title: Evaluating the impact of sleep on genome-wide methylation levels in college students

city: New Haven

first: Yong

last: Zhu

state: Connecticut

address: 60 College St

institute: Yale School of Public Health

summary: Approximately 4 μg of DNA was isolated from blood of each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit.  Of the 16 samples, 8 were from group 1 (CESD-H/TST-H; 5 female, 3 male) and 8 were from group 2 (CESD-H/TST-L; 5 female, 3 male).  All DNA samples were confirmed to be of high purity (A260/280: 1.7-2.0).  Pooled samples were prepared for each group by combining approximately 75 ng of DNA from each of the eight subjects.  These two samples were submitted to the Yale Genomics Core for epigenome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip, which measures the level of methylation β (a value ranging from 0 to 1, where 0 represents a completely unmethylated site and 1 a completely methylated site) at each of the 485,577 CpG sites on the array.  Illumina’s GenomeStudio software was used to calculate the degree of differential methylation by group for each CpG site on the array, and FDR-adjusted p-values (Q-values) were calculated for each site in order to adjust for multiple comparisons. CESD=depression score; TST=sleep score

overall_design: Blood-derived genomic DNA was isolated from 16 subjects; 8 each with high and low total sleep scores, respectively. DNA was pooled by group and genome-wide methylation profiling was performed.

first: Mary

last: Carskadon

first: Daniel

middle: I

last: Jacobs


title: Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 3)

status: Public on Aug 01 2016

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

type: Expression profiling by high throughput sequencing

summary: Understanding gene regulation in stem cells is key to understanding stem cell biology. Contrary to transcriptional regulation the function of alternative splicing (AS) in stem cells is poorly understood. Here we study function and mechanisms of AS in a powerful in vivo model for stem cell biology, the planarian S. mediterranea. Knockdown of AS factors, computational analyses of massive RNA-sequencing data, phenotyping, and biochemical binding assays revealed a stem cell specific AS program comprising hundreds of alternative exons, intron retention events, and microexons. The conserved AS factors CELF/MBNL are main regulators of this program. We show that they antagonize each other by directly promoting or repressing stem cell specific AS events. Knockdown of CELF/MBNL leads to defective regeneration by affecting self-renewal and differentiation, respectively. Thus, AS is of key importance for stem cell regulation in vivo and antagonistic regulation by CELF/MBNL is likely an ancestral feature of animal stem cells.

overall_design: mRNA profiles of various samples of planarian cells, including control and knockdowns of key splicing factors in whole worms, and FACS-purified fractions

first: Jordi

last: Solana

first: Marta

middle: R

last: Orejuela

first: Nikolaus

last: Rajewsky


title: Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection

city: beijing

first: kong

last: weiwen

address: Qinghua East Rd 35

country: China

institute: Beijing forestry university

summary:
Purpose:  The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection
Methods: mRNA profiles of anti-infection samples and interaction sample  were generate  by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using  SYBR Green assays
Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome.  There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification.
Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens.

sample_organism:
Cucumis sativus
Botrytis cinerea

platform_organism:
Cucumis sativus
Botrytis cinerea

overall_design: mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using  Illumina Hiseq 2500 .

first: Weiwen

last: Kong

first: Xiaoqing

last: He


title: Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNA) are non-coding RNAs that negatively regulate gene expression by preventing the translation of specific mRNA transcripts. Since miRNAs are stably expressed in bodily fluids, there is growing interest in profiling these miRNAs, as it is minimally invasive and cost-effective as a diagnostic matrix. A technical hurdle in studying miRNA dynamics is the ability to reliably extract miRNA as small sample volumes and low RNA abundance create challenges for extraction and downstream applications. The purpose of this study was to develop a pipeline for the recovery of miRNA using small volumes of archived serum samples. The RNA was extracted employing several widely utilized RNA isolation kits with and without addition of a carrier. We were able to profile miRNA levels in serum samples using the small RNA sequencing method on the Illumina platform and observed that successful sequencing cannot be predicted by substrate RNA quality. Although the carrier RNA had a significant impact on miRNA measurement, it did not enhance the mapping of any miRBase annotated sequences. However, some of the extraction procedures offer certain advantages: RNA extracted by TRIzol seemed to align to the miRBase best; extractions using TRIzol with carrier yielded higher miRNA-to-small RNA ratios and higher numbers of processed reads, but the majority of the reads were not aligning to miRBase. Our findings illustrate that miRNA extraction and quantification is influenced by the choice of methodologies and by careful selection of an extraction method, permitting archived serum samples to become valuable resources for high-throughput applications.

overall_design: Testing different RNA extraction procedures  for small RNA sequencing; The serum samples were obtained from the Department of Defense Serum Repository where they were stored at -30 C. These samples were used to conduct a pilot study with the purpose of determining suitable methods for these compromised samples before setting up a larger study. A subset of samples was pooled and divided into 350  L aliquots to be used in extractions. All procedures used 350  L of serum for miRNA extractions except the Qiagen miRNeasy Mini Kit, where 200  L of sample was used per extraction.

first: Raina

last: Kumar


title: Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

type: Genome binding/occupancy profiling by high throughput sequencing

summary: By analysis of ChIP-exo of FOXA1 in LNCaP,  we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis.

overall_design: We have performed ChIP-seq of eight chromatin remodeler factors.

first: Zhong

last: Chen


title: miRNA Profile in Three Different Normal Human Ocular Tissues by miRNA-Seq

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

summary: Since microRNAs (miRNAs) have been associated with eye diseases, our study aims to profile ocular miRNA expression in normal human eye tissue using miRNA-Seq in order to provide a foundation for future disease research. Total RNAs were extracted from normal human ciliary body (CB) (n=7), cornea (n=7), and trabecular meshwork (TM) (n=7) samples using mirVana total RNA isolation kit. The sequencing library was prepared using the Illumina TruSeq Small RNA Sample Prep kit and was sequenced using Illumina MiSeq. Generated sequence reads were trimmed and aligned against human reference database using the Bowtie software, and only exact matches to mature miRNAs from miRBase were included. miRTarBase database was used to analyze the gene targets of the miRNAs in our tissues, and expression of a few selected miRNAs were validated using droplet digital PCR (ddPCR). We found 378 miRNAs expressed collectively in our samples, of which miR-143-3p, miR-184, miR-26a-5p, and miR-204-5p were most abundantly expressed. With the expression patterns and gene targets, we identified several uniquely expressed miRNAs and created a profile of miRNAs known to target genes associated with keratoconus and glaucoma. Using ddPCR, we were able to validate the expression profile created using miRNA-Seq. For the first time, we profiled miRNA expression in three human ocular tissues using miRNA-Seq, identifying many miRNAs that had not been previously reported in ocular tissue. Knowing the expression of miRNAs in non-diseased eye tissues could help elucidate miRNA changes that accompany diseases such as glaucoma and keratoconus.

overall_design: This study profiled the expression of miRNAs in normal human ciliary body (n=7), cornea (n=7), and trabecualr meshwork (n=7) tissue

first: Michelle

last: Drewry


title: RNase ZS1-mediated UbL40 mRNA decay controls thermo-sensitive genic male sterility in hybrid rice

city: Guangzhou

first: Hai

last: Zhou

state: Guangdong

address: Wushan

department: College of Life Sciences

institute: South China Agricultural University

summary: Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 80% (2.6 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40) genes. RNase ZS1, a member of the evolutionarily conserved endonuclease, processed tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Over-expression of UbL401 and UbL404 in wild-type plants caused male sterility, whereas knockdown of UbL401 and UbL404 in tms5 plants partially restored the male fertility at restrictive temperatures. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications not only of rice but also of other crops.

overall_design: To address whether RNase ZS1 involves in mRNA metabolism, degradome sequencing was performed using RNA from young panicles of wild type (ZH11) and tms5 (Os02g12290iL1) plants grown at restrictive temperatures.

first: Chuxiong

last: Zhuang


title: Directional RNA-Seq analysis of Arabidopsis plants grown under Pi-deprived conditions

city: Newark

first: Vinay

middle: K

last: Nagarajan

state: DE

address: 15 Innovation Way

institute: University of Delaware

overall_design: PolyA+ RNA isolated from Col-0, hho2-1, phr1 and hho2phr1 grown on agar-solidified P- condition for 7d

first: Kashchandra

middle: G

last: Raghothama

first: Ajay

last: Jain


title: Revised annotation of Plutella xylostella microRNAs

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

summary: We used our newly ultra deep sequence data and bioinformatics to re-annotate P. xylostella genome for high confidence miRNAs with the correct 5p and 3p arm features. Furthermore, the whole genome was screened to identify potential miRNA binding sites using three target-predicting algorithms. Totally, 203 mature miRNAs were annotated, including 33 novel miRNAs.

overall_design: Two geographical populations of Diamondback moth larvae from Queensland (Gatton) and South Australia (Waite) were collected and reared on the cabbage plant at the University of Queensland in Australia. Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturer’s protocol (Life Technologies). The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software.

first: Sassan

last: Asgari


title: Prox1 (Prosper-related homeobox  1)  transcription factor depletion effect on CGTH-W-1  cells.

status: Public on Jul 31 2016

city: Warsaw

first: Katarzyna

last: Paczkowska

address: Roentgena 5

department: Department of Genetics

country: Poland

institute: Cancer Center - Institute

summary: Analysis of CGTH-W-1  follicular thyroid carcinoma cells transcriptome following  48 hrs siRNA-mediated depletion of PROX1. PROX1 is a homeobox transcription factor. PROX1  depletion decreases  migratory ability, motility and invasivness and induces profound cytoskeleton changes of CGTH-W-1  cells.  Results provide insight into the role of PROX1 in the thyroid cancer.

overall_design: Three biological replicates for a given condition

first: Magdalena

last: Rudzińska

first: Joanna

last: Ledwoń

first: Justyna

last: Sikorska

first: Agnieszka

last: Paziewska

first: Michal

last: Mikula

first: Jerzy

last: Ostrowski

first: Barbara

last: Czarnocka


title: Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians (dataset 1)

city: Berlin

first: Marta

last: Rodriguez Orejuela

address: Robert-Roessle str. 10 (H. 87)

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbruck Centrum

summary: Understanding gene regulation in stem cells is key to understanding stem cell biology.Contrary to transcriptional regulation the function of alternative splicing (AS) in stem cells is poorly understood. Here we study function and mechanisms of AS in a powerful in vivo model for stem cell biology, the planarian S. mediterranea. Knockdown of AS factors, computational analyses of massive RNA-sequencing data, phenotyping, and biochemical binding assays revealed a stem cell specific AS program comprising hundreds of alternative exons, intron retention events, and microexons. The conserved AS factors CELF/MBNL are main regulators of this program. We show that they antagonize each other by directly promoting or repressing stem cell specific AS events. Knockdown of CELF/MBNL leads to defective regeneration by affecting self-renewal and differentiation, respectively. Thus, AS is of key importance for stem cell regulation in vivo and antagonistic regulation by CELF/MBNL is likely an ancestral feature of animal stem cells.

overall_design: Sequencing of polyA-selected RNA from Schmidtea mediterranea individuals after control, smed-bruno-like(RNAi) and mbnl(RNAi) after 20,25,30 days after RNAi

first: Jordi

last: Solana

first: Manuel

last: Irimia

first: Salah

last: Ayoub

last: Orejuela

first: Vera

last: Zywitza

first: Marvin

last: Jens

first: Debashish

last: Ray

first: Quaid

middle: D

last: Morris

first: Timothy

last: Hughes

first: Benjamin

middle: J

last: Blencowe

first: Nikolaus

last: Rajewsky


title: CXCR5+ Follicular Cytotoxic T cells Control Viral Infection in B Cell follicles

city: Clayton

first: Yew Ann

last: Leong

state: Victoria

address: Wellington Road

department: BIochemistry

institute: Monash University

summary: Lymphocytic Choriomeningitis Virus (LCMV) specific CD8+ T cells (P14) were transferred into congenic WT mice followed by LCMV(DOCILE) infection. CXCR5-expressing (CXCR5+) or CXCR5 non-expressing (CXCR5-) P14 were purified on day 8 after infection, and total mRNA were sequenced from these populations. mRNA of P14 from uninfected mice (Naive P14) was also sequenced.

overall_design: Examination of mRNA level in CXCR5 expressing P14 (CXCR5+P14) and non-expressing P14 (CXCR5-P14) from LCMV infected mice day 8 post infection. mRNA of P14 from uninfected mice (Naïve P14) was also examined.

first: Yew

middle: A

first: Di

last: Yu


title: BAZ1B in Nucleus Accumbens Regulates Reward-Related Behaviors in Response to Distinct Emotional Stimuli

status: Public on Jul 30 2016

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: ATP-dependent chromatin remodeling proteins are being implicated increasingly in the regulation of complex behaviors, including models of several psychiatric disorders. Here, we demonstrate that Baz1b, an accessory subunit of the ISWI family of chromatin remodeling complexes, is upregulated in the nucleus accumbens (NAc), a key brain reward region, in both chronic cocaine-treated mice and mice that are resilient to chronic social defeat stress. In contrast, no regulation is seen in mice that are susceptible to this chronic stress. Viral-mediated overexpression of Baz1b, along with its associated subunit Smarca5, in mouse NAc is sufficient to potentiate both rewarding responses to cocaine, including cocaine self-administration, and resilience to chronic social defeat stress. However, despite these similar, proreward behavioral effects, genome-wide mapping of BAZ1B in NAc revealed mostly distinct subsets of genes regulated by these chromatin remodeling proteins after chronic exposure to either cocaine or social stress. Together, these findings suggest important roles for BAZ1B and its associated chromatin remodeling complexes in NAc in the regulation of reward behaviors to distinct emotional stimuli and highlight the stimulus-specific nature of the actions of these regulatory proteins.

overall_design: BAZ1B (WSTF) ChIP-seq of mouse. Cocaine vs Saline, 3 biological replicates. In social defeat model: Normal control vs Susceptible vs Resilient, 3 biological replicates.

first: HaoSheng

last: Sun

first: Ning-Yi

last: Shao

first: Li

last: Shen


title: High-throughput sequencing analysis identify miRNAs in 7dpf F1-zebrafish under β-diketone antibiotics exposure to F0-zebrafish

city: Wenzhou

first: Wang

last: hui

state: Zhejiang

address: Wenzhou Medical University Chashan Campus  Chashan University Town, Wenzhou,  Zhejiang Province

summary: Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day β-diketone antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution.

overall_design: Sample 1: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 12.5 mg/L.

first: Yuansi

last: Zheng


title: mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development [RNA-seq and mTAIL-seq Human and Drosphila]

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Eukaryotic mRNAs are subject to multiple types of tailing which critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAILseq (mRNA TAIL-seq or mTAIL-seq) with enhanced sequencing depth for mRNAs (by ~1000 fold compared to the previous version). The improved method allows us to investigate the regulation of poly(A) tail in Drosophila oocytes and embryos. We find that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAILseq data with ribosome profiling data, we find a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that  regulation of poly(A) tail in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Ten separate sets of TAIL-seq experiments were performed. Two sets of HeLa cells are untransfected normal cells. Eight sets of fly sample include a pair of wild type and mutant.

first: Mihye

last: Lee

first: Ahyeon

last: Son

first: Hyeshik

last: Chang

first: V

middle: N

last: Kim


title: Histone H3K4 trimethylation in rat peripheral nerve

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

summary: ChIP-seq of H3K4me3 in rat peripheral nerve was used to identify transcription start sites associated with Schwann cell-expressed genes. The analysis was performed in injured and control nerve to identify injury-responsive changes in Schwann cells.

overall_design: H3K4me3 ChIP samples were prepared from rat sciatic nerve at 1 day post-transection using both the distal stump of the injured nerve and the contralateral (sham) nerve.

first: Ki

last: Ma


title: Effect of Gfi1 36N variant on genome-wide H3K9 Acetylation patterns

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

summary: ChIP-Seq Analysis of H3K9Ac in pairs of mouse and human samples carrying either the Gfi136S or the GFi136N variants. The objective of the study was to identify the changes in H3K9 acetylation at gene promoters that occur in samples expressing the 36N variant of the Gfi1 gene.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 3 pairs of bone-marrow AML samples were obtained from mice where 1 mouse in each pair was homozygous for Gfi136S and 1 heterozygous for Gfi136N, or homozygous for 36N in one case. 2 pairs of AML samples were obtained from human patients were 1 patient was homozygous for Gfi1 36S and one was heterozygous for Gfi1 36N. H3 and H3K9Ac ChIP-Seq was carried out on each sample.

first: Lacramioara

last: Botezatu

first: Hideki

last: Makishima

first: Lars

middle: C

last: Michel

first: Tarik

last: Möröy

first: Cyrus

last: Khandampour


title: Deep transcriptome analysis of mouse embryonic fibroblast following simultaneous overexpression of Stella, Oct4 and Nanos2 (SON)

city: Mashhad

first: Moein

last: Farshchian

address: Vakilabad Highway

department: Department of Biology,Faculty of Science,

country: Iran

institute: Ferdowsi University of Mashhad

summary: We constructed a polycistronic lentiviral vector to overexpress 3 germ cell specific genes (Stella, Oct4 and Nanos2)  in mouse embryonic fibroblast (MEFs) and evaluated the transcriptome portrait in partially reprogrammed cells.We sequenced RNA samples from bulk cell population of two biological duplicates of MEF-GFP (control) and MEF-SON (overexpressed) 21 days post infection. Differential expression analysis of 50 M pair-end read per samples showed overexpression of neurogenesis, blood vessel and proliferation related genes and downregulation of chondroitin sulphate metabolic process, nitric oxide production and innate immune response genes.

overall_design: Examination of whole transcriptome following concurrent overexpression of Stella, Oct4 and Nanos2 in MEFs.

first: Olivier

last: Armant

first: Manuel

last: Irimia

first: Per

middle: L

last: Brattås

first: Maryam

middle: M

last: Matin

first: Ahmad

last: Bahrami


title: Genome-wide transcriptional analysis of PTTH-stimulated Bombyx prothoracic gland

status: Public on Jul 29 2016

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

institute: University of Alberta

summary: This is part of a cross-species approach to characterize transcriptional response of the insect prothoracic gland (PG) to the prothoracicotropic hormone (PTTH). Genome-wide response of the PG to PTTH was analyzed in vitro in Bombyx and in vivo in Drosophila, and the results were compared to identify common components in the PTTH signaling pathway.

overall_design: Bombyx PGs were incubated in vitro for 1 or 3 hours with or without 10 nM recombinant PTTH. 12-18 larvae were used to prepare each RNA sample, and the experiment was conducted twice. Total RNA samples from two independent preparations were combined to obtain a single RNA sample for each treatment, which was subjected to RNA-seq.

first: Naoki

last: Yamanaka

first: Christina

last: Brakken-Thal

first: Michael

middle: B

last: O'Connor


title: A multi-functional AAV-CRISPR-Cas9 and its host response

city: Boston

first: Alex

last: Ng

state: MA

address: 77 Avenue Louis Pasteur Rm 233

department: Genetics

institute: Harvard Medical School

summary: CRISPR-Cas9 delivery by AAV holds promise for gene therapy but faces critical barriers due to its potential immunogenicity and limited payload capacity. Here, we demonstrate genome engineering in postnatal mice using AAV-split-Cas9, a multi-functional platform customizable for genome-editing, transcriptional regulation, and other previously impracticable AAV-CRISPR-Cas9 applications. We identify crucial parameters that impact efficacy and clinical translation of our platform, including viral biodistribution, editing efficiencies in various organs, antigenicity, immunological reactions, and physiological outcomes. These results reveal that AAV-CRISPR-Cas9 evokes host responses with distinct cellular and molecular signatures, but unlike alternative delivery methods, does not induce detectable cellular damage in vivo. Our study provides a foundation for developing effective genome therapeutics

overall_design: mRNA-Seq from muscles (9 samples; 3 mice x 3 conditions) and lymph nodes (9 samples; 3 mice x 3 conditions).

first: Wei

last: Chew

middle: H


title: Co-assembly of stranded and unstranded RNA-seq data improves coding and noncoding transcriptome maps

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

summary: We want to develop transcriptome assembly pipeline that significantly improves the quality of the assemblies constructed using stranded and/or unstranded RNA-seq data.

overall_design: Transcriptome of mouse embryonic stem cells (mESC) were assembled using stranded and unstranded library generated by Illumina HiSeq 2000

first: S

last: Lee

first: J


title: DNA methylome patterns of zebrafish cells under cold pressure

city: Shanghai

first: Junfang

last: Zhang

address: Huchenghuan Road 999

department: College of fishery and life science

institute: Shanghai Ocean University

type: Methylation profiling by high throughput sequencing

summary: In this study, MeDIP-seq and RNA-seq were performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cell line (ZF4) and its variation under cold environment.This study puts a new insight into the genome-wide epigenetic regulation under cold environment.

overall_design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 5 days and 30 days, seperately. Each condition has three biological replica.

first: Bingshe

last: Han

first: Zuozhou

last: Chen

first: Wenhao

last: Li

first: Liangbiao


title: Bcl11b defect in a human severe combined immunodeficiency with multisystem anomalies

city: San Francisco

first: Divya

last: Punwani

state: CA

address: 555 Mission bay blvd south

department: Pediatrics

institute: University of California San Francisco

summary: Background: Severe combined immunodeficiency (SCID) is characterized by arrested T lymphocyte production and B lymphocyte dysfunction, resulting in life-threatening infections. Early diagnosis of SCID through population-based newborn screening (NBS) optimizes clinical management and outcomes, and also permits identification of previously unknown factors essential for human lymphocyte development. Methods: SCID was detected, prior to onset of infections, by NBS of T cell receptor excision circles, a biomarker for thymic output. Upon confirmation, the affected baby was treated by allogeneic hematopoietic cell transplantation (HCT). The genetic cause was sought by exome sequencing of the patient and parents, followed by functional analysis of a prioritized candidate gene using human hematopoietic stem cells (HSC) and zebrafish embryos. Results: An infant with leaky SCID, craniofacial and dermal abnormalities, and absent corpus callosum had his immune deficit fully corrected by HCT. Exome sequencing revealed a heterozygous, de novo, missense mutation pN441K in BCL11B. The mutant Bcl11b protein had dominant negative activity, abrogating the ability of wild type Bcl11b to bind DNA, arresting T cell lineage development and disrupting HSC migration, revealing a novel function of Bcl11b. The patient’s defects, recapitulated in Bcl11b-deficient zebrafish, were reversed by ectopic expression of intact, but not mutant, human BCL11B. Conclusions: Newborn screening facilitated treatment and identification of a novel etiology for human SCID. Coupling exome sequencing with candidate gene evaluation in human HSC and in zebrafish revealed that a constitutional BCL11B mutation causes human multisystem anomalies with SCID, while also revealing a novel, pre-thymic role for Bcl11b in hematopoietic progenitors.

overall_design: 3 samples were analyzed in duplicate, Sample 1 was human HSC transduced with GFP only lentivirus which served as controls, Sample 2 was human HSC transduced with lentivirus expressing FLAG-tagged WT BCL11B and GFP, Sample 3 was human HSC transduced with lentivirus expressing FLAG-tagged mutant BCL11B and GFP

first: Yong

first: Jason

last: Yu

first: Morton

last: Cowan

first: Sadhna

last: Rana

first: Antonia

last: Kwan

first: Aashish

last: Adhikari

first: Carlos

middle: O

last: Lizama

first: Bryce

last: Mendelsohn

first: Shawn

middle: P

last: Fahl

first: Ajithavalli

last: Chellappan

first: Rajgopal

last: Srinivasan

first: Steven

middle: E

last: Brenner

first: David

last: Wiest

first: Jennifer

last: Puck


title: Isolation and sequencing of AGO-bound RNAs reveals characteristics of stem-loop processing in vivo

city: Philadelphia

first: Ian

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

summary: MicroRNA precursors (pre-miRNAs) are short hairpin RNAs that are rapidly processed into mature microRNAs (miRNAs) in the cytoplasm. Due to their low abundance in cells, sequencing-based studies of pre-miRNAs have been limited. We successfully enriched for and deep sequenced pre-miRNAs in human cells by capturing these RNAs during their interaction with Argonaute (AGO) proteins. Using this approach, we detected > 350 pre-miRNAs in human cells and > 250 pre-miRNAs in a reanalysis of a similar study in mouse cells. We uncovered widespread trimming and non-templated additions to 3’ ends of pre-miRNAs and mature miRNAs. Additionally, we identified novel AGO2-cleaved pre-miRNAs and created an index for microRNA precursor processing efficiency. This analysis revealed a subset of pre-miRNAs that produce low levels of mature miRNAs despite abundant precursors, including an annotated miRNA in the 5’ UTR of the DiGeorge syndrome critical region 8 (Dgcr8) mRNA transcript. This led us to search for other AGO-associated stem-loops originating from other mRNA species, which identified hundreds of putative pre-miRNAs derived from mRNA sequences in both the mouse and human transcriptomes. Intriguingly, we found that iron responsive elements in ferritin heavy and light chain mRNAs are processed into AGO-associated stem-loops in both mouse and humans but do not produce functional small RNAs. In summary, we provide a wealth of information on mammalian pre-miRNAs, and identify novel microRNA and microRNA-like elements localized in mRNAs.

overall_design:
pre-miRNA-seq and miRNA-seq from HEK293T cells.  Reanalysis of HEK293T smRNA-seq, MEF pre-miRNA and MEF smRNA-seq (processed data for these Samples are linked below). The reanalyzed HEK293T Samples are from Series GSE66224 and consists of Samples GSM1617437 and GSM1617438. The reanalyzed MEF pre-miRNA and MEF smRNA-seq Samples were downloaded from European Nucleotide Archive (http://www.ebi.ac.uk/ena/) under the accession number PRJEB6756 (ERX525474 and ERX525475).
RNA-seq analysis of HEK293T cells following knockdown of DGCR8, DROSHA or Luciferase.

first: Sager

last: Gosai

first: Nate

last: Berkowitz

first: Brian

last: Gregory


title: PRC2 controls adult neuron identity and protects neurons against neurodegeneration

first: Josefa

last: Sullivan

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state in medium spiny neurons in the striatum of adult mice

summary: Normal brain function critically depends on the interaction between highly specialized neurons that operate within anatomically and functionally distinct brain regions. The fidelity of neuronal specification is contingent upon the robustness of the transcriptional program that supports the neuron type-specific patterns of gene expression. Changes in neuron type-specific gene expression are commonly associated with neurodegenerative disorders including Huntington’s and Alzheimer’s disease. The neuronal specification is driven by gene expression programs that are established during early stages of neuronal development and remain in place in the adult brain. Here we show that the Polycomb repressive complex 2 (PRC2), which supports neuron specification during early differentiation, contributes to the suppression of the transcription program that can be detrimental for the adult neuron function. We show that PRC2 deficiency in adult striatal neurons and in cerebellar Purkinje cells impairs the maintenance of neuron-type specific gene expression. The deficiency in PRC2 has a direct impact on a selected group of genes that is dominated by self-regulating transcription factors normally suppressed in these neurons. The age-dependent progressive transcriptional changes in PRC2-deficient neurons are associated with impaired neuronal function and survival and lead to the development of fatal neurodegenerative disorders in mice.

overall_design: Medium Spiny neuronal nuclei were isolated from adult mouse striata via NeuN-specific Flourescence Activated Nuclei Sorting.

first: Melanie

last: von Schimmelmann

first: Philip

last: Feinberg

first: Stacy

last: Ku

first: Ana

last: Badimon

first: Mary

last: Duff

first: Zichen

last: Wang

first: Alexander

last: Lachmann

first: Scott

last: Dewell

first: Avi

last: Ma'ayan

first: Ming-Hu

last: Han

last: Tarakhovsky

first: Anne

last: Schaefer


title: NFIB is a driver of SCLC initiation, progression and metastasis in mouse and marks metastatic disease in patients

city: Amsterdam

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

country: Netherlands

institute: NKI

summary: Small Cell Lung Cancer (SCLC) is the most aggressive type of lung cancer with early metastatic dissemination and invariable development of resistant disease for which no effective treatment is available to date. Mouse models of SCLC based on inactivation of Rb1 and Trp53 developed earlier showed frequent amplifications of two transcription factor genes: Nfib and Mycl. Overexpression of Nfib but not Mycl in SCLC mouse results in an enhanced and altered metastatic profile, and appears to be associated with genomic instability. NFIB promotes tumor heterogeneity with the concomitant expansive growth of poorly differentiated, highly proliferative, and invasive tumor cell populations. Consistent with the mouse data, NFIB expression in high-grade human neuroendocrine carcinomas correlates with advanced stage III/IV disease warranting its further assessment as a potentially valuable progression marker in a clinical setting.

overall_design: Genomic DNA from mouse small cell lung tumor samples was analyzed by mate pair sequencing and low coverage sequencing. And RNA from Nfib overexpressing mouse small cell lung cancer cell lines was further analyzed for high quality RNA profiles using Illumina Hiseq2500.  This series contains only RNA-seq data.

first: Ekaterina

last: Semenova

first: Min-chul

last: Kwon

first: Kim

last: Monkhorst

first: Ji-Ying

last: Song

first: Rajith

last: Bhaskaran

first: Ivo

last: Huijbers


title: The histone H3K9 demethylase KDM3A promotes anoikis through transcriptional activation of pro-apoptotic genes BNIP3 and BNIP3L

city: Worcester

first: Victoria

last: Pedanou

address: 364 Plantation St Room 670A

institute: Umass Medical School

summary: We isolated and sequenced the shRNA region of a pSM2 retroviral plasmid to identify which shRNAs were enriched in MCF10A cells grown in detached conditions versus the same MCF10A cells that were grown under normal, attached conditions.

overall_design: Comparison of the ratio of shRNA sequences between cells grown under normal conditions versus cells grown in detached conditions.

first: Michael

last: Green


title: shRNA cassette sequencing from disomic and trisomic fibroblasts cultured in the presence of shRNA kinome library for 14 days

city: Aurora

first: Ahwan

last: Pandey

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Center

summary: Kinome-wide shRNA screen to identify kinases differentially required for survival of cells disomic and trisomic for chromosome 21

overall_design: Cells were transduced in triplicate and propagated for 14 days to allow for enrichement or depletion of shRNAs from the population

first: Kelly

last: Sullivan

first: Leisa

last: Jackson

first: Joaquín

last: Espinosa


title: RNAseq from Dp16 and control mice

summary: RNA was sequenced from Normal and DP 16 mice to identify consistent changes in gene expression across cohorts

overall_design: Cells were cultured at subconfluency and RNA harvested for sequencing

first: L

last: Ligget

first: James

last: DeGregori


title: Circulating microRNA profiles during the bovine oestrous cycle

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

country: United Kingdom

institute: The Roslin Institute

summary: Up to 50% of ovulations go undetected in modern dairy herds due to attenuated oestrus behavior and a lack of high-accuracy methods for detection of fertile oestrus. This significantly reduces overall herd productivity and constitutes a high economic burden to the dairy industry. MicroRNAs (miRNAs) are ubiquitous regulators of gene expression during both health and disease and they have been shown to regulate different reproductive processes. Extracellular miRNAs are stable and can provide useful biomarkers of tissue function; changes in circulating miRNA profiles have been reported during menstrual cycles. This study sought to establish the potential of circulating miRNAs as biomarkers of oestrus in cattle using Illumina small-RNA sequencing.

overall_design: In this experiment a total of 24 bovine plasma samples were analysed using Illumina miRNA sequencing. These samples were collected at three time-points during a normal oestrous cycle from each of 8 animals (Day 0, Day 8 and Day 16 after oestrus) in a repeated-measures design. Therefore this study included 8 biological replicates for each of the three time-points analysed.

first: Xavier

last: Donadeu


title: Identification of New Branch Points and Unconventional Introns in Saccharomyces cerevisiae

city: Cambridge

first: Geneveive

last: Gould

state: Massachusetts

address: 77 Massachusetts Ave. 68-253

institute: MIT

summary: Spliced messages constitute one-fourth of  expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult.  We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. Applied to S. cerevisiae, Branch-seq detected 76% of expressed, annotated BPs and identified a comparable number of novel BPs.  We used RNA-seq to confirm associated 3'SS locations, identifying some 200 novel splice junctions, including an AT-AC intron.  We show that several yeast introns use two or even three different BPs, with effects on 3'SS choice, protein coding potential, or RNA stability and identify novel introns whose splicing changes during meiosis or in response to stress. Together, these findings reveal BP-based regulation and demonstrate unanticipated complexity of splicing in yeast.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces cerevisiae S288C

overall_design: 1 Lariat-seq experiment library. 3 barcoded Branch-seq libraries that make up one experiment. 26 RNA-seq samples, 2 biological replicates of each.

first: Genevieve

first: Christopher

last: Burge


title: Gene expression profiling of drug-tolerant persister BT474 breast cancer cells derived from lapatinib treatment

status: Public on Jul 28 2016

first: Matthew

last: Hangauer

institute: UC San Francisco

summary: Acquired drug resistance prevents targeted cancer therapy from achieving stable and complete responses. Emerging evidence implicates a key role for nonmutational mechanisms including changes in cell state during early stages of acquired drug resistance. Targeting nonmutational resistance may therefore present a therapeutic opportunity to eliminate residual surviving tumor cells and impede relapse. A variety of cancer cell lines harbor quiescent, reversibly drug-tolerant “persister” cells which survive cytotoxic drugs including targeted therapies and chemotherapies. These persister cells survive drug through nonmutational mechanisms which are poorly understood. Specifically targeting persister cells is a promising strategy to prevent tumor relapse. We sought to identify therapeutically exploitable vulnerabilities in persister cells using the HER2-amplified breast cancer line BT474 as an experimental model. Similar to other persister cell models, upon treatment with the HER2 inhibitor lapatinib (2uM concentration) for nine or more days, the majority of BT474 cells die, revealing a small population of quiescent surviving persister cells. Removal of lapatinib allows the persister cells to regrow and to re-acquire sensitivity to lapatinib. Subsequent lapatinib treatment re-derives persister cells. The reversibility of persister cell drug resistance indicates a nonmutational resistance mechanism. Here we provide RNAseq gene expression profiling data generated from parental BT474 cells compared to BT474 persister cells generated from nine days of treatment with 2 uM lapatinib. These data can be used to identify genes and pathways which are upregulated in persister cells, revealing potential therapeutic targets.

overall_design: 3 biological replicates of BT474 persister cells, two biological replicates of BT474 parental cells

first: Frank

last: McCormick

middle: T

last: McManus


title: Chx10 consolidates V2a interneuron identity through two distinct gene repression modes [ChIP-Seq]

city: Portland

first: Jae

middle: W

last: Lee

state: OR

address: 3181 SW Sam jackson Rd

institute: Oregon Health & Science University

summary: During development, two cell-types born from closely related progenitor pools often express the identical transcriptional regulators despite their completely distinct characteristics. This phenomenon highlights the necessity of the mechanism that operates to segregate the identities of the two cell-types throughout differentiation after initial fate commitment. To understand this mechanism, we investigated the fate specification of spinal V2a interneurons, which share important developmental genes with motor neurons (MNs). Here we demonstrate that the paired homeodomain factor Chx10 functions as a critical determinant for V2a fate and is required to consolidate V2a identity in postmitotic neurons. Chx10 actively promotes V2a fate, downstream of the LIM-homeodomain factor Lhx3, while concomitantly suppressing MN developmental program by preventing the MN-specific transcription complex from binding and activating MN genes. This dual activity enables Chx10 to effectively separate V2a and MN pathways. Together, our study uncovers a widely applicable gene regulatory principle for segregating related cell fates.

overall_design: ChIP DNA samples from Chx10-ESC-derived MNs were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2000. The peak calling was conducted with MACS software (Zhang et al., 2008). MEME-ChIP Suite (Bailey et al., 2009; Machanick and Bailey, 2011) and TOMTOM algorithm (Gupta et al., 2007) was used for motif analysis.

first: Ji-sun

last: Kwon

first: Soo-Kyung


title: Analysis of kidney macrophages' gene expression at steady state

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Analysis of gene expression (RNAseq) from isolated kidney macrophages injetced i.v. with PBS

overall_design: C57BL/6J mice were injected i.v. with PBS. One hour after injection, kidney macrophages were isolated (sorted by FACS) for gene expression analysis.

first: Frederic

last: Geissmann

first: Efstathios

last: Stamatiades


title: Chx10 consolidates V2a interneuron identity through two distinct gene repression modes [RNA-Seq]

overall_design: RNA samples from Chx10-ESC-derived MNs were prepared for sequencing according to the Illumina protocol, and sequenced on the Illumina HiSeq 2000. We will then compare the transcriptome changes between -Dox (no Chx10) and +Dox (Chx10) in order to identify genes rregulated by Chx10.


title: Chx10 consolidates V2a interneuron identity through two distinct gene repression modes


title: Characterization of t(15;21) translocations in myeloid disorders

city: Bari

first: Alberto

last: L'Abbate

address: via Orabona 4

department: Department of Biology

country: Italy

institute: University of Bari

summary: We report on two novel t(15;21) alterations [t(15;21)(q24;q22) and t(15;21)(q21;q22)], which led to concurrent disruption of RUNX1 and two translocation partner genes encoding for transcription factors (SIN3A, TCF12)

overall_design: Examination of four different patients with myeloid disorders. 2 out of 4 have been analyzed by means RNAseq

first: Doron

last: Tolomeo

first: Francesca

last: De Astis

first: Angelo

last: Lonoce

first: Crocifissa

last: Lo Cunsolo

first: Dominique

last: Mühlematter

first: Jacqueline

last: Schoumans

first: Peter

last: Vandenberghe

first: Achilles

last: Van Hoof

first: Orazio

last: Palumbo

first: Massimo

last: Carella

first: Tommaso

last: Mazza

first: Clelia

last: Storlazzi


title: ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: Histone acetylation, including acetylated H3K14 (H3K14ac), is generally linked to gene activation. Monomethylated histone H3 lysine 4 (H3K4me1), together with other gene-activating marks, denotes active genes. In contrast to usual gene-activating functions of H3K14ac and H3K4me1, we here show that the dual histone modification mark H3K4me1-H3K14ac is recognized by ZMYND8 (also called RACK7) and functions to counteract gene expression. We identified ZMYND8 as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 antagonizes the expression of metastasis-linked genes, and its knockdown increases the cellular invasiveness in vitro and in vivo. The plant homeodomain (PHD) and Bromodomain cassette in ZMYND8 mediates the combinatorial recognition of H3K4me1-H3K14ac and H3K4me0-H3K14ac by ZMYND8. These findings uncover an unexpected role for the signature H3K4me1-H3K14ac in attenuating gene expression and reveal a previously unknown metastasis-suppressive epigenetic mechanism in which ZMYND8's PHD-Bromo cassette couples H3K4me1-H3K14ac with repression of metastasis-linked genes.

overall_design:
i) ChIP-Seq data of ZMYND8, JARID1D, H3K4me1, H3K14ac, H3K4me3, and H3K27me3 in normal DU145 cells.
ii) ChIP-Seq data of H3K4me1 and H3K4me3 in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.
iii) RNA-Seq data in shLuciferase-, shJARID1D-, or shZMYND8-treated DU145 cells.

first: Min

last: Lee

first: Wei

last: Li


title: RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice

first: Lori

last: Sussel

address: 1775 Aurora Ct.

institute: University of Colorado

summary:
Aim: Transcriptional analysis of the colon of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control
Methods: 2 cm of the colon (as measured after the caecum) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: 53 genes with a p-value <0.05 were down-regulated and 36 were up-regulated. Among the changed genes are enteroendocrine hormones.
Conclusion: Nkx2.2 regulates enteroendocrine cell specification

overall_design: mRNA profiles of the colon of 6 week old control and Nkx2.2int mice were generated by deep sequencing, using Illumina HiSeq2000.

first: Stefanie

last: Gross


title: SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2) and screened for second-site mutations that attenuate the Fv'/Fm' decrease and lesion formation linked to the cat2-2 phenotype. A mutation in the transcriptional regulator SHORT-ROOT (SHR) of the GRAS family rescued the cell death phenotype of cat2-2 plants under photorespiration-promoting conditions in a SCR-independent way, and provoked perturbation of photorespiratory metabolites. SHR deficiency boosted ascorbate levels and prevented the oxidation of the glutathione pool in cat2-2 background upon exposure to photorespiratory stress. These results reveal an unanticipated role for SHR as a regulator of cellular redox homeostasis.

overall_design: Unstressed and stressed samples of 4 genotypes (Col-0, cat2, shr and cat2 shr) in triplicate

first: Kerchev

last: Pavel

first: Cezary

last: Waszczak

first: Frank

last: Van Breusegem


title: Polycomb Group Protein Pcgf6 Acts as a Master Regulator to Maintain Embryonic Stem Cell Identity

city: La Jolla

first: Tariq

last: Rana

state: California

address: 9500 Gilman Drive

institute: University of California San Diego

summary: We report that the PRC1 component polycomb group ring finger 6 (Pcgf6) is required to maintain embryonic stem cell (ESC) identity. In contrast to canonical PRC1, Pcgf6 acts as a positive regulator of transcription and binds predominantly to promoters bearing active chromatin marks. Pcgf6 is expressed at high levels in ESCs, and knockdown reduces the expression of the core ESC regulators Oct4,Sox2, and Nanog. Conversely, Pcgf6 overexpression prevents downregulation of these factors and impairs differentiation. In addition, Pcgf6 enhanced reprogramming in both mouse and human somatic cells. The genomic binding profile of Pcgf6 is highly similar to that of trithorax group proteins, but not of PRC1 or PRC2 complexes, suggesting that Pcgf6 functions atypically in ESCs. Our data reveal novel roles for Pcgf6 in directly regulating Oct4, Nanog, Sox2, and Lin28 expression to maintain ESC identity.

overall_design: To identify Pcgf6-bound genomic DNA regions in mouse embryonic stem cells, we fixed mouse ESCs and isolated Pcgf6-bound genomic DNA regions for deep sequencing analysis.

first: Chao-Shun

last: Yang


title: Human Corneal microRNA Expression Profile in Fungal Keratitis

city: Madurai

first: Bharanidharan

last: Devarajan

state: Tamil Nadu

address: 1,Anna nagar

department: Bioinformatics

country: India

institute: Aravind Medical Research Foundation

summary: MicroRNAs (miRNAs) are small, stable non-coding RNA molecules with regulatory function and marked tissue specificity that post-transcriptionally regulate gene expression, however their role in fungal keratitis remain unknown. Our purpose was to identify the miRNAs in human cornea from fungal keratitis patients and understand their key role in regulation of pathogenesis. Corneal samples from normal cadaver (n=3) and fungal keratitis (n=5) patients were pooled separately and total RNA was extracted. Deep sequencing was done using Illumina HiSeq1000 platform to identify miRNA profile. We identified seventy five differentially expressed miRNAs in fungal keratitis corneas. Select miRNAs were validated by real-time RT-PCR (Q-PCR). We predicted their role in regulating target genes in several pathways by combining miRNA target genes and pathway analysis, and mRNA expression of select target genes were further analysed by Q-PCR. MiR-21-5p, miR-223-3p, miR-146b-5p, miR-155-5p, miR-511-5p were found to be involved in inflammatory and immune responses, regulating Toll like receptor signaling pathways, which is of particular interest. MiR-451a with an increased expression in keratitis may have a role in wound healing by targeting Macrophage Migration Inhibitory Factor (MIF). Further, we highlighted that Neurotrophin signaling pathway may play a role in wound healing process. One novel miRNA was also detected in cornea. In conclusion, several miRNAs with high expression in fungal keratitis corneas point towards their role in regulation of pathogenesis. Further insights in understanding miRNAs role in wound healing and inflammation may help design new therapeutic strategies.

overall_design: Control and fungal keratitis, human corneal miRNA profiles were generated using IlluminaHiseq1000 platform

first: Lalitha

last: Prajna


title: Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (ChIP-Seq)

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary: To identify FHY3 associated genes in floral organ. We performed ChIP-seq using 35S:3FLAG-FHY3-3HA fhy3-4 tansgenic plants. A total of 21, 24 and 37 million reads were obtained from two replicates and input library, respectively, which were uniquely mapped to the Arabidopsis genome by Bowtie2 software resulting in 1885 FHY3 binding peaks. 84% of FHY3 binding sites (1580 loci) were subsequently assigned to genic regions and grouped into 2192 genes in flower.

overall_design: Inflorescence of  35S:3FLAG-FHY3-3HA fhy3-4 containing stage 8 and younger flowers were harvested for ChIP-seq analysis with anti-FLAG antibodies. No antibody served as negative control. The chromatin DNA from two distinct biological replicates and an input DNA sample were subjected to ultra-high-throughput Solexa (Illumina) sequencing.

first: Xigang

last: Liu

first: Renyi


title: Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ

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

overall_design: Refer to individual Series


title: Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)

summary: To identify FHY3 regulated genes in floral organ. We performed RNA-seq using Ler, ag-10, fhy3-68, ag-10 fhy3-68.

overall_design: Inflorescence of  Ler, ag-10, fhy3-68, ag-10 fhy3-68 containing stage 8 and younger flowers were harvested forRNA-seq analysis  two distinct biological replicates were subjected to ultra-high-throughput Solexa (Illumina) sequencing.


title: Effect of  from Human Umbilical Vein Endothelial Cells

status: Public on Jul 27 2016

city: Bad Nauheim

first: Oliver

middle: Andrew

last: Stone

address: Ludwigstr 43

department: Developmental Genetics

institute: Max Planck Institute

summary: We profiled global gene expression in primary human umbilical vein endothelial cells to determine the gene expression changes associated with knocking down PKM2 and p53. We identified a p53 dependent transcriptional response that remodels metabolism in cells lacking p53, thus limiting cell growth.

overall_design: Human Umbilical Vein Endothelial Cells were transfected with siRNA duplexes targeting PKM2 and / or p53, RNA was extracted and subjected to RNA sequencing

first: Didier

last: Stainier


title: Differential expression of genes in photoreceptor and other retinal cells in developing retina

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

summary: To analyze cell lineage specific global transcriptional changes during retinogenesis, we sequenced mRNA from developing retina fractioned to Cd73+ photoreceptors and Cd73- other cells, in addition to the whole retina at embryonic period.

overall_design: Examination of global mRNA expression patterns of mouse retinal cells by RNA sequence

first: Kazuko

last: Ueno


title: Regulation of genes expression in photoreceptor and other retinal cells by histone H3 tri-methylation at K27 during retinal development

summary: To analyze roles of histone H3 tri-methylation for transcription in retina, global transcription patterns of retinal cells of Ezh2, H3K27 methylase, knockout mice and control were examined

overall_design: Examination of global mRNA expression patterns of mouse retinal cells fractioned into Cd73+ photoreceptors and Cd73- other retinal cells at postnatal 12 mouse


title: Differential regulation of genes in photoreceptor and other neurons by histone H3 methylation at K4 and K27

summary: To analyze cell lineage specific transcriptional activation mechanisms during retinogenesis, we purified retinal cells into photoreceptors and other retinal cells, and performed ChIP sequence for H3K27me3 and H3K4me3.

overall_design: Examination of 2 different histone modifications in Cd73-positive (Cd73P) retinal cells and Cd73-nagative (Cd73N) retinal cells at 3 developmental timepoints.


title: End Sequence Analysis ToolKit (ESAT) expands the extractable information from single cell RNA-Seq data

first: Alan

last: Derr

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: Test data used for the evaluation of ESAT performance and results files for data from 3' and 5' end-sequencing RNA-Seq protocols and droplet-based single-cell RNA-Seq.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
Quantification and analysis of Tophat-aligned (v2.0.9) samples from mouse bone-marrow derived dendritic cells (mBMDC) timecourse (0, 2, 4 and 6 hours) post LPS stimulation and non-diabetic BBDR rat pancreatic islet cells.
Since end-sequencing (3' or 5') is used for all samples, alignments are only required for the R2 (sequence-containing) read.

first: Chaoxing

first: Rapolas

last: Zilionis

first: Sambra

last: Redick

first: Maxim

last: Artyomov

first: Manuel

last: Garber


title: MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

institute: Institute of cotton research of CAAS

summary:
Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum.

Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which is consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and Pectatelyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation.

Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culmand dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton.

overall_design: Total RNA was purified from stem apexes of three samples at the fifth true leaf stages and sequenced deeply using Illumina HiSeq 2000 system.

first: Xiongming

last: Du

first: Wenfang

last: Gong


title: Splicing towards noncoding isoforms in colorectal carcinoma is associated with tumor hypoxia and the DNA damage response

first: Danish

last: Memon

address: Robinson Way

institute: CRUK Cambridge Institute, University of Cambridge

summary: Tumor hypoxia is associated with poor patient outcome and resistance to therapy. It is associated with a rapid decline in protein production mediated through mTOR signalling. Here we show that it also leads to widespread changes in splicing and a global shift towards the expression of noncoding isoforms, thus providing a novel and orthogonal mechanism by which cells can modulate protein expression.

overall_design: Examination of mRNA levels in HCT116 cells after 0 hr, 1 hr, 2 hr and 24 hr in hypoxia. Three biological replicates each.

first: Keren

last: Dawson

first: Christopher

middle: S

last: Smowton

first: Wei

last: Xing

first: Caroline

last: Dive

first: Crispin

last: Miller


title: Deciphering the loss of fertility in ivermectin-treated Brugia malayi females in vitro: a transcriptomic approach [Study II]

city: Ste-Anne-de-Bellevue

first: Timothy

middle: G.

last: Geary

address: 21,111 Lakeshore Rd

department: Parasitology

institute: McGill University

summary: In this study, we analyzed transcriptomic profiles from ivermectin-treated and -untreated B. malayi adult females using Next Generation RNA Sequencing technology at different concentrations (100 nM, 300 nM and 1 µM) and time points (24, 48, 72 h, and 5 days). Our analysis revealed altered expression of multiple genes involved in meiosis, as well as oxidative phosphorylation which were significantly down-regulated as early as 24 hours post-exposure. RNA interference phenotypes of the orthologs of these down-regulated genes in C. elegans include “maternal sterile”, “embryonic lethal”, “larval arrest”, “larval lethal”, “reduced brood size” and “egg shape variable”. These changes reflect and provide insight into the mechanisms involved in ivermectin-induced reduction in microfilaria output and impaired fertility, embryogenesis, and larval development.

overall_design: Transcriptomic changes over several different time points and concentrations.

first: Cristina

last: Ballesteros

first: Lucienne

last: Tritten

first: Maeghan

last: O’Neill

first: Erica

last: Burkman

first: Weam

middle: I

last: Zaky

first: Jianguo

last: Xia

first: Andrew

last: Moorhead

first: Steven

last: Williams

middle: G


title: Epigenetic Alterations in Density Selected Human Spermatozoa for Assisted Reproduction

city: Guangzhou

first: Zhaofeng

last: Huang

state: Guangdong

address: 74# zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

summary: We report the histone retention loci alteration in human sperm cell genome  after density selection

overall_design: comparison the histone binding site alteration with high-throughput sequencing technique.

first: Bolan

last: Yu


title: Deciphering the loss of fertility in ivermectin-treated Brugia malayi females in vitro: a transcriptomic approach


title: Molecular signature of Cd73 positive and negative cells in developing retina

first: Sumiko

last: Watanabe


title: Loss of Trex1 in dendritic cells is sufficient to trigger systemic autoimmunity

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: Heidelberg University Hospital

summary: Biallelic defects of the gene encoding for the intracellular enzyme 3’ repair exonuclease (Trex)1 cause Aicardi-Goutières syndrome (AGS), a rare monogenic, lupus-like autoimmune disease, while heterozygous Trex1 loss of function alleles are associated with systemic lupus erythematosus (SLE). Trex1-/- mice develop lethal autoimmune multi-organ inflammation, which results from a chronic type I IFN response triggered by intracellular accumulation of a putative nucleic acid substrate of Trex1. This pathogenic nucleic acid is detected by the broadly, but not ubiquitously, expressed cytosolic DNA sensor cGAS, raising the question whether there are specific cell types that respond to Trex1 deficiency by production of IFN and induce autoimmunity. We generated mice with conditional knock out of the Trex1 gene and demonstrated that loss of Trex1 throughout the hematopoietic system and even selective loss in dendritic cells is sufficient to cause IFN release and autoimmunity. B cells showed no transcriptional response to Trex1 deficiency. Trex1-/- keratinocytes produced IFN but did not induce skin inflammation, whereas loss of Trex1 in cardiomyocytes triggered neither IFN response nor pathology. Trex1-deficient neurons and astrocytes did not release IFN in the CNS. In contrast, mice with selective inactivation of Trex1 in long-living CNS macrophages such as microglia locally produced IFN but did not reproduce the mild encephalitis seen in Trex1-/- mice. Collectively, individual cell types differentially respond to the loss of Trex1 and dendritic cells seem promising candidates for experiments addressing the molecular pathomechanism in Trex1 deficiency.

overall_design: We sorted CD19-positive B cells from spleens of Trex1fl/fl CD19-Cre+ and Trex1fl/fl CD19-Cre- mice and isolated total RNA for library construction to perform mRNA deep sequencing.

first: Katrin

last: Peschke

first: Mathias

last: Lesche

first: Andreas

last: Dahl

first: Rayk

last: Behrendt


title: Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells

city: Kyoto

first: Akira

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins.

overall_design: Methyl-seq analysis for undifferentiated induced pluripotent stem cell (iPSC) lines (n = 21), human dermal fibroblast (HDF, n = 1), human peripheral blood (n = 1), and human keratinocyte (n = 1), and ATAC-seq analysis for 2 iPSC lines and an embryonic stem cell (ESC) line with two different culture conditions. CTCF-ChIP-seq analysis for an ESC line.

first: Masatoshi

last: Nishizawa

first: Masahiro

last: Nakamura

first: Yoshinori

last: Yoshida


title: miRNA-seq study between Th0 and Th17 cells

city: Shanghai City

first: li

last: cao

address: 800 Xiangyin Road

department: Department of neurobiology

institute: second military medical university

summary: To explore the differences in miRNA profiles, naive CD4+CD62L+ helper T cells were  sorted by magnetic cell sorting from spleens of female C57BL/6 mice and were induced to differentiate into Th1 or Th17 cells, then total RNA was extracted and miRNA-seq were conducted. The results showed that many microTNAs presented a different expression pattern between Th1 and Th17 cells, which prompted us to further study their roles in Th117 differenciation.

overall_design: miRNA profiles of  Th0 and Th17 cells were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500

first: Li

last: Cao


title: RNAseq analysis of the duodenum of intestine-specific adult SD mutant mice

city: Aurora

first: Lori

last: Sussel

summary:
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/SD;Villin-Cre (SDint) mice versus control
Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: 206 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones.
Conclusion: The SD domain of Nkx2.2 regulates specification of some enteroendocrine cells

overall_design: mRNA profiles of the duodenum of 6 week old control and SDint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Stefanie

last: Gross


title: RNAseq analysis of the duodenum of intestine-specific adult Nkx2.2 mutant mice

summary:
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice versus control
Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: 184 genes with a p-value <0.05 were down-regulated and 211 were up-regulated. Among the down-regulated genes are most enteroendocrine hormones.
Conclusion: Nkx2.2 regulates enteroendocrine cell specification

overall_design: mRNA profiles of the duodenum of 6 week old control and Nkx2.2int mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.


title: RNAseq analysis of the duodenum of intestine-specific adult TN mutant mice

summary:
Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/TN;Villin-Cre (TNint) mice versus control
Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.
Results: 299 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones.
Conclusion: The TN domain of Nkx2.2 regulates specification of some enteroendocrine cells

overall_design: mRNA profiles of the duodenum of 6 week old control and TNint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.


title: RBFOX3/NeuN is required for hippocampal circuit balance and function

status: Public on Jul 26 2016

city: Taipei

first: Hsien-Sung

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

summary: RBFOX3 mutations are linked to epilepsy and cognitive impairments, but the underlying pathophysiology of these disorders is poorly understood. Here we report replication of human symptoms in a mouse model with disrupted Rbfox3. Rbfox3 knockout mice displayed increased seizure susceptibility and decreased anxiety-related behaviors. Focusing on hippocampal phenotypes, we found Rbfox3 knockout mice showed increased expression of plasticity genes Egr4 and Arc, and the synaptic transmission and plasticity were defective in the mutant perforant pathway. The mutant dentate granules cells exhibited an increased frequency, but normal amplitude, of excitatory synaptic events, and this change was associated with an increase in the neurotransmitter release probability and dendritic spine density. Together, our results demonstrate anatomical and functional abnormality in Rbfox3 knockout mice, and may provide mechanistic insights for RBFOX3-related human brain disorders.

overall_design: Two samples (one is from wild-type and the other is from Rbfox3 homozygous knockout mice)


title: Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

overall_design: Three lines of Alfalfa (salt-tolerant CW064027, salt-tolerant Bridgeview, salt-sensitive Rangelander) were grown on 3 different concentrations of salt.  For each cultivar-salt condition, 3 biological replicates were collected for a total of 27 samples.

first: Ali

last: Taheri

first: Margie

last: Gruber

first: Min


title: RNA-seq analysis of add-back rescued TALEN-mediated LATS2 knockout HeLa-S3 cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Chromatin modifying activities for construction of appropriate epigenetic landscapes by polycomb repressive complex 2 (PRC2) play an essential role in development and tumorigenesis. However, the spatiotemporal mechanisms by which PRC2 achieves diverse epigenomes for specific tissue or cellular contexts remain poorly understood. Here, we discovered that LATS2 knockout causes dysregulation of PRC2 and subsequent transcriptome changes for differentiation in both mouse and human cells. LATS2 depletion dependent dysregulation of PRC2 also effects H3K4me3 and forms negative feedback loop for maintenance of PRC2. Further analyses reveal that LATS2 on chromatin binds to EZH2 and LATS2 has ability to phosphorylate PRC2 in vitro. These LATS2 dependent H3K27me3 targets are highly induced during neurogenesis, and statistical analysis of glioblastoma multiforme reveals that LATS2-high cases show more dedifferentiated transcriptome and poor prognosis with silencing of H3K27me3 targets. These observations suggest that LATS2-mediated epigenome coordination is pivotal for development and disease, including cancer.

overall_design: mRNA of LATS2 KO HeLa-S3 cells rescued by empty vector, wild-type LATS2 or kinase-dead LATS2 were subjected to deep sequencing  profiling using Illumina HiSeq 2500

first: Shota

last: Motooka

first: Kosuke

last: Torigata


title: Multivalent Influenza DNA vaccine induces cross-reactive polyfunctional T lymphocytes and promotes rapid clearance of heterologous challenge strain in non-human primates

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: Recent avian and swine-origin influenza virus outbreaks illustrate the ongoing threat of influenza pandemic.  New vaccines that offer accelerated production and broader, more universal protection against drifted and shifted strains are needed. Here, we investigated a multivalent PMED DNA vaccine for the ability to induce antibody and T cell responses against four HA antigens, nucleoprotein and the ectodomain of M2 (M2e).

overall_design: Macaques in the Vaccinated and Control groups were intramuscularly anaesthetized with ketamine (10 mg/kg) and inoculated with a suspension containing 10^6.5 p.f.u. ml-1 of CA09 virus through a combination of intratracheal (4.5 ml), intranasal (0.5 ml per nostril), ocular (0.1 ml per eye) and oral (1 ml) routes (resulting in a total infectious dose of 10^7.4 PFU). Bronchoalveolar lavages were collected two weeks prior to challenge and at days 3, 7, and 10 post-infection. We performed microarray analysis on these samples.

first: Merika

last: Koday

first: Jolie

last: Leonard

first: Debra

last: Bratt

first: James

last: Fuller

first: Robert

last: Murnane

first: Todd

last: Reinhart

first: Amy

last: Hartman

first: Kelly

last: Stefano-Cole

first: Adriana

last: Forero

first: Juliet

last: Morrison

first: Deborah


title: Deep sequencing reveals mRNA recruitment in translation initiation

city: Beijing

first: Xiao-Dong

last: Su

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Science

institute: Peking University

summary: We studied the initiation signals located in the translational initiation region (TIR) and identified the role for recognition of the initiation signals in each individual stage during formation of the initiation complexes.

overall_design: Sequencing the randomized mRNA libraries captured by translation initiation complexes

first: Rong

last: Gao

first: Kai

last: Yu

first: Ju-Kui

last: Nie

first: Jian-Shi

last: Jin

first: Anders

last: Liljas


title: Single-cell analysis of allelic gene expression in pluripotency, differentiation and X-chromosome inactivation

city: Stockholm

first: Qiaolin

last: Deng

address: Berzelius väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: We sequenced the mRNAs of embryonic stem cells (ESCs)  cultured in different conditions. The two lines M (male) and F (female) used in this study were derived from E4 blastocysts of the same cross between a C57BL/6J (Mus musculus domesticus) and CAST/EiJ (Mus castaneus) male. mESCs were cultured in 2i and LIF as the ground state condition or in serum and LIF as the conventional condition. Epistem cell lines were also generated from the two lines by culturing them with Activin A and FGF2. In order to study more advanced development, we differentiated the two mESC lines through embryonic body formation to postmitotic motor neurons using retinoic acid and the smoothened agonist SAG. This differentiation process also results in the derivation of several types of interneurons.  We picked single cells from all different conditions and generated sequencing libraries using the Smart-seq2 and Tn5 protocol. For simplicity, we designate the different condition as ES2i, ES, Epi and Neuron from hereon. We also obtained preimplantation inner cell mass and epiblast cells from E3.5 ICM (inner cell mass) and E4.5 blastocysts of the crossbred mice (male CAST/EiJ × female C57BL/6J) as well as postimplantation epiblast cells from E5.5 embryos of C57BL/6J mice

overall_design: Examination of gene expression profile in individual male and female embryonic stem cell lines along developmental progression

first: Geng

last: Chen


title: RNA-seq analysis of immunogenic actions of metronomic cyclophosphamide treatment: dependence of gene responses on tumor model, mouse host, and drug schedule

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: RNA-seq analysis was performed using RNA isolated from three tumor models (GL261 glioma, LLC Lewis lung carcinoma, B16F10 melanoma) implanted subcutaneousy in C57BL/6 mice, or in ICR scid mice. Mice were untreated or were treated with cyclophosphamide (CPA) given on a 6-day repeating metronomic schedule (CPA/6d), except as noted. Results from these global transcriptome analysis indicated substantial elevation of basal GL261 immune infiltration and strong activation by CPA/6d treatment of GL261 immune stimulatory pathways and their upstream regulators, but without preferential depletion of negative immune regulators compared to LLC and B16F10 tumors. In LLC tumors, where CPA/6d treatment was found to be anti-angiogenic, CPA/6d suppressed VEGFA target genes and down regulated cell adhesion and leukocyte transendothelial migration genes. In GL261 tumors implanted in adaptive immune-deficient scid mice, where CPA/6d-induced GL261 regression is incomplete and late tumor growth rebound can occur, T cell receptor signaling and certain cytokine-cytokine receptor responses seen in B6 mice were deficient. Extending the CPA treatment interval from 6 to 9 days (CPA/9d) − which results in a strong but transient natural killer cell response followed by early tumor growth rebound − induced fewer cytokines and increased expression of drug metabolism genes. Taken together, these findings elucidate molecular response pathways activated by intermittent metronomic CPA treatment and identify deficiencies that characterize immune-unresponsive tumor models and drug schedules.

overall_design: RNA isolated from various tumor cell lines implanted s.c in C57BL/6 mice or scid mice, untreated or treated with cyclophosphamide (CPA) given on a metronomic schedule, were prepared and used for stranded or unstranded RNA-seq.

first: Junjie

last: Wu

middle: J


title: Pervasive effects of aging on gene expression in wild wolves

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

institute: Duke University

summary: We sequenced total RNA from whole blood samples of 27 wild gray wolves from Yellowstone National Park.

overall_design: Gene expression level analysis of both male and female wolves, ranging from ages 0.8-8.8 years.

first: Pauline

last: Charruau


title: Genome-wide maps of chromatin state in LATS2-knockout HeLa-S3 cell

first: Daisuke

last: Okuzaki

overall_design: Examination of 2 different histone modifications in parental wild-type HeLa-S3 and LATS2-knockout KO cells using Illumina HiSeq 2000.

first: Yasuyuki

last: Ohkawa

first: Kosuke

last: Torigata


title: Identification of genome wide targets of the hox protein Ultrabithorax (Ubx) in larval wing buds of Bombyx mori (Daizo)

city: Cambridge

first: Shreeharsha

last: Tarikere

address: 16 Divinity Avenue, Biolabs

department: Organismic and Evolutionary Biology

institute: Harvard University

summary: Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis. We have employed ChIP followed by illumina sequencing to identify the targets of Ubx in developing hind and fore wing buds of Bombyx larvae. This is a first next generation sequencing study in Lepidoptera in an attempt to understand wing development.

overall_design: Chromatin Immunoprecipitation (ChIP) was used to identify genome wide targets bound by Ubx in Bombyx larval wing buds. The experiment to enrich Ubx bound regions was carried out using a Bombyx N terminal-Ubx specific poylclonal antibody raised in Rabbit and purified against a Protein A column to obtain IgG fraction. An Immunoprecipitation (IP) with Normal Rabbit IgG was used as a negative control to eliminate the regions that pertained to non specific binding to an Immunogloubulin. The normalization of both ChIP and IgG was done against sequenced input chromatin. Two replicates of single end 36 bp reads were sequenced using Ilumina for all the three conditions and for both fore and hind wing tissue samples.The peaks common to both the replicates were considered after applying a FDR cutoff.The fore wing target set was used for comparison with the hind wing targets.

first: L

last: Shashidhara


title: A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species.

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

overall_design: Refer to individual Series


title: Identification of differentially expressed genes in fore and hind wing buds of IV instar larvae of Bombyx mori (Daizo)

summary: Amongst the various different insect groups, there is remarkable diversity in the number and size of wings. However the development of the basic body plan in insects is similar to a large extent. The genes of the hox complex regulate various pathways to bring about the development or modification of different organs. Ubx, a gene of the bithorax hox complex is expressed in the third thoracic segment of insects and is known to specify the fate of wing appendage in that segment.To understand the role of Ubx and how its regulatory mechanism has evolved through the course of evolution we have compared its genome wide targets in different insect orders. The identification of regulatory pathways and the key players Ubx regulates is crucial to understand how it has controlled wing development across insect orders. Our lab has previously identified direct targets of Ubx in Drosophila using ChIP-chip (Agrawal et al, 2011). To further our knowledge on the role of regulation in development and modification of hind wing appendage we have studied the targets in the hind wings of other insects (silk moth; Lepidoptera and honeybee; Hymenoptera) and performed a comparative analysis.To understand the differential development of wing appendages in insects we intend to compare the differential expression of fore and hind wing appendages in Diptera and Lepidoptera. We have employed RNA-seq using by illumina sequencing to identify the genes that are differentially expressed between fore and the hind wing bud of the Bombyx larvae. Only one replicate was performed as the intended study was to validate the differential targets in comparison to ChIP studies and other methods of select candidates.

overall_design: Total RNA was extarcted from wing buds of IV instar Bombyx larvae and sequenced on an illumina sequencer. Wing buds were collected directly in liquid nitrogen and 80 such buds each for fore and hind wing were collected from IV instar larvae. RNA was isolated from them and processed for Library preperation and illumina sequencing. One replicate was done as a supplement to ChIP studies.


title: Deciphering the loss of fertility in ivermectin-treated Brugia malayi females in vitro: a transcriptomic approach [Study I]

first: Timothy

last: Geary

state: Quebec

summary: In this study, we analyzed transcriptomic profiles from ivermectin-treated and -untreated B. malayi adult females using Next Generation RNA Sequencing technology at different concentrations (100 nM, 300 nM and 1 µM) and time points (24, 48, 72 h, and 5 days). Our analysis revealed altered expression of multiple genes involved in meiosis, as well as oxidative phosphorylation which were significantly down-regulated as early as 24 hours post-exposure. RNA interference phenotypes of the orthologs of these down-regulated genes in C. elegans include “maternal sterile”, “embryonic lethal”, “larval arrest”, “larval lethal”, “reduced brood size” and “egg shape variable”. These changes reflect and provide insight into the mechanisms involved in ivermectin-induced reduction in microfilaria output and impaired fertility, embryogenesis, and larval development.

overall_design: Transcriptomic changes over several different time points and concentrations.

first: Cristina

last: Ballesteros

first: Lucienne

last: Tritten

first: Maeghan

last: O’Neill

first: Erica

last: Burkman

first: Weam

last: Zaky

first: Jianguo

last: Xia

first: Andrew

last: Moorhead

first: Steven

last: Williams