

last: Enomoto

first: Rei

last: Kajitani

first: Takehiko

last: Itoh


title: Locally renewing resident synovial macrophages provide a protective barrier for the joint [RNA-seq]

first: Philipp

last: Kirchner

summary: Macrophages (MΦs) are considered to contribute to chronic inflammatory diseases such as rheumatoid arthritis 1. However, both the exact origin and role of MΦs during inflammatory joint disease remain unclear. Here, we used multiple fate-mapping approaches in conjunction with 3D-light-sheet fluorescence microscopy and single cell RNA sequencing to perform a comprehensive spatiotemporal analysis of the composition, origin and differentiation of MΦ subsets within the healthy and inflamed joint and subsequently studied their roles during arthritis. This approach revealed dynamic membrane-like structures consisting of a distinct population of CX3CR1+ tissue-resident MΦs that formed an internal immunological barrier at the synovial lining and physically secluded the joint. Barrier-forming MΦs displayed features otherwise typical of epithelial cells, and maintained their numbers through a pool of locally proliferating CX3CR1- mononuclear cells embedded into the synovial tissue. Unlike recruited monocyte-derived MΦs, which actively contributed to joint inflammation, such epithelial-like CX3CR1+ lining MΦs restricted the inflammatory reaction by providing a tight junction-mediated shield for intra-articular structures. Our data thus reveal an unexpected functional diversification among synovial MΦs and have important implications for the general role of MΦs in health and disease.

overall_design: mRNA profiles of sorted GFP+ lining macrophages and GFP- interstitial macrophages of healthy Cx3cr1-GFP mice and in vitro differentiated bone marrow-derived macrophages (BMDM) were generated by bulk RNA sequencing, in triplicate.

first: Gerhard

last: Krönke

first: Stephan

last: Culemann

first: Anika

last: Klingberg

first: Fulvia

last: Ferrazzi

first: Arif

last: Ekici


title: Impact of heavy atmospheric pollution on the transcriptome of Escherichia coli BW25113 and the adapted E. coli strain T56-1

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

summary: Expression profile of E. coli BW25113 grown under standard laboratory atmosphere with a fine particulate matter (PM2.5) concentration of 17 mg m-3, under urban polluted atmosphere with a PM2.5 of 230 mg m-3 or under diesel exhaust atmosphere with a PM2.5 of 613 mg m-3. Expression profile of the diesel exhaust atmosphere-adapted E. coli strain T56-1 grown under diesel exhaust atmosphere.

overall_design: Illumina RNA-seq of total RNA extracted from E. coli BW25113 grown in M9-glucose medium under standard laboratory atmosphere, under urban polluted atmosphere or under diesel exhaust atmosphere. Illumina RNA-seq of total RNA extracted from a E. coli strain (T56-1) evolved by adaptive laboratory evolution to grow faster in M9-glucose medium under diesel exhaust atmosphere. The adapted strain was transferred 56 times and Total RNA was extracted from T56-1 growing under diesel exhaust atmosphere.

first: Xiaochen

last: Shi

first: Tian

last: Zhang


title: Single-cell transcriptomic profiling of TAE684-sensitive, intermediate resistant and fully resistant Kelly cells.

summary: We performed single-cell RNA-seq analysis in TAE684-sensitive, intermediate resistant and fully resistant Kelly cells.

overall_design: Single-cell RNA-sequencing libraries of TAE684-sensitive, intermediate resistant and fully resistant Kelly cells using 10x Genomics technology.


title: Genome wide SMC1-mediated chromatin looping changes in shBORIS and shLUC resistant Kelly cells.

summary: We performed SMC1-mediated ChIA-PET analysis in both shBORIS and shLUC resistant Kelly cells.

overall_design: SMC1 ChIA-PET data from shBORIS and shLUC resistant Kelly cells were generated by deep sequencing using Illumina HiSeq 2000.

first: Daniel

last: Day


title: Global gene expression analysis in shBORIS and shLUC resistant Kelly cells.

first: Ruben

last: Dries

summary: We performed gene expression profiling by Affymetrix primeview array in both shBORIS and shLUC resistant Kelly cells.

overall_design: Expression profiles of  shBORIS and shLUC resistant Kelly cells using GeneChip® PrimeView™ Human Gene Expression Array, in duplicate,for a total of 4 individual samples.


title: Genome wide chromatin changes in TC-32 and TC-71 Ewing sarcoma cell lines.

summary: We performed ChIPseq on histone modification marks, transcriptional factors and chromatin architectural proteins in TC-32 and TC-71 Ewing sarcoma cell lines.

overall_design: ChIPseq profiles of  TC-32 and TC-71 Ewing sarcoma cell lines for 3 different marks (BORIS, H3K27ac, SMC1) were generated by next generation sequencing, in duplicate, using Illumina NextSeq 500, for a total of 16 individual samples.

first: David

last: Debruyne


title: Next Generation Sequencing Analysis of chemically reprogrammed osteoblasts from Beta-actin Wildtype (WT) Heterozygotes (HET) and knockout (KO) Mouse Embryonic Fibroblast (MEFs)

status: Public on Aug 06 2019

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: mRNA profiles of chemically reprogrammed osteoblasts from Beta-actin Wildtype (WT) Heterozygotes (HET) and knockout (KO) Mouse Embryonic Fibroblast (MEFs)

overall_design: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the changes of the global gene expression programs among the chemically reprogrammed osteoblasts from Beta-actin Wildtype (WT) Heterozygotes (HET) and knockout (KO) Mouse Embryonic Fibroblast (MEFs)

first: Xin

last: Xie

first: Tamara

last: Gjorgjieva

first: Nizar

last: Drou


title: Transcriptome of human T cell stimulated with anti-CD3 antibody.

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

summary:
Purpose: The aim of this study is the evaluation of differential gene expression profile by RNA-seq in response to anti-CD3 treatment in CD3 cells obtained from blood samples of healthy donors, to achieve a better understanding of the antibodies molecular mechanisms of action. In this study T cells were treated in the complex PBMC milieu, in a tentative to mimetize the natural ambient that occurs in a clinical administration of therapeutic anti-CD3.
Methods: Human peripheral blood mononuclear cells were purified from healthy volunteers blood and were cultured in the presence of the monoclonal antibody OKT3 or a recombinant fragment of humanized anti-CD3 (FvFcR) or recombinant fragment chimeric anti-CD3 (FvFcM). After 72 hours, CD3+ T cells were isolated by negative selection using magnetic beads and total RNA was extracted with the RNeasy kit (Qiagen). Paired-end cDNA reads (150bp) were generated using the HiSeq 2500 Sequencing system (Illumina) located at the NGS Overseas Project Manager, Next Generation Sequencing Division, Macrogen, Inc. (Seoul, Korea). Quality check of the paired-end reads was performed using FASTQC. The reads were aligned to the human genome refence downloaded from the UCSC Genome Browser database using open source segemehl_0_2_0. The aligned files were ordered and indexed using Samtools followed by read count using HTSeq-count. Statistical analysis was done using the R environment for statistical computing. Gene model quantification were performed using the Bioconductor package DESeq2.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the human genome and identified 7089 transcripts in the T cell stimulated with OKT3, 2425 transcripts with FvFc R and 1406 with FvFc M. RNA-seq data confirmed stable expression of some known housekeeping genes, and 3 of these were validated with qRT-PCR. We found 860 genes there are equally regulated among the treatments, considering a padj ≤ 0.05. Altered expression of 35 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: In conclusion, we had used a deep transcriptome sequencing method for comparing three anti-CD3 antibodies in terms of gene ontology enrichment and immunological markers expression. The present data showed that both recombinant antibodies induced a compatible expression profile, suggesting they could be tested as substitute in human pre-clinical trials. Moreover, the proposed methodology is amenable to be more generally applied for molecular comparison purposes.

overall_design: Comparison of differentially expressed genes in T cells stimulated with anti-CD3 antibodies.

first: Isabel

middle: G

last: Sousa

first: Kelly

middle: C

last: Simi

first: Tainá

first: Marcelo

last: Brigido


title: Investigation of bivalently marked promoters in patient-derived colorectal cancer stem cells by ChIP-seq, chromatin accessibility by ATAC-seq, and differential regulation of gene expression following EZH2 inhibition using RNA-seq.

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: We profiled changes in gene expression following EZH2 inhibition, in a patient-derived, cancer stem cell enriched model. Cells were treated with UNC1999, an EZH2 inhibitor, for 7 days, prior to processing for RNA-seq. In parallel, we identified H3K27me3 and H3K4me3 marked promoters using ChIP-seq at baseline in the same model, as well as chromatin accessibility using ATAC-seq.

overall_design:
Colorectal cancer stem cells were profiled for bivalently marked (H3K4me3), repressed (H3K27me3) and active (H3K4me3) promoters at baseline. Cells were treated with the EZH2 inhibitor UNC1999, and processed for RNA-seq. ChIP-seq data was used to determine whether the promoters of the differentially regulated genes were marked with repressive, active or bivalent marks. ATAC-seq was performed at baseline to determine chromatin accessibility and used for transcription factor motif analysis.
Raw data will be submitted to EGA due to patient privacy concerns.

first: Evelyne

last: Lima-Fernandes

first: Tiago

last: da Silva Medina

first: Alex


title: Genome wide chromatin changes in TAE684 sensitive and resistant Kelly cells.

summary: We performed ChIP-seq on MYCN in both TAE684 sensitive and resistant Kelly cells.

overall_design: ChIPseq profiles of TAE684 sensitive and resistant Kelly cells for MYCN were generated by next generation sequencing, in duplicate, using Illumina NextSeq 500, for a total of 8 individual samples.

first: Rani

last: George


title: Locally renewing resident synovial macrophages provide a protective barrier for the joint

first: Philipp

last: Kirchner

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

overall_design: Refer to individual Series


title: Genome wide chromatin changes in shBORIS and shLUC resistant Kelly cells.

first: Ruben

summary: We performed ChIPseq on histone modification marks, transcriptional factors and chromatin architectural proteins in both shBORIS and shLUC resistant Kelly cells.

overall_design: ChIPseq profiles of shBORIS and shLUC resistant Kelly cells for 4 different marks (BORIS, CTCF, SMC1, H3K27ac) were generated by next generation sequencing, in duplicate, using Illumina NextSeq 500, for a total of 20 individual samples.


title: Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

type: Non-coding RNA profiling by high throughput sequencing

summary: As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. During the premiotic stage, AGO18b primarily binds to 21-nt phasiRNAs with 5’-uridine and less binds to 24-nt phasiRNAs with 5’-adenosine, coincident with its enrichment of miR2275 required for the 24-nt phasiRNA production. MiR166a, the negative regulator of SAM, is mostly enriched among AGO18b-bound miRNAs, implicating a novel negative regulator of IM. We suggest that AGO18b regulates maize tassel development via both phasiRNAs and miRNA pathways.

overall_design: sRNA-Seq, mRNA-Seq and RIP-Seq for W22-ref and ago18b::mum samples, respectively. Both library type have two biological experiments. IgG samples were used as control for RIP-Seq. For RIP-Seq, we constructed two type libraries: short insertion for sRNAs and long insertion for mRNAs.

first: Yi

last: Zhang

first: Zuxin


title: Modeling Human Cancer-induced Cachexia (Mouse)

city: Charleston

first: Erin

last: Talbert

state: SC

address: 70 President Street

department: Pediatrics

institute: Medical University of South Carolina

summary:
Cachexia is a wasting syndrome characterized by pronounced skeletal muscle loss.  In cancer, cachexia associates with increased morbidity and mortality and decreased treatment tolerance.
Although advances have been made in understanding the mechanisms of cachexia, translating these advances to the clinic has been challenging. One reason for this shortcoming may be the current animal models that fail to fully recapitulate the etiology of
human cancer-induced tissue wasting. Because pancreatic ductal adenocarcinoma (PDA) presents with a high incidence of cachexia, we engineered a mouse model of PDA, that we named KPP. KPP mice, similar to PDA patients, progressively lose skeletal and adipose mass
as a consequence of their tumors. In addition, KPP muscles exhibit a similar gene ontology to cachectic patients. We envision the KPP model will be a useful resource for advancing our mechanistic understanding and ability to treat cancer cachexia.

overall_design: Comparison of gene expression from muscle of cachectic mice to control mice (n=2/group), for 4 mouse models of cancer cachexia

first: Denis

last: Guttridge


title: Direct and Specific Functional Evaluation of the Nrf2 and MafG Heterodimer by Introducing a Tethered Dimer into Small Maf-Deficient Cells

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

institute: Tohoku University


title: Circadian modulation of genome-wide RXR binding in mouse liver tissue

city: Lausanne

first: Nicolas

last: Guex

state: Vaud

address: Genopode, Dorigny Campus

department: CIG - Center for Integrative Genomics

institute: University of Lausanne

summary: RXR DNA-binding sites cluster together and toward promoter-riches region on chromatin landscape and boost gene expression.The RXR signal is highly correlated with Pol2 signal and even mimic the Pol-II profile upon some high expressed genes. Majority of RXR peaks are constant binding. Only 10% of RXR peak showed circadian rhythm, and only 10% of them associated with circadian expressed genes. The genes with and without RXR at their promoter exhibit different phases of Pol2 signal. And RXR is not the main driver for the circadian transcriptional output. Pathways analysis for target genes showed distinct pattern for genes with unique binding motif, they mainly involve in general fundamental pathways like cell cycle and cell check-point. While the genes with multiple binding motifs are involve in specific pathways like circadian and liver metabolism pathways.

overall_design: 7 sampling time points in C67Bl/6 male mice: ZT02, ZT06, ZT10, ZT14, ZT18, ZT22 and ZT26. All mice had food access in night time ZT12-24 with normal diet. We have ChIP and input for each analyzing time point but no replicate.

first: Khanh

last: Trang

first: Federica

last: Gilardi

first: Béatrice

last: Desvergne


title: Interplay between FACT subunit SPT16 and TRIM33 can remodel chromatin at macrophage distal regulatory elements

city: Fontenay aux roses

first: federica

last: ferri

address: 18 route du panorama

country: France

institute: cea


title: Modeling Human Cancer-induced Cachexia (Human)

overall_design: Comparison of gene expression from muscle of cachectic pancreatic cancer patients to control patients (n=5/group)


title: Interplay between FACT subunit SPT16 and TRIM33 can remodel chromatin at macrophage distal regulatory elements [ATAC-seq]

summary:
Although the advances in genome-wide approaches have elucidated the functions of macrophage-specific distal regulatory elements in transcriptional responses, chromatin structures associated with PU.1 priming and the underlying mechanisms of action of these cis-acting sequences are not characterized.
Here, we show that, in macrophages, FACT subunit SPT16 can bind to positioned nucleosomes directly flanking PU.1-bound sites at previously uncharacterized distal regulatory elements located near genes essential for macrophage development and functions. SPT16 can interact with the transcriptional co-regulator TRIM33 and binds to half of these sites in a TRIM33 dependent manner. Using the Atp1b3 locus as a model, we show that FACT binds to two positioned nucleosomes surrounding a TRIM33/PU.1-bound site in a region, located 35kb upstream the Atp1b3 TSS, that interact with the Atp1b3 promoter. At this -35kb region, TRIM33 deficiency leads to FACT release, loss of the two positioned nucleosomes, RNA Pol II recruitment and bidirectional transcription. These modifications are associated with higher levels of FACT binding at the Atp1b3 promoter, an increase of RNA Pol II recruitment and an increased expression of Atp1b3 in Trim33-/- macrophages.
Thus, sequestering of SPT16/FACT by TRIM33 at PU.1-bound distal regions might represent a new regulatory mechanism for RNA Pol II recruitment and transcription output in macrophages.

overall_design: ATAC-seq of wild-type and Trim33-/- bone marrow-derived macrophages (BMDM).

first: F

last: Ferri

first: P

middle: H

last: Romeo


title: needle1 (ndl1) encodes a mitochondria localized ATPase required for thermotolerant maize growth [greenhouse]

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

summary: RNA-seq was performed on 2-4mm WT and Bif1;Bif4 double heterozygous mutant maize tassels grown in a greenhouse

overall_design: 6 samples

first: M

last: Galli

first: A


title: needle1 (ndl1) encodes a mitochondria localized ATPase required for thermotolerant maize growth [field]

summary: RNA-seq was performed on 2-4mm WT and ndl1 mutant maize tassels

overall_design: 9 samples


title: Identification of a T follicular helper subset that drives anaphylactic IgE

city: Farmington

first: William

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: We report a rare population of IL-13-producing Tfh cells that were present with high-affinity IgE to allergens. These “Tfh13” cells have an unusual cytokine profile (IL-13hiIL-4hiIL-5hiIL-21lo), co-express BCL6 and GATA3 and were required for production of high- but not low-affinity IgE and accordingly, allergen-induced anaphylaxis.

overall_design: Single-cell RNA-seq from 1) Sorted Tfh cells (TCRβ+ CD4+ CD44+ PD-1+ CXCR5+) and 2) Total IL-4 4Get GFP reporter positive CD4 T cells (TCRβ+ CD4+ CD44+ GFP (IL-4)+) cells from day 7 mediastinal LN after Alternaria alternata (10μg) + NP-OVA (25μg) immunization (i.n.).

first: Uthaman

last: Gowthaman

first: Jennifer

middle: S

first: Biyan

first: Yisi

last: Lu

first: Wenzhi

last: Song

first: Julie

last: Joseph

first: Jake

last: Gertie

first: Lan

last: Xu

first: Magalie

last: Collet

first: Jessica

last: Grassmann

first: Tregony

last: Simoneau

first: David

last: Chiang

last: Berin

first: Joseph

middle: E

last: Craft

first: Jason

last: Weinstein

first: Adam

last: Williams

first: Stephanie

last: Eisenbarth


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [ago2KO s4U TT-SLAMseq]

city: Vienna

first: Brian

last: Reichholf

address: Doktor-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Argonaute (Ago)-bound microRNAs (miRNAs) silence mRNA expression in a dynamic and regulated manner to control organismal development, physiology and disease. Here, we employed metabolic sequencing of small RNAs for a comprehensive view on intracellular miRNA kinetics in Drosophila. Based on absolute biogenesis and decay rates, miRNAs rank among the fastest produced and most long-lived cellular transcripts, enabling them to reach >105 copies per cell at steady-state. Tight coupling of steps in biogenesis produces mature miRNAs within minutes and is effectively disrupted by pre-miRNA uridylation. In contrast, control over Ago protein homeostasis generates a kinetic bottleneck that cooperates with ncRNA surveillance to ensure faithful miRNA loading. Finally, regulated small RNA decay enables the rapid turnover of specific Ago1-bound miRNAs but not of Ago2-bound siRNAs, reflecting key differences in the robustness of small RNA silencing pathways. Our work opens new experimental avenues to deconvolute the timescales, molecular features, and regulation of small RNA silencing pathways in living cells.

overall_design: Combination of TT-seq with SLAM-seq, labelling Ago2KO Drosophila S2 cells for 5 minutes. Labelling was performed in three biological replicates, each replicate was once sequenced only as "input" and once as "bound" (TT-seq purified). Both "input" and "bound" underwent SLAMseq IAA treatment. Unlabelled input was sequenced once (prepared with NEBNext Ultra II Directional RNA Library Prep Kit). All Samples were analysed with slamdunk v0.3.4

first: Veronika

last: Herzog

first: Nina

last: Fasching

first: Raphael

last: Manzenreither

first: Ivica

last: Sowemimo

first: Stefan

middle: L

last: Ameres


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [nbrKO miRNA-seq]

overall_design: Wild-type Drosophila S2 cells, NbrKO, NbrKO expressing NbrWT, and NbrKO expressing a catalytically inactive version of Nbr were pelleted in two biological replicates. The libraries were analysed with the in-house smRNAseq pipeline (github.com/AmeresLab/smRNAseq), and each replicate was treated individually. Wild type are the positive control, and nbrKO the negative control, nbrKO + nbrWT is expected to result in smallRNA length profiles similar to wild-type, where nbrKO + nbrCM is used to test if nbr presence alone is sufficient to influence length profiles of small RNAs.


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [WT s4U time-course miRNA-seq]

overall_design: Wild-type cells were labelled in a s4U timecourse over 24h and samples were taken at the indicated timepoints. Isolated RNA was either sequenced untreated or following oxidation. Control camples are represented as "wt no s4U no IAA" for unlabelled (no s4U), untreated (without iodoacetamide) and no oxidation. Oxidised samples are indicated with "+ox". All samples were analysed with the in-house nextflow pipeline (github.com/AmeresLab/smRNAseq).


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [ago2ko s4U time-course miRNA-seq]

overall_design: Ago2KO Drosophila S2 cells were labelled with s4U in a timecourse and samples were taken at the indicated time points. The experiment was performed in biological duplicates where IDs 45493-45501 reflect the first replicate and 47117-47125 provide the second replicate. The libraries were prepared as a single batch per replicate. The time course was analysed using the in-house smRNAseq nextflow pipeline (available on github: github.com/AmeresLab/smRNAseq) both separately, and upon merging replicates of time points to facilitate more depth.


title: Analysis by RNA-seq of the changes in the transcriptome induced by cohesin inactivation

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

summary: The main objective of this study is to determine how cohesin influences transcription and compare these changes to changes previously observed in chromatin structure, which were previously determined by Mnase-seq

overall_design: Samples for RNA  were obtained from two different genetic backgrounds of S.cerevisiae cells (wild-type and scc1-73-W303 bar1∆ background). scc1-73 is a thermosensitive allele of the kleisin subunit of the mitotic cohesin complex that was used to analyze the effects of cohesin inactivation on chromatin. 2 samples for each genetic background (2 independent experiments) were collected at the G2/M transition.

first: Felix

last: Prado

first: Douglas

last: Maya-Miles

first: Marina

last: Murillo-Pineda

first: María

middle: J

last: Cabello-Lobato

first: Eloísa

last: Andújar

first: Mónica

last: Pérez-Alegre


title: Comparison of long non-coding RNA expression profiles in human periodontal tissue cells

city: Guangzhou

first: Liping

last: Wu

address: 56 Lingyuanxi Road

institute: Sun Yat-sen University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Human dental follicle cells (hDFCs) are precursor cells of periodontal development. Long non-coding RNAs (lncRNAs) have been revealed to be crucial factors that regulate a variety of biological processes; however, whether lncRNAs serve a role in human periodontal development remains unknown. Therefore, the present study used microarrays to detect the differentially expressed lncRNAs and mRNAs between hDFCs and human periodontal ligament cells (hPDLCs). Human dental follicle and periodontal ligament samples were obtained from four adolescents (2 males and 2 females) between 12 and 16 years old following premolar and immature impacted third molar (roots developed to <2/3 their full size) extraction for orthodontic reasons. To verify the reliability of the microarray data, six differentially expressed lncRNAs and six differentially expressed mRNAs were randomly selected for analysis of their expression levels by RT-qPCR.

overall_design: After primary culture, cells were passaged with a 1:3 ratio using 0.25% trypsin/EDTA (Gibco; Thermo Fisher Scientific, Inc.). The third-generation cells were used for subsequent experiments.

first: Y

middle: X

last: Liu

first: X

last: Hu


title: Gene expression data from nine pediatric glioblastoma tumor samples

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary: Expression data of a small series of pediatric glioblastomas were used as a control in a comparison with ependymoma tumors

overall_design: Total RNA from nine glioblastoma tumor samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays.

first: Kristian

last: Pajtler

first: Daisuke

last: Kawauchi


title: C. difficile-associated antibiotics prime the host for infection by a microbiome-independent mechanism

city: Cambridge

first: Jemila

last: Kester

state: MA

address: 32 Vassar Street, Bldg 16, Rm 436

institute: MIT

summary: The most clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Though most broad-spectrum antibiotics significantly disrupt the structure of the gut microbiota, only particular ones increase CDAD risk, suggesting additional factors might increase the risk from certain antibiotics. Here we show that commensal-independent effects of antibiotics collectively prime an in vitro germ-free human gut for CDAD. We found a marked loss of mucosal barrier and immune function with CDAD-associated antibiotic pretreatment distinct from pretreatment with an antibiotic unassociated with CDAD, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent host changes in the increased risk of CDAD with specific antibiotics. Our findings are contrary to the previously held belief that antibiotics allow for CDAD solely through disruption of the microbiome. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD, and to impact human tissue culturing protocols.

overall_design: Antibiotics used: Clindamycin, ciprofloxacin, tigecycline. Clindamycin and ciprofloxacin compared to untreated, while tigecycline compared to DMSO. 6 replicates per condition. Hi: Clindamycin 300ug/ml, Ciprofloxacin 200ug/ml, tigecycline 20ug/ml. Low: Clindamycin 3ug/ml, ciprofloxacin 5ug/ml, tigecycline 1ug/ml


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis

first: Brian

last: Reichholf

overall_design: Refer to individual Series


title: Prediction of Venetoclax Activity in Precursor B-ALL by Functional Assessment of Apoptosis Signaling

city: Ulm

last: Seyfried

address: Eythstr. 24

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

summary: Small molecule inhibitors of key apoptosis regulators have been developed that bind to anti-apoptotic molecules like BCL-2, leading to release of pro-apoptotic proteins and cell death induction. This study shows that functional analysis of the interplay of apoptosis regulators in precursor B-ALL predicts preclinical in vivo activity of the BCL-2 inhibitor venetoclax and provides a robust assay for upfront identification of leukemias eligible for therapy.

overall_design: Gene expression was measured using Affymetrix platform in 27 precursor B-ALL xenograft samples

first: Lüder

last: Hinrich Meyer


title: Analysis by Mnase-seq of the chromatin structure of wild type cells and cells in which chromatin structure is perturbed (histone H4 depletion) in the presence or absence of the kleisin subunit of cohesin, Scc1

last: Andujar

summary: The main objective of this study is to determine how cohesin influences chromatin structure and chromatin assembly during DNA replication

overall_design: Chromatin structure has been determined by MNase-seq in 4 different genetic backgrounds (wild-type, scc1-73, tHHF2 and tHHF2 scc1-73) in S.cerevisiae cells (W303 bar1∆ background). scc1-73 is a thermosensitive allele of the kleisin subunit of the mitotic cohesin complex that was used to analyze the effects of cohesin inactivation on chromatin. tHHF2 is a genetic background in which both loci that codify histone H4 are deleted and all histone H4 is expressed from a doxycycline regulatable promoter (tetON). Histone depletion was induced in G1 arrested cells changing the concentration of doxycicline (5 µg/ml ≈ wild type to 0.25 µg/ml = histone depletion). 2 samples for each genetic background (2 independent experiments) were collected at the G2/M transition.


title: needle1 (ndl1) encodes a mitochondria localized ATPase required for thermotolerant maize growth

first: Andrea

last: Gallavotti


title: Comparison of methods for the characterization of miRNAs from 200 µl of cerebrospinal fluid

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

summary: Cerebrospinal fluid (CSF) miRNAs have emerged as a potential low invasive diagnostic tool for central nervous system malignancies. However, they have not yet been implemented in the clinic since there is no standardized and simple method established. Another problem that it must be considered is that the amount of CSF that can be obtained from patients is very limited, especially from infants. With this in mind, we have compared six different methodologies to establish the best one for the detection of miRNAs using a minimum CSF volume. Four of them incorporated a EVs enrichment step and the other two extracted the miRNAs directly from crude CSF. The efficiency of each method was evaluated by quantitative PCR (qPCR) and smallRNA sequencing. Our results showed that, the Plasma/Serum RNA Purification kit (Norgen) and the proposed method combining the total exosome isolation reagent (Invitrogen) with the mirVana PARIS kit (Ambion) were the most efficient. However, the Norgen’s kit was the most reproducible protocol by qPCR and presented a user-friendly protocol. Therefore, we considered it as the most suitable method for detecting circulating and EVs-associated miRNAs using only 200 µl of CSF.

overall_design: Comparison of six methodologies for miRNAs analysis from 200 µl of cerebrospinal fluid. Of them, four incorporated a EVs enrichment step and the other two extracted the miRNAs directly from crude CSF. The efficiency of each method was evaluated by quantitative PCR (qPCR) and smallRNA sequencing. For this experiment a pool of samples was generated.

first: Endika

last: Prieto-Fernández

first: Félix

last: Royo

first: Esperanza

last: González

first: Juan

last: Lozano

first: Javier

last: Benito

first: África

last: García-Orad

last: Falcón-Pérez


title: Genome-wide profiling of Scc1 subunit  in wild type cells and in cells in which chromatin structure is perturbed (histone H4 depletion).

first: Eloisa

type: Genome binding/occupancy profiling by genome tiling array

summary: The main objective of this study is to determine how chromatin assembly during DNA replication influences cohesin deposition

overall_design: Cohesin deposition was determined by ChIP-on-ChIP  in 2 different genetic backgrounds (wild-type and  t::HHF2-W303 bar1∆ background) that carried a tagged version of SCC1 (SCC1-6HA).  t::HHF2 is a genetic background in which both loci that codify histone H4 are deleted and all histone H4 is expressed from a doxycycline regulatable promoter (tetON). Histone depletion was induced in G1 arrested cells changing the concentration of doxycicline (5 µg/ml ≈ wild type to 0.25 µg/ml = histone depletion). 2 samples for each genetic background (2 independent experiments) were collected at the G2/M transition. Each experiment carried a non-tagged version of the wild type strain. One of them was analyzed to determine all non-specific signal.

last: Prado

first: Douglas

last: Maya-Miles

first: Eloísa

last: Andújar

first: Mónica

last: Pérez-Alegre


title: T-cell receptor repertoire analysis of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody [TCR-seq]

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

summary: Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. IT1208 (IDAC Theranostics, Tokyo, Japan) is a humanized anti-CD4 immunoglobulin G1 (IgG1) monoclonal antibody with a defucosylated Fc region, which markedly enhances antibody dependent cellular cytotoxicity. In a first-in-human, phase I, open-label, dose-escalation study, we performed T cell repertoire analysis of T cell subsets in the tumors and peripheral blood mononuclear cells (PBMCs) to clarify T cell responses against IT1208 monotherapy in patients with advanced solid tumors.

overall_design: Four and seven patients were assigned to dose levels 1 (0.1mg/kg) and 2 (1.0 mg/kg), having gastrointestinal cancer. First patient in each cohort was treated as one dose of IT1208 on day 1 and other patients received two doses of IT1208 on day 1 and 8. To clarify T cell repertoire changes by IT1208 monotherapy, PBMC collection and tumor biopsy were conducted before the study treatment and just after dose-limiting toxicities evaluation period whenever possible. Then, we performed T cell receptor (TCR)-seq analysis by using Ion Proton or Ion Genestudio S5 sequencers.

first: Hiroyasu

last: Aoki

first: Satoshi

last: Ueha

first: Kohei

last: Shitara

first: Haru

last: Ogiwara

first: Tetsuya

last: Nakatsura

first: Toshihiro

last: Suzuki

first: Manami

last: Shimomura

first: Toshiaki

last: Yoshikawa

first: Kayoko

last: Shoda

first: Shigehisa

last: Kitano

first: Makiko

last: Yamashita

first: Takayuki

last: Nakayama

first: Akihiro

last: Sato

first: Sakiko

last: Kuroda

first: Masashi

last: Wakabayashi

first: Shogo

last: Nomura

first: Shoji

last: Yokochi

first: Satoru

last: Ito

first: Kouji

last: Matsushima

first: Toshihiko

last: Doi


title: Time-resolved small RNA sequencing unravels molecular principles of microRNA homeostasis [Ago1OE + TailorKO]

first: Brian

last: Reichholf

overall_design: Wild-type Drosophila S2 cells, TailorKO, FM-tagged Ago1 overexpression in wild-type background, Ago2KO, and FM-tagged Ago1-overexpression in Ago2KO background were subjected to biochemical purification of Argonaute ribonucleoprotein complexes and smallRNA sequencing in 2 or 3 replicates (as indicated). The libraries were first aligned to S2 viral genomes to eliminate contaminants, then to dm6 to determine mappers in ncRNA and coding regions in a hierarchical manner (rRNA, mitochondria, tRNA, snRNA, snoRNA, endo-siRNA, cisNAT, miRNA, intronic, exonic, TE, none).

first: Veronika

last: Herzog

first: Nina

last: Fasching

first: Raphael

last: Manzenreither

first: Ivica

last: Sowemimo

first: Stefan

last: Ameres


title: Transcriptomic analysis of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody  [3'SAGE-seq]

first: Shigeyuki

last: Shichino

summary: Immune checkpoint inhibitors such as anti-cytotoxic T-lymphocyte–associated antigen-4 and anti-programmed cell death-1 monoclonal antibodies (mAbs) agents or these combinations has improved outcomes of various cancers.However, still not a few patients fail to achieve clinical benefit, this highlights the importance of additional treatment to overcome its resistance. Previously, we showed that administration of the anti-CD4 mAb alone had strong anti-tumor effects that were superior to those elicited by CD25+ Treg depletion or other immune checkpoint mAbs in B16F10, Colon 26, or Lewis lung carcinoma subcutaneous tumor models. IT1208 (IDAC Theranostics, Tokyo, Japan) is a humanized anti-CD4 immunoglobulin G1 (IgG1) monoclonal antibody with a defucosylated Fc region, which markedly enhances antibody dependent cellular cytotoxicity. In a first-in-human, phase I, open-label, dose-escalation study, we performed transcriptomic analysis of tumors to clarify molecular responses against IT1208 monotherapy in patients with advanced solid tumors.

overall_design: Four and seven patients were assigned to dose levels 1 (0.1mg/kg) and 2 (1.0 mg/kg), having gastrointestinal cancer. First patient in each cohort was treated as one dose of IT1208 on day 1 and other patients received two doses of IT1208 on day 1 and 8. To clarify T cell repertoire changes by IT1208 monotherapy, PBMC collection and tumor biopsy were conducted before the study treatment and just after dose-limiting toxicities evaluation period whenever possible. Then, we performed transcriptomic analysis by using an Ion Proton sequencer.

first: Kohei

last: Shitara

first: Satoshi

last: Ueha

first: Hiroyasu

last: Aoki

first: Haru

last: Ogiwara

first: Tetsuya

last: Nakatsura

first: Toshihiro

last: Suzuki

first: Manami

last: Shimomura

first: Toshiaki

last: Yoshikawa

first: Kayoko

last: Shoda

first: Shigehisa

last: Kitano


title: TCR repertoire and transcriptomic analyses of advanced solid tumors in first-in-human phase 1 study of IT1208, a defucosylated humanized anti-CD4 depleting antibody

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


title: Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition [ExpressionArray]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Ovarian cancer (OC) cells exhibit varying extents of epithelial/mesenchymal phenotype, forming an EMT spectrum based on their EMT scores. Combining 450K DNA methylation array, ChIP-sequencing of five histone H3 marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3 and H3K9me3) and transcriptomic analyses, we examined the genome-wide epigenetic profiles of OC cell lines with progressive EMT phenotypes, including a knockdown model of EMT suppressor Grainyhead-like 2 (GRHL2) which showed intermediate state transition. We identified differentially methylated CpG sites (DMCs) associated with EMT genes, found mainly at the promoters of epithelial genes including CDH1, GRHL2 and genes with GRHL2 binding sites. This prompted us to further study the epigenetic role of GRHL2. GRHL2-knockdown resulted in CpG methylation gain at GRHL2 binding sites and at DMCs associated with epithelial genes. Importantly, the changes of histone modifications occurred in GRHL2-knockdown cells are also more prominent among epithelial genes and at GRHL2 binding sites—reduction in permissive marks H3K4me3 and H3K27ac; elevated repressive mark H3K27me3—similar to the transitions observed in a four-cell-line model representing the EMT spectrum. We tested the effects of GRHL2 overexpression in conjunction with epigenetic drugs 5-azacitidine, GSK126 and mocetinostat, all of which exerted MET effects to different extents, depending on the existing cell state. Overall, GRHL2 is required for the epigenetic and chromatin remodeling of epithelial genes during EMT/MET that control intermediate phenotype switching.

overall_design: The total RNA of 29 ovarian cancer cell lines (each with duplicates) were subjected to gene expression profiling

first: Vin

middle: Y

last: Chung

first: Tuan

middle: Z

first: Jieru

last: Ye

first: Meng

middle: K

last: Wong

first: Ruby

last: Huang


title: Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition

type: Methylation profiling by genome tiling array


title: Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition [RNA-seq]

overall_design: Total RNA of OVCA4209 control and GRHL2 knockdown (shGRHL2#12) cells were analyzed.

first: Shaveta

last: Goyal

first: Nur

last: Sapari

first: Richie

last: Soong


title: Genome wide chromatin changes in TAE sensitive and resistant Kelly cells [ChIP-seq]

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

institute: DFCI

summary: We performed ChIPseq on histone modification marks, transcriptional factors and chromatin architectural proteins in both TAE sensitive, resistant and JQ1-treated resistant Kelly cells.

overall_design: ChIPseq profiles of TAE sensitive and resistant Kelly cells for 6 different marks (BORIS, BRD4, CTCF, H3K27ac, H3K27me3, Pol2) were generated by next generation sequencing, in duplicate, using Illumina NextSeq 500, for a total of 40 individual samples.

first: David

last: Debruyne

first: Rani

last: George


title: Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition [ChIP-seq]

overall_design: ChIP samples of 5 histone marks (H3K4me3, H3K4me1, H3K27ac, H3K27ac, H3K9me3) from 6 cell lines were analyzed by Next-generation sequencing.

first: Heike

last: Wollmann

first: Ernesto

last: Guccione


title: Grainyhead-like 2 (GRHL2) and epigenetic remodeling in the intermediate states of epithelial-mesenchymal transition [MethylArray]

overall_design: 64 samples of genomic DNA (32 EOC cell lines in duplicates) were analyzed by Illumina Infinium 450K DNA methylation BeadChip array.


title: Interplay between FACT subunit SPT16 and TRIM33 can remodel chromatin at macrophage distal regulatory elements [ChIP-seq]

first: federica

last: ferri

summary:
Although the advances in genome-wide approaches have elucidated the functions of macrophage-specific distal regulatory elements in transcriptional responses, chromatin structures associated with PU.1 priming and the underlying mechanisms of action of these cis-acting sequences are not characterized.
Here, we show that, in macrophages, FACT subunit SPT16 can bind to positioned nucleosomes directly flanking PU.1-bound sites at previously uncharacterized distal regulatory elements located near genes essential for macrophage development and functions. SPT16 can interact with the transcriptional co-regulator TRIM33 and binds to half of these sites in a TRIM33 dependent manner. Using the Atp1b3 locus as a model, we show that FACT binds to two positioned nucleosomes surrounding a TRIM33/PU.1-bound site in a region, located 35kb upstream the Atp1b3 TSS, that interact with the Atp1b3 promoter. At this -35kb region, TRIM33 deficiency leads to FACT release, loss of the two positioned nucleosomes, RNA Pol II recruitment and bidirectional transcription. These modifications are associated with higher levels of FACT binding at the Atp1b3 promoter, an increase of RNA Pol II recruitment and an increased expression of Atp1b3 in Trim33-/- macrophages.
Thus, sequestering of SPT16/FACT by TRIM33 at PU.1-bound distal regions might represent a new regulatory mechanism for RNA Pol II recruitment and transcription output in macrophages.

overall_design: ChIP-seq profiling (H3K36me3, H379me2, SPT16, POLII) in Trim33-/- and WT bone marrow derived macrophages (BMDMs).

first: F

last: Ferri

first: P

last: Romeo


title: IFN-mediated negative feedback supports bacteria class-specific macrophage inflammatory responses

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Gene expression for mouse C57BL/6 bone marrow derived macrophages stimulated with a titration matrix of TLR4 and TLR2 ligand, KDO2-Lipid A and Pam3CSK4, respectively

overall_design: Gene expression for mouse C57BL/6 bone marrow derived macrophages stimulated with a titration matrix of TLR4 and TLR2 ligand, KDO2-Lipid A (KLA) and Pam3CSK4(P3C), respectively

first: Rachel

last: Gottschalk

first: Iain

middle: D

last: Fraser

first: Ronald

middle: N

last: Germain


title: YAP1 fusion proteins drive forebrain ependymoma tumorigenesis via the interaction with TEAD transcription factors

first: Marcel

last: Kool

summary: A mouse model has been generated resembling human YAP1 fusion-positive supratentorial ependymoma. We show that the YAP1-MAMLD1 fusion, which is the most recurrent fusion in this distinct type of ependymomas, is able to drive malignant transformation in mice. The resulting brain tumors resemble histo-molecular characteristics of their human counterparts.

overall_design: Ten mouse brain tumors induced by electroporating either a human YAP1-MAMLD1 fusion construct or a human C11orf95-RELA fusion construct into cerebral ventricular zone cells of fetal mice at E13.5 were profiled on the Affymetrix Mouse Genome mm430.2 array.

first: Kristian

last: Pajtler

first: Daisuke

last: Kawauchi


title: Inhibition of Tumor Growth and Metastasis by EMMPRIN Multiple Antigenic Peptide (MAP) Vaccination Is Mediated by Immune Modulation

city: Haifa

first: Michal (Miki)

middle: A.

last: Rahat

address: 7 Michal st.,

department: Immunology, Faculty of Medicine

country: Israel

institute: Carmel Medical Center & Technion-Israel Institute of Technology

summary: We report here that a EMMPRINs-specific cancer peptide vaccination, where the peptide was modified and synthesied as a multiple antigenic peptide (MAP), significantly inhibited tumor growth and metastases. Specifically, we describe changes in the gene expression profile as assessed by RNAseq in tumors derived from mice implanted with the colon tumorigenic carcinoma (CT26 cells), and vaccinated with either a control scrambled multiple antigenic peptide (Scr-MAP) or with an epitope-specific EMMPRIN multiple antigenic peptide (designated 161-MAP).

overall_design: Toral RNA from tumors from 3 mice in each group (Scr-MAP and 161-MAP vaccinated) were extracted, and RNAseq analysis revealed differentially expressed genes (DEGs).

first: Michal


title: Genomic and epigenomic predictors of response to Guadecitabine in relapsed/refractory Acute Myelogenous Leukemia

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: Guadecitabine is a second generation DNA methylation inhibitor with improved pharmacokinetics and clinical activity in relapsed/refractory AML (rrAML). Here we report genome-wide DNA methylation profiles in pre-treatment samples from 116 rrAML patients treated at therapeutic doses of guadecitabine in a phase I/II study. Response rate to guadecitabine was 22 % (16CR, 42 12CRi/CRp). There were no strong mutation or methylation predictors of response. Gene expression defined a subset of patients (~20%) that had (i) high DNMT3B and low CDKN2B, CTCF and CDA expression, (ii) enrichment for KRAS/NRAS mutations, (iii) frequent CpG island hypermethylation (iv) low LINE1 hypomethylation after treatment and (v) resistance to guadecitabine in both phase I (response rate 0 % vs 33 %, p=0.07) and phase II components of the study (response rate 5 % vs. 30 %, p=0.02). Multivariate analysis identified peripheral blood blasts and hemoglobin as predictors of response and cytogenetics, gene expression, RAS mutations and hemoglobin as predictors of survival. Thus, a subset of patients (∿ 20%) with rrAML are unlikely to benefit from single agent guadecitabine. In the remaining 80%, guadecitabine is a viable option with a median survival of ∿ 8 months and a three year survival rate of over 20%.

overall_design: Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of human genomic DNA from the whole blood of 116 patients with relapsed/refractory acute myeloid leukemia (rrAML) and peripheral blood from 5 healthy controls. Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

first: Woonbok

last: Chung

first: Andrew

last: Kelly

first: Patricia

last: Kropf

first: Henry

last: Fung

first: Xiang

last: Su

first: Gail

last: Roboz

first: Hagop

middle: M

last: Kantarjain

first: Mohammad

last: Azab

first: Jean-Pierre

last: Issa


title: Regulation of zebrafish dorsoventral patterning by phase separation of RNA-binding protein rbm14

status: Public on Aug 05 2019

city: Shanghai

first: Yue

last: Xiao

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: RNA-binding proteins with intrinsically disordered regions (IDRs) such as Rbm14 can phase separate in vitro. To what extent the phase separation contributes to their physiological functions is however unclear. Here we show that zebrafish rbm14 regulates embryonic dorsoventral patterning through phase separation. Zebrafish rbm14 morphants displayed dorsalized phenotypes associated with attenuated BMP signaling. Consistently, depletion of mammalian Rbm14 downregulated BMP regulators and effectors Nanog, Smad4/5, and Id1/2, whereas overexpression of the BMP-related proteins in the morphants significantly restored the developmental defects. Importantly, rbm14's IDR demixed into liquid droplets in vitro despite poor sequence conservation with its mammalian counterpart. While its phase separation mutants or IDR failed to rescue the morphants, its chimeric proteins containing an IDR from other phase-separation proteins were effective. Rbm14 complexed with proteins involved in RNA metabolism and phase separated into cellular ribonucleoprotein compartments. Consistently, RNA deep sequencing analysis on the morphant embryos revealed increased alternative splicing events as well as largescale transcriptomic downregulations. Our results suggest that Rbm14 functions in ribonucleoprotein compartments through phase separation to modulate multiple aspects of RNA metabolism. Furthermore, IDRs conserve in phase separation ability but not primary sequence and can be functionally interchangeable.

overall_design: Zebrafish embryo mRNA profiles of ctrl-MO and rbm14-MOs by deep sequencing at 10hpf and 24hpf. For each sample, 50 embryos were pooled.

first: Jiehui

last: Chen


title: Single cell RNA sequencing analysis of CD8+ T cell subsets following DENV-vaccine administration

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: PBMC-derived CD8 T cell activation and gene expression profiles were assessed 14 days following a single dose of a candidate live-attenuated tetravalent denge virus vaccine (DENVax). Three distinct populations of CD8+ T cells were isolated by flow cytometric sorting: 1) CD3+ CD8+ CD38- HLA-DR- T cells, 2) CD3+ CD8+ CD38+ HLA-DR+ T cells, and 3) CD3+ CD8+ CD71+ HLA-DR+ T cells

overall_design: Single cell RNA sequencing analysis of 3 different CD8 T cell populations present in a vaccine recpient 14 days post vaccine administration

first: Richard

last: Jarman

first: Jeffrey

last: Currier


title: Expression data from prostate cancer cell line PC3 with JunD knockdown and control cells

city: Atlanta

first: Bethtrice

last: Thompson-Elliott

state: GA

address: 223 James P. Brawley Dr. SW

department: Center for Cancer Research and Therapeutic Development

institute: Clark Atlanta University

summary: The development of prostate cancer occurs with uncontrolled cell proliferation which eventually leads to development of highly invasive intraductal carcinoma. This initiation of carcinogenesis in the prostate is primarily dependent on deregulation of genes that control cell proliferation and as a result causes either a loss of inhibitory controls of cell cycle progression or an upregulation of factors which stimulate cell proliferation. JunD, an AP1 transcription factor, has been shown to play an essential role in cell proliferation of PCa cells and regulation of genes required for cell cycle progression.

overall_design: We used gene expression profiling (microarray) to examine JunD's role in regulating genes that play a role in cell proliferation and are required for the progression of the cell cycle. Dataset includes 3 PC3 control replicates and 3 PC3-JunD knockdown replicates.

last: Elliott

first: Ana

middle: C

last: Millena

first: Lilya

last: Matyunina

first: Mengnan

last: Zhang

first: Nathan

last: Bowen

first: John

last: McDonald

first: Shafiq

last: Khan


title: The XPO1 inhibitor KPT-8602 synergizes with dexamethasone for the inhibition of acute lymphoblastic leukemia

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. Survival of ALL patients has improved significantly over the last 50 years. However, the current intensified chemotherapy is associated with serious short and long-term side effects in these young patients. Whereas KPT-8602 is a second generation exportin-1 (XPO-1) inhibitor with potent activity against ALL in pre-clinical models and with minimal effects on normal cells. In this study, we evaluated if synergistic ALL inhibition could be obtained by combining KPT-8602 with dexamethasone, vincristine or doxorubicin. Combination of KPT-8602 with dexamethasone showed the strongest synergistic effect on human B-ALL and T-ALL cell lines. This synergy was confirmed in vivo on three patient-derived ALL xenografts. Compared to single drug treatment, the drug combination caused increased apoptosis, reduced cell cycle gene expression and led to histone depletion. mRNA expression analysis and ChIP-seq revealed that addition of KPT-8602 to dexamethasone increased transcript level and binding of the glucocorticoid receptor, as well as NFKBIA expression. Dexamethasone concentrations could be reduced 5 to 10-fold in the presence of KPT-8602 to achieve the same level of NFKBIA induction as with dexamethasone alone. Our pre-clinical study demonstrates that combination of KPT-8602 and dexamethasone is highly synergistic in vivo. This opens the possibility to reduce dexamethasone concentrations and reduce side effects in future clinical trials.

overall_design:
RNA sequencing of ALL cell lines with different treatments: DMSO - dexamethasone (DEXA) - KPT-8602 (KPT) - combination of DEXA and KPT (COMBI)
ChIPmentation sequencing of ALL cell lines with different treatments: DMSO - dexamethasone (DEXA) - KPT-8602 (KPT) - combination of DEXA and KPT (COMBI)

first: Delphine

last: Verbeke

first: Jan

last: Cools


title: Beta cell dysfunction and identity loss induced by low dose of Interleukin-1β is associated with changes in histone acetylation and gene expression [ChIP-seq]

city: Copenhagen

first: Nils

middle: Billestrup

last: Billestrup

address: Bledamsvej

country: Denmark

institute: University of Copenhagen

summary: We report maturity loss and dysfunction of primary mouse islets exposed to prolonged low Interleukin-1B exposure is associated with a decreassed expresion of key beta cell genes and a decreased H3K27ac mark

overall_design: Examination of 3 histone modifications (H3K27ac; H3K27me3 and H3K4me3) in primary mouse islets exposed or non-exposed to Interleukin-1B for 10 days

first: Adriana

last: Ibarra Urizar

first: Michala

last: Prause

first: Matthew

last: Wortham

first: Yinghui

last: Sui

first: Peter

last: Thams

first: Maike

last: Sander

first: Gitte

last: Christensen


title: Transcriptome analysis of A549 cells expressing a SUMOylation-deficient TRIM28 mutant in the context of influenza A virus infection

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: Aim: Identify differentially expressed genes in human lung epithelial cells expressing a SUMOylation-deficient TRIM28 mutant (TRIM28 6KR) compared to TRIM28 wt.

overall_design: A CRISPR/Cas9-edited A549 TRIM28 knock-out (KO) single cell clone was reconstituted by lentiviral transduction to express either wild type (wt) TRIM28 or TRIM28 6KR. Cells were infected with influenza A virus (A/WSN/33) at MOI=10 PFU/cell or mock infected and RNA was extracted from three independent replicates at 6 hours post infection (hpi) and analysed by mRNA sequencing.

first: Nora

last: Schmidt

first: Benjamin

middle: G

last: Hale


title: Beta-cell dysfunction induced by non-cytotoxic concentrations of Interleukin-1β is associated with changes in expression of beta-cell maturity genes and associated histone modifications

overall_design: Refer to individual Series


title: Gene expression profile (GEP) of K562 cells expressing wtCALR, CALRins5 and CALRdel52

status: Public on Aug 04 2019

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
In this work, we compared gene expression profile (GEP) of K562 cells transduced with the retroviral vector  LCALRins5IDN or  LCALRdel52IDN with K562 cells transduced with LwtCALRIDN
In order to unravel MPL-independent mechanisms underlying the effect of CALR mutations on MPN pathogenesis, we analysed the transcriptional changes induced by the CALRins5 or CALRdel52 overexpression in K562 cells, which lack MPL expression

overall_design: In a set of three independent experiments, K562 cells were transduced with the LCALRwtIDN (CALR wild-type, CALRwt), LCALRdel52IDN (CALRdel52), LCALRins5IDN (CALRins5) retroviral vectors. After NGFR-based purification, the transduced cells were profiled by means of Affymetrix U219 Array

first: Simona

last: Salati

first: Elena

last: Genovese

first: Zelia

last: Prudente

first: Chiara

last: Carretta

first: Valentina

last: Pennucci

first: Samantha

last: Ruberti

first: Sebastiano

last: Rontauroli

last: Rossi

first: Roberta

last: Zini

first: Elisa

last: Bianchi

first: Enrico

last: Tagliafico


title: RNA-Seq study of blood collected from photosensitive and photorefractory blackheaded buntings exposed to first long day

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

institute: UNIVERSITY OF DELHI

summary: We report the mRNA found in blood of photosensitive and photorefractory migratory buntings. The aim of this study was to study the effect of first long day on the mRNA makeup of blood in birds from two different seasonal states.

overall_design: Study of total mRNA from blood in photosensitive and photorefractory buntings (SEB, REB), using Illumina sequencing.

first: Aakansha

last: Sharma

first: Subhajit

last: Das


title: Expression of target genes in itaconic acid cluster and electron transport chain in Aspergillus terreus NRRL1960 cultivated under low dissolved oxygen

city: Bangkok

first: Pajareeya

last: Sogserm

address: 254 Chulalongkorn University Institute Building 3, Phayathai Road, Pathum Wan

department: The Institute of Biotechnology and Genetic Engineering

country: Thailand

institute: Chulalongkorn University

summary:
Aim: We aimed to study the differential gene expressions of the target genes encoding H+-ATPase, the mitochondrial respiratory chain complex, and the alternative oxidase (AOX) in Aspergillus terreus NRRL1960 cultivated under low dissolved oxygen
Methods:The fermentation samples were collected for RNA extraction.The barcoded RNA libraries were prepared using Lexogen’s Quant-Seq 3’ mRNA seq kit (Ion Torrent, Lexogen, Vienna, Austria). DNA templates for sequencing were prepared from 200 bp v3 OT2 kit and the Ion One Touch 2 platform. Sequencing was performed on the Ion Proton by Ion Torrent Suite v5.0.4. Raw sequences form each sample were uploaded and the dapter sequences were trimmed. The reads were aligned to A. terreus NIH2624 genome references downloaded from http://fungi.ensembl.org/info/website/ftp/index.html using Star 2.4.1d. The bam index files were generated. The quantification of gene expression was performed by Htseq v0.6.0 with -f and -s options indicating bam inputs and un-stranded reads, respectively. Cuffdiff v.2.1.1 was used to estimate the transcript abundance with the -no-diff and default options to generate the differential analysis for each described comparison.
Results:From the gene expression (FPKM) results, genes in Cytochrome C complex and aoxA had the high expression level compared to pma encoding H+-ATPase. However, the different gene expression analysis results shown that the target genes in the mitochondrial respiratory chain complex were predominantly down regulated as observed from the log2(fold_change) less than -1 and and the gene encoding AOX (aoxA) were down regulated.
Conclusions: In this study, the transcriptomic analysis were performed for better understanding the biosynthesis pathway and the regulation of target genes in itaconic acid cluster and the ATP regeneration pathway.

overall_design: Nine samples were fungal mycelia collected from the fermentation broth at the end of the growth (at 48h) phase and those taken during the production phase (at 72, 96, 120, 144, 168, 192, 216, 240h). Transcription levels (FPKM) of the target genes of all sample were analyzed. The differential gene expression levels were the data of the gene expression  during the production phase (at 72, 96, 120, 144, 168, 192, 216, 240h) compared with that at the end of the growth (48 h).

first: Songserm

last: Pajareeya

first: Srimongkok

last: Piroonporn

first: Thitiprasert

last: Sitanan

first: Tanasupawat

last: Somboon

first: Assabumrungrat

last: Suttichai

first: Karnchanatat

last: Aphichart

first: Thongchul

last: Nuttha


title: RRM Transcription Factors Interact with NLRs and Regulate Broad-Spectrum Blast Resistance in Rice

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Nucleotide-binding site leucine-rich repeat (NLR) receptors perceive pathogen effectors and trigger plant immunity. However, the mechanisms underlying NLR-triggered defense responses remain obscure. The recently discovered Pigm locus in rice encodes a cluster of NLRs, including PigmR, which confers broad-spectrum resistance to blast fungus. Here, we identify PIBP1 (PigmR-INTERACTING and BLAST RESISTANCE PROTEIN 1), an RRM (RNA-recognition motif) protein that specifically interacts with PigmR and other similar NLRs to trigger blast resistance. PigmR-promoted nuclear accumulation of PIBP1 ensures full blast resistance. We find that PIBP1 and a homolog, Os06 g02240, bind DNA and function as unconventional transcription factors at the promoters of the defense genes OsWAK14 and OsPAL1, activating their expression. Knockout of PIBP1 and Os06g02240 greatly attenuated blast resistance. Collectively, our study discovers previously unappreciated RRM transcription factors that directly interact with NLRs to activate plant defense, establishing a direct link between transcriptional activation of immune responses with NLR-mediated pathogen perception

overall_design: Genome-wide analysis of the transcriptome of PIBP1 RNAi and corresponding wild type NIL-Pigm treatment with blast isolate TH12.

first: Keran

last: Zhai

first: Yiwen

first: Qun

last: Li

first: Zuhua

last: He


title: Transcriptome analysis of differentiated normal mouse urothelial organoids reveals novel pathways activated during urothelial differentiation

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

summary: Transcriptomic analysis revealed significant changes between organoids growing in full medium growth conditions (proliferative NMU-o) and deprived medium (differentiated NMU-o). Around 4100 genes are differentially expressed between both conditions. Moreover, GSEA analysis in proliferation showed pathways related to cell cycle, DNA repair, RNA biology and protein synthesis; in differentiation, pathways related to cellular traffic, cell-cell adhesion and notch signalling are up-regulated.

overall_design: We established normal mouse urothelial organoids (NMU-o) from 3 independent samples and further induced differentiation. For each individual sample we sequenced the corresponding proliferation and differentiation stages.

first: Catarina

middle: P

last: Santos

first: Irene

last: Millán

last: Carrillo-de Santa Pau

first: Francisco

last: Real


summary: Nucleotide-binding site leucine-rich repeat (NLR) receptors perceive pathogen effectors and trigger plant immunity. However, the mechanisms underlying NLR-triggered defense responses remain obscure. The recently discovered Pigm locus in rice encodes a cluster of NLRs, including PigmR, which confers broad-spectrum resistance to blast fungus. Here, we identify PIBP1 (PigmR-INTERACTING and BLAST RESISTANCE PROTEIN 1), an RRM (RNA-recognition motif) protein that specifically interacts with PigmR and other similar NLRs to trigger blast resistance. PigmR-promoted nuclear accumulation of PIBP1 ensures full blast resistance. We find that PIBP1 and a homolog, Os06 g02240, bind DNA and function as unconventional transcription factors at the promoters of the defense genes OsWAK14 and OsPAL1, activating their expression. Knockout of PIBP1 and Os06 g02240 greatly attenuated blast resistance. Collectively, our study discovers previously unappreciated RRM transcription factors that directly interact with NLRs to activate plant defense, establishing a direct link between transcriptional activation of immune responses with NLR-mediated pathogen perception.

overall_design: ChIP-Seq using leaves of the transgenic plants containing PIBP1-GFP


title: Beta cell dysfunction and identity loss induced by low dose of Interleukin-1β is associated with changes in histone acetylation and gene expression [RNA-seq]

first: Nils

last: Billestrup

overall_design: Examination of mRNA profile of primary mouse islets exposed or non-exposed to Interleukin-1B for 10 days

first: Adriana

last: Ibarra Urizar

first: Michala

last: Prause

first: Matthew

last: Wortham

first: Yinghui

last: Sui

first: Peter

last: Thams

first: Maike

last: Sander

first: Gitte

last: Christensen


title: Gene expression affected by loss-of- or gain-of-function of Dmrt3/Dmrta2 in the dorsomedial telencephalon

status: Public on Aug 03 2019

city: Kobe

first: Daijiro

last: Konno

address: 2-2-3 Minatojima Minamimachi Chuo-ku

department: Center for Developmental Biology (CDB)

institute: RIKEN

summary: We then examined the mutant mice that lack both Dmrt3 and Dmrta2 alleles, and found the size of the medial cortex including the hippocampus and the cortical hem was significantly reduced in mutant brains .To further investigate how Dmrt3 and Dmrta2 are involved in the development of the medial cortex, we applied gene expression profiling approach using whole genome DNA microarray to identify genes which are differentially expressed in Dmrt3/Dmrta2-knockdown cells. Cortical cells knocked-down both Dmrt3 and Dmrta2 exhibited a dramatic increase of Pax6 expression in the medial cortex, leading to the precocious neuronal differentiation, and simultaneous knockdown of Pax6 with Dmrt3/Dmrta2 rescued the phenotype. Our results unveil a key mechanism that mammalian Dmrt factors maintain more proliferative potential of neural progenitors by suppressing Pax6 expression in the developing cerebral cortex.

overall_design: We compared gene expression in cells transfected with control siRNAs, two different sets of Dmrt3/Dmrta2 siRNAs (set1 and set2), and a expression vector for Dmrta2, using 3  independent replicates in each group.