title: Med1 facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination.

city: New York

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

summary: Immunoglobulin class switch recombination (CSR) is initiated by the transcription-coupled recruitment of activation induced cytidine deaminase (AID) to immunoglobulin switch (S) regions. During CSR, the IgH locus undergoes dynamic three-dimensional structural changes in which promoters, enhancers and S regions are brought to close proximity. Nevertheless, little is known about the underlying mechanisms. Here we conditionally inactivated in B cells the Med1 subunit of mediator, a complex implicated in transcription initiation and long-range enhancer/promoter loop formation. We find that Med1-deficiency results in defective CSR, reduced acceptor switch region transcription and that this correlates with reduced long-range interactions between the acceptor switch regions and the Em enhancer, as determined by 4C-Seq. Our results implicate the mediator complex in the mechanism of CSR and are consistent with a model in which Med1 facilitates the transcriptional activation of switch regions and their long-range contacts with the IgH locus enhancers during CSR.

overall_design: 4C-seq data in resting and activated WT and Med1 mutant B cells. 4C bait was designed in the Eu enhancer of the Igh locus on chromosome 12. Primer sequences: 5’ TCTGTCCTAAAGGCTCTGAGA 3’ and 5’ GAACACAGAAGTATGTGTATGGA 3’.

first: Bernardo

last: San-Martin


title: RNAseq in IMR-32 neuroblastoma cells

status: Public on Feb 17 2016

city: Zurich

first: Claudia

last: Scheckel

state: NY

address: Schmelzbergstrasse 12

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital Zurich

type: Expression profiling by high throughput sequencing

summary: IMR-32 cells were subjected to lentiviral YRNA infection or nELAVL RNAi and/or UV stress followed by RNAseq analysis to monitor RNA level changes

overall_design: RNA from IMR-32 cells was Trizol extracted, Ribominus selected and submitted for high-throughput sequencing.

first: Elodie

last: Drapeau

first: Joseph

middle: D

last: Buxbaum

first: Robert

middle: B

last: Darnell


title: nELAVL HITS-CLIP in Alzheimer's Disease patients

summary: Human brain samples from control and advanced Alzheimer's Diseased subjects were subjected to HITS-CLIP to monitor nELAVL binding changes during AD progression

overall_design: Human brain samples were obtained from the Mount Sinai Brain Bank; samples were UV-irradiated and subjected to nELAVL HITS-CLIP (detailed desription in accompanying paper)


title: RNAseq in Alzheimer's Disease patients

summary: Human brain samples from control and advanced Alzheimer's Diseased patients were subjected to RNAseq analysis to monitor RNA level changes during AD progression

overall_design: Human brain samples were obtained from the Mount Sinai Brain Bank; RNA was Trizol extracted, Ribominus selected and submitted for high-throughput sequencing.


title: Comprehensive mutational analysis of primary and relapse acute promyelocytic leukemia

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: Acute promyelocytic leukemia (APL) is a subtype of myeloid leukemia characterized by   differentiation block at the promyelocyte stage. Besides the presence of chromosomal   rearrangement t(15;17) leading to formation of PML-RARA fusion, other genetic   alterations have also been implicated in APL. Here, we performed comprehensive   mutational analysis of primary and relapse APL to identify somatic alterations which   cooperate with PML-RARA in the pathogenesis of APL. We explored the mutational   landscape using whole-exome (n=12) and subsequent targeted sequencing of 398   genes in 153 primary and 69 relapse APL. Both primary and relapse APL harbored an   average of eight non-silent somatic mutations per exome. We observed recurrent   alterations of FLT3, WT1, NRAS and KRAS in the newly diagnosed APL, while   mutations in other genes commonly mutated in myeloid leukemia were rarely detected.   The molecular signature of APL relapse was characterized by emergence of frequent   mutations in PML and RARA genes. Our sequencing data also demonstrates incidence   of loss-of-function mutations in previously unidentified genes, ARID1B and ARID1A,   both of which encode for key components of the SWI/SNF complex. We show that   knockdown of ARID1B in APL cell line, NB4, results in large scale activation of gene   expression and reduced in vitro differentiation potential.

overall_design: Studying the effects of silensing ARID1B gene in NB4 cell lines

first: Vikas

last: Madan

first: Pavithra

last: Shyamsunder

first: Lin

last: Han

first: Anand

last: Mayakonda

first: Yasunobu

last: Nagata

first: Janani

last: Sundaresan

first: Deepika

last: Kanojia

first: Kenichi

last: Yoshida

first: Saravanan

last: Ganesan

first: Norimichi

last: Hattori

first: Noreen

last: Fulton

first: Kar-Tong

last: Tan

first: Tamara

last: Aplermann

first: Ming-Chung

last: Kuo

first: Shahrbano

last: Rostami

first: Jairo

last: Matthews

first: Masashi

last: Sanada

first: Li-Zhen

last: Liu

first: Yuichi

last: Shiraishi

first: Satoru

last: Miyano

first: Ezhilarasi

last: Chendamarai

first: Hsin-An

last: Hou

first: Gregory

last: Malnassy

first: Tobias

last: Ma

first: Manoj

last: Garg

first: Ling-Wen

last: Ding

first: Qiao-Yang

last: Sun

first: Wenwen

last: Chien

first: Takayuki

last: Ikezoe

first: Michael

last: Lill

first: Andrea

last: Biondi

first: Richard

middle: A

last: Larson

first: Bayard

middle: L

last: Powell

last: Lübbert

first: Wee

middle: J

last: Chng

first: Hwei-Fang

last: Tien

first: Michel

last: Heuser

first: Arnold

last: Ganser

first: Maya

last: Koren-Michowitz

first: Steven

middle: M

last: Kornblau

first: Hagop

last: Kantarjian

first: Daniel

last: Nowak

first: Wolf-Karsten

last: Hoffmann

first: Henry


title: The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

country: USA

institute: National Institutes of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We addressed the roles of three nucleosome spacing enzymes (ISW1, ISW2 and CHD1) in specifying chromatin organization in S. cerevisiae.

overall_design: Comparison of budding yeast nucleosome positions obtained using micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq). We sequenced nucleosomes from isogenic strains with the isw1Δ, isw2Δ or chd1Δ mutations in all combinations. We measured gene activity by ChIP-seq for the Rpb3 subunit of RNA polymerase II for some of these mutants.

first: Josefina

last: Ocampo

middle: V

first: Peter

middle: R

last: Eriksson

first: David

last: Clark


title: nELAVL HITS-CLIP in IMR-32 neuroblastoma cells

first: Claudia

last: Scheckel

summary: Non-stressed and UV-stressed IMR-32 cells were subjected to HITS-CLIP to monitor nELAVL binding changes during AD progression

overall_design: Nonstressed and stressed IMR-32 cells were UV-irradiated and subjected to nELAVL HITS-CLIP (detailed desription in accompanying paper)

first: Elodie

last: Drapeau

first: Joseph

last: Buxbaum

first: Robert

last: Darnell


title: nELAVL HITS-CLIP and RNA-seq in Alzheimer's Disease patients and IMR-32 neuroblastoma cells

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

overall_design: Refer to individual Series


title: Transcriptome analysis of Advanced glycation end products treated ligament cells

status: Public on Feb 16 2016

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

summary: Ossification of the posterior longitudinal ligament (OPLL) is formed by heterogeneous ossification of posterior longitudinal ligament. The patho-mechanism of OPLL is still largely unknown. Recently, disorders of metabolism are thought to be the center of many diseases such as OPLL.  Advanced glycation end product (AGE) are accumulated in many extracellular matrixes such as ligament fibers, and it can functions as cellular signal through its receptor (RAGE), contributing to various events such as atherosclerosis or oxidative stress. However, its role in OPLL formation is not yet known. Therefore, we performed high-through-put RNA sequencing on primary posterior longitudinal ligament cells treated with different doses of AGEs (1µM, 5µM and negative control), with or without BMP2 (1µM).

overall_design: mRNA profiles of Primary human posterior longitudinal ligament cells stimulated with various stimuli (Control, 1µM AGE-BSA, 5µM AGE-BSA, 1µM AGE-BSA with BMP2, 5µM AGE-BSA with BMP2) were generated by deep sequencing on Ion Proton

first: Zhimin

last: He


title: Genome-wide translational analysis of the effect of acute endurance exercise on mouse gastrocnemius

city: Tokorozawa

first: Hiroaki

last: Sako

country: Japan

institute: Waseda University

summary:
Purpose: The aim of this study is to investigate the translational regulation of skeletal muscle during acute endurance exercise.
Methods: We used mRNA-Seq and ribosome profiling to examine transcriptional and translational regulation, respectively.
Result: There were clear distinctions between the profiles of transcription and translation even at a basal condition. TOP-motif genes were translationally suppressed immediately after the exercise. Other genes, such as Slc25a25 was significantly translationally up-regulated presumably in a mTOR-independent manner.
Conclusion: There were diverse regulation between transcription and translation. Although many focused on overall protein synthesis to understand the effect of exercise, translational regulation of individual genes are required.

overall_design: Transcriptional and translational profiles of mouse gastrocnemius with or without acute endurance exercise were generated using Ion PGM sequencer.


title: RNA-Sequencing of HUVEC treated with Tie2 activating antibody

status: Public on Feb 15 2016

city: Irvine

first: Hosung

last: Bae

state: CA

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

summary: We analyzed genome-wide transcriptional changes induced by ABTAA+Ang2, using RNA-seq analysis of HUVECs

overall_design: Examination of 3 different antibodies treated to HUVEC to analyze the effect of Tie2 activation

first: Gou

last: Koh

first: Jin-Sung

last: Park


title: Genome-wide MAF1-dependent regulation of RNA polymerase III transcription [ChIP-Seq]

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

summary: In higher eukaryotes, an important mechanism to tune translation in different tissues and conditions is mTORC1-dependent regulation of tRNAs transcription by RNA polymerase III (Pol III), as the relative amount of tRNAs tightly coordinates with the translational needs of the cell. mTORC1 contributes to regulate protein synthesis through its direct substrate MAF1, which functions as a negative regulator of Pol III transcription in response to stimuli such as serum starvation or rapamycin treatment. Here, we applied ChIP-seq to examine the Pol III occupancy profile in human fibroblasts and report evidence of a genome wide, MAF1-dependent coordinated response to favorable or stress growth conditions. Strikingly, while a set of genes is extremely responsive in terms of Pol III binding, other genes are mostly unperturbed, yet associated with transcriptionally engaged polymerases as revealed by nascent EU-labeled RNA-seq (neuRNA-seq). As shown by DamIP-seq, the responsiveness of a subset of genes is tightly connected to the rapid and transient interaction of MAF1 with DNA-bound Pol III.

overall_design: We performed duplicate ChIP-seq experiments for the Rpc4 (POLR3D) subunit of RNA polymerase III in IMR90hTert cells grown in the presence of fetal bovine serum (FBS), serum starved (SS), serum starved and treated with insulin (SS+I), serum starved and treated with insulin and rapamycin (SS+R+I). Additional ChIP-seq profiles were generated in cells treated with MAF1 siRNAs and serum starved. MAF1 binding was addressed by DamIP-seq, using two replicates per clone of IMR90hTert cells expressing HA-tagged MAF1-DamK9A (2 different clones) or EGFP-DamK9A (2 different clones). To monitor dynamic transcription profiles we did neusRNA-seq in IMR90hTert cells EU-labeled or mock (DMSO)-labeled. For both DamIP-seq and neusRNA-seq, cells were either unperturbed or serum starved.

first: Andrea

last: Orioli

first: Viviane

last: Praz

first: Philippe

last: l'Hote

first: Nouria

last: Hernandez


title: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors

city: Cambridge

first: Omer

last: Yilmaz

state: MA

address: 77 Massachusetts Avenue, 76-353D

department: Biology

institute: Koch Institute for Integrated Cancer Research at MIT

summary: Little is known about how pro-obesity diets regulate tissue stem and progenitor cell function. Here we find that high fat diet (HFD)-induced obesity augments the numbers and function of Lgr5+ intestinal stem cells (ISCs) of the mammalian intestine. Like HFD, ex vivo treatment of intestinal organoid cultures with palmitic acid (PA), a constituent of the HFD, enhances the self-renewal potential of these organoid bodies. Mechanistically, HFD induces a robust peroxisome proliferator-activated receptor delta (PPAR-delta signature in intestinal stem and progenitor cells and pharmacologic activation of PPAR-delta recapitulates the effects that HFD has on these cells. Interestingly, HFD- and agonist-activated PPAR-delta signaling endows organoid-initiating capacity to non-stem cells and enforced PPAR-delta signaling permits these non-stem cells to form in vivo tumors upon loss of the tumor suppressor Apc. These findings highlight how diet-modulated PPAR-delta activation alters not only the function of intestinal stem and progenitor cells but also their capacity to initiate tumors.

overall_design: mRNA profiles of intestinal stem cells (GFP-Hi) and progenitors (GFP-Low) from WT or HFD fed mice were generated by deep sequencing using HiSeq 2000.


title: Age and Nursing Affect the Neonatal Porcine Uterine Transcriptome

city: New Brunswick

first: Caroll

last: Bagnell

state: New Jersey

address: 59 Dudley Road

department: Animal Sciences

institute: Rutgers University

summary: Age- and lactocrine-sensitive elements of the neonatal porcine uterine developmental program are undefined. Here, effects of age and nursing for 48 h from birth (postnatal day = [PND] 0) on the uterine transcriptome at PND 2 were identified using RNA sequencing.

overall_design: Pig uterine tissues were obtained from neonatal gilts (n = 4/group) within 1 h of birth [postnatal day (PND) 0], or 48 h after nursing ad libitum (PND 2N), or feeding a commercial milk replacer (PND 2R).

first: Carol

first: Frank

middle: F

last: Bartol


title: Ribosome profiling of harringtonine-treated SUM1315 cells

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: SUM1315 were treated with harringtonine, and an untreated control sample was taken. Ribosome profiling was performed on these samples.

overall_design: 1 treated and 1 untreated sample

first: Fabricio

last: Loayza-Puch

first: Jelle

last: Zijlstra

first: Joachim

last: Oude Vrielink

first: Rui

last: Lopes

first: Alejandro

middle: P

last: Ugalde

first: Axel

last: Bex

first: Reuven

last: Agami


title: Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Significance of RNA methylation in the context of HIV-1 infection in human T cells

overall_design: MeRIP-Seq of Control and HIV-infected MT4 T-Cells

first: Gianluigi

last: Lichinchi

first: Shang

last: Gao

first: Yogesh

last: Saletore

first: Vikas

last: Bansal

first: Tariq

last: Rana


title: Genome-wide MAF1-dependent regulation of RNA polymerase III transcription

first: Nicolo

last: Riggi


title: RNA-seq analysis of hair follicle stem cell transcriptome upon loss of the transcription factor FOXC1

first: Kenneth

last: Lay

address: 1230 York Avenue

institute: The Rockefeller University

summary: We report downstream gene expression changes in stem cells of the adult mouse hair follicle upon conditional ablating of the transcription factor Forkhead Box C1 transcription factor (FOXC1). Hair follicles undergo cycles of rest (telogen; Tel) and regeneration (anagen; Ana). As such, we performed our analysis on these two different stages of hair follicles.

overall_design: mRNA-sequencing of WT vs. Foxc1-conditional or inducible KO (Foxc1-cKO or iKO) hair follicle stem cells (HFSCs) purified from mouse dorsal back skin by flow-activated cell sorting (FACS).

first: K

first: E

last: Fuchs


title: Genome-wide MAF1-dependent regulation of RNA polymerase III transcription [RNA-Seq]

first: Andrea

last: Orioli

first: Viviane

last: Praz

first: Philippe

last: l'Hote

first: Nouria

last: Hernandez


title: Transcriptome analysis in Haematococcus pluvialis: astaxanthin induction by salicylic acid (SA) and jasmonic acid (JA)

city: Zibo

first: chunxiao

last: meng

state: Shandong

address: No. 266 Xincun West Road, Zhangdian District

institute: Shandong University of Technology

summary: Haematococcus pluvialis transcriptome analysis

overall_design:
The genetic transcriptome details of astaxanthin biosynthesis were analysed by exposing the algal cells to 25 mg/L of SA and JA for 1, 6 and 24 hours, plus to the control (no stress).
SRP062153
PRJNA292140

first: Zhengquan

first: Chunxiao

last: Meng


title: Genome-wide CRISPR-Cas9 screens reveal loss of redundancy between PKMYT1 and WEE1 in Glioblastoma stem-like cells

city: Seattle

first: Patrick

last: Paddison

state: WA

address: 1100 Fairview Ave N, C3-187

institute: Fred Hutchinson Cancer Research Center

summary: To identify new therapeutic targets for Glioblastoma (GBM), we performed genome-wide CRISPR-Cas9 "knockout" (KO) screens in patient-derived GBM stem-like cells (GSCs) and human neural stem/progenitors (NSCs), non-neoplastic stem cell controls, for genes required for their in vitro growth.  Surprisingly, the vast majority GSC-lethal hits were found outside of molecular networks commonly altered in GBM and GSCs (e.g., oncogenic drivers).  In vitro and in vivo validation of GSC-specific targets revealed several strong hits, including the wee1-like kinase, PKMYT1/Myt1.  Mechanistic studies demonstrated that PKMYT1 acts redundantly with WEE1 to inhibit Cyclin B-CDK1 activity via CDK1-Tyr15 phosphorylation and to promote timely completion of mitosis in NSCs.  However, in GSCs, this redundancy is lost, likely as a result of oncogenic signaling, causing GBM-specific lethality.

overall_design: A whole-genome CRISPR-Cas9 knockout screens targeting over 18,000 genes using the all-in-one LV-sgRNA:Cas9 platform system were performed using a “shot gun” approach by transducing 2 GBM patient-derived isolates and 2 human neural stem cell isolates with the pool library (2 biological replicates), and cultures were outgrown for ~3 weeks.  The end time point of each screen was compared to day 0 in order to determine which sgRNAs were overrepresented or underrepresented in the population.

first: Chad

last: Toledo

first: Yu

last: Ding

first: Ryan

last: Basom

first: Jeffery

last: Delrow

first: James

last: Olson


title: MSI2 is required for maintaining activated myelodysplastic syndrome stem cells

first: Alexendar

middle: Reinaldo

last: Perez

department: Computational Biology

institute: Memorial Sloan Kettering

summary: Analysis of musashi2 contribution towards maintaing myelodysplastic phenotype in stem cells. We find that musashi2 plays an integral role in maintaining the myelodysplastic phenotype

overall_design: Control, NUP98-HOXD13; NHD13, NHD13/MSI2 bone marrow was transplated allowed to engraft into lethally irradiated congenic CD45.1 animals. Mice were then fed doxycycline to induce MSI2 overexpression.  Mice were induced for 3 months and then CD45.2 Lineage lo Sca1+ and Kit+ cells were sorted and then assessed for gene expression.

first: Michael

last: Kharas


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Liver_mRNA]

city: Princeton

first: Jeff

last: Aaronson

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the liver of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Striatum_miRNA]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the striatum of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Cortex_miRNA]

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the cortex of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: Global Translational Impacts of the Loss of the tRNA Modification t6A in Yeast

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

summary: The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The importance of t6A in decoding has been studied for the past 40 years, but the cellular role has remained unclear. In this work, we examined the genome-wide effect to translation during the absence of t6A. In accordance with the previous experiments using single gene reporters, absence of t6A led to a increase of upstream non-AUG initiation of translation and increased translation ambiguities. Surprisingly, absence of t6A did not lead to a global and cataclysmic frame-shifting, but instead occurred only in a few genes. Restoration of protein homeostasis through the overexpression of Unfolded Protein Response (UPR) factors or the addition of L-homoserine suppressed the slow growth phenotype seen in t6A-defcient strains.

overall_design: 4 samples

middle: C

last: Thiaville

first: Rachel

last: Legendre

first: Diego

last: Rojas-Benítez

first: Agnès

last: Baudin-Baillieu

first: Isabelle

last: Hatin

first: Guilhem

last: Chalancon

first: Alvaro

last: Glavic

first: Valérie

last: de Crécy-Lagard


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Striatum_mRNA]

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the striatum of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: Identification of a Molecular Signature for Acute Lyme Disease by Human Transcriptome Profiling

city: San Francisco

first: Charles

last: Chiu

address: 185 Berry Street, Box 0134

department: Laboratory Medicine

institute: University of California, San Francisco

summary: Lyme disease is challenging to diagnose, as clinical manifestations are variable and current tools to detect nucleic acid or antibody responses from Borrelia burgdorferi infection have low sensitivity.  Here we conducted the first study of the global transcriptome of patients with Lyme disease to identify potential diagnostic biomarkers.  Twenty-nine patients were enrolled and compared to 13 healthy controls at three time points after infection.  Fifteen publicly available transcriptome datasets from patients in vivo or infection models in vitro were used to assess specificity of differentially expressed genes (DEGs).  We found that Lyme disease results in profound and sustained changes in the patient transcriptomes, with a specific signature that shares ≤44% DEGs with other infections.

overall_design: Gene expression profile from peripheral mononuclear blood cells (PBMC) of Lyme disease patients against healthy controls was undertaken. A total of 29 Lyme disease patients were sampled at 3 time points: acute Lyme pre-treatment (V1), 3 weeks later, immediately following completion of a standard course of antibiotics (V2), and 6 months following treatment completion (V5). 13 healthy controls were also sampled at one time point. Total RNA was extracted from 10e7 PBMC, followed by mRNA purification, paired-end barcode library preparation and sequencing on an Illumina Hiseq 2000.

first: Jerome

last: Bouquet

middle: Y


title: BET inhibition releases the Mediator complex from specific cis elements in acute myeloid leukemia cells (ChIP-Seq II)

status: Public on Mar 01 2016

city: Cold Spring Harbor

first: Anand

middle: S

last: Bhagwat

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Genome occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of Brd4 with or without Doxycycline treatment to induce Med12 or Med23 shRNAs in MLL-AF9 transformed acute myeloid leukemia cells (RN2)

first: A

first: C

last: Vakoc


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Cortex_mRNA]

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the cortex of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.


title: Discovery and profiling conserved and novel miRNAs involved in ovule development of Ginkgo biloba by deep sequencing

status: Public on Feb 12 2016

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: High-throughput small RNA sequencing were performed to identify a large number of miRNAs and their targets in mature  G. biloba ovules. Our study is the first to provide useful information for uncovering the regulatory networks of miRNAs in basal gymnosperm G. biloba ovules.

overall_design: small RNA sequencing in ovules of G. biloba

first: Jian

middle: G

last: Zhao


title: Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

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

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Refer to individual Series


title: Small RNA profiles of the rice non-pollen male sterile line Wuxiang S reveal miRNAs involved in the fertility transition

status: Public on Feb 14 2016

city: Wuhan city

first: Hongyuan

last: zhang

state: Hubei Provinve, P.R. China

address: Wuhan Academy of Agricultural Sciences, Hanshi Road, Huangpi District, Wuhan,430065, Hubei Province, China

institute: Wuhan Academy of Agricultural Sciences

summary: Illumina sequencing was employed to examine the expression profiles of rice anther miRNAs from the a non-pollen male sterile line Wuxiang S (WXS), one of photo-thermo sensitive genical male sterile (PTGMS) line rice, during in the fertility transition stage. A total of 493 known miRNAs and 273 novel miRNAs were identified during rice anther development. Based on the number of sequencing reads, a total of 26 miRNAs were discovered to be significant difference expression between WXS(S, Sterility) and WXS(F, Fertility), and the results were partially validated by qRT-PCR. Among these, 11 miRNAs were decreased and 15 miRNAs were increased in WXS(S) compared with WXS(F). The expression patterns for targets of osa-miR156a-j, osa-miR3879, osa-miR159c/d/e, osa-miR171a/c/e/i, osa-miR398b, osa-miR164d, osa-miR528 and osa-miR408 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. These targets have previously been reported to be related with pollen development and male sterility, suggesting that miRNAs might act as regulators of rice anthers. Furthermore, miRNA editing events were observed. The U-to-C and U-to-A editing phenomenon was validated by molecular cloning and sequencing.

overall_design: Examine small RNA profiles change of four tissues of the rice non-pollen male sterile line Wuxiang S under two different environments.

last: Zhang

first: Jihong

last: Hu

first: Yi

last: Ding


title: Gene expression profiles of MBP-specific T cells during experimental autoimmune encephalomyelitis

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: 2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF.

overall_design: 2nd generation sequencing of MBP-specific T cells retrieved from blood and CNS compartments during experimental autoimmune encephalomyelitis

first: Christian

last: Schläger

first: Henrike

last: Körner

first: Francesca

last: Odoardi

first: Alexander

last: Flügel

first: Thomas

last: Lingner

last: Salinas-Riester


title: Tcf1 and Lef1 establish CD8+ T cell identity via their intrinsic histone deacetylase activity

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University


title: RNA Sequencing of default, melanocyte biased and enteric human neural crest populations (NC) and neuroectoderm (CNS)

city: New York

first: Lorenz

last: Studer

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We have generated expression profiles of three different neural crest populations from human embryonic stem cells.  These profiles were compared to a neuroectoderm population.  We find that the neural crest populations are separable and distinct.

overall_design: All cell types were differentiated from human embryonic stem cells.  Neural crest populations were sorted on day 12 for CD49.  The neuroectoderm cells were unsorted and harvested on day 12 of differentiation.

first: Faranak

last: Fattahi


title: Impact of Tcf1 and Lef1 deficiency on mature CD8 thymocytes

summary: Comparison of transcriptome between control and Tcf1/Lef1-deficient mature CD8 thymocytes

overall_design: Control mice or those are deficient for Tcf1 and Lef1 transcription factors (deleted by CD4-Cre) were used to isolate thymocytes. The thymocytes were surface-stained to identify TCRbeta high, CD69–, CD24– CD8+ subsets. These cells were sorted for RNAseq analysis.

first: Hai-Hui

last: Xue


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [AllelicSeries_6month_TissueSurvey_mRNA]

first: Jeff

last: Aaronson

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 6 month old knock-in mice with CAG lengths of 175 along with littermate control wild-type animals.

overall_design: mRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Brown Adipose tissue, White Adipose tissue around Gonad,  White Adipose tissue around Intestine, Brain - Brainstem, Brain - Cerebellum, Brain - Hippocampus, Brain - Hypothalamus/Thalamus, Corpus callosum, Gastrocnemius, Heart, and Skin of 6 month old knock-in mice with CAG lengths of 175 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [striatum; cortex; liver; tissue survey]

overall_design:
Refer to individual Series
Langfelder 2016 (PMID 26900923) discusses data in GSE65770 GSE65772 GSE65774 GSE65775.
Langfelder 2018 (PMID 29324753) discusses data in GSE65769 GSE65771 GSE65773.


title: flavodentata

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

institute: INRA

summary: Study of the role of the FLV/DOT4 protein in post-transcriptional regulation of chloroplast gene expression. DOT4 is a pentatricopeptide repeat protein targeted to the chloroplast which regulates the editing of the rpoC1 transcript

overall_design:
The editing level of rpoC1 varies from one tissue to the other and because the main macroscopic phenotype of the flv/dot4 mutant are white leaf margins. We compared  the leaf border to the leaf center of wild-type Col0 plants but also the leaf borders of col0 and flv/dot4 knock out mutants by sequencing total RNA depleted from rRNA  to get a global view of gene expression (including post-transcrional modifications) of the 3 plant genomes: nucleus, chloroplast and mitochondria.
mRNA seq on wild-type Col and FLV mutants knock out.

first: Etienne

last: Delannoy

first: Sandrine

last: Balzergue

first: Rémi

last: Bounon

first: Véronique

last: Brunaud

first: Marie-Laure

last: Martin-Magniette


title: Genome-wide MAF1-dependent regulation of RNA polymerase III transcription [DamIP-Seq]

first: Nicolo

last: Riggi

address: Bugnon 25

institute: CHUV

summary: In higher eukaryotes, an important mechanism to tune translation in different tissues and conditions is mTORC1-dependent regulation of tRNAs transcription by RNA polymerase III (Pol III), as the relative amount of tRNAs tightly coordinates with the translational needs of the cell. mTORC1 contributes to regulate protein synthesis through its direct substrate MAF1, which functions as a negative regulator of Pol III transcription in response to stimuli such as serum starvation or rapamycin treatment. Here, we applied ChIP-seq to examine the Pol III occupancy profile in human fibroblasts and report evidence of a genome wide, MAF1-dependent coordinated response to favorable or stress growth conditions. Strikingly, while a set of genes is extremely responsive in terms of Pol III binding, other genes are mostly unperturbed, yet associated with transcriptionally engaged polymerases as revealed by nascent EU-labeled RNA-seq (neuRNA-seq). As shown by DamIP-seq, the responsiveness of a subset of genes is tightly connected to the rapid and transient interaction of MAF1 with DNA-bound Pol III.

overall_design: We performed duplicate ChIP-seq experiments for the Rpc4 (POLR3D) subunit of RNA polymerase III in IMR90hTert cells grown in the presence of fetal bovine serum (FBS), serum starved (SS), serum starved and treated with insulin (SS+I), serum starved and treated with insulin and rapamycin (SS+R+I). Additional ChIP-seq profiles were generated in cells treated with MAF1 siRNAs and serum starved. MAF1 binding was addressed by DamIP-seq, using two replicates per clone of IMR90hTert cells expressing HA-tagged MAF1-DamK9A (2 different clones) or EGFP-DamK9A (2 different clones). To monitor dynamic transcription profiles we did neusRNA-seq in IMR90hTert cells EU-labeled or mock (DMSO)-labeled. For both DamIP-seq and neusRNA-seq, cells were either unperturbed or serum starved.

first: Andrea

last: Orioli

first: Viviane

last: Praz

first: Philippe

last: L'Hote

first: Nouria

last: Hernandez


title: Restrictions in amino acid availability revealed by differential ribosome codon reading

first: Koos

last: Rooijers

institute: Netherlands Cancer Institute


title: m1A marks translation initiation sites in human and mouse messenger RNA

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Homo sapiens
Mus musculus


title: Histone H4 acetylation and epigenetic reader Brd4 are critial regulators of pluripotency in embryonic stem cells

status: Public on Feb 11 2016

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania

summary: Histone H4ac and Brd4 are critical for ESCs

overall_design: 12 samples: 2 replicates for each ChIP, 2 replicates for each input sample.

first: Michelle

last: Gonzales-Cope

first: Simone

last: Sidoli

first: Natarajan

last: Bhanu

first: Kyoung-Jae

first: Benjamin

last: Garcia


title: To identify and study the regulation of cellulosic enzymes in a biomass degrading gut fungal isolate from horse (Piromyces sp. finn)

city: University of California Santa Barbara

last: O’Malley

address: Engineering 2 Bldg

department: Chemical Engineering

institute: UC Santa Barbara

summary: Here, we develop a systems-level approach leveraging powerful next generation sequencing, proteomics and phenotypic studies to rapidly obtain an integrated view of lignocellulose degradation in the earliest free living fungi

overall_design: RNA-seq of Piromyces grown on Glucose, Cellulose, Cellulobiose, Avicel, Filter paper, and time-course of transient glucose pulse (catabolite repression).  N>=2

first: Kevin

last: Solomon

first: Charles

last: Haitjema

first: John

middle: K

last: Henske

first: Sean

last: Gilmore

first: Diego

last: Borges-Rivera

first: Michael

last: Theodorou

first: Anna

last: Lipzen

first: Igor

last: Grigoriev

first: Aviv

last: Regev

first: Dawn

last: Thompson


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Liver_miRNA]

first: Jeff

last: Aaronson

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on tissue samples from the liver of 2, 6, and 10 month old knock-in mice with CAG lengths of 20, 80, 92, 111, 140, 175 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [Chip-Seq]

city: SAN FRANCISCO

first: Benoit

middle: G.

last: Bruneau

address: 1650 OWENS STREET

institute: GLADSTONE INSTITUTES

summary:
Genome-wide occupancy analysis of TBX5, NKX2-5 and GATA4  in differentiating WT, Nkx2-5KO (NKO), Tbx5KO (TKO) and Nkx2-5;Tbx5KO (DKO) cells at the cardiac precursor (CP) and cardiomyocyte (CM) differentiation stages.

Analysis of TBX5, NKX2-5 and GATA4 occupancy a and gene expression in WT, Tbx5KO, Nkx2-5KO and DoubleKO precursor (CP) and mature (CM) in vitro differentiated cardiomyocytes.

overall_design:
We performed ChIP-exo experiments for NKX2-5, TBX5 and GATA4 in differentiating WT, Nkx2-5KO (NKO), Tbx5KO (TKO) and Nkx2-5;Tbx5KO (DKO) cells at the CP and CM stages.
ChIP-exo was performed according to methods published previously (Boyer et al., 2005; Serandour et al., 2013; Wamstad et al., 2012) using specific antisera to TBX5 (sc-17866 XS, lot no. B1213), NKX2-5 (sc-8697 XS, lot no. B1213), and GATA4 (sc-1237 XS, lot no. B1213) on chromatin isolated from 10 mill. cells. Re-ChIP-exo was performed from 40 mill cells, combining methods published previously (Serandour et al., 2013; Shankaranarayanan et al., 2011).

ChIP-exo Analysis:
Barcoded libraries were single-end 50bp sequenced on an Illumina HiSeq 2500 instrument. Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using bowtie2 (ChIP-seq, ChIP-exo) (Langmead and Salzberg, 2012). Samtools was then used to retain reads that had a mapq score of 30 or greater (Li et al., 2009), thereby ensuring that each mapped uniquely to the genome assembly. The 5' -most position of reads that mapped to the reference strand and the 3â??-most position of reads that mapped to the non-reference strand were identified for each read as the actual edges of each exonuclease-treated fragment. The genome was divided into 20bp genomic bins and a normalized tag density was calculated for each genomic bin 'i' as follows:

    tag density(i)=([#tags within 75bp of i] X [total# genomic bins])/(total #of tags)

To identify broad regions of binding, bins with tag densities of greater than 100 were merged to generate a peak list for each sample. Within 1kb of each region, strand-specific single-base-resolution tag densities were calculated for each dataset by dividing each region into 1bp bins, then counting the number of tags within 5bp of each bin. For each region of binding, the footprint for each bound region was defined as the span from the peak position of '+' strand binding to the peak position of '-' strand binding as seen from the high-resolution tag densities. For subsequent analyses, any overlapping footprint for replica/factor/stage/genotype was merged to generate an average footprint list. Only average footprints present in at least two replicas of the same factor, stage and genotype were considered (Final Average Footprints).

first: Luis

last: Luna-Zurita


title: MicroRNAs for fine-tuning of mouse Embryonic Stem Cell fate decision through regulation of TGF-β signaling

city: Heraklion, Crete

first: Christiana

last: Hadjimichael

address: Nikolaou Plastira 100

department: Institute of Molecular Biology and Biotechnology (IMBB)

country: Greece

institute: Foundation for Research and Technology - Hellas (FORTH)

summary: Over the past years, microRNAs (miRNAs) have emerged as crucial factors that regulate self-renewal and differentiation of embryonic stem cells (ESCs). Although much is known about their role in maintaining ESC pluripotency, the mechanisms by which they affect cell fate decisions remain poorly understood. By performing deep sequencing to profile miRNAs expression in mouse ESCs (mESCs) and differentiated embryoid bodies (EBs), we identified four differentially expressed miRNAs. Among them, miR-191 and miR-16-1 are highly expressed in ESCs and repress Smad2, the most essential mediator of Activin-Nodal signaling, resulting in the inhibition of mesendoderm formation. miR-23a, which is also downregulated in the differentiated state, suppresses differentiation towards the endoderm and ectoderm lineages. We further identified miR-421 as a differentiation-associated regulator through the direct repression of core pluripotency transcription factor Oct4 and BMP-signaling components, Smad5 and Id2. Collectively, our findings uncover a regulatory network between the studied miRNAs and both branches of TGF-β/BMP signaling pathways revealing their importance for ESC lineage decisions.

overall_design: miRNA profiles of ESCs and differentiated EBs D8 were generated by deep sequencing, in duplicate, using ION TORRENT PGM platform

first: Christoforos

last: Nikolaou

first: Joseph

last: Papamatheakis

first: Androniki

last: Kretsovali


title: miR-195-5p Regulates Hair Follicle Inductivity of Dermal Papilla Cells by Suppressing Wnt/β-catenin Activation

city: Ghantou

first: Yang

last: Liu

state: Guangdong

address: No.22, Xingling Street, Jinping District

department: Department of Histology and Embryology

institute: Shantou University Medical College

summary: We performed microarray analysis to detect the differential expression of miRNAs in early- vs. late-passage DP cells by microarray profiling of the total of 1924 hsa-miRNAs (miRNAs)

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In the study presented here, the human scalp specimens were obtained from selected face-lift surgeries of healthy patients . We randomly select three dermal papilla cell strains to subculture and compare the differential expression of miRNAs in early- vs. late-passage DP cells by microarray analysis


title: Gene expression profiling of Drosophila melanogaster 30 minutes after alcohol exposure

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

summary: We sequenced mRNA extracted from heads of a D. melanogaster population that was sedated with a stream of ethanol saturated vapor, 30 minutes before RNA extraction; and from an age-matched untreated control group. Differential gene expression between the two groups was calculated and reported.

overall_design: Examination of mRNA levels in heads of D. melanogaster adult females after ethanol exposure was performed using next generation sequencing (NGS) technology.

first: Andrzej

middle: Z

last: Pietrzykowski


title: Comprehensive Evaluation of AmpliSeq Transcriptome, a Novel Targeted Whole Transcriptome RNA Sequencing Methodology for Global Gene Expression Analysis.

city: Milwaukee

first: Wenli

last: Li

state: Wisconsin

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Background: Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis.  However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeqTM Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq.To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs).
Results: Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson’s r=0.92) and Ion Torrent Proton (Pearson’s r=0.92). We used ROC, Matthew’s correlation coefficient and RMSD to determine the overall performance characteristics. All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations.
Conclusions: Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy.

overall_design: Comprehensive, performance evaluation of AmpliSeq Transcriptome to standard whole-transcriptome RNA-sequencing methods for large-scale, genome-wide differential gene expression analysis. We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs).

first: Amy

last: Turner

first: Praful

last: Aggarwal

first: Andrea

last: Matter

first: Erin

last: Storvick

first: Donna

last: Arnet

first: Ulrich

last: Broeckel


title: Redefining the translational status of 80S monosomes

city: Darlinghurst

last: Heyer

state: NSW

address: 384 Victoria Street

department: Genomics & Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remains controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ~590 nucleotides and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.

overall_design: We examined the translational status of single 80S ribosomes using ribosome profiling, and compared these monosome footprints to both polysome ribosome footprints and general ribosome profiling.  RNASeq libraries were also prepared from the overall sample input.

first: E

first: J

last: Moore


title: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis [RNA-Seq]

first: Benoit

last: Bruneau

summary: Analysis of the changes in gene expression during in vitro cardiomyocyte differentiation due to the lack of Tbx5, Nkx2-5 or both.

overall_design:
We performed RNA-seq in WT, Tbx5KO (TKO), Nkx2-5KO (NKO) and Tbx5KO;Nkx2-5KO (DKO) cells at the cardiac precursor (CP) and cardiomyocyte (CM) differentiation stages.
Total RNA was isolated from 3 mill cells using TRizol Reagent. RNA-seq libraries were prepared according to NuGEN Ultralow V2 kit and paired-end 100bp sequenced on an Illumina HiSeq 2500 instrument.
Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using tophat2 (RNA-seq) (Kim et al., 2013). For each gene, reads were counted, and counts-per-million (CPM) calculated using featureCounts (Liao et al., 2014). Finally, edgeR was used to perform differential expression analyses (Robinson et al., 2010).

first: Luis

last: Luna-Zurita


title: Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis

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

overall_design: Refer to individual Series

first: Bogac

middle: L

last: Kaynak


title: Identification of genes that may predict response to azacitidine treatment.

status: Public on Feb 10 2016

city: Prague 2

first: Monika

last: Belickova

address: U nemocnice 1

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

summary: Azacitidine (AZA) is a hypomethylating drug used to treat disorders associated with myelodysplasia and related neoplasms. Approximately 50% of patients do not respond to AZA and have very poor outcomes. It is of great interest to identify predictive biomarkers for AZA responsiveness. Therefore, we searched for specific genes whose expression level was associated with response status.Using microarrays, we analyzed gene expression patterns in bone marrow CD34+ cells from 32 patients with myelodysplastic syndromes, chronic myelomonocytic leukemia, and acute myeloid leukemia with myelodysplasia-related changes before AZA therapy.

overall_design: Total RNA was isolated from bone marrow CD34+ cells obtained from myelodysplasia and related neoplasms  patients who underwent treatment with 5-azacytidine (AZA, Vidaza). Using Illumina Human HT-12 v. 4 microarrays, we assayed gene expression profiles in patient CD34+ cells before AZA treatment in order to collect basic data for search for markers of the prediction of therapy response.


title: C9orf72 BAC Transgenic Mice Display Typical Pathologic Features of ALS/FTD

city: Los Angeles

first: Jacqueline

middle: Gire

last: O'Rourke

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

summary: Noncoding expansions of a hexanucleotide repeat (GGGGCC) in the C9orf72 gene are the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia. Here we report transgenic mice carrying a bacterial artificial chromosome (BAC) containing the full human C9orf72 gene with either a normal allele (15 repeats) or disease-associated expansion (~100–1,000 repeats; C9-BACexp). C9-BACexp mice displayed pathologic features seen in C9orf72 expansion patients, including widespread RNA foci and repeat-associated non-ATG (RAN) translated dipeptides, which were suppressed by antisense oligonucleotides targeting human C9orf72. Nucleolin distribution was altered, supporting that either C9orf72 transcripts or RAN dipeptides promote nucleolar dysfunction. Despite early and widespread production of RNA foci and RAN dipeptides in C9-BACexp mice, behavioral abnormalities and neurodegeneration were not observed even at advanced ages, supporting the hypothesis that RNA foci and RAN dipeptides occur presymptomatically and are not sufficient to drive neurodegeneration in mice at levels seen in patients.

overall_design: To compare the RNA Seq profiles from the cortex and spinal cord of transgenic mice expressing unexpanded human C9orf72 (F08, n=4), expanded human C9orf72 (F112, n=3/4), and nontransgenic controls (n=4).

first: Robert

middle: H

last: Baloh


title: RNA-sequencing based analysis of Listeria monocytogenes 10403S::ΔBCHL Prha-sigH and  ΔBCHL Prha

city: Ithaca

first: Martin

last: Wiedmann

state: NY

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

summary: In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ΔBCHL Prha-sigH and  ΔBCHL Prha.  RNA-seq was performed on ΔBCHL Prha-sigH and  ΔBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. To identify sigH-dependent promoters, a new method of moving sliding windows of 50 nt along the whole genome was used to compare the normalized RNA-seq coverage (NRC) between the two strains. Using the standard whole gene differential expression analysis, significant upregulation of 5 genes in 4 operons was found in the sigH overexpressing strain. While with the sliding windiow analysis, 2 additional σH-dependent promoters were identified. Our results show that three σH-dependent transcritption units that encode competence proteins, including the comEABC , comGABCDEFG and coiA.

overall_design: Transcriptome profiles of L. monocytogenes 10403S::ΔBCHL Prha-sigH and  ΔBCHL Prha were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Yichang

last: Liu

first: Renato

last: Orsi


title: Feedback regulation of cholesterol metabolism by LeXis, a lipid-responsive non-coding RNA

first: Ascia

last: Eskin

state: California

address: 695 Charles Young Drive South  Gonda 5554

department: Human Genetics

institute: UCLA

summary: Abstract: The LXR and SREBP transcription factors are key regulators of cellular and systemic cholesterol homeostasis. The molecular mechanisms that integrate these pathways are incompletely understood. Here we show that ligand activation of LXRs in liver not only promotes cholesterol efflux, but also simultaneously inhibits cholesterol biosynthesis. We further identify the long non-coding RNA LeXis as an unexpected mediator of this effect. LeXis is robustly induced in mouse liver in response to western diet feeding or pharmacologic LXR activation. Expression of LeXis in liver inhibits cholesterol biosynthesis and lowers plasma cholesterol levels. Reciprocally, knockdown of LeXis increases hepatic cholesterol content and raises plasma cholesterol levels. LeXis interacts with the heterogeneous nuclear ribonucleoprotein Raly and regulates its binding to cholesterol biosynthetic gene promoters. These studies outline a regulatory role for a non-coding RNA in lipid metabolism and advance our understanding of the mechanisms orchestrating systemic sterol homeostasis.

overall_design: Global RNA expression from primary hepatocytes treated with or without GW3965 were compared by RNA-Seq.

first: Tamer

last: Sallam


title: New insights into the Plasmodium vivax transcriptome using RNA-seq

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

institute: Nanyang Technological University

summary: Transcription profile of the Plasmodium vivax intraerythrocytic cycle

overall_design: Total RNA in Plasmodium vivax strain at every 6 hour of intraerythrocytic cycle using RNA-seq

first: Lei

last: Zhu

first: Sachel

last: Mok

first: Peter

last: Preiser


title: Comparative transcriptome of the fertile and sterile buds of genic multiple-allele inherited male sterile AB line in Chinese cabbage

city: Shenyang

first: Chang

address: Dongling street

institute: Shenyang agriculture university

summary: we performed transcript profiling of male sterile and fertile buds from a multiple-allele inherited male sterile AB line using the Illumina high-throughput sequencing platform and analyzed differential gene expression at the transcriptional level.

overall_design:
Examination of mRNA levels in sterile and fertile buds of chinese cabbage

Please note that the 'Table_S*.xls' files contain the further-processed supplementary data. The data processing details are provided in the readme.xlsx.

first: Hui

last: Feng


title: Histone H3 lysine 4 acetylation-methylation dynamics define breast cancer subtypes [RNA-seq]

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: The onset and progression of breast cancer are linked to genetic and epigenetic changes that alter the normal programming of cells. Epigenetic modifications of DNA and histones contribute to chromatin structure that results in the activation or repression of gene expression. Several epigenetic pathways have been shown to be highly deregulated in cancer cells. Targeting specific histone modifications represents a viable strategy to prevent oncogenic transformation, tumor growth or metastasis. Methylation of histone H3 lysine 4 has been extensively studied and shown to mark genes for expression; however this residue can also be acetylated and the specific function of this alteration is less well known. To define the relative roles of histone H3 methylation (H3K4me3) and acetylation (H3K4ac) in breast cancer, we determined genomic regions enriched for both marks in normal-like (MCF10A), transformed (MCF7) and metastatic (MDA-MB-231) cells using a genome-wide ChIP-Seq approach. Our data revealed a genome-wide gain of H3K4ac associated with both early and late breast cancer cell phenotypes, while gain of H3K4me3 was predominantly associated with late stage cancer cells. Enrichment of H3K4ac was overrepresented at promoters of genes associated with cancer-related phenotypic traits, such as estrogen response and epithelial-to-mesenchymal transition pathways. Our findings highlight an important role for H3K4ac in predicting epigenetic changes associated with early stages of transformation. In addition, our data provide a valuable resource for understanding epigenetic signatures that correlate with known breast cancer-associated oncogenic pathways.

overall_design: RNA-Seq of cell lines MCF10A, MCF7 and MDA-MB-231.

first: Terri

last: Messier

first: Gordon

last: Jonathan

first: Joseph

last: Boyd

first: Coralee

last: Tye

first: Gillian

last: Browne

first: Janet

last: Stein

first: Jane

last: Lian

first: Gary


title: Expression data from fully-expanded leaflet of Bambara groundnut (S19-3 genotype)

city: Nottingham

first: Venkata Suresh

last: Bonthala

address: Wollaton Road

department: School of Computer Science

country: United Kingdom

institute: University of Nottingham

summary: Low temperature stress in a number of African countries, such as Botswana, at night can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, we made an attempt to identify and analyze the genes and gene modules associated with low temperature stress response in bambara groundnut using the cross-species microarray technique, as bambara groundnut has no microarray chip, coupled with network-based analysis.

overall_design: Two plants of the bambara groundnut genotype ‘S19-3’ were grown in controlled environment growth rooms at Sutton Bonington Campus, University of Nottingham under a 12 hour photoperiod and at a constant temperature of 27°C.  Plants were grown in soil columns containing a growing medium of 1 part John Innes 2 compost to 1 part sand, and were watered as required. A single, fully-expanded leaflet was sampled from each of the three plants growing at 27°C, snap frozen in liquid nitrogen and stored at -80°C. Plants were given a further 3 days at 27°C to recover from sampling before being moved to a controlled environment room at 23°C. On the fifth day at 23°C a single fully-expanded leaflet was sampled and stored, as described above. After 3 further days plants were moved to 18°C, and then five days later were sampled again.

first: Venkata

first: Katie

last: Mayes

first: Sean

first: Festo

last: Massawe

first: Jamie

last: Twycross


title: Inhibitors of the histone lysine demethylase KDM1A are broadly efficacious in AML by evicting the enzyme from chromatin [ChIP-Seq]

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Examine the distribution of KDM1A and the histone H3K4me2 mark on chromatin following treatment with two distinct classes of KDM1A inhibitors - an irreversible inhibitor (RN-1) and a reversible inhibitor (GSK690)

overall_design: 15 samples total from two treated cell lines - 9 from Kasumi-1 and 6 from SKNO-1.  Controls included were input DNA isolated from the treated cells.

first: John

last: McGrath

first: Kaylyn

last: Williamson

first: Patrick

last: Trojer

first: Charlie

last: Hatton


title: Inhibitors of the histone lysine demethylase KDM1A are broadly efficacious in AML by evicting the enzyme from chromatin


title: Transcriptome sequencing of human fetal heart

city: stanford

first: chunjiang

last: he

address: 265 campus drive

institute: stanford university

summary: We sequenced 2 heart samples from human fetal donors and detected the differential expressed mRNAs and lncRNAs. The network of significant differential expressed transcripts could be associated to developmental program.

overall_design: examination mRNA and lncRNA expression in heart tissues

first: Chunjiang

last: He

first: Kitchener

middle: D

last: Wilson

first: Haodi

last: Wu

first: Joseph


title: Inhibitors of the histone lysine demethylase KDM1A are broadly efficacious in AML by evicting the enzyme from chromatin [RNA-Seq]

summary: Investigating the effects of two different classes of KDM1A inhibitors on the transcriptome of AML cell lines

overall_design: 16 different samples with biological replicates.  Treatment for 24 and 72 hours with an irreversible KDM1A inhibitor (RN-1) or a reversible KDM1A inhibitor (GSK690) or an inactive isomer of the latter (GSK690*).


title: Probing Xist RNA structure in cells using Targeted Structure-Seq

status: Public on Feb 09 2016

city: West Haven

first: Matthew

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.

overall_design: Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.

first: Rui

last: Fang

first: Walter

middle: N

last: Moss

first: Michael

last: Rutenberg-Schoenberg


title: Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles

city: Kansas City

first: Lane

last: Christenson

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function.  While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased.  Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix.  Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle.

overall_design: Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles

first: R

last: Navakanitworakul

first: L


title: Chimeric RNA profiling demonstrates an association of alveolar rhabdomyosarcoma with specific stages of normal myogenesis

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

summary: Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts.

overall_design: Discovering fusion genes from muscle differentiated mesenchymal stem cells

first: Hui

last: Li


title: RNA-seq analysis of Selaginella kraussiana leaf, rhizophore, seedling and stem

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: Annotation of the draft assembly of selaginella kraussiana

overall_design: Total RNA obtained from the leaf, rhizophore, seedling and stem.


title: m1A marks translation initiation sites in human and mouse messenger RNA [Sequencing]

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

institute: Sheba Medical Center

summary: We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel sequencing

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Homo sapiens
Mus musculus

overall_design: Identification of m1A modified sequences in human, mouse and yeast cell lines

first: Dan

last: Dominissini

first: Chuan

first: Gideon

last: Rechavi


title: High-throughput measurements of fitness effects of mutations in the yeast U3 snoRNA

city: Edinburgh

first: Olga

middle: Anna

last: Puchta

address: Crewe Road

department: MRC Human Genetics Unit IGMM

institute: University of Edinburgh

summary: We used a molecular barcoding approach to quantify the fitness of ~60,000 randomly mutated variants of the Saccharomyces cerevisiae U3 snoRNA (the data were further used to calculate a map of intragenic epistatic interactions within this RNA molecule, as descibed in Puchta et al. 2016)

sample_organism:
Saccharomyces cerevisiae
synthetic construct

overall_design: We generated two independent mutant libraries ('Small' with ~3 and 'Big' with ~10 SNPs per allele) on centromeric plasmid, with 20nt random barcodes placed in a non-transcribed region downstream of the gene (PE Samples 30-37 - paired-end sequencing of: U3, 70nt linker and 20nt barcode); next we performed competition experiments in several conditions (E1-5) on populations of yeast cells transformed with both libraries and measured frequencies of mutated variants in time-points during the experiment by deep sequencing of barcodes (Samples 1-29).

first: Grzegorz

last: Kudla


title: ChIP-seq of three core components of the circadian clock (BMAL1, CLOCK and CRY1) in unsynchronized human U2OS cells

city: Lausanne

first: Laura

last: Symul

state: Station 15

address: EPFL SV IBI UPNAE, AAB 039

department: SV-IBI

institute: EPFL

summary: The human osteosarcoma cell line U2OS contains a functional circadian clock but expresses only a few rhythmic genes. We identified by ChIP-seq analysis 3040 binding sites of the circadian transcription factors BMAL1, CLOCK, and CRY1 in the genome of U2OS cells, comparable to the number found in highly rhythmic tissues like liver.

overall_design: ChIP was performed as described previously (Rey et al, 2011; doi:10.1371/journal.pbio.1000595) using confluent desynchronized U2OS cells and BMAL1, CLOCK, and CRY1-antibodies.  Immunoprecipitated chromatin (10 ng DNA of 8 independent BMAL1 ChIPs with enrichment levels > 80-fold, 9 ng DNA of a CRY1 ChIP with 10-fold enrichment, and 8 ng DNA of a CLOCK ChIP with 40-fold enrichment) was used for library preparation. Three lanes of the BMAL1 library, and one lane each of the CRY1 and CLOCK library were sequenced on the Illumina Genome Analyzer IIx using Single-Read Cluster Generation Kit and 36 Cycle Sequencing Kit v2  (Lausanne Genomics Technologies Facility).

first: Julia

last: Stefanski


title: The RNAseq of 79 small cell lung cancer (sclc) and 7 normal control

city: Gaithersburg

first: Dong

last: Shen

state: MD

address: MedImmune Way

department: Translational Science

institute: Medimmune

summary: Even though small cell lung cancer (SCLC) has entered the age of broad genomic analysis, platinum-based chemotherapy remains the standard care for SCLC. Topotecan is the only approved agent for recurrent or progressive SCLC (1).  In the absence of well-defined genomic biomarkers, clinical efficacy signals in genomically distinct subsets of SCLC could have been missed. Serine/Arginine Splicing Factor 1 (SRSF1) is a member of SR protein family. The deleterious consequences of overexpression of the SRSF1 proto-oncogene in human cancers suggest that there are complex mechanisms and pathways underlying SRSF1-mediated transformation (2). Whole exome and transcriptome sequencing of primary tumor SCLC from 99 Chinese patients has identified SRSF1 DNA amplification and mRNA over-expression which predicts poor survival in Chinese SCLC patients. In vitro and in vivo studies have demonstrated that SRSF1 is essential for tumorigenecity of SCLC and plays a key role in DNA repair and chemo-sensitivity.

overall_design: We did RNAseq on 79 small cell lung cancer patients' tumor sample and 7 normal lung tissue. We normalized the RNAseq data and did differential expression analysis.  The deleterious consequences of overexpression of the SRSF1 proto-oncogene in human cancers suggest that there are complex mechanisms and pathways underlying SRSF1-mediated transformation.

first: Brandon

last: Higgs

first: Shen

last: Dong


title: Antisense Transcripts Impede Uridylation-induced Exonucleolytic Degradation to Generate Guide RNAs

status: Public on Feb 08 2016

city: boston

first: Ruslan

last: Afasizhev

address: 72 East Concord Street, Evans, Room 426

department: Department of Molecular & Cell Biology

institute: Boston University

summary: Small non-coding RNA biogenesis typically involves cleavage of structured precursors by RNase III-like endonucleases. However, guide RNAs that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5′ triphosphate characteristic of transcription start site and possess U-tail indicative of 3′ processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase and 3′-5′ DSS1 exonuclease, and three additional subunits. This complex, termed mitochondrial 3′ processome (MPsome), is responsible for primary uridylation of ~800-nt gRNA precursors, their processive degradation to a mature length of 50-60 nt, and secondary U-tail addition. Both strands of gRNA gene are transcribed giving rise to sense and antisense precursors of similar size. Head-to-head hybridization of these transcripts blocks symmetrical 3′-5′ degradation at the fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5′ extremity of a primary molecule by uridylation-induced, antisense transcription-controlled exonucleolytic degradation.

overall_design:
1. we first sequenced guide RNA precursor (Gel-fractioned total cellular RNA 600-1500nt was used) transcripts from three replicates to study the their tail features and also validate observation of sense/antisense accumulation upon perturbation of pre-processing complex based on few cases.

2. we then sequenced mitochondrial small RNA and built a reference for small RNAs using our custom algorithm. We then took the mitochondrial small RNA data and uncovered the sense/antisense pair.

3. We then used CLIP-Seq data to investigate in vivo binding sites and, together with RNA IP-Seq data to understand what determine the relative abundance of sense and antisense pair of the duplex.

4. We used sequenced small mitochondrial RNA in different RNAi experiments (For RNAi experiments, 30-70nt RNA fraction was gel-isolated from total cellular RNAs) to understand which protein will affect the Utail length in mature small mitochondrial RNA.

first: Liye

last: Zhang


title: Global transcriptome profiling of the 482N1 mouse metastasis-derived cell line, with or without Arntl2 knockdown

city: Stanford

first: Jennifer

last: Brady

state: CA

address: 269 Campus Drive

institute: Stanford University

summary: In order to determine the role of the transcription factor Arntl2 in regulating metastatic ability and identify Arntl2-dependent transcriptonal targets in metastatic lung adenocarcinoma, we sequenced the mRNA from 3 mouse metastasis cell lines. Each of these cell lines (482N1shLuciferase, 482N1shArntl2#1, and 482N1shArntl2#2) were derived from the same parental cell line, 482N1. 482N1 was derived from a lymph node metastasis of a Kras LSL G12D, p53 flox/flox 129S1/SvlmJ mouse model of metastatic lung adenocarcinoma. A comparison of shLuciferase and shArntl2 cell lines reveals Arntl2-dependent changes in the metastatic transcriptome.

overall_design: This study includes 6 samples: 2 biological replicates of 482N1 shLuciferase, 2 biological replicates of 482N1 shArntl2#1, and 2 biological replicates of 482N1shArntl2#2. Poly-A RNA was isolated and prepared for sequencing using the Illumina TruSeq RNA kit (v2) to generate 100bp paired end reads. Reads were aligned to mm10.

middle: J

first: Monte

last: Winslow


title: Expression profiling by high throughput sequencing of tumors derived from human prostate epithelial cells transformed with the oncogenes N-Myc and myrAKT1.

status: Public on Feb 06 2016

city: Seattle

first: John

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

summary:
MYCN amplification and overexpression are common in neuroendocrine prostate cancer (NEPC). However, the impact of aberrant N-Myc expression in prostate tumorigenesis and the cellular origin of NEPC have not been established. We define N-Myc and activated AKT1 as oncogenic components sufficient to transform human prostate epithelial cells to prostate adenocarcinoma and NEPC including the small cell prostate carcinoma (SCPC) variant with phenotypic and molecular features of aggressive, late-stage human disease. We directly show that prostate adenocarcinoma and NEPC can both arise from a common epithelial clone. Further, N-Myc is required for tumor maintenance and destabilization of N-Myc through Aurora A kinase inhibition reduces tumor burden. Our findings establish N-Myc as a driver of NEPC and a target for therapeutic intervention.
Expression profiling by high throughput sequencing of experimentally generated human tumors with mixed NEPC and prostate adenocarcinoma.

overall_design: Gene expression analysis of laser capture microdissected NEPC and adenocarcinoma from three independent engineered human tumors of mixed NEPC and prostate adenocarcinoma phenotype.


title: RNA sequencing of Brassica napus seeds at different developmental stages

city: Beibei

first: Huafang

last: Wan

state: Chongqing

address: Tiansheng

institute: Southwest University

summary: Understanding the regulation of lipid metabolism is vital for genetic engineering of Brassica napus (B. napus) to increase oil yield or modify oil composition. We report the application of Illumina Hiseq 2000 for transcriptome profiling of seeds of B. napus at different developmental stages, which may uncover the dynamic changes in lipid metabolism and reveal key genes involved in lipid biosynthesis and degradation. Total RNA from developing seeds at 2, 4, 6, and 8 weeks after pollination (WAP) were isolated and sequenced separately. The gene expression levels of all samples were quantified and normalized by the DESeq normalization. We found that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. Two genes, encoding for acetyl-CoA carboxylase and acyl-ACP desaturase, might be critical for fatty acid biosynthesis in oil rape seeds. This study provides insight into the mechanism underlying lipid metabolism and reveals candidate genes that are worthy of further investigation for their values in genetic engineering of B. napus.

overall_design: Whole Transcriptome profiling of developing Brassica napus seeds at 2, 4, 6, 8 WAP by RNA sequencing using Illumina HiSeq 2000.

first: Qing

last: Xiong

first: Wei

last: Qian


title: Gene expression profile of Foxf1 induced tumor progression in a mouse model of prostate cancer

city: Cincinnati

first: Vladimir

last: Kalinichenko

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary: We report the gene expression profile of Foxf1 induced tumor progression in a mouse model of prostate cancer.  Foxf1 was over expressed using lentivirus and confirmed with both qPCR and western blot.  Gene Ontology analysis showed significant elevation of components of Erk5 MAPK signaling.

overall_design: RNA was pooled from three separate control and Foxf1 over expressing TRAMP tumors after three weeks post-implantation into the subcutaneous compartment of syngenic mice

first: Tanya

middle: V

last: Kalin


title: Intralipid protects the heart in late pregnancy against ischemia/reperfusion injury

city: Berlin

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

institute: Charite University Hospital

summary:
The heart of late pregnant (LP) rodents is more prone to ischemia/reperfusion (I/R) injury compared to non-pregnant rodents.
We hypothesized that Intralipid (ITLD) protects the heart in LP rodents against I/R injury.  We performed genome-wide expression profiling to identify the underlying mechanisms.

overall_design: Female LP rat hearts were subjected to ischemia followed by reperfusion with vehicle or ITLD (one bolus of 5mg/kg).


title: An essential role for UTX in resolution and activation of bivalent promoters

status: Public on Feb 05 2016

city: Houston

first: Alin

last: Tomoiaga

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

summary: In the present study, we show that UTX plays an essential role in resolving and activating many retinoic acid (RA)-inducible bivalent genes during the RA-driven differentiation of mouse ESCs treated with a physiologically relevant RA concentration (0.2 μM). We showed that UTX loss and UTX knockdown interfered with the RA-induced differentiation of mouse ESCs. Therefore, our findings indicate that the UTX-mediated resolution and activation of many RA-inducible bivalent genes, including numerous Hoxa-d cluster genes, are required for RA-driven differentiation of mouse ESCs.

overall_design: ChIP-Seq data for H3K4me3 and H3K27me3 were generated along with input data for mouse stem cells with wild type or UTX-depleted genotype and with or without RA treatment.

first: Min

last: Li


title: Reference annotation for small RNA-producing genes in maize

city: State College

first: Michael

last: Axtell

state: PA

address: University Park

institute: Penn State University

summary: The goal of the project is to produce a standard annotation of the loci producing small RNAs in the maize genome. To achieve this goal we produced small RNA libraries from four different maize tissues, which will allow the identification of tissue-specific small RNA expression. The availability of bilogical replicates for three of the four tissues analyzed will guarantee robustness in the small RNA genes identification process.

overall_design: sRNA profile of maize expanded leaf, wrapped leaf, pollen and embryo, collected from B73 wt plants grown under control conditions. Leaves and pollen samples are replicated three times, embryo one time.

first: Ceyda

last: Coruh

first: Alice

last: Lunardon


title: Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)

first: Susanne

last: Wells

state: Ohio

address: 3333 Burnet Ave.

summary: We report the first RNA-Seq experiments profiling the effects of DEK loss in HNSCC. Our data also incorporates HPV+ and HPV- tumors to idenfity HPV-dependent and -independent gene signatures.

overall_design: RNA-Seq of DEK-dependent gene signatures in HNSCC cell lines

first: Allie

last: Adams


title: Genome wide analysis of liver histone H3K9 acetylation after partial hepatectomy in glucose-treated and control mice.

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

summary: We report the results of AcH3K9 ChIP-Seq on regenerating liver harvested 12 h after partial hepatectomy (PH) from mice treated with supplemental parenteral dextrose (to delay onset of PH-induced hypoglycemia) or vehicle (as control).

overall_design: Examination of the effect of delaying PH-induced hypoglycemia on histone H3K9 acetylation in regenerating liver.

first: David

middle: A

last: Rudnick

middle: F


title: Suppression of NAF-1 in Breast Cancer Cells Reduces their Tumorigenicity by Interfering with Cellular Iron Distribution and Metabolism and Ensuing ROS Formation and Apoptosis

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

summary: Nutrient autophagy factor 1 (NAF-1) is an iron-sulfur protein found on the outer mitochondrial membrane and the ER. Recent studies highlighted an important role for NAF-1 in regulating autophagy via interaction with BCL-2. We recently reported that the level of NAF-1 is elevated in cancer cells and that NAF-1 is required for tumor growth. Here we report that shRNA suppression of NAF-1 results in the activation of apoptosis in xenograft tumors and cancer cells grown in culture. Suppression of NAF-1 resulted in a depletion in the cytosolic iron pool, facilitated uptake of iron, and accumulation of iron and ROS in mitochondria, a shift to glycolysis and glutaminolysis, and the activation of cellular stress pathways associated with HIF1α, AMPK and mTOR. Suppression of NAF-1 in breast cancer cells appears therefore to reduce their tumorigenicity by interfering with cellular iron distribution and energy metabolism resulting in the activation of apoptosis.

overall_design: Examination of the effect of suppression of NAF-1 in the breast cancer cell line MCF-7. Two sample types were analyzed, MCF-7 suppressed for NAF-1 and MCF-7 Empty vector control, three replicates for each.

first: Sarah

last: Holt

first: Merav

last: Darash–Yahana

first: Yang

middle: S

last: Sohn

first: Luhua

last: Song

first: Ola

last: Karmi

first: Sagi

last: Tamir

first: Dorit

last: Michaeli

first: Mark

last: Paddock

first: Patricia

last: Jennings

first: José

last: Onuchic

first: Ioav

last: Cabantchik

first: Rachel

last: Nechushtai

first: Ron

last: Mittler

first: Eli

last: Pikarsky


title: Global analysis of genome accessibility in hair follicle stem cells

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

summary: Quiescent stem cells are periodically activated to maintain tissue homeostasis or occasionally called into action upon injury. Molecular mechanisms that constitutively maintain stem cell identity or promote stem cell proliferation and differentiation upon activation have been extensively studied. However, it is unclear how quiescent stem cells maintain identity and reinforce quiescence when they transition from quiescence to activation. Here we show mouse hair follicle stem cell compartment induces a transcription factor, Foxc1, when activated. Importantly, deletion of Foxc1 in the activated but not quiescent stem cells compromises stem cell identity, fails to re-establish quiescence and subsequently drives premature stem cell activation.These findings uncover a dynamic, cell-intrinsic mechanism employed by hair follicle stem cells to reinforce stemness in response to activation.

overall_design: Accessible chromatin regions were profiled using ATAC-seq, enriched peak regions were used to infer transcription factor binding sites.

first: Julie

last: Siegenthaler

first: Robin

last: Dowell

first: Rui

last: Yi


title: Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: In the process of translation, ribosomes first bind to mRNAs (translation initiation) and then move along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By employing three types of RNA-seq methods, we experimentally and computationally resolved elongation speed at individual gene level and under physiological condition in human cells. We proposed the elongation velocity index (EVI) as a relative measure and successfully distinguished slow-translating genes from the background translatome. The proteins encoded by the low-EVI genes are more stable than the proteome background. In normal cell and lung cancer cell comparisons, we found that the relatively slow-translating genes are relevant to the maintenance of malignant phenotypes. In addition, we identified cell-specific slow-translating codons, which may serve as a causal factor of elongation deceleration.

overall_design: We sequenced mRNA, translating mRNA (RNC-mRNA) and ribosome footprints in normally growing HeLa cells.

first: Xinlei

last: Lian

first: Jiahui

last: Guo

first: Wei

last: Gu

first: Yizhi

last: Cui

first: Jingjie

last: Jin

first: Jiayong

last: Zhong

first: Tong


title: Impact of Tcf1 and Lef1 deficiency on histone marks and Tcf1 binding in CD8 T cells

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

summary: Comparison of epigenome and Tcf1 occupancy between control and Tcf1/Lef1-deficient CD8 T cells

overall_design:
Control mice or those are deficient for Tcf1 and Lef1 transcription factors (deleted by CD4-Cre) were used to isolate thymocytes. The thymocytes were surface-stained to identify TCRbeta high, CD69–, CD24– CD8+ subsets. These cells were sorted for ChIPseq  analysis of various histone marks.
Control mice or those are deficient for Tcf1 (deleted by CD4-Cre) were used to isolate thymocytes. The splenocytes were surface-stained to identify TCRbeta high, CD8+ subsets. These cells were sorted for ChIPseq analysis of Tcf1 binding locations.

first: Hai-Hui

last: Xue


title: Capturing pairwise and multi-way chromosomal conformations using C-walks

status: Public on Feb 04 2016

city: Rehovot

first: Pedro

last: Olivares-Chauvet

address: 234 Hertzl Street

department: Department of Computer Science and Applied Mathematics/Department of Biological Regulation

institute: Weizmann Institute of Science

summary: Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs), are highly conserved between cell types and species. Whether pairwise loops synergize to form higher order structures is still unclear. Here we develop a conformation capture approach to study higher order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains. The data captured a hierarchical chromosomal structure at varying scales. Inter-chromosomal contacts constitute only 7-10% of the pairs and are restricted by the TAD structure of the interfacing chromosomes. About half of the C-walks stay within one chromosome, and almost half of these are restricted to intra-TAD spaces. Analysis of nested topological motifs suggests hierarchical chromosomal structure is present also within TADs. Targeted analysis of thousands of 3-walks anchored at strongly expressed genes support nested, rather than hub-like, chromosomal topology at active loci. Polycomb-repressed HOX domains are shown by the same approach to form synergistic hubs. Together, the data suggest that chromosomal territories, TADs, and intra-TAD loops are primarily driven by nested, possibly dynamic, pairwise contacts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Unbiased shotgun sequencing of 1pg samples of chromosome conformation campture (3C) template for the assembly of chromosome walks (c-walks) on K562 and mES in addition to 3-way 4C for the assesment of active chromatin hubs (human;K562) and polycomb domains on HOX gene clusters (mouseES).
Hi-C (mouseES) : in-nucleus ligation 3C; biotin fill-in was omitted. Digested with 15 µl HC DpnII (NEB 50,000 U/ml).

first: Amos

last: Tanay


title: ChIP-seq of MYST acetyltransferases in RKO cell line

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

summary: Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

first: Celine

last: Roques

first: Jacques

last: Côté


title: MAFG is a transcriptional repressor of bile acid synthesis and metabolism (ChIP-seq)

city: Los Angeles

first: Thomas

last: Vallim

address: 650 Charles E. Young Drive South, A2-237 CHS

institute: UCLA

summary: Specific bile acids are potent signaling molecules that modulate metabolic pathways affecting lipid, glucose and bile acid homeostasis, and the microbiota. Bile acids are synthesized from cholesterol in the liver, and the key enzymes involved in bile acid synthesis (Cyp7a1, Cyp8b1) are regulated transcriptionally by the nuclear receptor FXR. We have identified an FXR-regulated pathway upstream of a transcriptional repressor that controls multiple bile acid metabolism genes. We identify MafG as an FXR target gene and show that hepatic MAFG overexpression represses genes of the bile acid synthetic pathway and modifies the biliary bile acid composition. In contrast, loss-of-function studies using MafG(+/-) mice causes de-repression of the same genes with concordant changes in biliary bile acid levels. Finally, we identify functional MafG response elements in bile acid metabolism genes using ChIP-seq analysis. Our studies identify a molecular mechanism for the complex feedback regulation of bile acid synthesis controlled by FXR.

overall_design: ChIP-Seq analysis for livers overexpressing BLRP-tagged MafG and BLRP control

first: T

last: de Aguiar Vallim

first: Casey

last: Romanoski


title: Reversion to naïve human pluripotency creates a new methylation landscape devoid of blastocyst or germline memory

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: Human embryonic stem cells (hESCs) typically exhibit "primed" pluripotency, analogous to stem cells derived from the mouse post-implantation epiblast. This has led to a search for growth conditions that support self-renewal of hESCs akin to hypomethylated naïve epiblast cells in human pre-implantation embryos. We have discovered that reverting primed hESCs to a hypomethylated naïve state or deriving a new hESC line under naïve conditions results in the establishment of Stage Specific Embryonic Antigen 4 (SSEA4) negative hESC lines with a transcriptional program resembling the human pre-implantation epiblast. In contrast, we discovered that the methylome of naïve hESCs in vitro is distinct from the human epiblast in vivo with loss of DNA methylation at primary imprints and a lost "memory" of the methylation state of the human oocyte. This failure to recover the naïve epiblast methylation landscape appears to be a consistent feature of self-renewing hypomethylated naïve hESCs in vitro.

overall_design: This data includes 25 RNA-seq and 18 BS-seq datasets

first: Wanlu

last: Liu


title: MAFG is a transcriptional repressor of bile acid synthesis and metabolism

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

overall_design: Refer to individual Series