title: small RNA-seq from metanephros (ENCSR000AFU)

summary:
The libraries contained in this experiment come from human fetal kidney tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: small RNA-seq from diencephalon (ENCSR000AFR)

status: Public on Mar 18 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

type: Expression profiling by high throughput sequencing

summary:
The libraries contained in this experiment come from human fetal diencephalon tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: small RNA-seq from frontal cortex (ENCSR000AFS)

summary:
The libraries contained in this experiment come from human fetal frontal cortex tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: small RNA-seq from heart (ENCSR000AFT)

summary:
The libraries contained in this experiment come from human fetal heart tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: small RNA-seq from cerebellum (ENCSR000AFQ)

summary:
The libraries contained in this experiment come from human fetal cerebellum tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: small RNA-seq from GM12878 (ENCSR000AEJ)

summary:
The libraries contained in this experiment come from independent growths of cell line GM12878.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Temperature Sensitive Remodeling of Fruit Fly Physical Chromosomal Domains upon Heat Shock

city: Atlanta

first: Chun-hui

last: Hou

address: 1510 Clifton Rd NE

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Metazoan chromosomes in interphase nucleus are partitioned into discrete three dimensional physical domains which confine epigenetically modified chromatin and are relative stable across different cell types even species1-4. Physical domains are segregated preferentially at DNase I hypersensitive sequences of high density of active gene and insulator proteins which are hypothesized contributing together to domain border formation3,4. However, whether physical domain structure can be maintained without insulator proteins and transcription is unknown5-8. Transcription of most genes and the insulator proteins binding can be severely impaired in heat shocked (HS) fruit fly nuclei9.  Here we show that chromatin contact frequency increases within and decreases beyond ~100kb after HS respectively accompanied by repartitioning of the Drosophila chromosomes into a different array of physical domain. Prominently, domains tend to merge because borders disappeared are more than borders newly emerged which are located more frequently in repressive chromatin. In contrast to previous hypothesis1,3,4, changes in insulator proteins enrichment and RNAPII show no noticeable difference at lost or emerged borders. Our results show a metazoan genome can be quickly reconfigured as cells undergo brief physiological stress. In addition to insulator proteins and transcription, we speculate that extra trans-factors binding and various biological activities are required for the establishment and maintenance of physical domains. Moreover, we found long-range chromatin interaction network is reshaped after HS implying long-range chromatin interactions can be formed due to domain level reorganization of chromosomes despite functional relevance. We anticipate our analysis to be a starting point for more intensive experimental investigation into the elusive mechanisms behind the physical domain partition and dynamic reconfiguration of metazoan genomes.

overall_design: We carried out Hi-C experiments using HindIII and ChIP experiments with antibodies against BEAF, CP190, CTCF, SuHw and RNAPII on heat shocked Kc167 cells and generated two Hi-C libraries and five ChIP-seq libraries which were sequenced paired-end on Illumina HiSeq2000 platform. Five ChIP libraries are indexed with Illumina index sequencing primers.

first: Chunhui

first: Li

last: Li

first: Ming

last: Hu

first: Zhaohui

middle: S

last: Qin

first: Victor

middle: G

last: Corces


title: Identification of transcripts whose abundance changes in response to acute switches in DSX isoform in the ovary and testis

status: Public on Mar 17 2016

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: RNAseq of dissected adult ovary and testis after DSX isoform is switched using temperature inducible alleles or constructs.

overall_design: Biological duplicates were sequenced for each genotype at each condition.

first: Erin

last: Jimenez

first: Cale

last: Whitworth

first: Emily

last: Clough

first: Yoo-Ah

last: Kim

first: Harold

middle: E

last: Smith

first: Teresa

middle: M

last: Przytycka

first: Stephen

last: Goodwin

first: Mark

last: Van Doren


title: small RNA-seq from urinary bladder (ENCSR000AFP)

summary:
The libraries contained in this experiment come from human fetal urinary bladder tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Impact of Tcf1 and Lef1 deficiency on mSin3A distribution 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 mSin3A distribution 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 splenocytes. The splenocytes were surface-stained to identify TCRbeta high CD8+ subsets. These cells were sorted for ChIPseq analysis.

first: Hai-Hui

last: Xue


title: Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis

city: Hwasun, Jeollanam-do

first: Young-Kook

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary: Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells while we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3′ end, yielding miRNAs from the 5′ strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.

overall_design: Two independent sequencing experiments (set 1 and set 2, respectively) were performed using 9 samples.

first: Narry


title: small RNA-seq from K562 (ENCSR000AES)

first: ENCODE

last: DCC

summary:
The libraries contained in this experiment come from independent growths of cell line K562.  They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size.  These data were collected as part of the RNA Evaluation Study.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Gene expression in human glioblastoma specimens

city: Houston

first: Amy

middle: B

last: Heimberger

state: TX

address: 1400 Holcombe Blvd., FC7.2000

department: Neurosurgery

institute: The University of Texas MD Anderson Cancer Center

summary: We assessed global gene expression changes in 32 human glioblastoma specimens

overall_design: Human mRNA profiles of 32 glioblastoma specimens, were obtained by sequencing on Illumina HiSeq 3000

first: Konrad

last: Gabrusiewicz

first: Benjamin

last: Rodriguez


title: small RNA-seq from lung (ENCSR000AFW)

summary:
The libraries contained in this experiment come from human fetal lung tissue from independent donors. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: BBBomics - Human Blood Brain Barrier Transcriptomics Hub [miRNA-seq]

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available;of which, the human microvascular endothelial cell line (hCMEC/D3) is  the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain  features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs.

overall_design: We have developed blood brain barriers transcriptomics landscape using RNA and micro RNA sequencing data obtained from replicates of hCMEC/D3 BBB cell line.

first: Krishna

middle: R

last: Kalari

first: Karunya

middle: K

last: Kandimalla


title: BBBomics - Human Blood Brain Barrier Transcriptomics Hub [RNA-seq]

summary: Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available; of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain  features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs.

overall_design: We have developed blood brain barriers transcriptomics landscape using RNA sequencing and micro RNA seqeuncing data obtained from replicates of hCMEC/D3 BBB cell line.


title: Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

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

overall_design: Refer to individual Series


title: BBBomics - Human Blood Brain Barrier Transcriptomics Hub


title: Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

summary: Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue.

overall_design: We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

first: Alexey

middle: V

last: Pindyurin

first: Ludo

last: Pagie

first: Elena

middle: N

last: Kozhevnikova


title: Genome-wide analysis of chronic inflammation induced gene expression in livers isolated from either wild type or ApoE-Cyp7a1 transgenic animals.

city: Boston

first: Daniel

last: Okin

state: MA

address: 55 Fruit St, BUL148

department: Department of Medicine, Division of Pulmonary and Critical Care

institute: Massachusetts General Hospital

summary: Analysis of whole genome expression changes in livers from wild type animals and animals with a liver specific transgenic over expression of Cyp7a1. Mice were given a chronic, repetitive administration of LPS for 7 days. Our prior analysis had indicated that inflammation suppresses Cyp7a1 and that this leads to accumulation of intermediates in the mevalonate biosynthesis pathway. Here, we hypothesized that over expression of Cyp7a1 would not affect the changes in transcriptional state due to chronic administration of LPS. We provide gene expression data which evaluates this question. Here we find that over expression of Cyp7a1 minimally alters the transcriptome of livers in an untreated state, and that it has small effects on the response to chronic LPS.

overall_design: Total RNA isolated from livers of wild type and liver specific Cyp7a1 transgenic animals treated with or without recurrent, daily LPS injections (1.5mg/kg) for 7 days. There are two biological replicates per condition. Samples are a matrix of all conditions reported as FPKMs.

first: Ruslan

last: Medzhitov


title: Codon usage and 3′ UTR length determine maternal mRNA stability in zebrafish

city: Kita-ku

first: Yuichiro

last: Mishima

state: Kyoto

address: Motoyama, Kamigamo,

department: Department of Frontier Life Sciences

country: Japan

institute: Kyoto Sangyo University

summary: The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3′ UTR, with long 3′ UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3′ UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes.

overall_design: zebrafish embryonic mRNA profile at 2 different stages (2 hpf and 6 hpf) in wildtype and 3 additional conditions (miR-430 inhibition, RNApol II inhibition and CNOT7 inhibition) at 6 hpf. All experiments are performed as triplicates


title: High-throughput sequence data of ChIP performed with anti-SMARCAD1 (ASNA) or anti-CBP actibodies.

city: Nagasaki

first: Masamichi

last: Doiguchi

address: Sakamoto 1-12-4

institute: University of Nagasaki

summary: Histone acetylation and nucleosome remodeling play a pivotal role in transcriptional regulation. While histone acetylase and ATP-dependent chromatin remodeling activities have been well characterized, how the two activities are coordinated remains to be uncovered. We discovered ATP-dependent histone H2A acetylation activity in Drosophila nuclear extracts. This activity was column-purified and demonstrated to be composed of CBP and SMARCAD1, which belongs to the Etl1 subfamily of the Snf2 family of helicase-related proteins. SMARCAD1 enhanced acetylation of H2A K5 and K8 by CBP in nucleosomes in an ATP-dependent fashion. Expression array analysis of S2 cells having ectopically expressed SMARCAD1 revealed up-regulated genes. Using native genome templates of these up-regulated genes, we found that SMARCAD1 activates their transcription in vitro. Knockdown analysis of SMARCAD1 and CBP indicated overlapping gene control, and ChIP-seq analysis of these commonly controlled genes showed that CBP is recruited to the promoter prior to SMARCAD1. Moreover, Drosophila genetic experiments demonstrated interaction between SMARCAD1/Etl1 and CBP/nej during development. The interplay between the remodeling activity of SMARCAD1 and histone acetylation by CBP sheds light on chromatin and the genome-integrity network.

overall_design: Examination of 2 different protein in 1 cell type.

first: Takashi

last: Ito


title: Sensory experience restricts cortical plasticity by inducing IGF-1 in VIP neurons

first: Ivo

last: Spiegel

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary: RNA-seq libraries purified from the visual cortices of neurons expressing Emx-, GAD2-, PV-, SST-, or VIP-Cre using the Ribotag allele.  Seq libraries are provided from mice raised in standard housing, or housed in the dark for two weeks (dark-housed), or dark-housed and then exposed to light for 1, 3, or 7.5 hours.  These seq libraries represent the genetic response of distinct types of cortical interneurons to altered sensory experience.

overall_design: To explore how sensory experience affects gene expression, we examined this process in the visual cortex of adult mice that were housed in standard conditions, in complete darkness (i.e. dark-housed), or dark-housed and then exposed to light for increasing amounts of time. We generated mice that were heterozygous for alleles of either Emx-,Gad2-,Sst-,Vip- or Pv-Cre, and were also heterozygous for the Rpl22-HA (RiboTag) allele, which expresses an HA-tagged ribosomal protein specifically in Cre-expressing neurons. We performed RNA-Seq on RNA isolated from the dark-housed/light-exposed RiboTag-mice; Experiments were done in 3 biological replicates and the visual cortices of 3 mice were pooled per sample at each time-point and for each Cre line.

first: Alan

last: Mardinly

first: David

middle: A

last: Harmin

first: Michael

last: Greenberg


title: Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (RNA-Seq)

city: Uppsala

first: Anna

last: Åsman

address: PO Box 7080

department: Molecular Sciences

country: Sweden

institute: Swedish University of Agricultural Sciences (SLU)

summary: The plant pathogen Phytophthora infestans encodes four distinct Ago proteins. To identify the sRNA repertoire associated with each PiAgo protein, Ago-sRNA co-immunoprecipitation and sRNA sequencing were carried out. 20-22 nucleotide (nt) sRNAs were identified as the main interaction partners of PiAgo1 and high enrichment of 24-26 nt sRNAs was seen in the PiAgo4-bound sample. The majority of PiAgo-associated sRNAs derived from transposable elements (TEs). The frequencies and sizes of TE-derived sRNAs in the different PiAgo libraries suggested diversified roles of the PiAgo proteins in control of different TE classes. We further provide evidence for involvement of PiAgo1 in the P. infestans miRNA pathway. Protein-coding genes are likely to be regulated by the shared action of PiAgo1 and PiAgo5, as demonstrated by analysis of differential expression. An abundance of sRNAs from genes encoding host cell death-inducing CRN effectors was bound to PiAgo1, implicating this protein in regulation of the expanded CRN gene family. These findings highlight the different roles played by Ago proteins in an economically important plant pathogenic oomyce

overall_design: Transcriptome sequencing from duplicate samples of strain 88069 mycelium

first: Johan

last: Fogelqvist

first: Ramesh

last: Vetukuri

first: Christina

last: Dixelius


title: Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (small RNA-Seq)

overall_design: The number of small RNA samples sequenced from each Argonaute immunoprecipitation were: PiAgo1-IP, three; PiAgo3-IP, one; PiAgo4-IP, two; PiAgo5-IP, one. Control GFP immunoprecipitation: GFP-IP, two. Control input Ago1: two. Total number of samples: eleven.


title: Transcriptome of Colletotrichum graminicola wild-type and and mutant isolates during infection of Zea mays leaf sheaths

city: Lexington

first: Lisa

last: Vaillancourt

state: Kentucky

address: 201F Plant Science Building

department: Plant Pathology

institute: University of Kentucky

summary: Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of pathogenic development *in planta*: melanized appressoria that form on the host surface prior to penetration; biotrophy, characterized by colonization of living host cells; and necrotrophy, characterized by host cell death and symptom development. An improved filtering algorithm and a Mixed Effects Generalized Linear Model (GLM) were developed and applied to an existing Illumina transcriptome dataset, substantially increasing the statistical power of the analysis of *C. graminicola* gene expression during infection and colonization. Additionally, the *in planta* transcriptome of the wild-type was compared with that of a mutant strain impaired in the establishment of biotrophy, allowing detailed dissection of events occurring specifically during penetration, and during early versus late biotrophy. Results indicated that there is a continuum of activities that occur during colonization of maize by *C. graminicola*, and that boundaries drawn between the three recognizable phases are artificial. More than 2000 fungal genes were differentially transcribed in waves during appressorial maturation, penetration, and colonization. Secreted proteins and membrane receptors were over-represented among the differentially expressed genes, suggesting that the fungus engages in an intimate and dynamic conversation with the host, beginning prior to penetration. This communication process is likely to involve reception of plant signals that trigger subsequent developmental progress in the fungus, as well as the production of signals that induce responses in the host. Later phases of biotrophy were more similar to necrotrophy, with increased production of secreted proteases, inducers of plant cell death, hydrolases, and membrane bound transporters for the uptake and egress of potential toxins, signals, and nutrients. The differentially expressed genes could be used as landmarks to more accurately identify developmental progress in compatible versus incompatible interactions involving genetic variants of both host and pathogen.

overall_design:
Analysis of C. graminicola colonization stages: pre-penetration appressoria (PA), early biotrophic phase (BP), and the switch from biotrophy to necrotrophy (NP), in two different isolates, a wild-type (WT) and a non-pathogenic mutant (MT). There are 3 biological replicates per stage, except for the MTBP treatment with only 2 biological replicates. A total of four lanes (i.e. technical replicates) of data were generated for WTAP; one lane each was produced for WTBT and WTNT; and two lanes each were produced for MTAP and MTBT. The technical replicates for each treatment were pooled.

The wild type strains of this study were submitted in GSE34632. The new wild type Samples combined reps. The attached excel file describes the Sample to Sample associations.

first: Ester

last: Buiate

first: Maria

last: Torres

first: Noushin

last: Ghaffari

first: Charles

last: Johnson


title: Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements


title: Dicer-independent RNA-directed DNA methylation in Arabidopsis [methylC-seq]

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 and some RdDM mutants

overall_design: MethylC-Seq: 8 mutants examined, nrpd1-3, nrpe1-11, dcl2/3/4, rdr1/2/6, ddc, met1-1, dcl1-100, ago4/6

first: Dong-Lei

last: Yang

first: Kai

last: Tang


title: A screen for cis-regulatory elements for murine miR-142 using an sgRNA library prepared by Molecular Chipper technology

city: New Haven

first: Jijun

last: Cheng

state: CT

address: 10 Amistad St.., Rm 214K

department: Genetics

institute: Yale University

summary: CRISPR-based loss-of-function screens have been proven powerful to identify genetic regulators in mammalian cells, but current approaches for single guide RNA (sgRNA) library construction are expensive and difficult to be adapted in most laboratories. Here, we present a Molecular Chipper technology for inexpensive and easily customizable sgRNA library generation, and a proof-of-principle screen that identifies novel cis-regulatory regions for miR-142 biogenesis.  This method will be useful for functional interrogation of non-coding elements in mammalian genomes

overall_design: 12 biological samples were sequenced from three biological replicates (Sam1, Sam2 and Sam3 below). Each biological replicate was sorted into neg-GFP, low-GFP, med-GFP and high-GFP populations for sequencing library construction. An unsorted sample is included.

first: Jun

last: Lu


title: A fully validated blood stem/progenitor cell regulatory network reveals mechanisms of cell state stabilisation

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

summary: The aim of this study was to determine the genomic binding sites of important haematopoietic transcription factors in haematopoietic cell lines.

overall_design: 416Bs cells were fixed with either 1 or 0.4 % formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and specific antibodies were used to pull down the transcription factors of interest after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced.

first: Judith

last: Schütte

first: Huange

last: Wang

first: Stella

last: Antoniou

first: Andrew

last: Jarrett

first: Nicola

last: Wilson

first: Joey

last: Riepsaame

first: Fernando

middle: J

last: Calero-Nieto

first: Silvia

last: Basilico

first: Sarah

last: Kinston

first: Rebecca

last: Hannah

first: Mun

middle: C

last: Chan

first: Sylvia

middle: T

last: Nurnberg

first: Willem

middle: H

last: Ouwehand

last: Bonzanni

first: Marella

middle: F

last: de Bruijn

first: Berthold

last: Göttgens


title: Short RNAs expression profiling in circulating CD34+ cells from Primary Myelofibrosis patients and from normal controls pooled bone marrow CD34+ cells.

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

summary: We report the application of Illumina short RNA sequencing for characterization and discovery of miRNAs and moRNAs, and for identification of differentially expressed small RNAs in circulating CD34+ cells from Primary Myelofibrosis (PMF) patients and from normal controls pooled bone marrow CD34+ cells.

overall_design: Short RNAs sequencing for miRNA quantification, discovery and characterisation.

first: Alessandro

last: Vannucchi


title: RNA-seq time-course analysis of the transcriptional dynamics of the two root-infecting fungi Colletotrichum tofieldiae (mutualistic) and Colletotrichum incanum (pathogenic) and their plant host Arabidopsis thaliana during root colonization

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

summary: The objective of this study was on the one hand to compare the transcriptional dynamics of mutualistic Colletotrichum tofieldiae and pathogenic Colletotrichum incanum during colonization of Arabidopsis roots and on the other hand also examine the corresponding host responses

sample_organism:
Arabidopsis thaliana
Colletotrichum tofieldiae
Colletotrichum incanum

overall_design: Arabidopsis seeds that were either untreated (mock) or inoculated with Colletotrichum tofieldiae (isolate 0861) or Colletotrichum incanum (isolate MAFF230704) were grown in normal (P+) or low (P-) phosphate conditions. Roots (with/without fungal colonization) were collected at 6, 10, 16, and 24 days post inoculation (dpi). Additionally, C. tofieldiae and C. incanum in vitro hyphae were collected after two days growth in liquid Mathur’s medium. For each condition three replicates were obtained.

first: Stéphane

last: Haqcuard

first: Kei

last: Hiruma

first: Paul

last: Schulze-Lefert

first: Richard

last: O'Connell


status: Public on Mar 16 2016

city: Foshan

first: Ying

last: Yang

state: China/Guangdong

address: Xianhu road

country: China

institute: Foshan University

summary: Effect of High Temperature on Immune Response of Grass Carp (Ctenopharyngodon idellus) by Transcriptome Analysis

overall_design: To understand the immune response mechanisms of this fish in high temperature circumstance, the transcriptomic profiles of the spleens from grass carp groups undergoing heat stress and normal temperature were investigated.


title: Global gene transcriptional profiles of  RAW 264.7 cells following the infection with Brucella abortus wild and mutant strains

city: Seoul

first: Myunghwan

last: Jung

address: 1 Gwanak-ro

department: Veterinary Medicine

institute: Seoul National University

summary:
We focused on whether transposon mutagenesis in Brucella abortus could induce difference in the trascriptional responses of RAW 264.7 cell infection model compared to the wild strain infected RAW 264.7 cells.
The function of genes in Brucella abortus was analyzed through the identified differences in gene expression between RAW 264.7 cell infected with wild and mutant strains.

overall_design: We analyzed altered transcription in RAW 264.7 cells at 0, 6, 12, and 24 h following the infection with 10 MOI of Brucella abortus wild and mutant strains.

first: Jung

last: Myunghwan

first: Yoo

last: Sang


title: Staufen Negatively Modulates MicroRNA Activity in Caenorhabditis elegans

city: Worcester

first: Isana

last: Veksler-Lublinsky

address: 373 Plantation Street

department: Molecular Medicine

institute: University of Massachusetts Medical School

summary: The double-stranded RNA-binding protein Staufen has been implicated in various posttranscriptional gene regulatory processes. Here, we demonstrate that the Caenorhabditis elegans homolog of Staufen, STAU-1, functionally interacts with microRNAs. Loss-of-function mutations of stau-1 significantly suppress phenotypes of let-7 family microRNA mutants, a hypomorphic allele of dicer and a lsy-6 microRNA partial loss-of-function mutant. Furthermore, STAU-1 modulates the activity of lin-14, a target of lin-4 and let-7 family microRNAs, and this modulation is abolished when the 3' untranslated region of lin-14 is removed. Deep sequencing of small RNA cDNA libraries reveals no dramatic  change in the levels of microRNAs, or other small RNA populations between wild-type and stau-1 mutants, with the exception of certain endogenous siRNAs in the WAGO pathway. The modulation of microRNA activity by STAU-1 does not seem to be associated with the previously reported enhanced exogenous RNAi (Eri) phenotype of stau-1 mutants, since eri-1 exhibits the opposite effect on microRNA activity. Altogether, our results suggest that STAU-1 negatively modulates microRNA activity downstream of biogenesis, possibly by competing with microRNAs for binding on the 3' untranslated region of target mRNAs

overall_design: Deep-sequencing was performed on cDNA libraries made from total RNA from young adults populations of two strains: wild-type (N2) and  stau-1(tm2266), in three biological replicates each strain.

first: Zhiji

last: Ren

first: David

last: Morrissey

first: Victor

last: Ambros


title: Derivation and differentiation of haploid human embryonic stem cells [RNA-Seq 2]

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution.

overall_design: RNA sequencing analysis was performed on a total of 2 samples of in vitro fertilization (IVF) control embryonic stem cell lines.

first: Dieter

last: Egli

first: Nissim

last: Benvenisty


title: Transcriptome assay of materal mRNA degradation in Btg4-deleted oocytes

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

summary: We analyzed the functions of BTG family proteins in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in BTG4-deleted oocytes, and identified the BTG4 target genes in oocyte cyplasmic maturation.

overall_design: 2 WT oocyte samples at GV stage, 2 WT oocyte samples at MII stage, 2 Btg4-/- oocyte samples at GV stage and 2 Btg4-/- oocyte samples at MII stage?2 WT embryo samples at zygote stage, 2 WT embryo samples at 2-cell stage, 2 Btg4-/- embryo samples at zygote stage and 2 Btg4-/- embryo samples at 2-cell stage , and a WT GV oocyte, a WT MII oocyte, a Erk-/- GV oocyte and a Erk-/- MII oocyte are performed RNA sequencing.

first: Chao

last: Yu

first: Shu-Yan

last: Ji

first: Yujiao

last: Dang


title: Dynamic epigenetic changes to VHL occurs with sunitinib in metastatic clear cell renal cancer

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary: The role of epigenetic changes, relative to mutations, with targeted therapy

overall_design: 70 Biopsy and Nephrectomy Samples analyzed by methylCap-seq DNA methylation

first: Fiach

last: O'Mahony

first: Grant

middle: D

last: Stewart

first: Thomas

last: Powles

first: Tim

last: De Meyer

first: Geert

last: Trooskens

first: Christophe

last: Van Neste


title: GAS5 controls Nodal autocrine in Human Embryonic Stem Cells Self-Renewal through competing endogenous mechanism

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: Long non-coding RNAs (lncRNAs) are recently characterized players that are involved in the regulatory circuitry of self-renewal in human embryonic stem cells (hESCs). However, the specific roles of lncRNAs in this circuitry are poorly understood. Here, we determined that growth-arrest-specific transcript 5 (GAS5), which is a known tumor suppressor and growth arrest gene, is abundantly expressed in the cytoplasm of hESCs and essential for hESC self-renewal. GAS5 depletion in hESCs significantly impaired their pluripotency and self-renewal ability, whereas GAS5 overexpression in hESCs accelerated the cell cycle, enhanced their colony formation ability and increased pluripotency marker expression. By RNA sequencing and bioinformatics analysis, we determined that GAS5 activates NODAL-SMAD2/3 signaling by sustaining the expression of NODAL, which plays a key role in hESC self-renewal but not in somatic cell growth. Further studies indicated that GAS5 functions as a competing endogenous RNA (ceRNA) to protect NODAL mRNA against degradation and that GAS5 transcription is directly controlled by the core pluripotency transcriptional factors (TFs). Taken together, we suggest that the core TFs, GAS5 and NODAL-SMAD2/3 form a feed-forward loop to maintain the hESC self-renewal process. These findings are specific to ESCs and did not occur in the somatic cell lines we tested; therefore, our findings also provide evidence that the functions of lncRNAs vary in different biological contexts.

overall_design: We analyzed long non-coding RNAs in two hESC cell lines (X-01 and H1), and found GAS5 is highly expressed and functional in maintaining hESC self-renewal. We generate stable overexpressed or knockdown hESC cell lines using lentiviral approach. We transfected cells initialy after passage, and lentiviruses are added with daily medium change for three days (at a final concentration of 10^5 IU/ml). Puromycin is added for selection and supplied with daily medium change. Stable cell lines are established after two passages and verified under fluorescence scope. Total RNAs and miRNAs are extracted separately of all three cell lines (LV-NC, LV-GAS5 and LV-shGAS5) and put to sequencing.

first: Yue

last: Wang

first: Houqi

last: Liu


title: Mathematical modeling of Trypanosoma brucei transcription

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. In this study, we refined the previously published mathematical model for bloodstream form parasites and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Through this study, we conclude that lLevels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting acquisition of new control mechanisms during adaptation to mammalian parasitism.

overall_design: Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro  PCF and in duplicate from in vitro T. brucei  Lister427, to understand global differntial gene transcription.

first: Enoch

last: Antwi

first: Jurgen

last: Haanstra

first: Bryan

last: Jensen

first: Dorothea

last: Droll

first: Federico

last: Rojas

first: Igor

last: Minia

first: Monica

last: Terrao

first: Clementine

last: Merce

first: Keith

last: Matthews

first: Peter

last: Myler

first: Marilyn

last: Parsons

first: Christine

last: Clayton


title: To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages

city: Chongqing

first: quan

last: sun

address: Chongwen road 2#

department: College of Bioinformation

institute: Chongqing University of Posts and Telecommunications

summary:
Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism
Methods: shoot apical mRNA and miRNA in two nulliplex branch and two normal branch cotton of three development stages were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
Results: we found 3 825 and 353 specific stage differnent expressed genes in pre-budding stage of island cotton and upland cotton, respectively. In miRNA, we found 16 and 18 specific stage differnent expressed miRNA in pre-budding stageof island cotton and upland cotton, respectively.
Conclusions: Our study represents the genes and miRNA control development of lateral branch and regulate flowering time at same times.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Shoot apical mRNA and miRNA of normal branch cotton and nulliplex branch botton were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Quan

last: Sun

first: Yingfan

last: Cai


title: Comparison of Glomerular and Podocyte mRNA Profiles in eNOS-/- Diabetic Mice Induced by Streptozotocin

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

summary: We compared mRNA profiles of isolated glomeruli versus sorted podocytes between diabetic and control mice. IRG mice crossed with eNOS-/- mice were further bred with podocin-rTTA and TetON-Cre mice to permanently label podocytes before the diabetic injury. Diabetes was induced by injection of streptozotocin. mRNA profiles of isolated glomeruli and sorted podocytes from diabetic and control mice at 10 weeks after induction of diabetes were examined. Consistent with the previous reports, expression of podocyte-specific markers in the glomeruli were down-regulated in the diabetic mice compared to controls. However, these differences disappeared when mRNA levels were corrected for podocyte number per glomerulus. Interestingly, the expression of these markers was not altered in sorted podocytes from diabetic mice, suggesting that the reduced expression of podocyte markers in isolated glomeruli is likely a secondary effect of reduced podocyte number, rather than the loss of differentiation markers. Analysis of the differentially expressed genes in diabetic mice also revealed distinct up-regulated pathways in the glomeruli (mitochondrial function and oxidative stress) and podocytes (actin organization). In conclusion, our data suggest that podocyte-specific gene expression in transcriptome obtained from the whole glomeruli may not represent those of podocytes in the diabetic kidney.

first: Jia

last: Fu

first: Kyung

last: Lee

first: Weijia

last: Zhang

first: Wu

last: He

last: Chuang

first: Zhihong

last: Liu

first: John


title: Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [RNA-seq]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue.

overall_design: RNA sequencing of 3 samples, each using 2 biological replicates.

first: Alexey

last: Pindyurin

first: Ludo

last: Pagie

first: Joris

last: van Arensbergen


title: Differential gene expression of the nosocomial pathogen Enterococcus faecalis subjected to metal stress

city: Freiburg

first: Emanuel

last: Clauss-Lendzian

address: Hugstetter Straße 55

institute: University Medical Center

summary:
Emerging antibiotic resistance among clinically relevant bacteria, paired with their ability to form biofilms on medical and technical devices, represents a serious problem in terms of effective and long-term decontamination in health care environments and gives rise to an urgent need for new antimicrobial materials. Here we present the first study of the impact of AGXX®, a novel broad-spectrum antimicrobial surface coating consisting of micro galvanic elements formed by silver and ruthenium, on the transcriptome of the nosocomial pathogen Enterococcus faecalis. E. faecalis was subjected to metal stress by growing it for different periods of time in the presence of AGXX® or silver-coated steel meshes. Subsequently, total RNA was isolated and next-generation RNA sequencing was performed to analyze variations in gene expression levels in the presence of the antimicrobial materials with focus on known stress genes. Exposure to AGXX® had a large impact on the transcriptome of E. faecalis.
After 24 minutes almost 1/5 of the E. faecalis genome displayed differential expression. At each time-point the cop operon was strongly up-regulated, providing indirect evidence for the presence of free Ag+-ions. Moreover, exposure to AGXX® induced a broad general stress response in E. faecalis. Genes coding for the chaperones GroEL and GroES as well as the Clp proteases ClpE and ClpB were among the top up-regulated heat shock genes. Furthermore, differential expression of genes coding for thioredoxin, superoxide dismutase and glutathione synthetase indicates a high level of oxidative stress. We postulate a mechanism of action where the combination of Ag+-ions and reactive oxygen species generated by AGXX® results in a synergistic antimicrobial effect, which is superior to that of conventional silver coatings.

overall_design: Gene expression analysis of Enterococcus faecalis 12030 either subjected to metal stress by exposure to an antimicrobial AGXX®- or Ag-coated V2A steel mesh or exposed to an uncoated V2A steel mesh or left untreated performing RNA Sequencing with an Ion ProtonTM Sequencer and subsequent data analysis with a T-REx RNA-Sequencing expression analysis pipeline.

first: Anne

last: de Jong

first: Uwe

last: Landau

first: Carsten

last: Meyer

first: Jan

last: Kok

first: Elisabeth

last: Grohmann


title: Dicer-independent RNA-directed DNA methylation in Arabidopsis [small RNA-seq 2]

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

institute: Purdue University

summary: Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4/nrpd1 and nrpd1 mutants

overall_design: 2 samples examined, dcl2/3/4/nrpd1 and nrpd1

first: Dong-Lei

last: Yang

first: Kai

last: Tang


title: Derivation and differentiation of haploid human embryonic stem cells [RNA-Seq 1]

first: Ido

last: Sagi

overall_design: RNA sequencing analysis was performed on a total of 15 samples, including haploid and diploid human parthenogenetic embryonic stem cells at different differentiation states and cell cycle phases.

first: Dieter

last: Egli

first: Nissim

last: Benvenisty


title: Dicer-independent RNA-directed DNA methylation in Arabidopsis [small RNA-seq 1]

summary: Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4, dcl1/2/3/4 and WT

overall_design: 3 samples examined, WT, dcl2/3/4 and dcl1/2/3/4


title: Nucleosome Positioning Dynamics Through the Yeast Metabolic Cycle

status: Public on Mar 15 2016

first: Iestyn

last: Whitehouse

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

summary: We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression.

overall_design: Examination of nucleosome positions and transcriptional output through metabolic oscillations in budding yeast.

first: Nicolas

last: Nocetti


title: Derivation and differentiation of haploid human embryonic stem cells

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets

city: Los Angeles

first: Yibin

last: Wang

state: Ca

institute: University of California Los Angeles

summary: In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. We report a systematic study of small RNA-mediated endonucleolytic cleavage in mouse through integrative analysis of small RNA and degradome sequencing data without imposing any bias towards known small RNAs. Hundreds of small cleavage-inducing RNAs and their cognate target genes were identified, significantly expanding the repertoire of known small RNA-guided cleavage events. Strikingly, both small RNAs and their target sites demonstrated significant overlap with retrotransposons, providing evidence for the long-standing speculation that retrotransposable elements in mRNAs are leveraged as signals for gene targeting. Furthermore, our analysis showed that the RNA cleavage pathway is also present in human cells but affecting a different repertoire of retrotransposons. These results show that small RNA-guided cleavage is more widespread than previously appreciated. Their impact on retrotransposons in non-coding regions shed light on important aspects of mammalian gene regulation.

overall_design: rRNA depleted RNA sequencing was done for four stages of testis development.

first: Ashley

last: Cass

first: Xinshu

last: Xiao


title: Single cell transcriptome analysis of mouse carotid body glomus cells

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: CARL Building room 264 Research Drive

institute: Duke University

summary: The carotid body (CB) is a major arterial chemoreceptor containing glomus cells whose activities are regulated by changes in arterial blood contents including oxygen. We employed the single cell RNASeq method by performing next-generation sequencing on single glomus cellderived cDNAs to eliminate contamination of genes derived from other cell types present in the CB. This study has generated a CB expression profile containing novel glomus cell specific genes. The wealth of information provided through this study offers a valuable foundation for identifying molecules functioning in the CB.

sample_organism:
Mus musculus
Mus musculus x Mus spretus

platform_organism:
Mus musculus
Mus musculus x Mus spretus

overall_design: 8 single CB glomus cells that were confirmed expressing tyrosine hydroxylase (Th), ubiquitin carboxyl-terminal esterase L1 (Uchl1) and potassium channel subfamily K member 3 (Kcnk3) were harvested from P4-5 wild type mice and subjected to single-cell RNA-Seq

first: Ting

last: Zhou

first: Ming-Shan

last: Chien


title: Enhanced methylome sequencing by recovery of unsequenceable fragments

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

summary: Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A,T-rich DNA library that leads to major PCR biases that may confound methylation analysis. Here we report a method that enables accurate methylation analysis, by rebuilding the damaged DNA library after bisulfite treatment. This recovery after bisulfite treatment (ReBuilT) approach enables PCR-free bisulfite sequencing from low nanogram quantities of genomic DNA. We applied the ReBuilT method for whole methylome analysis of the A,T rich genome of Plasmodium berghei. We demonstrate substantial improvements in coverage and the reduction of sequence-context biases as compared to classical methylome analysis. Our method will be widely applicable for accurate, quantitative methylation analysis, even for technically challenging genomes, and where limited sample DNA is available.

overall_design: From the same DNA sample we prepared 3 PCR-free Bisulfite-Seq replicates (ReBuilT) and 2 standard Bisulfite-Seq replicates (PCR-BS).

first: Gordon

last: McInroy

first: Eun

last: Raiber

first: Katarzyna

last: Modrzynska

first: Pieter

last: van Delft

first: Shankar

last: Balasubramanian


title: Time-course transcriptome of wild-type Arabidopsis leaf

city: Pohang

first: Hee Jung

last: Koo

address: Hyojadong San 31

institute: Pohang University of Science and Technology

summary: During the senescence stage, leaves undergo degeneration and relocate nutrients accumulated during the growth stage to sink parts such as seeds, critically contributing to plants’ productivity and fitness. Here, we asked how leaf transcriptome is regulated during the senescence stage by performing directional sequencing of total and small RNAs for the entire lifespan of Arabidopsis leaves.

overall_design: The total RNA and small RNA profiles of the Arabidopsis leaf along lifespan (14 and 7 time points, respectively) were generated by next-generation sequencing using Illumina Hiseq2000. Two independent biological replicates were used for each experiment.

first: Hye Ryun

last: Woo

first: Jeongsik

last: Kim

first: Hyobin

last: Jeong

first: Pyung Ok

last: Lim

first: Daehee

last: Hwang

first: Hong Gil

last: Nam


first: Yibin

last: Wang

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Small RNA sequencing libraries were generated for H1, mouse whole brain at developmental stage E10 as well as mouse testis and cerebellum developmental stages E14, E18, post-natal 3 weeks, and post-natal 6 months

first: Ashley

last: Cass

first: Xinshu

last: Xiao


title: Identification of DNA methylation-independent epigenetic events underlying clear cell renal cell carcinoma

first: Gangning

last: Liang

address: 1441 Eastlake Ave, NOR 7344

department: Urology

institute: University of Southern California

summary: Alterations in chromatin accessibility independent of DNA methylation can affect cancer-related gene expression, but are often overlooked in conventional epigenomic profiling approaches. In this study, we describe a cost-effective and computationally simple assay called AcceSssIble to simultaneously interrogate DNA methylation and chromatin accessibility alterations in primary human clear cell renal cell carcinomas (ccRCC). Our study revealed significant perturbations to the ccRCC epigenome, and identified gene expression changes that were specifically attributed to the chromatin accessibility status whether or not DNA methylation was involved. Compared to commonly mutated genes in ccRCC, such as the von Hippel-Lindau (VHL) tumor suppressor, the genes identified by AcceSssIble comprised distinct pathways and more frequently underwent epigenetic changes, suggesting that genetic and epigenetic alterations could be independent events in ccRCC. Specifically, we found unique DNA methylation-independent promoter accessibility alterations in pathways mimicking VHL deficiency. Overall, this study provides a novel approach for identifying new epigenetic-based therapeutic targets, previously undetectable by DNA methylation studies alone, that may complement current genetic-based treatment strategies.

overall_design: Examination of 3 different histone modifications in 2 patient tumor and adjacent normal samples.

first: Elinne

last: Becket


title: Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis

city: Toronto

first: Shivani

middle: Nainesh

last: Kamdar

state: Ontario

address: 60 Murray Street, L6-304B

department: Cancer Biology

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Background: Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation marks by performing whole-genome next generation sequencing in representative normal and prostate cancer-derived cell lines in order to determine functional pathways and key genes regulated by these epigenomic modifications in cancer. Results: Our cell line model shows disruption of hydroxymethylation distribution in cancer, with global loss and highly specific gain in promoter and CpG island regions. Significantly, we observed locus-specific retention of hydroxymethylation marks in specific intronic and intergenic regions which may play a novel role in the regulation of gene expression in critical functional pathways, such as BARD1 signaling and steroid hormone receptor signaling in cancer. We confirm a modest correlation of hydroxymethylation with expression in intragenic regions in prostate cancer, while identifying an original role for intergenic hydroxymethylation in differentially expressed regulatory pathways in cancer. We also demonstrate a successful strategy for the identification and validation of key candidate genes from differentially regulated biological pathways in prostate cancer. Conclusion: Our results indicate a distinct function for aberrant hydroxymethylation within each genomic feature in cancer, suggesting a specific and complex role for the deregulation of hydroxymethylation in tumorigenesis, similar to methylation. Subsequently, our characterization of key cellular pathways exhibiting dynamic enrichment patterns for methylation and hydroxymethylation marks may allow us to identify differentially epigenetically modified target genes implicated in prostate cancer tumorigenesis.

overall_design: Methylation profiles of representative normal prostate cell line RWPE-1 and prostate adenocarcinoma cell line 22Rv1 were generated by MBD capture followed by high-throughput sequencing on the HiSeq 2500 (Illumina), in triplicate.  Hydroxymethylation profiles of RWPE-1 and 22Rv1 were generated by hMeSeal followed by high-throughput sequencing on the HiSeq 2500 (one replicate each). Additional hydroxymethylation profiling for RWPE-1 was generated by hMeDIP followed by high-throughput sequencing on the HiSeq 2000 (Illumina).

first: Linh

last: Ho

first: Ken

last: Kron

first: Ruth

last: Isserlin

first: Theodorus

last: van der Kwast

first: Alexandre

last: Zlotta

first: Neil

last: Fleshner

first: Gary

last: Bader

first: Bharati

last: Bapat


title: Transposable elements and their KRAB-ZFP controllers regulate gene expression in adult tissues

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

summary: The tetrapod-restricted KRAB-containing zinc finger proteins (KRAB-ZFPs) are essential early embryonic controllers of transposable elements (TEs), which they repress via their cofactor KAP1 and associated effectors through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched several murine TEs with their cognate KRAB-ZFP. This revealed an unexpected level of granularity in their interactions, with KRAB-ZFPs recognizing TEs from more than one subfamily, TEs recruiting more than one KRAB-ZFP, and spatially and temporally differential KRAB-ZFP-mediated regulation of TEs and nearby genes. Most importantly, we discovered that the KRAB/KAP1 system controls TEs in adult tissues, in cell culture and in vivo, where they partner up to regulate the expression of cellular genes. Therefore, TEs and KRAB-ZFPs establish widely active transcription networks that regulate not only development but probably also many physiological events. Given the high degree of species-specificity of both TEs and KRAB-ZFPs, these results have important implications for studying and understanding the biology of higher vertebrates, including humans.

overall_design: Analysis of transcriptional profiles of KAP1 or ZFP932/Gm15446 KO cells or tissues, and ZFP932 and Gm15446 ChIPseq in murine ES and C2C12 cells.

first: Gabriela

last: Ecco

first: Marco

last: Cassano

first: Annamaria

last: Kauzlaric

first: Didier

last: Trono


first: Yibin

last: Wang

overall_design: Degradome sequencing libraries were generated for cerebellum 6 months post-natal, testis 6 months post-natal, and H1 human embryonic stem cells.

first: Ashley

last: Cass

first: Xinshu

last: Xiao


title: RNA-seq analysis of control and podoplanin knockdown lymphatic endothelial cells

status: Public on Mar 14 2016

city: Boston

first: Noorjahan

last: Panjwani

address: 136 Harrison Ave

department: Ophthalmology

institute: Tufts University

summary: To determine the transcriptome changes after podoplanin was knocked down in human lymphatic endothelial cells

overall_design: Human lymphatic endothelial cells were transfected with control siRNA and podoplanin siRNA (N=2 for each group). After 48 hours, total RNA was isolated and processed for RNA-seq.

first: Wei-Sheng

last: Chen


title: Effect of tail domain and kinase domain mutations in BMPR2 on gene expression in rat Hc92 cells studied by RNA-Seq

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

institute: Vanderbilt University

summary: We sequenced RNA from rat Hc92 cells transformed with empty vector, tail domain BMPR2 and kinase domain BMPR2 knockout vectors

overall_design: Comparison of Hc92 cells lacking BMPR2 tail domain vs those lacking BMPR2 kinase domain, using empty vector treated cells as control for both.


title: Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA binding proteins

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA


title: Long RNAs expression profiling of 20 Italian Large White pig backfat

city: Bologna

first: Roberta

last: Davoli

state: Bologna

address: Viale G. Fanin, 46

department: DISTAL

institute: Bologna University

summary: We report the application of Illumina RNA sequencing for characterization and discovery of genes and transcripts in Italian Large Whtie pig backfat tissue.

overall_design: RNAs sequencing for long RNA quantification, discovery, characterisation and differential expression evaluation.

first: Paolo

last: Zambonelli

first: Enrico

last: Gaffo

first: Stefania

last: Bortoluzzi


title: Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA binding proteins [iPS]

summary: Alternative splicing (AS) plays a critical role in cell fate transitions, development and disease. Recent studies have shown that AS also influences pluripotency and somatic cell reprogramming. We profiled transcriptome-wide AS changes that occur during reprogramming of fibroblasts to pluripotency. This analysis revealed distinct phases of AS during reprogramming, including a splicing program that is unique to transgene-independent iPS cells. Changes in the expression of alternative splicing factors Zcchc24, Esrp1, Mbnl1/2 and Rbm47 were demonstrated to be key contributors to phase-specific AS. RNA binding motif enrichment analysis near alternatively spliced exons provided further insight into the combinatorial regulation of AS during reprogramming by different RNA binding proteins. Ectopic expression of Esrp1 enhanced reprogramming, in part by modulating the AS of the epithelial specific transcription factor Grhl1.These data represent a comprehensive temporal analysis of the dynamic regulation of AS during the acquisition of pluripotency.

overall_design: Mouse embryo fibroblasts were isolated from an E12.5 embryo that was homozygous for a TET-OP-OKSM polycistronic transgene targeted to the collagen 1A locus and homozygous for rtTA targeted to the Rosa26 locus.  Therefore the expression of the “4 factors/Yamanaka factors” that induce pluripotency can be induced with doxycycline treatment. Using this model we isolated RNA in triplicate over a timecourse of 0, 4, 7, 10, 15, 20, days of dox treatment as well as 3 transgene independent clones.  Ssea1 MACS purification (Miltenyi Biotec) was used at each time point except zero.

first: Russ

last: Carstens


title: Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

city: Irvine

first: Klemens

last: Hertel

address: 19182 Jamboree Rd. 811 Med Sci I, C270

department: MMG

institute: UCI

summary: Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects.

overall_design: HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturer’s protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

first: Maliheh

last: Movassat

first: Tara

middle: L

last: Crabb

first: Anke

last: Busch

first: Chengguo

last: Yao

first: Derrick

last: Reynolds

first: Yongsheng

last: Shi


title: Identification of conserved and species-specific microRNAs in tea plant (Camellia sinensis) by deep sequencing

city: Hefei

first: chaoling

last: Wei

state: Anhui

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: In this study, it is noticeable that 32 tea-specific miRNAs were confirmed on the base of genome survey, using deep sequencing and microarray hybridization, and many miRNAs might associate with secondary metabolites synthesis.

overall_design: Leaves, buds and roots were collected

first: Xiao

last: Zhang

first: Chaoling


title: Induction of insulin gene transcription by Gli-similar Krüppel-like zinc finger protein 3, Glis3, in αTC1-9 cells

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: In this study, we examined the effect of  Glis3 on the transcriptional activation of  gene expression, including insulin gene, in pancreatic α-cell line, αTC1-9,  which do not express the insulin gene. We demonstrate that Glis3 induces the transcription of the insulin and identified a number of other genes that are induced by Glis3.

overall_design: Using ChIP-Seq we map the genome-wide sites with which Glis3 is associated. From this the consesus Glis3 binding site was calculated. This study shows that Glis3 is recruited to the proximal promoter of the insuln gene inthe pancreatic α-cell line, αTC1-9.

first: Yukimasa

last: Takeda

first: Gary

last: Zeruth

first: Kilsoo

last: Jeon

first: Hong

middle: S

last: Kang

first: Pengyi

last: Yang

first: Anton

last: Jetten


title: nanoCAGE reveals 5’ UTR features that define specific modes of translation of functionally related mTOR-sensitive mRNAs

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

summary: mTOR regulates mRNA translation. Whereas ribosome-profiling suggested that mTOR exclusively stimulates translation of TOP (containing a 5’-terminal oligopyrimidine [5’TOP] motif) and TOP-like mRNAs, polysome-profiling implied that mTOR also modulates translation of non-TOP mRNAs. We show that ribosome-, but not polysome-profiling, is biased towards identification of TOP mRNAs as differentially translated while obscuring detection of changes in non-TOP mRNA translation. Transcription start site profiling by Nano-Cap Analysis of Gene Expression (nanoCAGE) revealed that many mTOR-sensitive mRNAs do not have 5’TOP motifs. Moreover, nanoCAGE showed that 5’ UTR features distinguish two functionally and translationally distinct subsets of mTOR-sensitive mRNAs: i) those with short 5’ UTRs enriched for mitochondrial functions such as respiration, that are translated in an eIF4E, but not eIF4A1-dependent manner and ii) mRNAs encoding proliferation- and survival-promoting proteins, that harbor long 5’ UTRs, and require both eIF4E and eIF4A1 for their efficient translation. Selective inhibition of translation of mRNAs harboring long 5’ UTRs via suppression of eIF4A leads to uncoupling of expression of proteins involved in respiration (e.g. ATP5O) from those protecting mitochondrial integrity (e.g. BCL-2) ultimately resulting in apoptosis. Conversely, simultaneous translational downregulation of both long and short 5’ UTR mRNAs by mTOR inhibitors results in suppression of mitochondrial respiration and predominantly cytostatic effects.  Therefore, 5’ UTR features define differential modes of translation of functionally distinct mTOR-sensitive mRNAs, which explains discrepancies between the effects of mTOR and eIF4A inhibitors on neoplastic cells.

overall_design: Determination of 5'UTR lengths using nanoCAGE in MCF7 cells


title: Single-cell RNA-seq transcriptome profiling of Prdm1+ lineages in E9.5 mouse placenta

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

summary: Our goal was to transcriptionally profile Prdm1+ cell lineages of maternal and embryonic origin in mid-gestation mouse placenta in order to study vascular mimicry and additional processes in the placenta.

overall_design: Profiling of 61 single cells and 17 clusters of 2 or 3 cells chosen based on expression of Prdm1, a paternally inherited Prdm1-Venus fluorescent reporter, progenitor trophoblast marker Gjb3 and spiral artery trophoblast giant cell marker Prl7b1.

first: A

last: Mould

first: E

last: Robertson

last: Bikoff


title: Toxic gain of function from mutant FUS protein is crucial to trigger cell autonomous motor neuron loss

city: Charlestown

first: Clotilde

last: Lagier-Tourenne

state: MA

address: Bldg. 114 16th Street, Room 3125

department: Neurology

institute: Massachusetts General Hospital

summary: FUS is an RNA-binding protein involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cytoplasmic FUS-containing aggregates are often associated with concomitant loss of nuclear FUS. Whether loss of nuclear FUS function, gain of a cytoplasmic function, or a combination of both lead to neurodegeneration remains elusive. To address this question, we generated knock-in mice expressing mislocalized cytoplasmic FUS and complete FUS knock-out mice. Both mouse models display similar perinatal lethality with respiratory insufficiency, reduced body weight and length, and largely similar alterations in gene expression and mRNA splicing patterns, indicating that mislocalized FUS results in loss of its normal function. However, FUS knock-in mice, but not FUS knock-out mice, display reduced motor neuron numbers at birth, associated with enhanced motor neuron apoptosis, which can be rescued by cell-specific CRE-mediated expression of wild-type FUS within motor neurons. Together, our findings indicate that cytoplasmic FUS mislocalization not only leads to nuclear loss of function, but also triggers motor neuron death through a toxic gain of function within motor neurons.

overall_design: Total RNA from brains of E18.5 knock-in (FusΔNLS/ΔNLS), and knock-out (Fus-/-) mice and their control littermates were extracted with Trizol and libraries were prepared for RNA sequencing and RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Generation sequencing (RASL-seq) (Li et al. 2012; Zhou et al. 2012). For the RNA-seq experiment, biological replicates were used with n=4-5 knock-in animals per group (4 wild-type and 5 homozygous FusΔNLS) and n=5 knock-out animals per group (5 wild-type and 5 homozygous Fus-/-). For the RASL-seq analysis, biological replicates were used with n=4 knock-in animals per group (4 wild-type, 4 heterozygous and 4 homozygous FusΔNLS) and n=5 animals per group (5 wild-type and 5 homozygous Fus-/- knock-out).

first: Luc

last: Dupuis

first: Erik

last: Storkebaum

first: Xiang-Dong

last: Fu


title: Prdm1

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Comparisons of Control and Schizophrenia-Patient derived hiPSC-derived NPCs

city: New York

first: Kristen

last: Brennand

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary:
Cell-based models of many neurological and psychiatric diseases, established by reprogramming patient somatic cells into human induced pluripotent stem cells (hiPSCs), have now been reported.  While numerous reports have demonstrated that neuronal cells differentiated from hiPSCs are electrophysiologically active mature neurons, the “age” of these cells relative to cells in the human brain remains unresolved.  Comparisons of gene expression profiles of hiPSC-derived neural progenitor cells (NPCs) and neurons to the Allen BrainSpan Atlas indicate that hiPSC neural cells most resemble first trimester neural tissue.  Consequently, we posit that hiPSC-derived neural cells may most accurately be used to model the early developmental defects that contribute to disease predisposition rather than the late features of the disease. Though the characteristic symptoms of schizophrenia SZ generally appear late in adolescence, it is now thought to be a neurodevelopmental condition, often predated by a prodromal period that can appear in early childhood. Postmortem studies of SZ brain tissue typically describe defects in mature neurons, such as reduced neuronal size and spine density in the prefrontal cortex and hippocampus, but abnormalities of neuronal organization, particularly in the cortex, have also been reported. We postulated that defects in cortical organization in SZ might result from abnormal migration of neural cells. To test this hypothesis, we directly reprogrammed fibroblasts from SZ patients into hiPSCs and subsequently differentiated these disorder-specific hiPSCs into NPCs. SZ hiPSC differentiated into forebrain NPCs have altered expression of a number of cellular adhesion genes and WNT signaling.
Methods: We compared global transcription of forebrain NPCs from six control and four SZ patients by RNAseq.
Results:  Multi-dimensional scaling (MDS) resolved most SZ and control hiPSC NPC samples; 848 genes were significantly differentially expressed (FDR<0.01)
Conclusions: The WNT signaling pathway was enriched 2-fold (fisher exact test p-value = 0.031).

overall_design: 1-2 independent differentiations (biological replicates) for each of four control and four schizophrenia patients were analyzed; samples were generated in parallel to neuron RNAseq data.

first: Gang

last: Fang


title: Multiphasic and dynamic changes in alternative splicing during induction of pluripotency are coordinated by numerous RNA binding proteins [ESRP DKO]

first: Yi

last: Xing

overall_design: ES cells from 3 independent E3.5 blastocysts from either Control (Esrp1 WT/WT; Esrp2 -/-) or Esrp DKO (Esrp1 floxed/floxed; Esrp2 -/-) were transfected with pLVX-EGFP-Cre, puro selected and RNA was isolated 6 days later.

first: Russ

last: Carstens


title: IGF2BP3 controls cancer cell invasiveness by modulation RISC function

status: Public on Mar 12 2016

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

summary: The goal of this study was to determine IGF2BP3 regulation of RNA targets in human pacreatic ductal adenocarcinoma cell lines

overall_design: Included are iCLIP-seq libraries for IGF2BP3 from PL45 and Panc1 PDAC cell samples, RIP-seq samples from PL45 and Panc1 PDAC cells, RNA-seq data sets from control and IGF2BP3 knockdown in PL45 and Panc1 PDAC cells, and small RNA-seq samples from Panc1 cells

first: Hanane

last: Ennajdaoui

middle: M

first: Sol

last: Katzman

first: Jeremy

last: Sanford


title: Sequence-Targeted Nucleosome Sliding in vivo

city: Eugene

first: Jeffrey

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon


title: Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling

summary: RNA sequencing was performed on various W303 variants to determine effects of nucleosome repositioning on transcript abundance

overall_design: RNA sequencing was carried out in multiple backgrounds to determine effects of nucleosome repositioning in various contexts. For engineered chromatin remodeling factors, a catalytically inactive control was included.

first: Toshio

last: Tsukiyama

first: Gregory

last: Bowman


title: Global view of mRNA uridylation in Arabidopsis

status: Public on Mar 11 2016

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

summary: To obtain a global view of mRNA uridylation in Arabidopsis, we generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant. The TAIL-seq protocol was recently developed to deep-sequence the 3' ends of RNAs (Chang et al., 2014).

overall_design: We generated TAIL-seq libraries from WT plants, urt1 and xrn4 single mutants, and urt1 xrn4 double mutant.

first: Hélène

last: Zuber


title: Genome-wide distribution of Pbx1/2/3 in mouse cortex at embryonic day 15.5 [ChIP-seq]

city: san francisco

first: olga

last: golonzhka

address: 1550 4th street

department: psychiatry

institute: UCSF

summary: We demonstrate using conditional mutagenesis that Pbx1, with and without Pbx2+/ sensitization, regulates regional identity and laminar patterning of the developing mouse neocortex in cortical progenitors (Emx1-Cre) and in newly generated neurons (Nex1-Cre). Pbx1/2 mutants have three salient molecular phenotypes of cortical regional and laminar organization: hypoplasia of the frontal cortex, ventral expansion of the dorsomedial cortex, and ventral expansion of Reelin expression in the cortical plate of the frontal cortex, concomitant with an inversion of cortical layering in the rostral cortex. Molecular analyses, including PBX ChIP-seq, provide evidence that PBX promotes frontal cortex identity by repressing genes that promote dorsocaudal fate.

overall_design: Chromatin immunoprecipitation was performed using antibody against Pbx1/2/3 (sc-888, Santa Cruz). Wild type E15.5 mouse whole cortex was used for the analysis.

first: John

last: Rubenstein

first: Olga

last: Golonzhka


title: Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis and global view of mRNA uridylation in Arabidopsis


title: Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

summary: Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler

overall_design: Matched MNase digests from W303 strain variants during log growth (OD600=0.4-0.6) were subject to paired-end sequencing for nucleosome mapping. For effects of the engineered fusion remodeling protein, a catalytically inactive (ATPase dead D513N) variant was included as a control.


title: Store-operated Ca2+ entry in follicular T cells controls humoral immune responses and autoimmunity

status: Public on Mar 10 2016

city: Würzburg

first: Martin

last: Vaeth

address: Versbacher Str. 9

department: Institute of Systems Immunology

institute: Julius-Maximilians University of Würzburg

summary: T follicular helper (TFH) cells promote affinity maturation of B cells in germinal centers (GCs), whereas T follicular regulatory (TFR) cells limit GC reaction. Store-operated Ca2+ entry (SOCE) through Ca2+ release-activated Ca2+ (CRAC) channels mediated by STIM and ORAI proteins is a fundamental signaling pathway in T lymphocytes. Here we show that SOCE is required for the differentiation and function of both TFH and TFR cells. Conditional deletion of Stim1 and Stim2 genes in T cells or Treg cells results in spontaneous autoantibody production and humoral autoimmunity. Conversely, antibody-mediated immune responses following viral infection critically depend on SOCE in TFH cells. Mechanistically, STIM1 and STIM2 control early TFR and TFH cell differentiation through NFAT-mediated IRF4, BATF and Bcl-6 expression. SOCE plays a dual role in GC response by controlling TFH and TFR cell function, thus enabling protective B cell responses and preventing humoral autoimmunity.

overall_design: RNAseq analyses of WT and Stim1Stim2 DKO follicular T cells and non-follicular T cells; 4-6 mice per cohort in duplicates. Mice were infected for 10 days with LCMV.

first: Stefan

last: Feske


title: Genome-wide identification of CCA1-bound genes in Arabidopsis by ChIP-Seq

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

institute: Nagoya University

summary: LHY and CCA1 encode single MYB transcription factors, involved in circadian clock. However, direct target genes of LHY and CCA1 in a genomic scale were largely unknown. To reveal bound genes by CCA1, chimeric protein CCA1-FLAG was expressed under CCA1 promoter in cca1 lhy (CCA1pro:CCA1-FLAG/ cca1 lhy). ChIP was performed using anti-FLAG antibody (F3165; SIGMA), which was bound to Dynabeads Protein G (100-03D; Life Technologies), and ChIP DNA were analyzed by IonPGM or Illumina GAII.

overall_design: Chromatin immunoprecipitation was performed for CCA1-FLAG-expressing Arabidopsis. ChIP DNA was analyzed 2 types of deep sequencers (Illumina GAII and IonPGM).

first: Takamasa

last: Suzuki


title: Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome

city: Magdalenka

first: Agnieszka

last: Szostak

address: Postępu, Jastrzębiec

country: Poland

institute: Institute of Genetics and Animal Breeding PAS

summary: The optimal ratio of omega-6 to omega-3 polyunsaturated fatty acids (PUFAs) is important for keeping homeostasis of biological processes and metabolism, yet the underlying biological mechanism is poorly understood. The objective of this study was to identify changes in the pig liver transcriptome induced by a diet enriched with omega-6 and omega-3 fatty acids, and to characterize the biological mechanisms related to PUFA metabolism.  Polish Landrace pigs (n =12) were fed diet enriched with linoleic acid (LA, omega-6) and alpha-linolenic acid (ALA, omega-3 family) or standard diet as a control. The fatty acids profiling was assayed in order to verify how feeding influenced the fatty acids content in liver, and subsequently next-generation sequencing (NGS) was used to identify differentially expressed genes (DEG) between transcriptomes between dietary groups. The biological mechanisms and pathway interaction networks were identified by analysis in DAVID and Cytoscape tools. Fatty acids profile analysis indicated a higher contribution of PUFAs in liver for LA and ALA-enriched diet group, particularly for the omega-3 fatty acids family, but not omega-6. Next-generation sequencing identified 3,565 DEG, 1,484 of which were induced and 2,081 were suppressed by PUFA supplemenation. Low ratio of omega-6/-3 fatty acids resulted in modulation of fatty acids metabolism pathways and over-representation of genes involved in membrane composition, signal transduction and immune response pathways.  In conclusion, a diet enriched with omega-6 and omega-3 fatty acids altered the transcriptomic profile of the pig liver and affected a set of genes involved in metabolic pathways important to animal health status.

overall_design: Hepatic mRNA profiles of Polish Landrace pig breed fed two different diets, were generated by deep sequencing, using Illumina MiSeq. Experimental diet was enriched with polyunsaturated fatty acids (omega-6 and omega-3), while standard diet remain as a cotrol. 2 pooled samples each containing RNA extracts from 6 individuals livers were analyzed.

first: Magdalena

last: Ogłuszka

first: Marinus

last: te Pas

first: Ewa

last: Poławska

first: Paweł

last: Urbański

first: Edyta

last: Juszczuk-Kubiak

first: Tadeusz

last: Blicharski

first: Chandra

last: Shekhar Pareek

first: Jenelle

middle: R

last: Dunkelberger

first: Jarosław

middle: O

last: Horbańczuk

first: Mariusz

last: Pierzchała


title: Expression profiling of IL-13 stimulated PBMCs with and without an IL-13R antagonist

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

country: Australia

institute: WEHI

summary: This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs).

overall_design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.

first: Monther

last: Alhamdoosh

first: Milica

last: Ng

first: Nicholas

last: Wilson

first: Huy

last: Huynh

first: Michael

first: Matthew

middle: E

last: Ritchie


title: Impact of URT1-mediated uridylation on small RNA tailing in Arabidopsis

first: Dominique

last: Gagliardi

summary: To analyse the impact of URT1-mediated uridylation on miRNA and siRNA tailing, we deep-sequenced small RNA libraries for WT and urt1 duplicate samples at the same developmental stage that was analyzed by TAIL-seq, i.e., two-week-old seedlings.

overall_design: Examination of miRNA and siRNA tailing in WT and urt1 samples.

first: Hélène

last: Zuber


title: RNA sequencing of WT and Uhrf1 KO  iNKT cells

city: Shanghai

first: Yu

last: Cui

state: Shanghai

address: Yueyang road 320

institute: Chinese Academy of Sciences

summary: Deletion of Uhrf1 resulted in stage 1-specific defects during iNKT cell development. To investigate the molecular mechanism, we sorted WT and Uhrf1-KO stage 1 iNKT cells and performed RNA-seq. By comparing gene expression profile, we found metabolic defects in Uhrf1-KO stage 1 iNKT cells. The expression of CD71 (Tfrc), two subunits of CD98 (Slc3a2 and Slc7a5) and Glut3 (Slc2a3) was reduced in stage 1 iNKT cells. Besides, the downstream pathways of AKT-mTOR axis were significantly reduced. Collectively, our results suggest that Uhrf1 is required for iNKT cell development by regulating the Akt-mTOR signaling pathway.

overall_design: We first sorted WT and Uhrf1-KO stage 1 iNKT cells, extracted the mRNA and performed RNA-seq. We then analyzed the differentially expressed genes and performed KEGG pathway analysis. We used RT-PCR to verify the expression of the key nutrient related genes (Tfrc, Slc3a2, Slc7a5 and Slc2a3) and used flow cytometry to test the protein level of metabolic related molecules. Besides, we also analyzed the expression of genes of mTOR downstream pathways to demonstrate that Uhrf1 mediated AKt-mTOR axis regulates iNKT cell development.

first: Xufeng

last: Chen


title: Identification of chromatin accessibility domains in EMT and breast cancer stem cell formation.

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary: Epithelial-mesenchymal transition (EMT), the process whereby cells gain migratory and invasive properties characteristic of mesenchymal cells, plays a central role in embryogenesis and wound healing in a wide range of tissues. However, EMT has also been linked to the formation of cancer stem cells (CSCs). Many of the signaling pathways involved in EMT have also been implicated in CSC formation but the processes that contribute uniquely to CSC formation remain elusive. We have previously demonstrated that PKCθ activation is critical for EMT induction and concomitant CSC formation in the breast cancer luminal epithelial cell line, MCF7. To discover how PKC-induced alterations in the epigenome influence the EMT and CSC formation in MCF-7 cells, we employed a combination of expression profiling and Formaldehyde Assisted Regulatory Elements (FAIRE)-sequencing in order to reveal novel links between gene expression and DNA accessibility changes after PKCθ activation. We found that, during EMT, increases in accessibility generally occurred in regions away from transcription start sites, low in CpG, enriched with chromatin marks of enhancer elements and motifs for FOX, AP1, TEAD and AP2. Increases in FOX and AP-1 motif accessibility were associated with genes that exhibited increased expression in CSC, while increased AP-2 accessibility was associated with genes that had higher expression in non-CSCs. This study revealed novel regions of DNA accessibility induced by PKC that contribute to the understanding of how epigenomic plasticity of cells undergoing EMT leads to the activation of genes that drive the CSC program.

overall_design: 2 biological samples were analysed with 2 biological replicates each and a mixed total input.

first: Anjum

last: Zafar

first: Sudha

last: Rao


title: Comparison of transcriptomes in class-B GATA mutants with cytokinin treatments

city: Freising

first: Quirin

middle: Ludwig

last: Ranftl

address: Emil-Ramann-Straße 4

department: Wissenschaftszentrum Weihenstephan

institute: TU München

summary:
We have used Agilent whole genome arrays (v4) to compare the gene expression changes between 14 days-old Arabidopsis seedlings with or without cytokinin treatments in wild type as well as the following mutant genotypes: gnc gnl (AT5G56860, AT4G26150),  gata16 gata17 gata17l (AT5G49300, AT3G16870, AT4G16141), gnc gnl gata16 gata17 gata17l (AT5G56860, AT4G26150, AT5G49300, AT3G16870, AT4G16141)
Three independent biological samples were prepared for each genotype. Experiment was performed in two rounds: Col-0_1, gnc gnl, quintuple and Col-0_2, triple.

overall_design: Three replicate measurements of three biological samples were prepared for each genotype.

first: Claus

last: Schwechheimer

first: Carina

last: Behringer


title: Identification of enhancers in EMT and breast cancer stem cell formation

summary: Epithelial-mesenchymal transition (EMT), the process whereby cells gain migratory and invasive properties characteristic of mesenchymal cells, plays a central role in embryogenesis and wound healing in a wide range of tissues. However, EMT has also been linked to the formation of cancer stem cells (CSCs). Many of the signaling pathways involved in EMT have also been implicated in CSC formation but the processes that contribute uniquely to CSC formation remain elusive. We have previously demonstrated that PKCθ activation is critical for EMT induction and concomitant CSC formation in the breast cancer luminal epithelial cell line, MCF7. To discover how PKC-induced alterations in the epigenome influence the EMT and CSC formation in MCF-7 cells and MDA-MB-231, we employed a combination of expression profiling and ChIP-sequencing of H3K4me1 and H3K27ac.

overall_design: 3 biological samples were analyzed with two different chromatin marks.


title: Dichloroacetate (DCA) prevents cisplatin-induced nephrotoxicity without compromising its anti-cancer properties.

status: Public on Mar 09 2016

summary: The aim of this study was to compare the transcriptional changes that occur in the kidneys of mice administered cisplatin or DCA, or both, by RNA-seq.

overall_design: generation of RNA-seq datasets from mice subjected to 4 different treatments. 3 biological replicates per treatment. Saline treatment is control.

first: Angelo

last: Theodoratos

first: Philip

middle: G

last: Board