title: Mapping of DHT-responsive or -independent AR-binding sites induced by activated Src in prostate cancer cell lines

status: Public on Dec 20 2016

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center


title: The Human Initiator Is a Distinct and Abundant Element That Is Precisely Positioned in Focused Core Promoters

city: La Jolla

first: Long

last: Vo ngoc

state: California

address: 9500 Gilman Dr

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7,678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1 core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.

overall_design: Transcription Start Site (TSS) mapping with two 5'GRO-seq experiments (including or excluding an RNA fragmentation step) using MCF-7 cells

first: James

middle: T

last: Kadonaga


title: Mapping of DHT-responsive or -independent AR-binding sites induced by activated Src in prostate cancer cell lines [RNA-seq]

state: NY

summary: Building on the observation that metastatic, castration-resistant prostate cancer (CRPC) correlates with activation of Src-family tyrosine kinases, we showed that the expression of activated Src renders LNCaP androgen-independent.  Here, we report on RNA-seq and/or AR ChIP-seq analyses of LNCaP, LNCaP[Src], VCaP, 22Rv1 cells grown in the presence or absence of 10 nM DHT for 16h, or LuCaP35.1 tumors grown in androgen-supplemented vs. castrated mice (androgen-dependent vs. castration-resistant). We identify an 11-gene Src-induced signature found only in CRPC in response to DHT, and moreover, the differentail expression of a subset (DPP4, BCAT1, CNTNAP4, CDH3) correlates with earlier PC metastasis onset and poorer survival.

overall_design: RNA-seq of NGS libraries and sequencing of prostate cancer cell lines. 16 samples are seqeunced.  For VCaP, LnCap, LnCap-SRC, 22RV1, and LNCap-C4-2, we have both DHT treated and control cell lines.  For LuCaP 35.1 cell line, xenografted scid mice tumors are seqeucned, 3 androgen-dependent and 3 castration-recurrent samples ar sequenced.

first: Irwin

middle: H

last: Gelman


title: N6-methyladenosine (m6A) sequencing of messenger RNAs in acute myeloid leukemia (AML) cells with and without knockdown of FTO

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To identify potential mRNA targets of FTO whose m6A levels are influenced in acute myeloid leukemia (AML) cells, we conducted m6A-seq for mRNA isolated from MA9.3ITD cells with and without knockdown of FTO

overall_design: We lentivirally transduced pLKO.1-shFTO (i.e., shFTO) or pLKO.1 empty vertor (i.e., shNS) into human MA9.3ITD (human CD34+ hematopoietic stem/progenetor cells stably infected by MLL-AF9 and FLT3-ITD) AML cells and then selected positively infected cells under selection of puromuycin (0.5ug/ml). Two stable lines including one FTO-knockdown cell line (i.e., shFTO) and one control line (i.e., shNS) were selected for genome-wide m6A-sequencing (m6A-Seq) assays. The m6A-seq procedure was performed as detailed in Dominissini’s method (Dominissini D., et al. Nat Protocols. 2013; 8: 176-189.). Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. M6A antibody (Synaptic Systems) was applied for m6A pull down. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.

first: Rui

last: Su

first: Sigrid

last: Nachtergaele

first: Lei

last: Dong

first: Chuan

last: He


title: A transcription factor pulse can prime chromatin for heritable transcriptional memory [RNAseq]

status: Public on Dec 21 2016

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

summary: To indentify genes displaying long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed RNAseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any genes respond more/faster in a second stimulation than in the first.

overall_design: Genome expression by RNAseq in uninduced Bcell (C10 cell line), after induction Cebpa for 6h (Cebpa6h) or not induced (Control6h), after 6 days of wash (Cebpa6h/Control6h_Chase6d) and (re-)induction of C/EBPa for 13h (Cebpa6h/Control6h_Chase6d_Cebpa13h) .

first: Aimee

last: Badeaux

first: Samuel

first: Thomas

last: Graf

first: Denis

last: Thieffry

first: Yang

last: Shi


title: mRNA sequencing in acute myeloid leukemia (AML) cells with and without knockdown of FTO

summary: To identify the expression of mRNAs after knockdown of FTO, we performed RNA-Seq in MA9.3ITD cells with or without knockdown of FTO.

overall_design: We lentivirally transduced pLKO.1-shFTO (i.e., shFTO) or pLKO.1 empty vertor (i.e., shNS) into human MA9.3ITD (human CD34+ hematopoietic stem/progenetor cells stably infected by MLL-AF9 and FLT3-ITD) AML cells and then selected positively infected cells under selection of puromuycin (0.5ug/ml). The knockdown efficiency was confirmed by qPCR and western. Two stable lines including one FTO-knockdown cell line (i.e., shFTO) and one control line (i.e., shNS) were selected for RNA-Seq. Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.


title: Integrated genomic analyses of de novo pathways underlying atypical meningiomas [ChIP-Seq]

city: New Haven

first: Akdes

last: Serin Harmanci

state: Connecticut

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

institute: Yale University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells (hESCs), thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways.

In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation.

The H3k27ac ChIP-seq data for 15 benign meningiomas and 2 dura samples listed below were created by Dr. Justin Cotney in Dr. James Noonan’s lab at Yale and previously published in a paper by our group with Drs. Cotney and Noonan as co-authors (Clark et al. Science, 2013). Sample IDs: MN-297, MN-288, MN-292, MN-163, MN-1037, MN-105, MN-201, MN-249, MN-191, MN-1066, MN-169, MN-291, MN-24, MN-79, MN-1044, CONTROL1, CONTROL2.

In this study, we used these benign meningioma H3k27ac ChIP-seq data as controls and compared them to the newly created ChIP-seq data. Sample IDs: MN-54, MN-97 and MN-171.

This GEO entry contains ChIP-seq results for both data sets.

overall_design: Analysis of meningioma H3k27ac ChIP-Seq data for each mutation subtype and grade

middle: S

last: Harmanci

first: Mark

last: Youngblood

first: Murat

last: Gunel


title: Next gen RNA sequencing of mouse acute myeloid leukemia

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Trascriptome analysis of aml samples were performed

overall_design: NRAS depended and independent AML mouse models sequenced using Illumina HiSeq 2000

first: Craig

middle: E

last: Eckfeldt

middle: A


title: Sequencing of messenger RNAs with N6-methyladenosine modifications in acute myeloid leukemia (AML) with and without forced expression of FTO

summary: To identify potential mRNA targets of FTO whose m6A levels are affected by FTO in acute myeloid leukemia (AML) cells, we conducted m6A-seq for messenger RNAs isolated from AML cells with and without forced expression of FTO.

overall_design: We retrovirally transduced MSCV-PIG-FTO (i.e., human FTO) or MSCV-PIG (i.e., CTRL/Control) into human MONOMAC-6/t(9;11) AML cells and then selected individual stable clones under selection of puromuycin (0.5ug/ml). Four stable lines including two each FTO-overexpressing lines (i.e., FTO+ 1 and FTO+ 2; or FTO_1 and FTO_2) and control lines (i.e., WT 1 and WT 2; or Ctrl_1 and Ctrl_2) were selected for genome-wide m6A-sequencing (m6A-Seq) assays. The m6A-seq procedure was performed as detailed in Dominissini’s method (Dominissini D., et al. Nat Protocols. 2013; 8: 176-189.). Polyadenylated RNA was extracted using FastTrack MAG Maxi mRNA isolation kit (Life technology). RNA fragmentation Reagents (Ambion) was used to randomly fragment RNA. M6A antibody (Synaptic Systems) was applied for m6A pull down. And final library preparation was constructed by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Final library was quantified by BioAnalyzer High Sensitivity DNA chip then deeply sequenced on the Illumina HiSeq 2500.

first: Hengyou

last: Weng

first: Xiaocheng

first: Zhixiang

last: Zuo

first: Zejuan

last: Li


title: Crystal structure of Pseudomonas aeruginosa RsaL bound to promoter DNA reaffirms its role as a global regulator involved in quorum-sensing

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

summary: Pseudomonas aeruginosa possesses at least three well-defined quorum-sensing (QS) (las, rhl, and pqs) systems. These QS systems control a variety of important functions including virulence. RsaL is a QS repressor that reduces QS signal production and ensures homeostasis by functioning in opposition to LasR. However, its regulatory role in signal homeostasis remains elusive. Here, we conducted a ChIP-seq assay and revealed that RsaL bound to two new targets, the intergenic regions of PA2228/PA2229 and pqsH/cdpR, which are required for PQS synthesis. Deletion of rsaL reduced the transcription of pqsH and cdpR, thus decreasing PQS signal production. The ΔrsaL strain exhibited increased pyocyanin production and reduced biofilm formation, which are dependent on CdpR or PqsH activity. In addition, we solved the structure of the RsaL-DNA complex at a 2.4 Å resolution. Although the overall sequence similarity is quite low, RsaL folds into a HTH-like structure, which is conserved among many transcriptional regulators. Complementation results of the rsaL knockout cells with different rsaL mutants further confirmed the critical role of the DNA-binding residues (including Arg20, Gln27, Gln38, Gly35, Ser37, and Ser42) that are essential for DNA binding. Our findings reveal new targets of RsaL and provide insight into the detailed characterization of the RsaL-DNA interaction.

overall_design: ChIP-seq of RsaL in Pseudomonas aeruginosa

first: Haihua

last: Liang


title: Integrated genomic analyses of de novo pathways underlying atypical meningiomas [H3k27me3 ChIP-Seq]

summary: Meningiomas are mostly benign brain tumors, with a potential for becoming atypical or malignant. Based on comprehensive genomic, transcriptomic and epigenomic analyses of meningiomas, we compared benign tumors to atypical ones. We show that the vast majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent mutations in SMARCB1. These tumors harbor increased H3K27me3 repressive signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells (hESCs), thereby phenocopying a more primitive cellular state. Consistent with this observation, and based on differential gene expression analysis as well as correlation of mRNA:miRNA regulatory networks, atypical meningiomas exhibit up-regulation of EZH2, the catalytic subunit of the PRC2 complex, well as the E2F2 and FOXM1 transcriptional networks that promote proliferation through activation of the cell cycle pathways. In addition, based on H3K27ac ChIP-seq analysis, we show atypical tumors to display an activated super-enhancer near the meningeal identity transcription factor ZIC1, leading to its transcriptional upregulation. Importantly, these primary atypical meningiomas do not harbor activating TERT promoter mutations, which have been reported in atypical tumors that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas, differentiating their profile from benign and progressed tumors and establishing novel therapeutic targets.

overall_design: Analysis of meningioma H3k27me3 ChIP-Seq data for each mutation subtype and grade.


title: A transcription factor pulse can prime chromatin for heritable transcriptional memory [ChIPseq]

first: samuel

summary: To investigate the epigenetic control of long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed ChIPseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any proteins/histone marks are retained.

overall_design: Genome binding/occupancy of transcription factor Pu1 and histones (H3K4me1/2/3 and H3K27me3) by ChIPseq in uninduced Bcell (Control), after induction Cebpa for 6h (Pulse) and after 6 days of wash (Chase).


title: Cdx and T Brachyury co-activate growth signaling in the embryonic axial progenitor niche.

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: In vertebrate embryos, anterior tissues are generated early, followed by the other axial structures that emerge sequentially from a posterior growth zone. The genetic network driving posterior axial elongation in mice, and its disturbance in mutants with posterior truncation are not yet fully understood. We show that the combined expression of Cdx2 and T Brachyury is essential to establish the core signature of posterior axial progenitors. Cdx2 and T Brachyury are required for extension of a similar trunk portion of the axis. Simultaneous loss of function of these two genes disrupts axial elongation to a much greater extent than each single mutation alone. We identify and validate common targets for Cdx2 and T Brachyury in vivo including Wnt and Fgf pathway components active in the axial progenitor niche. Our data demonstrate that integration of the Cdx/Hox and T Brachyury transcriptional networks controls differential axial growth during vertebrate trunk elongation.

overall_design: ChIP-seq for several transcription factors and histone mark H3K27ac, ATAC-seq and RNA-seq in Epiblast stem cells (EpiSCs) and early stage embryos.

first: S

last: Amin

first: R

last: Neijts

last: Simmini

first: C

last: van Rooijen

middle: C

last: Tan

first: L

last: Kester

first: Van

last: Oudenaarden

first: M

middle: P

last: Creyghton

first: J


title: Clonal conversion of B-lymphoid leukemia reveals cross-lineage transfer of malignant states.

city: Linkoping

first: Rajesh

last: Somasundaram

address: Dept of Clinical and Experimental Medicine (IKE)

department: Microbiology and Molecular Medicine

country: Sweden

institute: Linkoping University

summary: Even though leukemia is considered as confined to one specific hematopoietic cell type, cases of acute leukemia of ambiguous lineage and patients relapsing in phenotypically altered disease suggest that a malignant state may be transferred between lineages. Because B-cell leukemia is associated with mutations in transcription factors of importance for stable preservation of lineage identity we here investigated the potential lineage plasticity of leukemic cells. We report that primary pro-B leukemia cells from mice carrying heterozygous mutations in either of or both the Pax5 and Ebf1 gene, commonly mutated in human leukemia, can be converted into T-lineage leukemia cells. Even though the conversion process involved global changes in gene expression and lineage restricted epigenetic reconfiguration, the malignant phenotype of the cells was preserved enabling them to expand as T-lineage leukemia cells in vivo. Furthermore, while the transformed pro-B cells displayed plasticity towards myeloid lineages, the converted cells failed to cause myeloid leukemia after transplantation. These data provide evidence that a malignant phenotype can be transferred between hematopoietic lineages. This has important implications for modern cancer medicine because lineage targeted treatment of leukemia patients can be predicted to provoke the emergence of phenotypically altered sub-clones causing clinical relapse.

overall_design: ATAC-seq: Briefly, for T cell conditions primary leukemic ProB cells from mouse transheterozygote for Ebf1 +/- Pax5+/-  (TH-LN683) were cocultured either on OP9 or OP9-DL1, CD19+Thy1.2- (Day2), CD19+Thy1.2+ (Day6) and CD19-Thy1.2+ (Day 14) cells were sorted. For myeloid conditions TH-LN381 cells were transduced with pMIG or C/EBPα-ER-pMIG and CD19+CD11b- (Day 1), CD19+CD11b+ (Day 2), CD19-CD11b+ (Day 5) were sorted.  Lineage-KIT+Sca1+ (LSK) cells from Wt mouse were cultured either on B or T or Myeloid conditions and the CD19+, Thy1.2+ and CD11b+ cells were used as reference cell types in our assay. Eighty thousand cells from each type were washed in ice cold PBS prior to the assay.  Libraries were single-end sequenced on a NexSeq500. The data was mapped to mm10 using and Tag directories with reads mapped to the mitochondrial chromosome filtered out and UCSC BedGraph files normalized to 10M total mapped reads were created using the HOMER platform ATAC-seq peaks were identified using findPeaks.pl in HOMER. RNA-Seq: Briefly, for T cell conditions primary leukemic ProB cells from mouse transheterozygote for Ebf1 +/- Pax5+/-  (TH-LN377  & 619) was transduced either with ICN1-pMIG or pMIG retrovirus and were cocultured on OP9 for 14 days.  CD19+ (from pMIG) or Thy1.2+ (from ICN1-pMIG) cells were sorted.  For invitro myeloid differentiation experiment cells (TH-LN381 and 619) were transduced with pMIG or C/EBPα-ER-pMIG. After 5 days CD19+11b- (from pMIG) and CD19-CD11b+ (C/EBPα-ER-pMIG ) cells  were sorted.  For T cell kinetics experiment primary leukemic ProB cells (TH-LN683) was cocultured either on OP9 or OP9-DL1, CD19+Thy1.2+ (Day6) and CD19-Thy1.2+ (Day 14) cells were sorted. For myeloid kinetics experiment TH-LN381 cells were transduced with pMIG or C/EBPα-ER-pMIG and CD19+CD11b- (Day 1), CD19+CD11b+ (Day 2), CD19-CD11b+ (Day 5) were sorted.  Lineage-KIT+Sca1+ (LSK) cells from Wt mouse were cultured either on B or T or Myeloid conditions and the CD19+, Thy1.2+ and CD11b+ cells were sorted and used as reference cell types in our assay. RNA were extracted with Qiagen RNaeasy Micro Kit. Librarys were constructed using Nugen's Ovation Ultralow Library systems and were subsequently for 76 cycles of NextSeq500 sequencing generating 20-30 million reads/sample. Data analysis was performed by aligned to mouse reference genome (mm10 /GRCm38) and analysed using the HOMER platform.

first: Josefine

last: Åhsberg

first: Kazuki

last: Okuyama

first: Jonas

last: Ungerbäck

first: Henrik

last: Lilljebjörn

first: Thoas

last: Fioretos

first: Tobias

last: Strid


title: KSHV Infection Mimics the Hypoxic Response Based on Next-Generation Sequencing [miRNA-Seq]

city: Bethesda

first: Coralie

last: Viollet

state: MD

address: 10 Center Dr

institute: NIH/NCI

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: Kaposi’s sarcoma associated-herpesvirus (KSHV) causes several hyperproliferative disorders, including Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. KSHV encodes for a number of microRNAs (miRNAs), and KSHV infection can affect the expression of cellular miRNAs. Hypoxia has been shown to induce KSHV reactivation, directly induce several KSHV lytic genes, and also induce the most abundant latent viral protein, LANA.  Also, several KSHV proteins can stabilize and increase the cellular levels of hypoxia-inducible factor (HIF-1α). However, the degree to which hypoxic pathways are utilized by KSHV has yet to be determined.
Methods: We investigated the interplay between hypoxia and KSHV infection by comparing the 31effects of hypoxia and KSHV infection on miRNA and mRNA expression, and by examining the 32effects of hypoxia on uninfected and KSHV-infected cells. This was accomplished using next-33generation sequencing (NGS), qRT-PCR, Taqman assays, and pathway analysis.
Results: NGS analysis of human mRNAs revealed striking similarities (~34%) between the transcriptomic response to hypoxia and the transcriptomic response to KSHV infection. Additionally, hsa-miR-210, a key hypoxia-inducible miRNA with pro-angiogenic and anti-apoptotic properties, was found significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Finally, KSHV infected cells differed somewhat in their response to hypoxia compared to KSHV-uninfected controls.
Conclusions: These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and induces miR-210 up-regulation. The understanding of how these miRNAs, genes and pathways are regulated by HIF-1α and KSHV infection are essential to a better understanding of the biology of KSHV-associated diseases.

sample_organism:
Homo sapiens
Human gammaherpesvirus 8

overall_design:
6 samples analyzed. Two experimental conditions: hypoxic uninfected cells (SLK cells) and hypoxic chronically KSHV-infected cells (SLKK cells) (n=3). Two sequencing platforms: microRNA-Seq and mRNA-Seq.
This hypoxia study was compared to a previously published normoxia study available on GEO (GSE62830).

first: Viollet

last: Coralie

first: Yarchoan

last: Robert

first: Ragoussis

last: Jiannis

first: Reczko

last: Martin


title: Fusion Negative Rhabdomyosarcoma Cell Lines

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

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

overall_design: Refer to individual Series


title: Gene Expression Profiling of Fusion Negative Rhabdomyosarcoma Cell Lines

summary: We analyzed the expression of two fusion-negative established Rhabdomyosarcoma cell lines. Together with Chip-seq, we were able to identify transcribed loci bound by myogenic regulatory transcription factors (MYF5 and MYOD) that pertain to embryonic muscle development and cell cycle regulation pathways.  Keywords: rhabdomyosarcoma, gene expression profiling, RD, Rh18

overall_design: We compared the transcription profiles of 2 FN-RMS cell lines by RNA-seq analysis.

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: Characterization of chromatin and gene expression changes during fasting in mouse liver [RNA-Seq]

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: During fasting the liver supplies the organism’s energy demands by producing glucose and ketones. Fuel production during fasting is temporally organized whereby glucose serves as the major fuel produced in short-term fasting while ketones are produced in longer fasts as gluconeogenic precursors deplete1. However, the regulatory process dictating this temporally-organized metabolic output is unexplored. Here we show that a cascade of transcription factors (TFs) sequentially activated by hormonal signals, TF gene expression and assisted loading onto specific ‘fasting enhancers’ generate a framework for the temporal organization of fuel production during fasting.  Fasting led to massive chromatin re-organization, exposing enhancers in which a complex set of regulatory signals converge to regulate transcription. Glucagon secreted in early fasting activates cAMP responsive element binding protein (CREB) leading to increased expression of many TF genes, including CCAAT enhancer binding protein β (C/EBPβ) which relaxes chromatin, thereby potentiating glucocorticoid receptor (GR) binding to fasting enhancers upon its activation by corticosterone in mid-term fasting. Then, GR augments glucagon-dependent gluconeogenesis but also supports a peroxisome proliferator receptor α (PPARα)-dependent ketogenic gene program to sustain ketogenesis during prolonged fasting. Our results bridge over a long-lasting gap between the characterized temporal organization of fuel output during fasting and the undefined role of transcription and chromatin regulation in generating this output. Because a de-regulated response to fasting is a hallmark of diabetes progression, these findings may promote our understanding of this complex disease

overall_design: characterization of liver gene expression changes during fasting using RNA-seq

first: Ido

last: Goldstein

first: Gordon

middle: L

last: Hager


title: Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and gene regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains. We found that early non-CG methylation accumulation at super-enhancers in both fetal brain and organoids marks forthcoming transcriptional repression in the fully developed brain. 74% of 35,627 demethylated regions identified during organoid differentiation overlapped with fetal brain regulatory elements. Interestingly, pericentromeric repeats showed widespread demethylation in multiple types of in vitro human neural differentiation models but not in fetal brain. Our study reveals that organoids recapitulate many epigenomic features of mid-fetal human brain and also identified novel non-CG methylation signatures of brain development.

overall_design: MethylC-seq and RNA-seq of Cerebral Organoids differentiation

first: Chongyuan

last: Luo

first: Madeline

last: Lancaster

first: Rosa

last: Castanon

last: Nery

first: Juergen

last: Knoblich


title: Lineage-specific and non-specific cytokine-sensing genes respond differentially to the master regulator STAT5

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

country: China

institute: Zhejiang University

summary: STAT5, a member of the family of Signal Transducers and Activators of Transcription senses cytokines and controls the biology of cell lineages, including mammary, liver and T cells. Here we show that STAT5 activates lineage-specific and widely expressed genes through different mechanisms. STAT5 preferentially binds to promoter sequences of cytokine-responsive genes expressed across cell types and to putative enhancers of lineage-specific genes. While chromatin accessibility of STAT5-based enhancers was dependent on cytokine exposure, STAT5-responsive promoters of widely expressed target genes were generally constitutively accessible. While the contribution of STAT5 to enhancers is well established, its role on promoters is poorly understood. To address this we focused on Socs2, a widely expressed cytokine-sensing gene. Upon deletion of the STAT5 response elements from the Socs2 promoter, cytokine induction was abrogated, while basal activity remained intact. Our data suggest that promoter-bound STAT5 modulates cytokine responses and enhancer-bound STAT5 is mandatory for gene activation.

overall_design: ChIP-seq for STAT5, GR, H3K27ac and Dnase-seq in mammary tissues from wild-type (WT) and Socs2-Δs (Mut) at pregancy day 13 (p13), lactation day 1 (L1) and involution day 1 (I1). mRNA-seq in WT and Socs2-Δs mammary gland at mid-pregancy (p13).

first: Xianke

last: Zeng

first: Michaela

last: Willi

first: Ha

middle: Y

last: Shin

first: Lothar

last: Hennighausen


title: Integrated analysis of mRNA-seq and miRNA-seq in the liver of Pelteobagrus vachelli in response to hypoxia

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

summary: we used next-generation sequencing technology to characterise mRNA-seq and miRNA-seq of control- and hypoxia-treated P. vachelli livers to elucidate the molecular mechanisms of hypoxia adaptation. We were able to find miRNA-mRNA pairs using bioinformatics analysis and miRNA prediction algorithms.

overall_design:
Examination of 2 different oxygen-treated in Pelteobagrus vachelli (Repeat each treatment has three biology).
-----------------------------------
This represents the microRNA component only

first: Guosong

last: Zhang


title: RNA-seq analysis of differential gene expression in liver from Holstein Friesian bulls undergoing diet restriction and compensatory growth

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

summary: The objective of this study was to examine changes in hepatic gene expression of growing bulls during a period of dietary energy restriction followed by a period of subsequent realimentation and compensatory growth. Purebred Holstein Friesian bulls (n=20) were assigned to one of two feeding treatments (i) restricted feed allowance for 125 days (n=10) followed by ad libitum access to feed for a further 55 days or (ii) a control group with ad libitum access to feed through out the 180 days trial (n=10).  The first 125 days of the trial were denoted as Peirod 1, during which treatment groups were fed differentially. The subsequent 55 days, denoted as Period 2 during which all bulls were fed ad libitum. All bulls received the same diet of 70% concentrate 30% grass silage through out the experimental trial,with the amount of feed provided different dependnet on each treatment group. At the end of each period, 10 animals from each treatment group (10, restricted fed and 10 ad libitum fed) were slaughtered and hepatic tissue collected within thirty minutes of slaughter. RNA was extracted and hepatic gene expression was examined using RNAseq technology and bioinformatic analysis. During the differential feeding period, over-represented pathways including amino acid and lipid metabolism, protein synthesis and cell cycle/proliferation were identified, which indicate alterations in metabolic and growth rate in the liver during dietary restriction . During the realimentation period, pathways involved in cell cycle and cell growth as well as protein synthesis were over-represented, with the direction of fold changes opposite to that of these pathways in Period 1. This information can be exploited in genomic breeding programmes to assist selection of cattle with a greater ability to compensate following a period dietary restriction.

overall_design: 40 liver RNA samples were analysed in total. 10 samples were from liver biopsies collected at the end of a period of dietary restriction (d 125) and 10 samples were from liver biopsis collected after 55 days of compensatory growth (d 55 of re-alimentation). In addition,  RNA was also analyzed from 10 samples collected from animals fed ad libitum at each of these two timepoints.

first: David

last: Kenny

first: Alan

last: Kelly

first: Paul

last: Cormican

first: Sinead

last: Waters


title: Integrated genomic analyses of de novo pathways underlying atypical meningiomas

first: Akdes

last: Serin Harmanci

type: Methylation profiling by genome tiling array


title: ChIP-seq of Active Histone Mark (H3K27ac) and Myogenic Regulatory Factors (MYF5 and MYOD) in Fusion Negative Rhabdomyosarcoma Cell Lines

first: Javed

last: Khan

summary: We performed Chip-seq analysis of Myogenic Regulatory Transcription Factors (MYF5 and MYOD) in Fusion Negative Rhabdomyosarcoma cell lines. Endogenous MYF5/H3K27ac Chip-seq was performed in Rh18 cells and MYOD-H3K27ac Chip-seq was performed in RD cells, given that these cell lines express these proteins in a mutually-exclusive manner. Analysis revealed a common subset of enhancer and promoter regions bound by these transcription factors that are enriched for cell cycle regulation and embryonic muscle development pathways.  Keywords: rhabdomyiosarcoma, Chip-seq, chromatin, Transcription factos, MYF5, MYOD

overall_design: 5 samples are deposited including input DNA controls for each of 2 cell lines.

first: Berkley

last: Gryder

first: Marielle

last: Yohe

first: Xinyu

last: Wen


title: Characterization of chromatin and gene expression changes during fasting in mouse liver [Dnase-Seq]

first: Songjoon

last: Baek

overall_design: characterization of liver chromatin landscape during fasting using Dnase-I hypersensitive assay

first: Ido

last: Goldstein

first: Gordon

last: Hager


title: Nucleosome dynamics in human colorectal cancer specimens reveal activation of a CNOT3-regulated pathway of embryonic stem cell self-renewal

city: Boston

first: Paloma

last: Cejas

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
Temporal chromatin dynamics can reveal transcriptional determinants of cell differentiation, and we reasoned that dynamic changes in nucleosome configuration might similarly disclose transcriptional regulators in cancer. To this end, we identified thousands of cis-regulatory sites where chromatin marks and configuration in human CRCs differed from those in their respective precursor adenomas. (based on H3K4me2 mark).
At such sites in selected cases, we observed an abundance of sequence motifs and binding of CNOT3, which is overexpressed in scattered tumor cells in cases associated with unfavorable prognosis. In primary CRCs and cell lines, CNOT3 binding is highly enriched at genes that correspond to both the active and silenced limbs of the ESC gene signature expressed in aggressive carcinomas and these arms respond in coordinated, opposite fashion to CNOT3 loss.

overall_design: H3K4me2 ChIPseq analysis of human primary adenomas and matched colorectal carcinomas. CNOT3 ChIPseq analysis of the human colorectal cancer cell line (HCT116) and of two primary colorectal carcinomas. RNAseq analysis of HCT116 control and CNOT3 depleted cells.

first: Alessia

last: Cavazza

first: Chandri

last: Yandava

first: Víctor

last: Moreno

last: Horst

first: Juan

last: Moreno-Rubio

first: Emilio

last: Burgos

first: Marta

last: Mendiola

first: Len

last: Taing

first: Ajay

last: Goel

first: Jaime

last: Feliu

first: Ramesh

last: Shivdasani


title: Embryonic VHL-HIF signaling defines dynamic heart metabolic compartments essential for cardiac maturation

status: Public on Dec 19 2016

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: While gene regulatory networks involved in cardiogenesis have been characterized, the role of bioenergetics remains less studied. Here we show that until midgestation, myocardial metabolism is compartmentalized, with a glycolytic signature restricted to compact myocardium contrasting with increased mitochondrial oxidative activity in the trabeculae. HIF1a regulation mirrors this pattern, with expression predominating in compact myocardium and scarce in trabeculae. By midgestation, the compact myocardium downregulates HIF1a and switches toward oxidative metabolism. Deletion of the E3 ubiquitin ligase Vhl results in HIF1a hyperactivation, disrupting metabolic compartmentalization and blocking the midgestational shift toward oxidative phosphorylation. Moreover, the altered glycolytic signature induced by HIF1 trabecular activation precludes regulation of genes essential for cardiac conduction system establishment. Our findings reveal VHL-HIF-mediated metabolic compartmentalization in the developing heart and the connection between metabolism and myocardial differentiation. These results highlight the importance of bioenergetics in ventricular myocardium specialization and its potential relevance to congenital heart disease.

overall_design: RNA was isolated from individual E12.5 embryonic hearts after removal of the atria and valvular region. KOs and control littermates were matched by somite count, and a total number of 3 KOs and 3 controls from 3 independent litters were used. For RNA extraction, QIAzol Lysis Reagent (Qiagen; CA; USA) and the miRNeasy Mini Kit (Qiagen; CA; USA) were used. RNA was quantified and its purity checked with a NanoDrop ND-1000 spectophotometer (Thermo Scientific; MA; USA). RNA integrity was verified with an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA). Index-tagged cDNA libraries were constructed from 500 ng of total RNA using the TruSeq RNA Sample Preparation v2 Kit (Illumina; CA; USA). Libraries were quantified by Quant-iT™ dsDNA HS assay in a Q-bit fluorometer (Life Technologies; CA; USA). Average library size and size distribution were determined by DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using 10mM Tris-HCl, pH8.5 containing 0.1% Tween 20 and then applied to an Illumina flow cell for cluster generation (True Seq SR Cluster Kit V2 cBot) and sequencing-by-synthesis. Single reads of length 75bp were generated with the TruSeq SBS Kit v5 (Illumina; CA; USA) on the Genome Analyzer IIx platform, following the standard RNA sequencing protocol. Reads were further processed using the CASAVA package (Illumina; CA; USA) to split reads according to adapter indexes and produce fastq files.

first: I

last: Menendez-Montes

first: B

last: Escobar

last: Palacios

first: M

last: Gómez

first: J

last: Izquierdo-Garcia

first: L

last: Flores

last: Jiménez-Borreguero

last: Aragones

last: Ruiz-Cabello

last: Torres

first: S

last: Martin-Puig


title: 5-hydroxytryptamine synthesized in the Aorta-Gonad-Mesonephros regulates hematopoietic stem and progenitor cell survival

city: beijing

first: Lv

last: Junhua

state: beijing

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: Whole-genome gene expression analysis was performed using the AGMs from two littermate pairs of tph2+/+, tph2+/- or tph2-/- at E11.5. The total RNA was extracted using TRNzol  (Tiangen, Beijing) and cDNA samples were sequenced using Illumina HiSeq3000 (RiboBio Co. Ltd, Guangzhou). The reference Mus musculus genome and gene information were downloaded from the National Center for Biotechnology Information Database (NCBI:  http://www.ncbi.nlm.nih.gov/).

overall_design: Examination of gene expression levels in the AGMs of tph2+/+, tph2+/- or tph2-/- at E11.5

first: Junhua

last: Lv

first: Lu

last: Wang

first: Ya

last: Gao

first: Feng

last: Liu


title: Transcriptome profiling of single HEK293 cells with UMIs on Ion Torrent Proton (Run 20160225)

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: 5' selective RNA-seq of 76 Single HEK293 cells RNAseq profiling with N6H4 unique molecular identifiers processed on a Fluidigm C1.

overall_design: Single cell HEK293 cell 5' selective RNAseq profiling, 76 cells, unique molecular identifiers, custom library preparation.

last: Arguel

first: K

first: A

last: Paquet

first: P

last: Barbry

first: R

last: Waldmann


title: Comparison of transciptome of hiPS-MSC versus MSC (2D culture) and  analyze regulated trascripts during differentiation of hiPS-MSC and MSC on a 3D scaffold

city: Ioannina

first: Carol

last: Murphy

address: Panepistimioupoli

department: Biomedical reseach

country: Greece

institute: FORTH-IMBB

summary:
Expression data from hiPS lines after commitment towards mesenchymal lineage (hiPS-MSC) and expression data of mesenchymal lines (MSC), used as positive control of commitment. Following this, hiPS-MSC and MSC are seeded on scaffold to differentiate in a ligamentous (middle) and osseous (edges) part  (post 21 days 3D differentiation)
We used microarrays to validate efficient commitment of hiPS to generate hiPS-MSC and do whole transcriptome comparison of hiPS-MSC vs isolated MSC (positive control) and then compare the enhanced biological functions after differentiation of these cells on a scaffold

overall_design: 3 different hiPSMSC lines and 3 independent MSC isolated populations were selected (before and after seeding and differentiating on the scaffold) for RNA extraction and hybridization on Affymetrix microarrays. We sought to validate that the regulated trascriptomes of hiPS-MSC are highly similar to isolated primary MSC

first: Athena

last: Kyrkou


title: UMI-based, single cell RNA sequencing of human nasal epithelial cells grown for 52 days at air liquid interface

summary: 5' selective RNA-seq of 96 single cells from human nasal epithelial cells. Cells grown for 52 days at an air liquid interface. RNAseq profiling  was performed with N4H4 unique molecular identifiers processed on a Fluidigm C1. Sequencing was performed on a Ion Proton (Life Technologies).

overall_design: Single cell from human nasal epithelium. 5' selective RNAseq profiling, 96 cells, unique molecular identifiers, custom library preparation.

last: Ruiz-Garcia

last: Zaragosi


title: UMI-based, single cell RNA sequencing of human nasal epithelial cells grown for 33 days at air liquid interface

summary: 5' selective RNA-seq of 96 single cells from human nasal epithelial cells. Cells grown for 33 days at an air liquid interface. RNAseq profiling  was performed with N4H4 unique molecular identifiers processed on a Fluidigm C1. Sequencing was performed on a Ion Proton (Life Technologies).


title: Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

summary: RNA-Seq analysis was performed to assess how a glucose-supplemented diet and/or a hyl-2 mutation altered the transcriptome. Comparison analysis of transcripts associated with anoxia sensitive animals (hyl-2(tm2331) mutation or a glucose diet) revealed 199 common transcripts encoded by genes with known or predicted functions involving innate immunity, cuticle function (collagens) or xenobiotic and endobiotic phase I and II detoxification system.

overall_design: mRNA profiles of OP50-fed C. elegans, glucose-fed C. elegans (N2 strain),  OP50-fed C. elegans altered in ceramide metabolism (due to a hyl-2(tm2031) mutation),  and glucose-fed C. elegans altered in ceramide metabolism  were generated by RNA-Seq, in triplicate, using an Illumina HiSeq2000.  Transcriptome data were then used for a comprehensive quantitative analysis of differential gene regulation in hyl-2(tm2031) and glucose-fed C. elegans.

first: Mary

last: Ladage

first: Skylar

middle: D

last: King

first: David

last: Burks

first: Daniel

last: Quan

first: Anastacia

middle: M

last: Garcia

middle: K

first: Pamela

last: Padilla


title: Ovarian microRNA profile of long-living Ames dwarf mice during aging

city: Orlando

first: Augusto

last: Schneider

state: FL

address: 6900 Lake Nona Blvd

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

summary: Ovarian tissue was collected at 5-6 months and at 21-22 months of age for miRNA sequencing. We detected a total of 404 miRNAs in the ovarian samples, from which the abundance of 22 and 33 miRNAs changed with age in N and df/df mice, respectively. Of these, only three miRNAs were commonly regulated with age between N and df/df mice, indicating a very divergent miRNA profile between genotypes. We also detected that 46 miRNAs were regulated between N and df/df mice, of which 23 were regulated exclusively in young mice, 12 exclusively in old mice and 12 commonly regulated at young and old ages. Many genes likely to be targeted by these miRNAs are involved in the FoxO, mTOR, PI3k/Akt and insulin signaling pathways. These results suggest that the aging process has a differential impact on the ovarian miRNA profile in df/df mice, and suggest that these miRNAs can be central players in the maintenance of a younger ovarian phenotype.

overall_design: Ovarian miRNA profile of 6 and 22 month old Ames dwarf (df/df) and Normal (N/df) female mice. Twenty mice were used in this study, for each age/genotype 5 ovarian samples were processed.

first: Scot

last: Matkovic

first: Berta

last: Victoria

first: Lina

last: Spinel

first: Andrzej

last: Bartke

first: Pawel

last: Golusinski

first: Michal

last: Masternak


title: Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 2]

city: Durham

first: Nahid

last: Iglesias

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary: Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

overall_design: sRNA-seq analysis to characterize priRNA1-mediated secondary siRNA generation in WT and D580A Ago1

first: Ruchi

last: Jain

first: Danesh

last: Moazed


title: Expression data form hiPS lines, HEFs fibroblasts and HUES

first: Carol

last: Murphy

summary:
Comparison of transciptome before and after complete reprogramming of human fibroblasts back to pluripotency
We used microarrays to validate complete reprogramming of human fibroblasts and do whole transcriptome comparison of derived iPS versus a human embryonic stem cell line (HUES1)

overall_design: 3 different hiPS lines, the original cell type used for reprogramming (HEFs) and the embryonic cell line HUES1 were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to validate that the expression of hiPS that we generated from reprogramming of fibroblasts are highly similar to a commercial embryonic stem cell line.

first: Athena

last: Kyrkou


title: Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 1]

overall_design: sRNA-seq analysis to identify sRNA bound specifically to Ago1 in the nucleus


title: Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation

summary:
Small-RNA (sRNA)-guided transcriptional gene silencing by Argonaute (Ago)-containing complexes is fundamental to genome integrity and epigenetic inheritance. The RNA cleavage (“Slicer”) activity of Argonaute has been implicated in both sRNA maturation and target RNA cleavage. Typically, Argonaute slices and releases the passenger strand of duplex sRNA to generate active silencing complexes, but it remains unclear whether slicing of target nascent RNAs, or other RNAi components, also contributes to downstream transcriptional silencing. Here, we develop a strategy for loading the fission yeast Ago1 with a single-stranded sRNA guide, which bypasses the requirement for slicer activity in generation of active silencing complexes. We show that slicer-defective Ago1 can mediate secondary sRNA generation, H3K9 methylation, and silencing similar to or better than wild-type and associates with chromatin more efficiently. The results define an ancient and minimal sRNA-mediated chromatin silencing mechanism, which resembles the germline-specific sRNA-dependent transcriptional silencing pathways in Drosophila and mammals.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ChIP-Seq]

overall_design: ChIP-seq analysis of H3K9me2 levels showing that Ago1 slicing activity is not required for priRNA1-dependent H3K9me2 at ura4+


title: Transcriptome profiling of single HEK293 cells with UMIs sequenced on Ion Torrent Proton (Run 20151215)

first: Kevin

last: Lebrigand

summary: 5' selective RNA-seq of 47 Single HEK293 cells  RNAseq profiling  with N4H4 unique molecular identifiers processed on a Fluidigm C1.

overall_design: Single cell HEK293 cell 5' selective RNAseq profiling, 47 cells, unique molecular identifiers, custom library preparation.

first: M

last: Arguel

first: K

first: A

last: Paquet

first: P

last: Barbry

first: R

last: Waldmann


title: HEK293 cells 100 cell RNAseq profiling  on Ion Proton

summary: Five  libraries  from 100 HEK293 cells  each were prepared using a Smartseq based custom library preparation approach with unique molecular identifiers. One batch of 2 replicates (A) and one batch of 3 replicates (B) were prepared from different cell cultures. Libraries were sequenced on an Ion Proton

overall_design: HEK293 cell  (100 cells)  5' selective RNAseq profiling, N4H4 unique molecular identifiers, 2 replicates (A) and 3 replicates (B)


title: HEK293 cells 100 cell RNAseq profiling  on Illumina NextSeq 500

summary: Three libraries  from 100 HEK293 cells  each were prepared using a Smartseq based custom library preparation approach with unique molecular identifiers. Libraries were sequenced on a Illumina NextSeq 500

overall_design: HEK293 cell  (100 cells)  5' selective RNAseq profiling, N4H4 unique molecular identifiers, 3 replicates


title: A cost effective single cell RNA sequencing approach for the Fluidigm C1

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


title: Genome-wide transcriptome of the coleoptile and the first leaf treated by white light or shade in rice seedlings

city: Shanghai

first: Lin

last: Li

address: 2005 Songhu Road

institute: Fudan University

summary: Purpose: In order to figure out the tissue-specific mechanism in rice, we collected coleoptiles and the first leaves separately from the seedlings treated by 1 hr shade or white light for RNA sequencing.

overall_design: Methods:Coleoptiles were collected from two-day-old rice seedlings grown under white light treated with or without 1hr shade for RNA sequencing. The first leaves were collected from three-days-old rice seedlings grown under white light treated with or without 1 hr shade for RNA sequencing. 2x150 bp paired end RNA-sequencing was conducted using an Illuminia Hi-seq 2500 platform from Genergy Biotech Co. Ltd. (Genergy, Shanghai, China).

first: Huihui

last: Liu

first: Chuanwei

last: Yang


title: Chemical inhibitors of the Mycobacterium tuberculosis DosRST two-component regulatory system

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: The purpose of this study was to discover and characterize small molecule inhibitors of the M. tuberculosis DosRST two-component regulatory pathway. The impact of three novel DosRST regulon inhibitors on gene expression was studied in wild type M. tuberculosis and a DosRS mutant strain.

overall_design: Mtb strain CDC1551 or the CDC1551 (DdosRS mutant) was grown in standing T-25 flasks in 8 mL of medium seeded an initial OD of 0.1.  Cultures were treated with 40 mM of HC101A, HC102A, HC103A or a DMSO control.  Following 6 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq.

first: Huiqing

last: Zheng

first: Benjamin

last: Johnson

first: Christopher

last: Colvin

middle: B


title: Loss of mouse P2Y6 nucleotide receptor is associated with physiological macrocardia and amplified pathological cardiac hypertrophy

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: The study of the mechanisms leading to cardiac hypertrophy is essential to better understand cardiac development and regeneration. Pathological conditions such as ischemia or pressure overload can induce a release of extracellular nucleotides within the heart. We recently investigated the potential role of nucleotide P2Y receptors in cardiac development. We showed that adult P2Y4-null mice displayed microcardia resulting from defective cardiac angiogenesis. Here we show that loss of another P2Y subtype called P2Y6, a UDP receptor, was associated with a macrocardia phenotype and amplified pathological cardiac hypertrophy. Cardiomyocyte proliferation and size were increased in vivo in hearts of P2Y6-null neonates, resulting in enhanced post-natal heart growth. We then observed that loss of P2Y6 receptor enhanced pathological cardiac hypertrophy induced after isoproterenol injection. We identified an inhibitory effect of UDP on in vitro isoproterenol-induced cardiomyocyte hyperplasia and hypertrophy.   The present study identifies mouse P2Y6 receptor as a regulator of cardiac development and cardiomyocyte function. P2Y6 receptor could constitute a therapeutic target to regulate cardiac hypertrophy.

overall_design: WT and P2Y6 KO mice aged between 8 and 12 weeks were intraperitoneally injected with 50 mg/kg/day isoproterenol or saline solution, daily during 7 days, then hearts were harvested and weighted. Ventricles were then stored for RNA extraction.

first: Sophie

last: Clouet

first: Larissa

last: Di Pietrantonio

first: Evangelos-Panagiotis

last: Daskalopoulos

first: Hrag

last: Esfahani

first: Michael

last: Horckmans

first: Marion

last: Vanorlé

first: Anne

last: Lemaire

first: Jean-Luc

last: Balligand

first: Christophe

last: Beauloye

first: Jean-Marie

last: Boeynaems

first: Didier

last: Communi


title: Destabilization of B2 RNA by EZH2 activates the stress response

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary: More than 98% of the mammalian genome is noncoding and interspersed transposable elements account for ~50% of noncoding space. Here, we demonstrate that a specific interaction between the Polycomb protein, EZH2, and RNA made from B2 SINE retrotransposons controls stress-responsive genes in mouse cells. In the heat shock model, B2 RNA binds stress genes and suppresses their transcription. Upon stress, EZH2 is recruited and triggers cleavage of B2 RNA. B2 degradation in turn upregulates stress genes. Evidence indicates that B2 RNA operates as "speed bumps" against advancement of RNA Polymerase II and temperature stress releases the brakes on transcriptional elongation. These data attribute a new function to EZH2 that is independent of its histone methyltransferase activity and reconcile how EZH2 can be associated with both gene repression and activation. Our study reveals that EZH2 and B2 together control activation of a large network of genes involved in thermal stress.

overall_design: In this study the following samples and conditions were tested: 1) NIH/3T3 cells (2x biol.replicates) transfected with a scramble LNA have been either subjected to heat shock (45C - post-H/S cells) or incubated in normal temperature (37C- control cells - pre-H/S cells) for 15 minutes. Subsequently cells were subjected:  i) fixation with formaldehyde for ChIP-sequencing (Ezh2,Suz12, H3K27me3, Pol II S2 P and B2-CHART (with two different probes) sequencing, ii)  to Trizol RNA extraction for RNA-sequencing and short-RNA-sequencing, 2) NIH/3T3 cells (2x biol.replicates)  transfected with an LNA against B2 RNA  were subjected: i) fixation with formaldehyde for ChIP-sequencing ( Pol II S2 P),  ii)  to Trizol RNA extraction for RNA-sequencing and short-RNA-sequencing. 3) NIH/3T3 cells (2x biol.replicates) transfected with an LNA against Ezh2  were subjected  to Trizol RNA extraction for RNA-sequencing and short-RNA-sequencing. 4) RNA was extracted from undifferentiated mouse ES cells for short-RNA sequencing. Because of single-end 50 nt sequencing, full length B2 RNA or fragments of >50 nt in short-RNA-seq would appear as 50-nt reads. In order to get a better insight into such cases we have also sequenced the short-RNA libraries with miseq in order to produce single end 200nt long reads that would span the full length of B2 RNA.

first: Hsueh-Ping

last: Chu

first: Jeannie

middle: T

last: Lee


title: Transcriptome profiling of single HEK293 cells with UMIs on Ion Torrent Proton (Run 20150702)

first: Kevin

last: Lebrigand

summary: 5' selective RNA-seq of 38 Single HEK293 cells RNAseq profiling with N4H4 unique molecular identifiers processed on a Fluidigm C1.

overall_design: Single cell HEK293 cell 5' selective RNAseq profiling, 38 cells, unique molecular identifiers, custom library preparation.

first: M

last: Arguel

first: K

first: A

last: Paquet

first: P

last: Barbry

first: R

last: Waldmann


title: RNAseq from mouse hippcampus

city: Newcastle upon Tyne

first: David

last: Elliott

address: 1 Central parkway

department: Institute of Genetic Medcine

country: United Kingdom

institute: Newcastle University

summary: The RNA binding protein T-STAR controls alternative splicing of important synaptic proteins, and of its paralog SLM1, but its overall functions or physiological importance are unknown. These RNAseq analyses use dissected material from wild type and T-STAR knock out mice. The aim was to identify gene expression changes in the absence of T-STAR protein.

overall_design:
RNAseq reads were taken from wild type mice and mice with homozygous deletions of the Khdrbs3 gene
Wild type Ammon's Horn, homozygote Khdrbs3 Ammon's Horn, wild type Dentate Gyrus.

first: Ingrid

last: Ehrmann


title: Small RNA and PARE sequencing in rice (photoperiod sensitive male sterility lines and wild type) panicles under long-day and short-day conditions

status: Public on Dec 18 2016

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Purpose: The goals of this study are to detect the small RNAs generated from the PMS1T gene and the cleavage sites mediated by small RNAs (microRNAs or phasiRNAs).
Methods: The rice panicles were collected in liquid nitrogen and their total RNA were extracted for library construction and subsequent sequencing on an Illumina HiSeq 2000.
Results: Using an optimized data analysis workflow, we mapped a series of small RNAs generated from the PMS1T region of the rice genome; most of these small RNAs were 21-nt phasiRNAs. The results from PARE sequencing validated the cleavage site on the PMS1T transcript, with the cleavage mediated by miR2118.
Conclusions: Our results show that the 21-nt phasiRNA generated from the PMS1T transcript are associated with photoperiod-sensitive male sterility in rice.

overall_design: The young panicles  were collected for the sequencing from different sizes of genotypes Nongken 58S and NIL(MH), plus transgenic plants, all grown under long-day (daylength>14 h) and short-day (daylength<13.5 h) conditions.

first: Yourong

last: Fan

first: Jiangyi

last: Yang

first: Sandra

last: Mathioni

first: Jinsheng

last: Yu

first: Xuefei

first: Qinghua

last: Zhang

first: Zhaoxia

last: Cai

first: Caiguo

last: Xu

first: Xianghua

last: Li

first: Jinghua

last: Xiao

first: Qifa


title: Identification of Zfs1 RNA targets

status: Public on Dec 17 2016

city: Cambridge

first: Francisco

last: Navarro

address: Downing St

department: Department of Plant Sciences

institute: University of Cambridge

summary: We report RNAs associated with Zfs1 protein, identified by RIP-Seq, and also RNA differentially expressed in the zfs1∆ mutant

overall_design: RNA-seq experiments were performed from cells growing in minimal media (EMM) at 25°C. In immunoprecipiation experiments, RNA associated with Zfs1-TAP protein was sequenced (strain FR1401). RNA associated to GFP-TAP protein was also sequenced to control for inespecific binding (strain FR1424). In differentially expression experiments, RNA was extracted from the wild type strain (PN4)  and from  the zfs1∆ mutant (FR434)

first: Probir

last: Chakravarty

first: Paul

last: Nurse


title: RNA-seq analysis of gliotactin (Gli)-knockdown Drosophila melanogaster posterior midguts enterocytes (EC)

city: Los Angeles

first: Martin

last: RESNIK DOCAMPO

address: 610 Charles E young Dr East

department: MCDB

institute: UCLA

summary: The goal of this study is to analyze changes in gene expression produced in posterior midguts after knocking down Gli in enterocytes (EC) during 9 days. Gli was depleted from ECs using a drug-inducible version of the binary GAL4-UAS system in combination with UAS-GLI-RNAi. Targeted gene expression using the 5966GS-GAL4 driver is observed in adult ECs when flies are fed the progesterone analog RU486 (RU+); addition of ethanol is used as a control (RU-), providing cohorts of isogenic individuals with or without induction of the Gli-RNAi transgene.

overall_design: Seventy-five female 5966GS-GAL4 Gli-RNAi posterior midguts per condition (RU+ and RU-) were dissected. Each condition was sequenced in triplicate, using Illumina HiSeq 2000.

last: Resnik-Docampo

first: D

last: Jones


title: Identification of Breast Cancer Associated Variants That Modulate Transcription Factor Binding

city: Charlottesville

first: Michael

last: Guertin

state: Virginia

address: 1340 Jefferson Park Ave

institute: University Of Virginia

summary: GWAS have discovered thousands of genomic loci that are associated with disease risk and quantitative traits, but most of the variants responsible for risk remain uncharacterized. The vast majority of GWAS-identified loci contain non-coding SNPs and defining molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter Transcription Factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. We employed an integrative genomics approach to identify candidate TF binding motifs that confer breast cancer-specific phenotypes identified by GWAS. We performed de novo motif analysis of regulatory elements, analyzed evolutionary conservation of identified motifs, and assayed TF footprinting data to identify sequence elements that recruit TFs and maintain chromatin landscape in breast cancer-relevant tissue and cell lines. Regulatory elements for MCF10A were mapped with ATAC-seq.We identified top candidate causal SNPs that are predicted to alter TF binding, within breast cancer-relevant regulatory regions, and in strong linkage disequilibrium with the GWAS SNPs. This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk.

overall_design: Map the hypersensitve regions in breast cancer specific cell lines. Identfy TF motifs that underlie the overexpressed regions. Using GWAS ipute causal SNPs that could disrupt TF binding site. Five biological replicate libraries were prepared and sequenced paired end (2x75).

first: Ninad

last: Walavalkar


title: Cooperation between H3K27me3 and non-CG methylation in epigenetic regulation of genes in rice.

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C or T) contexts is a hallmark of transposon silencing in plants. However, relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. Here, we show that SDG711, a rice E(z) homolog, is required to maintain H3K27me3 of many developmental genes after shoot meristem to leaf transition and that many H3K27me3-marked developmental genes are also methylated at non-CG sites in the body regions. SDG711-binding and SDG711-mediated ectopic H3K27me3 also target genes methylated at non-CG sites. Conversely, mutation of OsDRM2, a major rice CHH methyltransferase, resulted in loss of SDG711-binding and H3K27me3 from many genes and their de-repression. Furthermore, we show that SDG711 physically interacts with OsDRM2 and a putative CHG methylation-binding protein. These results together suggest that the repression of many developmental genes may involve both DRM2-mediated non-CG methylation and PRC2-mediated H3K27me3 and that the two marks are not generally mutually exclusive but may cooperate in repression of developmentally regulated genes in rice.

overall_design: Genome-wide mapping of H3K27me3 and/or DNA methylation in WT, SDG711 overexpression, and osdrm2 mutant. Meterials and sequencing for BS-seq of WT and SDG711 overexpression are harvested or done at the same time.

first: Shaoli

last: Zhou

first: Xiaoyun

last: Liu

first: Chao

first: Daoxiu


title: Transcriptome assay of maternal mRNA degradation in ERK-deleted oocytes

status: Public on Dec 16 2016

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

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

overall_design: a WT GV oocyte, a WT MII oocyte, a Erk-/- GV oocyte and a Erk-/- MII oocyte are performed RNA sequencing.

first: Yinli

first: Yujiao

last: Dang


title: Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET1]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: In multicellular organisms, dedicated regulatory circuits control cell-type diversity and response. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. We present CRISP-seq, an integrated method for massively parallel single-cell RNA-seq and CRISPR pooled screens. We show that profiling the perturbation and transcriptome in the same cell, enables to elucidate, the function of multiple factors and their interactions. In this benchmarking study, we applied this technology to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors controlling the commitment toward different cell lineages or the inflammatory and antiviral pathways. CRISP-seq thereby emerges as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits.

overall_design:
Transcriptional and CRISPR profiles from single myeloid cells, infected with lentiviral vectors carrying different gRNAs, were generated by deep sequencing of tens of thousands of single cells, sequenced in several batches in an Illumina Nextseq 500.

Experiment was paired-end, but read2 was used to read cell and molecule barcodes only.

Additional details about experimental design (associating each single cell with its amplification batch and index sorting readout) available as Series supplementary file.

first: Diego

last: Jaitin

first: Assaf

last: Weiner

last: Yoffe


title: Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq

overall_design: Refer to individual Series


title: Genome-wide DNA methylation analysis of livers obtained from 2-stage carcinogenesis model in rats

city: Osaka

first: Ko

last: Omura

address: 2-1-6 Kashima yodogawa-ku

country: Japan

institute: Astellas Pharma Inc.

summary: Identification of epigenetic alterations in the early stage of carcinogenesis promises a great contribution for mechanism analysis and marker exploration for the drug development. For this purpose, we conducted comprehensive analyses for DNA methylation and gene expression in livers obtained from a rat 2-stage carcinogenesis study using nitrosodiethylamine, thioacetamide, methapyrilene and acetaminophen as an initiator and phenobarbital as a promoter. Here, we report the result of MeDIP-seq using methylated DNA enriched by MBD2-protein in rat livers. Comprehensive gene expression analysis was also conducted using same liver samples. The obtained tag sequences were mapped onto rat genome and arbitrary tag count values were calculated and used as each gene DNA methylation state. Using these methylation and gene expression data, pathway analyses for each treatment was performed. The data indicated that livers accompanying preneoplastic legions acquired carcinogenic character of DNA methylation and immune-response related pathways were affected.

overall_design:
DNA methylation status of livers obtained from 2-stage carcinogenesis model in rats. Examination of 2 different histone modifications in 2 cell types.

This submission represents the DNA methylation component of study.

first: Takeki

last: Uehara

first: Yuji

last: Morikawa

first: Hitomi

last: Hayashi

first: Kunitoshi

last: Mitsumori

first: Keiichi

last: Minami

first: Masayuki

last: Kanki

first: Hiroshi

last: Yamada

first: Atsuhi

last: Ono

first: Tetsuro

last: Urushidani


title: Perturb-seq: Dissecting molecular circuits with scalable single cell RNA profiling of pooled genetic screens

first: Atray

last: Dixit

address: 415 Main Street

institute: MIT

summary:
Methods: We create a CRISPR vector containing a polyadenylated RNA barcode and couple it with droplet scRNA-seq to get a large scale transcriptional measurements of perturbations
Results: We were able to perform regulatory inference of gene function, observe nonlinear interactions, and perform downsampling analysis to show that gene signature effects can be seen with as few as 10's of cells while gene level phenotypes, depending on effects size would require 100's of cells
Conclusion: Perturb-seq presents a scalable paradigm for obtaining rich genomic profiles of perturbations

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
scRNA-seq with pooled CRISPR-KO perturbations in 200,000 cells across six screens unstimulated BMDC, BMDC stimulated at 3hr, TFs in K562 at 7 and 13 days post trasnduction, and 13 days at a higher MOI of perturbations,

*Note: that the raw SRA data consists of BAM files not FASTQ files

first: Oren

last: Parnas

first: Biyu

last: Li

first: Jenny

last: Chen

first: Charles

last: Fulco

first: Livnat

last: Jerby-Arnon

first: Nemanja

last: Marjanovic

first: Danielle

last: Dionne

first: Tyler

last: Burks

first: Raktima

last: Raychndhury

first: Britt

last: Adamson

first: Thomas

last: Norman

first: Eric

middle: S

last: Lander

first: Jonathan

last: Weissman

first: Nir

last: Friedman

first: Aviv

last: Regev


title: Knockout of miR-221 and miR-222 reveals overlapping and specific function between paralogous miRNAs

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

summary: MicroRNAs (miRNAs) regulate the expression of mRNAs through sequence-specific binding into their 3′ untranslated region (UTR). The seed sequence of miRNAs is the key determinant to recognize the target sites. The paralogous miRNAs, which share the same seed sequences but differ in their 3′ parts, are known to regulate largely overlapping group of miRNAs. However, there is still no study which analyzes the functional difference among paralogous miRNAs. In this study, we compared the function between paralogous miRNAs, miR-221 and miR-222. By employing nuclease-mediated genome engineering technique, we established the knockout cell lines for these miRNAs, and analyzed their difference in target regulation precisely. We found that miR-221 and miR-222 suppress the previously identified targets, CDKN1B and CDKN1C, differentially. From the transcriptome analyses, we also found that large number of different transcripts with independent functions respond exclusively only to each of miR-221 and miR-222, respectively. Therefore, the miRNAs with common seed sequences can exert dissimilar function by regulating different groups of target mRNAs. This study illustrates that more researches are required to establish the rules of target site recognition by miRNAs.

overall_design: The mRNAs from each of four different cell lines (WT, 221KO, 222KO, DKO) were applied for RNA-seq.


title: Identification of PU. 1 target genes in mouse developing pro-B cells

city: London

first: Rodney

middle: Peter

last: DeKoter

state: Ontario

address: 1151 Richmond St

department: Microbiology and Immunology

institute: Western University

summary: We examined expression of PU.1 target genes in mouse developing pro-B cells by RNA sequencing (RNA-seq). Our goal was to determine the PU.1 target genes specificly required at the pro-B cell stage in B cell development.

overall_design: A PU.1 doxycycline-inducible mouse pro-B cell line (i660 BM) was used. Description: PU.1 expression was induced for 48 hours using doxycycline at the concentration of 70ng/ml, followed by RNA extraction. Non-induced cells were used as controls. qPCRs were performed in order to validate the samples before high-throughput sequencing. Three PU.1 induced samples and three PU.1 non-induced samples were submitted to sequencing.

first: Carolina

last: Batista


title: PU.1

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


title: Genomic-wide PU.1 binding in mouse developing pro-B cells

summary: We examined the genomic PU.1 binding profile in mouse developing pro-B cells by using chromatin immunoprecipitation following high-throughput sequencing (ChIP-seq). Our goal was to determine the genes regulated by PU.1 specifically at the pro-B cell stage in B cell development.

overall_design: A PU.1 doxycycline-inducible pro-B cell line (i660 BM) was used in these set of experiments. Description: PU.1 was induced for 24 hours using doxycycline at the concentration of 70ng/ml, followed by chromatin immunoprecipitation protocol. Non-induced cells were used as controls. qPCRs were performed in order to validate the immunoprecipitations before high-throughput sequencing. Two PU.1 induced samples and one input DNA sample (non-immunoprecipitated chromatin) were submitted to sequencing.


title: Chromatin remodeler Fun30-Fft3 disassembles nucleosomes to facilitate RNAPII elongation in fission yeast

city: Houston

first: Junwoo

last: Lee

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary:
Purpose: The ultimate goal of this study is the identification of transcription elongation-related chromatin remodeler and its in vivo mechanism in fission yeast through Next-generation sequencing (NGS) based ChIP-seq technique.
Methods: Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP  lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP  lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in  Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit.
Results: RNAPII and factor ChIP-seq in various mutants of chromatin remodelers showed that FUN30 family promotes transcription at gene coding regions. RNAPII ChIP-seq in fft3Δ, spt16-1 and fft3Δspt16-1 demonstrated that RNAPII regulation function of Fft3 is largely overlapped with that of Spt16. Histone H3 ChIP-seq results in  fft3Δ and spt16-18 demonstrated that Fft3 is major chromatin remodeler to promote nucleosome turnover through nucleosome disassembly. Finally, histone H3 and RNAPII ChIP-seq in fft3Δ, H3/H4DD and  fft3Δ H3/H4DD were showed that Fft3 facilitates RNAPII elongation at ORF regions through nucleosome barrier regulation.
Conclusions: Fun30-Fft3 is major chromatin remodeler to facilitate RNAPII elongation by nucleosome disassembly-driven nucleosome barrier alleviation in fission yeast.

overall_design: ChIP-seq samples of phosphorylated at Ser2 of CTD or unphosphorylated at CTD of RNAPII, chromatin-associated factors and histone H3 in various fission yeast mutants

first: Eun

last: Choi

first: Hogyu

last: Seo

first: Keunsoo

last: Kang

first: Joshua

last: Gilmore

first: Mike

last: Washburn

first: Jerry

last: Workman

first: Daeyoup


title: Niche WNT5A regulates expression of the actin regulatory pathway in regenerating repopulating hematopoietic stem cells

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

summary: We here show that the niche regulates the quality of the hematopoietic stem cells (HSCs) that are regenerated after transplantation. We find that a reduced level of Wnt5a in the niche regenerates dysfunctional HSCs, which do not successfully engraft secondary recipients. In particular, RNA sequencing shows a dysregulated Zeb1-associated gene expression of multiple genes involved in the small GTPase-dependent actin polymerization pathway. Misexpression of these genes results in reduced ability to direct polarized F-actin localization, leading to defects in adhesion, migratory behavior and homing to the bone marrow of secondary recipients. Our study further shows that the Wnt5a-haploinsufficient environment similarly affects BCR-ABLp185+ cells, which, in 42% of the studied recipients, fail to generate leukemia and, in the remaining cases, fail to transfer leukemia to secondary hosts. Thus, we show that Wnt5a in the niche is required to regenerate HSCs and leukemic cells with functional ability to rearrange the actin cytoskeleton which is required for successful engraftment.

overall_design: Hematopoietic stem cells are regenerated in WT or Wnt5a-haploinsufficient niches. We profile LSK hematopoiteic stem cells after transplantation and three cell populations from the niche environment: endothelial cells (EC), osteoblastic cells (OBC), and mesenchymal cells (MSC)

first: C

last: Schreck

first: Robert

middle: A

last: Oostendorp


title: Novel gene expression profile of women with intrinsic skin youthfulness by transcriptome sequencing

city: Redwood city

first: Anne

last: Chang

state: CA

address: 450 Broadway street, Pavilion C

department: Dermatology

institute: Stanford University School of Medicine

summary: Our study is an unbiased, whole transcriptome search for genes associate with intrinsic skin youthfulness in healthy volunteers that is controlled for co-variates. We identify novel candidate skin youthfulness genes and detail why they are highly worthy of future study. Of particular interest are PHLDA1, a follicle stem cell marker, and HAS2-AS1, a non-coding gene.  We demonstrate that immunologic gene sets are the most significantly altered in skin youthfulness,suggesting the immune system plays an important role in skin youthfulness, a finding that has notpreviously been recognized.

overall_design: Identify genes associated with intrinsic skin youthfulness in healthy volunteers  from sun protected skin.

first: Jin

last: Xu


title: Transcriptomic analysis reveals mechanisms of sterile and fertile flowers differentiation and development in Viburnum macrocephalum f. keteleeri

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We sequenced mRNA from fertile and sterile flowers growing V. macrocephalum f. keteleeri inflorescence using the Illumina HiSeq2500 platform to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for sterile and fertile flowers differentiation and development in flowering plant.

overall_design: Examination of mRNA levels in fertile and sterile flowers growing V. macrocephalum f. keteleeri inflorescence

first: Zhao

middle: G

last: Lu


title: Bisulfite sequencing with Daphnia highlights a role for epigenetics in regulating stress response to Microcystis through preferential differential methylation of serine and threonine amino acidsing bi-sulfite treatment

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

institute: Ghent University

summary: Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways.  Here, we focus on genome-wide methylation patterns in the micro-crustacean Daphnia magna, a model organism in ecotoxicology and risk assessment, exposed to the toxic cyanobacterium Microcystis aeruginosa. Bisulfite sequencing of exposed and control animals highlighted differential methylation patterns in Daphnia upon exposure to Microcystis primarily in exonic regions. These patterns are enriched for serine/threonine amino acid codons and genes related to protein synthesis, transport and degradation. Furthermore, we observed that genes with differential methylation corresponded well with genes susceptible to alternative splicing in response to Microcystis stress. Overall, our results suggest a complex mechanistic response in Daphnia characterized by interactions between DNA methylation and gene regulation mechanisms. These results underscore that DNA methylation is modulated by environmental stress and can also be an integral part of the toxicity response in our study species.

overall_design: Examination of cytosine methylation in DNA samples in Daphnia magna following bisulfite treatment. DNA samples were harvested from Daphnia exposed to Microcystis as well as unexposed Daphnia

first: Dieter

last: De Coninck

first: Eline

last: Beert

first: Colin

last: Janssen

first: Luisa

last: Orsini

first: Michael

middle: E

last: Pfrender

first: Ellen

last: Decaestecker

first: Karel

last: De Schamphelaere


title: Gene expression profiling of cell subpopulations from a mouse model of glioma

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: As a starting point for dissecting the cellular heterogeneity of gliomas, different subpopulations from a CRISPR mouse model of glioma were profiled for gene expression. Because we initially identified these astrocyte subpopulations in the mouse brain, we first sought to determine whether their malignant analogues are present in mouse models of glioma. Towards this, we recently developed a mouse model of malignant glioma, one that utilizes E16.5 IUE approaches in combination with CRISPR mediated gene editing, where we use IUE to introduce gRNA vectors to delete NFI, PTEN, and p53, CAS9, and a GFP reporter, resulting in the generation of malignant glioma at P70. Using the GFP label to distinguish tumor from normal brain tissue, along with FACS-based selection against the glioma stem cell (GSC) and endothelial cells (see methods), we screened our tumor models for the presence of these prospective astroglial populations in the non-GSC fractions of these tumors.

overall_design: Gene expression profiles (by RNA-seq) were taken of mouse glioma cells of three different populations.

first: Fengju

last: Chen

first: Benjamin

last: Deneen


title: Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET2]

first: Ido

last: Amit

overall_design: DNA sequencing of guide RNA targeted loci for several CRISPR pools.  Libraries were generated using primer flanking the target region for bulk population of cells, and sequenced on the Illumina MiSeq.

first: Diego

last: Jaitin

first: Assaf

last: Weiner

last: Yoffe


title: RNAseq analysis of two independent stains of C57BL/6J-Plat-/- mice and wild-type C57BL/6J.

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals. However, gene-deficient mice generated by using 129-derived embryonic stem (ES) cells may carry large segments of 129 DNA, even when extensively backcrossed to reference strains, such as C57BL/6J, and this may confound interpretation of experiments performed in these mice. Tissue plasminogen activator (tPA), encoded by the PLAT gene, is a fibrinolytic serine protease that is widely expressed in the brain. A large number of neurological abnormalities have been reported in tPA-deficient mice. The studies here compare genes differentially expressed in the brains of Plat-/- mice from two independent Plat-/- mouse derivations to wild-type C57BL/6J mice. One strain denoted “Old” was constructed in ES cells from a 129 mouse and backcrossed extensively to C57BL/6J, and one denoted “New” Plat-/- mouse was constructed using zinc finger nucleases directly in the C57BL/6J-Plat-/- mouse strain. We identify a significant set of genes that are differentially expressed in the brains of Old Plat-/- mice that preferentially cluster in the vicinity of Plat on chromosome 8, apparently linked to more than 20 Mbp of DNA flanking Plat being of 129 origin. No such clustering is seen in the New Plat-/- mice.

overall_design: Whole-transcriptome profiling of the cerebral cortex of wild-type control C57BL/6J mice and two independent Plat-/- mice strains on the C57BL/6J background.

first: Daniel

last: Lawrence

first: Thomas

last: Bugge


title: Transcriptome profiles of cirrhotic liver treated with lysophosphatidic acid pathway inhibitors

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Cirrhosis is a milieu that develops hepatocellular carcinoma (HCC), the second most lethal cancer worldwide. HCC prediction and prevention in cirrhosis are key unmet medical needs. Here we have established an HCC risk gene signature applicable to all major HCC etiologies: hepatitis B/C, alcohol, and non-alcoholic steatohepatitis. A transcriptome meta-analysis of >500 human cirrhotics revealed global regulatory gene modules driving HCC risk and lysophosphatidic acid pathway as a central chemoprevention target. Pharmacological inhibition of the pathway in vivo reduced tumors and reversed the gene signature, which was verified in organotypic ex vivo culture of patient-derived fibrotic liver tissues. These results demonstrate the utility of clinical organ transcriptome to enable a strategy, reverse-engineering precision cancer prevention.

overall_design: Cirrhosis-driven hepatocellular carcinoma (HCC) was induced in rats by weekly administration of low-dose diethylnitrosamine (low-dose DEN rat). HCC chemopreventive effects of lysophosphatidic acid (LPA) pathway inhibitors, AM063 (autotaxin [ATX] inhibitor) and AM095 (LPA receptor 1 [LPAR1] inhibitor), was examined.

first: Shigeki

last: Nakagawa

first: Lan

last: Wei

first: Won-Min

last: Song

first: Xiaochen

last: Sun

first: Anu

last: Venkatesh

first: Nicolas

last: Goossens

first: Anna

middle: P

last: Koh

first: Kenneth

last: Tanabe

first: Bryan

last: Fuchs


title: Genome-wide study of OsNF-YB1 regulatory network in rice

city: Shanghai

first: Jingjng

last: Xu

address: 300, Fenglin road

institute: SIPPE


title: Identification of Macrophage Inhibitory Factor as the Parthanatos Dependent AIF Associate Nuclease

city: Baltimore

first: Stephen

middle: Matthew

last: Eacker

state: MD

address: 733 N. Broadway Suite 731

department: Neurology

institute: Johns Hopkins University

summary: Inhibition or genetic deletion of poly(ADP-ribose) polymerase-1 (PARP-1) is profoundly protective against a number of toxic insults in many organ systems1,2. In the brain the molecular mechanisms underlying PARP-1-dependent cell death (parthanatos) involves mitochondrial apoptosis-inducing factor (AIF) release and translocation to the nucleus resulting in chromatinolysis3-5. However, it is not known how AIF induces chromatinolysis and neuronal death in parthanatos3. Here we show through an unbiased screen of a ~16K human protein microarray followed by a second siRNA-based screen for protection against PARP-1- dependent cell death, that macrophage migration inhibitory factor (MIF)6 is an AIF associated nuclease that is required for cell death following N-methyl-D-aspartate (NMDA) glutamate receptor excitotoxicity and N-methyl-N-nitroso-N- nitroguanidine (MNNG) toxicity in primary neuronal cultures and focal stroke in mice. MIF contains a central four stranded mixed β-sheet flanked by two α- helices on both sides with an αβββαβ topology which is the structural core of many proteins belonging to the PD-D/E(X)K nuclease-like superfamily. MIF possesses previously unknown Mg2+/Ca2+-dependent nuclease activity, cleaving genomic DNA into large 20-50 kb fragments. AIF recruits MIF to the nucleus after NMDA treatment to induce DNA damage and cell death. Disruption of the AIF-MIF interaction prevents MIF recruitment to the nucleus and protects neurons from NMDA excitotoxicity and ischemic injury. Mutation of Glu22 to Gln in the catalytic nuclease domain completely blocks MIF’s nuclease activity, which almost completely inhibits DNA damage and cell death in vitro and in vivo. These findings reveal that MIF is recruited by AIF to the nucleus where it functions as a parthanatos dependent AIF associated nuclease that induces chromatinolysis and neuronal death, providing a new therapeutic target for stroke and other disorders involving parthanatos.

overall_design: Examination of 2 different histone modifications in 2 cell types.

first: Yingei

last: Wang

first: Ted

last: Dawson


title: Whole eye transcriptome generated in Abca4-/-Rdh8-/- mice  to identify changes in gene expression after light exposure

city: Cleveland

first: Tanu

last: Parmar

state: OH

address: 2085 adelbert road

department: Department of Ophthalmology and Visual Sciences

institute: Case Western Reserve University

summary: RNA-Seq has revolutionized transcriptome profiling with precise identification of even low expressing and novel transcripts. Goal of the current study was to identify novel gene signatures/biological pathways which are expressed in the early stage after light exposure in our disease model to identify transcriptional mis-regulation followed by validation using quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods

overall_design: Whole eye mRNA profiles of 6 week old Abca4-/-Rdh8-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. Cuffdiff was used for differential gene analysis. qRT–PCR validation was performed using SYBR Green assays

first: Akiko

last: Maeda

first: Ernest

last: Chan


title: Genome-wide characterization of cis-acting DNA targets of OsNF-YB1 in rice

summary: OsNF-YB1 is a transcription factor that plays important roles during rice grain filling. OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and OsNF-YB1 RNAi lines showed retardation in grain filling and produced small grains with chalky endosperm as well as the altered starch quality. To reveal the transcriptional regulatory framework of OsNF-YB1, we determined OsNF-YB1 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 933 binding peaks distributed 743 neighbor genes. OsNF-YB1 directly regulates genes involved in nutrient transport including sugar and amino acids, and interestingly, different from the reported binding site of NF-Y complex, the GCC-box (a binding motif of ERF transcription factors) was enriched in the binding peaks of OsNF-YB1.

overall_design: Examination of 8-12 days after fertilization (DAF) OsNF-YB1-GFP rice caryopsis coat (The starchy endosperm and embryo of caryopses were removed, and the remaining structure was termed the caryopsis coat) with GFP antibody and Input serves as control.

first: Jingjing

first: Hongwei

last: Xue


title: A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors

status: Public on Dec 15 2016

city: Cambridge

first: Donald

last: Bryant

state: MA

address: 65 Landsdowne Stree

department: Biological and Biomedical Sciences

institute: Harvard University

summary: Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013):  https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration.

overall_design: To identify transcripts that are essential for regeneration and to provide a resource for axolotl researchers we profiled 42 samples across 16 tissues, from distinct locations among intact and regenerating limbs, relevant cell types, and other progenitor-rich samples using RNA-sequencing. The SRA study accession for these data is: SRP065567. The BioProject accession is:  PRJNA300706.  The TSA accession for the transcripome assembly is:  GFBM000000000.

first: Jessica

middle: L

last: Whited


title: Predominant TRUB1-dependent pseudouridylation of mammalian mRNA via a predictable and conserved code

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: In this accession we provide pseudouridylation measurements upon knockdown and/or overexpression three pseudouridine synthases, two of which (TRUB1 and PUS7) we find to be with predominant activity on mammalian mRNA.

overall_design: Examination of pseudouridylation upon genetic perturbation of three pseudouridine synthases

first: Modi

last: Safra


title: HiC of selected non-small cell lung carcinoma cell lines

city: Worcester

first: Job

last: Dekker

state: Massachusetts

address: 368 Plantation Street

department: Program in Systems Biology

institute: UMass Medical School

summary: Utilizing HiC to characterize the three-dimensional architecture of two NSCLC lines: NCIH460A, NCIH460B.

overall_design: Cell lines are cultured in accordance with supplier protocols and assayed following the Dekker Lab's HiC Assay protocol: http://www.jove.com/video/1869/hi-c-a-method-to-study-the-three-dimensional-architecture-of-genomes. http://www.jove.com/video/1869/hi-c-a-method-to-study-the-three-dimensional-architecture-of-genomes

first: John

last: Stamatoyannopoulos