title: Genome‐wide analysis of pre‐mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: A-seq

first: Andreas

middle: R

last: Gruber

overall_design: 3' ends of transcripts were profiled by high-throughput sequencing in HEK 293 cells under normal conditions, and in HEK 293 cells depleted of 3' end processing factors CF Im 68 and CstF-64.

first: Georges

last: Martin

first: Walter

last: Keller

first: Mihaela

last: Zavolan


title: The structure of human Argonaute-2 in complex with miR-20a

status: Public on May 12 2012

city: Cold Spring Harbor

first: Astrid

last: Haase

state: NY

address: One Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: Argonaute proteins lie at the heart of the RNA-Induced Silencing Complex (RISC), wherein they use small RNA guides to recognize targets. Some Argonaute proteins can directly cleave their targets, whereas others recruit co-factors to repress independently of “slicing.” Prior studies established the architecture of Argonaute proteins; however, we have not yet had a detailed picture of an Argonaute whose biochemical and biological functions were well established. Here we describe the crystal structure of human Argonaute-2 bound to miR-20a at 2.2 Å resolution. Overall architecture and domain organization is shared with its prokaryotic counterparts, though Ago2 is somewhat more open, with its PAZ domain further removed from the other domains. The miRNA is anchored at both ends by the Mid and PAZ domains but makes several kinks and turns along the binding groove. The RNA confers remarkable stability on the Argonaute protein, locking this otherwise flexible enzyme into a stable conformation.

overall_design: total small RNAs (19-29nt) and small RNAs associated with purified hArgonaute2 purified from SF9 cells. These were processed and sequenced on Illumina GA-II platform.

first: Elad

last: Elkayam

first: Claus-D

last: Kuhn

first: Ante

last: Tocilj

middle: D

first: Emily

middle: M

last: Greene

first: Gregory

middle: J

last: Hannon

first: Joshua-Tor

last: Leemor


title: Whole transcriptome sequencing reveals dynamic RNA changes in the aging rat brain

status: Public on May 10 2012

city: Liverpool

first: Shona

middle: Hiedi

last: Wood

address: Crown street

department: Functional and Comparative Genomics

country: United Kingdom

institute: University of Liverpool

type: Expression profiling by high throughput sequencing

summary: Using RNA-seq, 9 cerebral cortex RNA samples were sequenced from 6 month (n=3, 6 individuals pooled), 12 month (n=3, 6 individuals pooled) and 28 month (n=3, 6 individuals pooled) rats. Allowing brain aging in the cerebral cortex to be assessed.

overall_design: Transcriptional profiling of the ageing cerebral cortex at 6, 12 and 28 months

middle: H

first: Thomas

last: Craig

first: Yang

last: Li

first: Brian

last: Merry

first: João

middle: P

last: de Magalhães


title: Identification of microRNAs association with Rheumatoid Arthritis Synovial Fibroblasts using the Human TNF Transgenic Mouse Model

status: Public on May 14 2012

city: Varkiza

first: Martin

last: Reczko

address: 34 Fleming Street

department: Institute of Molecular Oncology

country: Greece

institute: BSRC A. Fleming

summary: OBJECTIVE: MicroRNAs (miRNAs, miRs), a class of small non-coding RNA molecules, are posttranscriptional regulators involved in a plethora of cellular functions and have been proposed as potential therapeutic targets in various diseases, including rheumatoid arthritis (RA). In this study, we sought to discover novel miR associations in synovial fibroblasts (SFs), a key cell type mediating RA pathogenesis, by performing miR expression profiling on cells isolated from the human TNF transgenic mouse model (TghuTNF or Tg197). METHODS: miR expression in SFs isolated from 8-week-old, fully diseased TghuTNF and WT littermate control mice were determined by deep sequencing of small RNAs and the arthritic profile was established by pairwise comparisons of the two groups. qRT-PCR analysis was utilised for profile validation purposes and miR quantitation in patient SFs. Dysregulated miR target genes and pathways were predicted via bioinformatic algorithms.

overall_design: Synovial Fibroblasts isolated from TghuTNF mice (2 x biological replicates) and control WT littermate mice (2 x biological replicates)

first: Ioannis

last: Pandis

first: Niki

last: Karagianni

first: Maria

middle: C

last: Denis

first: Carme

last: Camps

first: Artemis

middle: G

last: Hatzigeorgiou

first: Jiannis

last: Ragoussis

first: George

last: Kollias


title: RNA-seq from ENCODE/LICR

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yin Shen mailto:y7shen@ucsd.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

Using RNA-Seq (Mortazavi et al., 2008), high-resolution genome-wide maps of the mouse transcriptome across multiple mouse (C57Bl/6) tissues and primary cells were generated.

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols (http://genome.ucsc.edu/ENCODE/protocols/cell/mouse).
RNA-Seq
RNA samples from tissues and primary cells were extracted from Trizol® according to protocol (Invitrogen). PolyA+ RNA was purified with the Dynabeads mRNA purification kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al., 2009).
Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA. Alignment to the mouse genome was performed using TopHat (Trapnell et al., 2009). Wig files were generated by TopHat and expression levels were calculated with Cufflinks (Trapnell et al., 2010).

first: Yin

last: Shen

first: Bing

last: Ren


title: Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia

status: Public on May 11 2012

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

type: Methylation profiling by high throughput sequencing

summary: We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from CLL patient and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1764 gene promoters were identified as being differentially methylated between the two groups. Aberrant hypermethylation was found in all HOX gene clusters and a significant number of WNT signaling pathway genes. The genes that were frequently hypermethylated were typically associated with histone H3 lysine 27 tri-methylation or bivalent domains in normal B-cells. An additional 152 genes were found to be differentially methylated between normal naïve and memory B-cells. Of these 152 genes, 123 were hypomethylated in memory B-cells when compared to naïve B-cells. Overall, CLL B-cells had methylation patterns more similar to memory B-cells than naïve B-cells. Cluster analysis showed that the tissue-specific methylated genes separated CLL samples into two groups with differential ZAP70 methylation status. Hypomethylation occurred more frequently in the gene body including introns, exons, and 3'-UTRs in CLL. The hypomethylation in the NFATc1 P2 promoter and first intron correlated with up-regulation of both NFATc1 RNA and protein expression levels in CLL suggesting that an epigenetic mechanism is involved in the constitutive activation of NFAT activity in CLL cells. This comprehensive DNA methylation map will further our understanding of the epigenetic contribution to cellular dysfunction in CLL.

overall_design: To perform a genome-wide analysis of DNA methylation in CLL, we applied the Reduced Representation Bisulfite Sequencing (RRBS) to CD19+ B-cells isolated from normal control and CLL peripheral blood samples.  The genomic DNA from each sample was digested with the methylation-insensitive restriction enzyme MspI (restriction site, CCGG) and ligated to Illumina sequencing adaptors containing methylated cytosine residues. The ligated MspI fragments were size-selected, treated with sodium bisulfite, and amplified by PCR. The PCR products were purified and sequenced using Illumina GAIIx sequencer with a read length of 52 or 76bp.  11 CLL B-cell samples, 3 normal control samples including one each of normal CD19+, CD19+/ IgD+ naïve, and CD19+/CD27+ memory B-cell sample and three CLL cell lines (Mec-1, Mec-2, and Wac-3) were used. We generated 20-30 million Illumina sequencing reads for each sample.


title: Heat-shock protein 90 globally targets paused promoters and regulates environment-induced gene expression

status: Public on May 15 2012

city: Basel

first: Cem

last: Sievers

address: Mattenstrasse

country: Switzerland

institute: ETH Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study we provide evidence that Hsp90 binds chromatin at specific sites close to several TSS in Drosophila S2 cell line. In addition of finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic Hsp90 binding sites coinciding with non-annotated transcription start sites. Interestingly, this set includes promoters for primary transcripts of microRNA genes, thereby expanding the scope of Hsp90 to transcriptional control of many genes. We finally conclude that Hsp90 contacts NelfE and thus regulates pol II pausing.

overall_design: Our Dataset comprises of 1 ChIP-seq sample using chromatin from S2 cells which was immunoprecipitated, using antibodies against Drosophila Hsp90. The two biological replicates are submitted along with the input replicates.

first: Ritwick

last: Sawarkar

first: Renato

last: Paro


title: Identification of Transcription Factor MEF-2::GFP Binding Regions in L1

status: Public on May 09 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_3071
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP301(official name : OP301 genotype : unc119(ed3);wgIs301(mef-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MEF-2::EGFP fusion protein is expressed in the correct mef-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MEF-2 transcription factor. made_by : R Waterston ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs301(mef-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene mef-2; Strain OP301(official name : OP301 genotype : unc119(ed3);wgIs301(mef-2::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The MEF-2::EGFP fusion protein is expressed in the correct mef-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MEF-2 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: A novel miRNA produced during lytic HSV-1 infection is important for efficient replication in tissue culture.

status: Public on May 08 2012

city: Albany

first: April

last: Burch

address: 120 New Scotlant Ave

department: Infectious Diseases

institute: Wadsworth Center/ SUNY Albany/ Berkshire School

summary: We report a HSV-1 encoded miRNA present during lytic infection that influences replication efficiency in a tissue culture model.  miRNAs were identified using high-throughput sequencing of HSV-1 infected epithelial cells.  Functional assays were performed by mutating the miRNA coding region and testing grow of the mutant in vitro.

overall_design: Construction of a miRNA library and sequencing to reveal novel viral miRNAs from lytically infected cells

first: Daniel

last: Munson


title: Identification of Transcription Factor FOS-1::GFP Binding Regions in L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_3587
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene fos-1; Strain OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius


title: Identification of Transcription Factor ZK377.2::GFP Binding Regions in L2

summary:
modENCODE_submission_3591
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene sax-3; Strain OP355(official name : OP355 genotype : unc-119(ed3) III; wgIs355(ZK377.2::TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The sax-3::EGFP fusion protein is expressed in the correct sax-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the sax-3 transcription factor. The sax-3 gene is encoded by the ZK377.2 CDS. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong


title: Identification of Transcription Factor NHR-77::GFP Binding Regions in L2

summary:
modENCODE_submission_3595
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-77;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-77; Strain OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mike

last: Snyder


title: Identification of Transcription Factor NHR-116::GFP Binding Regions in L2

summary:
modENCODE_submission_3598
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-116;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-116; Strain OP226(official name : OP226 genotype : unc119(ed3);wgIs226(nhr-116::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-116 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-116::EGFP fusion protein is expressed in the correct nhr-116 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-116 transcription factor. made_by : M Sarov ); temp (temperature) 20 degree celsius

first: Cindie

last: Slightam


title: Identification of Transcription Factor FOS-1::GFP Binding Regions in L4

summary:
modENCODE_submission_3588
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene fos-1; Strain OP304(official name : OP304 genotype : unc119(ed3);wgIs304(fos-1::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The FOS-1::EGFP fusion protein is expressed in the correct fos-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the FOS-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Stuart

last: Kim


title: Identification of Transcription Factor F45C12.2::GFP Binding Regions in L1

summary:
modENCODE_submission_3600
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP212(official name : OP212 genotype : unc-119(ed3); wgIs212(F45C12.2:TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov ); Developmental Stage: fed L1; Genotype: unc-119(ed3); wgIs212(F45C12.2:TY1 EGFP FLAG; unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene F45C12.2; Strain OP212(official name : OP212 genotype : unc-119(ed3); wgIs212(F45C12.2:TY1 EGFP FLAG; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F45C12.2::EGFP fusion protein is expressed in the correct F45C12.2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F45C12.2 transcription factor. made_by : Mihail Sarov ); temp (temperature) 20 degree celsius

first: John

last: Murray


title: mRNA-seq of Physcomitrella protonema responding to 1 hr red light in wild type and the phytochrome-deficient mutant

city: Taipei

first: Shih-Long

last: Tu

address: 128, Sec 2, Academia Rd,Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica

summary: The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID:  .

overall_design: 4 samples, dark-grown wild-type and pubs hy2 protonema as time 0 control, followed by red light irradiation for one hour respectively

first: Yu-Rong

last: Chen

first: Yi-shin

last: Su


title: Identification of Transcription Factor NHR-77::GFP Binding Regions in L3

summary:
modENCODE_submission_3596
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-77;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene nhr-77; Strain OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette


title: Identification of Transcription Factor NHR-77::GFP Binding Regions in L4

summary:
modENCODE_submission_3597
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; Transgene: nhr-77;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene nhr-77; Strain OP353(official name : OP353 genotype : unc119(ed3);wgIs353(nhr-77::TY1 EGFP FLAG;unc119) outcross : 3 transgene : nhr-77 tags : Bombard tag : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-77::EGFP fusion protein is expressed in the correct nhr-77 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-77 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov


title: Identification of Transcription Factor GEI-11::GFP Binding Regions in L2

status: Public on May 07 2012

first: DCC

last: modENCODE

summary:
modENCODE_submission_3149
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

first: Anthony

last: Hyman


title: Identification of Transcription Factor F16B12.6::GFP Binding Regions in L1

summary:
modENCODE_submission_3148
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP114(official name : OP114 genotype : unc119(ed3);wgIs114(F16B12.6::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F16B12.6::EGFP fusion protein is expressed in the correct F16B12.6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F16B12.6 transcription factor. made_by : R Waterston ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs114(F16B12.6::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene F16B12.6; Strain OP114(official name : OP114 genotype : unc119(ed3);wgIs114(F16B12.6::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The F16B12.6::EGFP fusion protein is expressed in the correct F16B12.6 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the F16B12.6 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder


title: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

summary: The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the non-coding DNA surrounding their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac).  Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here we provide genomic maps of H3K4me1/me3 and H3K27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that: (i) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression; (ii) in early embryos, the peaks of H3K27ac enrichment are bound by pluripotent factors such as Nanog; (iii) the degree of evolutionary conservation is higher for enhancers that become marked by H3K27ac at the end of gastrulation suggesting their implication in the establishment of the most conserved (phylotypic) transcriptome that is known to occur later at the pharyngula stage.

overall_design: ChIP-seq analysis of H3K4me3, H3K4me1 and H3K27ac at four developmental time-points (dome, 80% epiboly, 24hpf and 48pf) of zebrafish embryogenesis.

last: Bogdanović

first: Ana

last: Fernandez-Miñan

first: Juan

last: Tena

first: Elisa

last: de la Calle-Mustienes

first: Carmen

last: Hidalgo

first: Simon

last: van Heeringen

first: Gert

last: Veenstra

first: José

middle: L

last: Gómez-Skarmeta


title: Identification of Transcription Factor DAF12::GFP Binding Regions in L3

summary:
modENCODE_submission_3147
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP167(official name : OP167 genotype : unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : S Kim ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene daf-12; Strain OP167(official name : OP167 genotype : unc119(ed3);wgIs167(daf-12::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The DAF-12::EGFP fusion protein is expressed in the correct daf-12 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the DAF-12 transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

last: Raha


title: Identification of Transcription Factor SEA2::GFP Binding Regions in L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_3082
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by :  ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene sea-2; Strain OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by :  ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

last: Snyder

first: Debasish

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Transcriptome sequencing of 7 tissues of S. lycopersicum and 2 of its closely related wild ancestor S. pimpinellifolium

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

summary: Transcriptome analysis of 7 tissues of commercial tomato (S. lycopersicum cv MoneyMaker) and its wild red-fruited ancestor (S. pimpinellifolium LA0722) genotypes performed to assess expression level of tomato transcriptome and to aid whole genome annotation. Sequencing of fruit at 3 different developmental stages will help to assess gene regulation through ripening.

sample_organism:
Solanum lycopersicum
Solanum pimpinellifolium

overall_design: Plants of S. lycopersicum (cv MoneyMaker) or S. pimpinellifolium (LA0722) were grown in soil-filled pots in greenhouse under controlled conditions in Long day (16 hours light, 8 hours dark). RNA was extracted from different tissues according to published methods(López-Gómez and Gomez-Lim, 1992). cDNA was produced according to the SMART cDNA PCR synthesis kit (Clontech) but using the SuperScriptII Reverse Transcriptase (Invitrogen), their quantity and quality were evaluated respectively by Nanodrop spectrophotometer and Agilent Bioanalyzer (DNA12000 assay). Tissues used for cDNA synthesis in S. lycopersicum were: root, stem, leaf, flower and fruit at 3 different maturation stages: mature green, breaker and ripe. S. pimpinellofolium tissues used for synthesis were leaf and berry ripe.  cDNA libraries were produced following the 454 Titanium Rapid Library Preparation protocol instructions, then fixed to micro beads and clonally amplified by emulsion PCR (emPCR Method Manual-Lib-L). The beads have been enriched to keep only those carrying identical PCR products, and then each sample has been loaded on a half picotiter plate to obtain at least 350000 reads with a medium length of 400bp. Each sample was sequenced on a half picotiterplate.

first: Marco

last: Pietrella

first: Giovanni

last: Giuliano

first: Fabio

last: Fuligni

first: Gianluca

last: De Bellis


title: Identification of Transcription Factor Pdpl1_DPL1::GFP Binding Regions in L1

summary:
modENCODE_submission_3075
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); Developmental Stage: fed L1; Genotype: unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene dpl-1; Strain YL425(official name : YL425 genotype : unc-119(ed3) III; vrIs69[pDPL-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); temp (temperature) 20 degree celsius

first: Mike

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

last: Waterston


title: Identification of Transcription Factor CES1::GFP Binding Regions in L1

summary:
modENCODE_submission_3076
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ); Developmental Stage: fed L1; Genotype: unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene ces-1; Strain OP174(official name : OP174 genotype : unc-119(ed3); wgIs174(ces-1::TY1 EGFP FLAG;unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The CES-1::EGFP fusion protein is expressed in the correct ces-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CES-1 transcription factor. made_by : S. Kim ); temp (temperature) 20 degree celsius

first: Robert

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

last: Raha


title: Identification of Transcription Factor Pefl1_EFL1::GFP Binding Regions in L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_3074
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); Developmental Stage: fed L1; Genotype: unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene efl-1; Strain YL424(official name : YL424 genotype : unc-119(ed3); vrIs68[pEFL-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

last: Snyder

first: Debasish

first: Ashish

last: Agarwal


title: Identification of Transcription Factor Ppie1_DPL1::GFP Binding Regions in YA

summary:
modENCODE_submission_3073
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); Developmental Stage: Young Adult; Genotype: unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene dpl-1; Strain YL390(official name : YL390 genotype : unc119(ed3); vrIs48 [pPIE-1::DPL-1::GFP FLAG: DPL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); temp (temperature) 20 degree celsius

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of Transcription Factor Ppie1_EFL1::GFP Binding Regions in YA

summary:
modENCODE_submission_3072
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); Developmental Stage: Young Adult; Genotype: unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene efl-1; Strain YL445(official name : YL445 genotype : unc119(ed3); vrIs81 [pPIE-1::EFL-1::GFP FLAG: EFL-1 3?UTR genotype : unc-119 (+)] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description :  made_by :  ); temp (temperature) 20 degree celsius


title: Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [dorsal root ganglia]

status: Public on May 06 2012

city: Nantong

first: xiaosong

last: gu

state: Jiangsu

address: 19 Qixiu Road

country: China

institute: Nantong University

summary: We applied Solexa sequencing technology to identify rat microRNA genes in dorsal root ganglia (DRGs) following sciatic nerve resection. Using Solexa sequencing, computational analysis and Q-PCR verification, 114 novel miRNAs in rats were discovered and identified, of which 52 novel miRNAs were first reported in rat DRGs and 62 novel miRNAs were produced at days 1, 4, 7 and 14 after sciatic nerve resection. These data provide an important resource relating to the role and regulation of miRNAs for future studies relating to peripheral nerve injury and regeneration.

overall_design: 18-30 nt small RNAs from 30 Thirty Sprague-Dawley (SD) rats were sequenced at one Solexa lane

first: Shiying

last: Li

first: Bin

last: Yu

first: Xiaosong

last: Gu


title: Identification of Transcription Factor CEH-26::GFP Binding Regions in LE

summary:
modENCODE_submission_3068
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ); Developmental Stage: late embryo; Genotype: unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene ceh-26; Strain OP500(official name : OP500 genotype : unc119(ed3);wgIs500(ceh-26::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The CEH-26::EGFP fusion protein is expressed in the correct ceh-26 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-26 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

first: Mike

first: Cindie

last: Slightam

first: Stuart

last: Kim

last: Murray


title: Identification of Transcription Factor NHR11::GFP Binding Regions in L2

summary:
modENCODE_submission_3079
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-11; Strain OP305(official name : OP305 genotype : unc119(ed3);wgIs305(nhr-11::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The NHR-11::EGFP fusion protein is expressed in the correct nhr-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-11 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: John

first: Robert

last: Waterston

first: Mark

last: Gerstein

last: Niu


title: PAR-CLIP of RBM4 and HIF-2a

city: Ottawa

first: Jim

last: Uniacke

address: 451 Smyth

institute: University of Ottawa

summary: To identify which mRNAs bind to RBM4/HIF-2a

overall_design: Two PAR-CLIPs were performed: One of an RBM4 immunoprecipitation, and the other of a HIF-2a immunoprecipitation and excising the associated RBM4 band.

first: James

first: Chet

middle: E

last: Holterman

first: Gabriel

last: Lachance

first: Aleksandra

last: Franovic

first: Mathieu

last: Jacob

first: Marc

last: Fabian

first: Josianne

last: Payette

first: Martin

last: Holcik

first: Arnim

last: Pause

first: Stephen

last: Lee


title: Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]

first: xiaosong

last: gu

summary:
We applied Solexa sequencing technology to identify rat microRNA genes in proximal sciatic nerve following sciatic nerve resection. Using Solexa sequencing, computational analysis and Q-PCR verification, 93 novel miRNAs in rats were discovered and identified, of which 42 novel miRNAs were first reported in proximal sciatic nerve of rat and 51 novel miRNAs were produced at days 1, 4, 7 and 14 after sciatic nerve resection. These data provide an important resource relating to the role and regulation of miRNAs for future studies relating to peripheral nerve injury and regeneration.
Keywords: Small RNA sequencing

overall_design: 18-30 nt small RNAs from proximal sciatic nerve of 30 Thirty Sprague-Dawley (SD) rats were sequenced at one Solexa lane

first: Shiying

last: Li

first: Bin

last: Yu

first: Xiaosong

last: Gu


title: Identification of protein-RNA interactions in Drosophila using RIP-Seq

status: Public on May 05 2012

city: Farmington

first: Brenton

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

summary:
The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared and sequenced. Sequence reads were aligned to the D. melanogaster reference genome Dm3 using TopHat and expression levels were quantitated using cufflinks. This work was funded as part of the modENCODE project by NHGRI.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: At least two biological replicates were performed for each protein studied. In addition, control experiments were performed in which cells were transfected with the same vector lacking an open reading frame.

first: Sara

last: Olson

first: Michael

last: Duff

first: Gemma

last: May

first: Bob

last: Obar

first: Spyros

last: Artavanis-Tsakonas

first: Susan

last: Celniker


title: A unifying model for mTORC1-mediated regulation of mRNA translation

status: Public on May 03 2012

city: Cambridge

first: Carson

last: Thoreen

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Ribsome profiling analysis of mRNA translation in mouse cells under conditions of mTOR activiation or inhibition.

overall_design: embryonic fibroblasts from 4EBP1/2 p53 mutants treated with Torin1

first: Lynne

last: Chantranupong

first: Heather

last: Keys

first: Tim

last: Wang

first: Nathanael

middle: S

last: Gray

first: David

last: Sabatini


title: RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.

status: Public on May 04 2012

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

institute: Stanford

summary: We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. Second, we discovered thousands of novel splice junctions, the majority of which modify existing gene structures. Third, we curated a confident set of 6686 non-coding transcripts in 3859 genomic loci. Many of these non-coding RNAs are also developmentally regulated, which suggests that they may play important roles during embryogenesis. Finally, we found hundreds of contigs that cannot be aligned to the reference genome, which indicates that the current genome (XenTro3) is still unfinished. Our results will aid in the full assembly and annotation of the Xenopus tropicalis genome.

overall_design: Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole

first: Meng

last: Tan

first: Kin

middle: F

first: Arielle

last: Yablonovitch

first: Andrea

last: Wills

first: Julie

last: Baker

first: Wing

last: Wong

first: Jin

middle: B


title: Mutant p53 cooperates with ETS2 to promote etoposide resistance

city: Jackson

first: Luis

middle: A

last: Martinez

state: MS

address: 1500 North State St

department: Biochemistry

institute: University of Mississippi Medical Center

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Identification of Transcription Factor LIN15B::GFP Binding Regions in L4

first: DCC

last: modENCODE

summary:
modENCODE_submission_3078
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene lin-15B; Strain OP184(official name : OP184 genotype : unc119(ed3);wgIs184(lin-15B::TY1 EGFP FLAG;unc119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The LIN-15B::EGFP fusion protein is expressed in the correct lin-15B spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-15B transcription factor. made_by : S Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster

city: heidelberg

first: michael

middle: thomas

last: bocker

address: Im Neuenheimer Feld

country: Germany

institute: DKFZ Heidelberg

type: Methylation profiling by genome tiling array

first: Michael

middle: T

last: Bocker

first: Francesca

last: Tuorto

first: Günter

last: Raddatz

first: Tanja

last: Musch

first: Feng-Chun

last: Yang

first: Mingjiang

last: Xu

first: Frank

last: Lyko

first: Achim

last: Breiling


title: Co-dependency of H2B monoubiquitination and nucleosome re-assembly on Chd1

status: Public on May 02 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Monoubiquitination of histone H2B on lysine 123  (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively.  Many of the factors such as Rad6/Bre1, the Paf1 complex, and the Bur1/Bur2 complex were identified to be required for proper histone H3K4 and H3K79 trimethylation, and were shown to function by regulating H2BK123ub levels.  Here, we have identified Chd1 as a factor that is required for proper maintenance of H2B monoubiquitination levels, but not for H3K4 and H3K79 trimethylation.  Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation.   Our data shows that nucleosomal occupancy is reduced in gene bodies in both CHD1 null and K123A backgrounds. We have also demonstrated that Chd1’s function in maintaining H2BK123ub levels is conserved from yeast to human. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo, and points to a role for Chd1 in positively regulating gene expression through promoting nucleosome re-assembly coupled with H2B monoubiquitination.

overall_design:
Examination of two histone modifications in wild-type and Chd1 null yeast strains using ChIP-seq.
Expression profiling in wild-type and Chd1 null yeast strains using RNA-seq.

last: Garrett

first: Jung-shin

last: Lee

first: Ali

last: Shilatifard


title: The SEC family of RNA Polymerase II elongation factors: gene target specificity and transcriptional output

summary: The elongation stage of transcription is a highly regulated in metazoan. We previously purified the AFF1/AFF4-containing Super Elongation Complex (SEC) as a major regulator of development and cancer pathogenesis. Here, we report the biochemical isolation of SEC-like 2 (SEC-L2) and SEC-like 3 (SEC-L3) containing AFF2 and AFF3 in association with P-TEFb, ENL, and AF9. The SEC family members demonstrate high levels of Pol II CTD kinase activity, however, only SEC is required for the proper induction of the HSP70 gene upon stress. Genome-wide mRNA-seq analyses demonstrate that SEC-L2-3 control the expression of different subsets of genes, while AFF4/SEC plays a more dominant role in rapid gene expression in cells. MYC is one of the direct targets of AFF4/SEC, and the SEC requirement to the MYC gene regulates its expression in different cancer cells bearing either acute myeloid or lymphoid leukemia. These findings suggest that AFF4/SEC could be a potential therapeutic target for the treatment of leukemia or other cancers associated with MYC overexpression.

overall_design: RNA-seq in human embyonic kidney 293T cells of wild-type and after RNAi of AFF2, AFF3, AFF4.  ChIP-seq of AFF4 and Pol2 in human 293T cells.

first: Zhoujuan

last: Luo


title: MORC family ATPases required for heterochromatin condensation and gene silencing

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

institute: UCLA

summary: Transposable elements (TEs) and DNA repeats are commonly targeted by DNA and histone methylation to achieve epigenetic gene silencing.  We isolated mutations in two Arabidopsis genes, CRT1 and CRH6, which cause de-repression of DNA-methylated genes and TEs, but no losses of DNA or histone methylation.  CRT1 and CRH6 are members of the conserved Microrchidia (MORC) ATPase family, predicted to catalyze alterations in chromosome superstructure.  The crt1 and crh6 mutants show decondensation of pericentromeric heterochromatin, increased interaction of pericentromeric regions with the rest of the genome, and transcriptional defects that are largely restricted to loci residing in pericentromeric regions.  Knockdown of the single MORC homolog in Caenorhabditis elegans also impairs transgene silencing.  We propose that the MORC ATPases are conserved regulators of gene silencing in eukaryotes.

overall_design: For Col wild type control and each of two T-DNA mutants, a single sample each of small RNA (sRNA), mRNA-Seq, 5'-methylcytosine DNA methylation (BS-Seq), ChIP H3K9me2 histone methylation, and ChIP H3 histone control.  For each of two EMS mutants, and as controls, their respective backgrounds, two batches of single mRNA samples, with the first batch also having a single mRNA sample for a double EMS mutant. For a wild type control and crh6 mutant strain, Hi-C was performed to characterize genome organization.

first: Guillaume

last: Moissiard

first: Joshua

last: Cary

first: Suhua

last: Feng

first: Allison

last: Billi

first: Hume

last: Stroud

first: Dylan

last: Husmann

first: Ye

last: Zhan

first: Bryan

middle: R

last: Lajoie

first: Rachel

last: McCord

first: Christopher

last: Hale

first: Wei

first: Scott

middle: D

last: Michaels

first: Alison

last: Frand

first: Matteo

last: Pellegrini

first: Job

last: Dekker

first: John

middle: K

last: Kim

first: Steve

last: Jacobsen


title: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (MeDIP-Seq)

first: michael

last: bocker

summary: Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we used the mammalian Hoxa cluster of developmental genes as a model system to follow changes in DNA modification patterns during retinoic acid induced differentiation. We found the inactive cluster to be marked by defined patterns of 5-methylcytosine (5mC). Upon the induction of differentiation, the active anterior part of the cluster became increasingly enriched in 5-hydroxymethylcytosine (5hmC), following closely the colinear activation pattern of the gene array, which was paralleled by the reduction of 5mC. Depletion of the 5hmC generating dioxygenase Tet2 impaired the maintenance of Hoxa activity and partially restored 5mC levels. Our results indicate that gene specific 5mC-5hmC conversion by Tet2 is crucial for the maintenance of active chromatin states at lineage-specific loci.

overall_design: Examination of 5-methylcytosine (MeDIP-seq) and 5-hydroxymethylcytosine (hMeDIP-seq) at the HOXA cluster in 2 different developmental stages of a pluripotent cancer cell line.

first: Michael

last: Bocker

first: Francesca

last: Tuorto

first: Günter

last: Raddatz

first: Tanja

last: Musch

first: Feng-Chun

last: Yang

first: Mingjiang

last: Xu

first: Frank

last: Lyko

first: Achim

last: Breiling


title: MiR-27a-3p in peripheral blood mononuclear cells as a potential marker for pancreatic cancer screening

city: Shanghai

first: xiaolin

last: wang

address: 180 Feng Lin Rd

institute: Zhongshan Hospital, Fudan University

summary: Background & Aims: MicroRNAs have been shown to offer great potential in the diagnosis of cancer. We aimed to identify microRNAs in peripheral blood mononuclear cells (PBMCs) for diagnosing pancreatic cancer (PC). Methods: PBMCs microRNA expression was investigated in three independent cohorts including 352 participants (healthy, benign pancreatic/peripancreatic diseases (BPD), and PC). First, we used sequencing technology to identify differentially expressed microRNAs in 60 PBMCs samples for diagnosing PC. Quantitative reverse-transcriptase polymerase chain reaction assay was then applied to evaluate the expression of selected microRNAs. A logistic regression model was constructed using an independent cohort. Area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. Results: We found that PBMCs miR-27a-3p could efficiently discriminate PC from BPD (AUC=0.840; 95% CI, 0.787 to 0.885; sensitivity=82.2%, specificity=76.7%). A panel composed of PBMCs miR-27a-3p and serum CA19-9 provided a high diagnostic accuracy in differentiating PC from BPD in the clinical setting (AUC=0.886; 95% CI, 0.837 to 0.923; sensitivity=85.3%, specificity=81.6%). The satisfactory diagnostic performance of the panel persisted regardless of disease status (AUCs for tumour-node-metastasis stagesⅠ,Ⅱ, and Ⅲ were 0.881, 0.884, and 0.893, respectively).  Conclusion: PBMCs miR-27a-3p could be a potential marker for PC screening. A panel composed of PBMCs miR-27a-3p and serum CA19-9 has considerable clinical value in diagnosing early-stage PC. Therefore, patients who would have otherwise missed the curative treatment window can benefit from optimal therapy.

overall_design: Examination of different MicroRNA profiles in 3 types of PBMCs samples

first: Wansheng

last: Wang

first: Lingxiao

last: Liu

first: Guoping

last: Li

first: Yi

last: Chen

first: Changyu

first: Dayong

last: Jin

first: Xiaolin


title: Identification of Transcription Factor EOR-1::GFP Binding Regions in L3

first: DCC

last: modENCODE

summary:
modENCODE_submission_3155
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.  Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene eor-1; Strain OP81(official name : OP81 genotype : unc-119(ed3) III; wgIs81 [unc-119(+) eor-1::TY1::EGFP::3xFLAG] outcross : 0 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain.  The EOR-1::EGFP fusion protein is expressed in the correct eor-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EOR-1 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong

first: Mike

last: Snyder

first: Cindie

last: Slightam

first: Stuart

last: Kim

first: John

last: Murray

first: Robert

last: Waterston

first: Mark

last: Gerstein

first: Wei

last: Niu

first: Judi

last: Janette

first: Debasish

last: Raha

first: Ashish

last: Agarwal

first: Valerie

last: Reinke

first: Mihail

last: Sarov

first: Anthony

last: Hyman


title: Identification of intermediate-sized non-coding RNAs involved in the UV-induced DNA damage response in C. elegans

status: Public on May 01 2012

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR.

overall_design: Examination of intermediate-sized transcripts (70-500nt) in L4 larvae of C. elegans strains, including wild-type (N2), UV-irradiated (N2-UV100J/m2) and NER-deficient mutant (xpa-1) strains.

first: Aqian

last: Li

first: Yunfei

last: Wang


title: Expression profiling of Drosophila testes

first: Sidi

last: Chen

department: Biology

institute: MIT

summary: We performed mRNA-seq of dissected testes of multiple Drosophila species and RNAi animals

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

overall_design: mRNA seq of testis

first: Manyuan

last: Long

first: Kevin

last: White

first: Xiaochun

last: Ni

first: Ben

last: Krinsky

first: Yong

last: Zhang

first: Maria

last: Vibranovski

first: Nicholas

last: VanKuren


title: Mutant p53 cooperates with ETS2 to promote etoposide resistance [ChIP-Seq]

first: Luis

last: Martinez

summary: Mutant p53 (mtp53) promotes chemotherapy resistance through multiple mechanisms including disabling pro-apoptotic proteins and by regulating gene expression. Analysis of promoter regions identified through CHIP-on-CHIP and CHIP-SEQ platforms reveal that the ETS motif (EBS) is prevalent within predicted mtp53 binding sites. We demonstrate that mtp53 regulates gene expression through EBS in promoters, and that ETS2 mediates the interaction with this motif. Importantly, we identified TDP2, a 5’-tyrosyl DNA phosphodiesterase involved in the repair of DNA damage caused by etoposide, as a transcriptional target of mtp53. We demonstrate that suppression of TDP2 sensitizes mtp53 expressing cells to etoposide, and that mtp53 and TDP2 are frequently overexpressed in human lung cancer; thus, our analysis identifies a potentially “druggable” component of mtp53’s gain-of-function activity.

overall_design: Comparison of two different transcriptional binding analysis (ChIP-on-ChIP and ChIP-Seq) for the identification of novel mutant p53 binding.

first: Phi

middle: M

last: Do

first: Lakshman

last: Varanasi

first: Song

last: Fan

first: Chunyang

first: Lwona

last: Kubacka

first: Virginia

last: Newman

first: Krishna

last: Chauhan

first: Silvano

last: Daniels

first: Maurizio

last: Boccetta

first: Michael

last: Garrett

first: Runzhao


title: Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

city: Rehovot

first: Omri

last: Wurtzel

address: Hertzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes we identified 113 sRNAs and 70 asRNAs, significantly increasing the repertoire of non coding RNAs in this species.  Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5’ UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such lasRNA/operon structure, termed "excludon", might represent a novel form of regulation in bacteria.

sample_organism:
Listeria monocytogenes EGD-e
Listeria innocua Clip11262

overall_design: Construction of consensus TSS-maps in Listeria monocytogenes and Listeria innocua by applying 5'-end sequencing on samples in different conditions and genetic backgrounds.

first: Nina

last: Sesto

first: J

last: Mellin

first: Iris

last: Karunker

first: Sarit

last: Edelheit

first: Christophe

last: Becavin

first: Cristel

last: Archambaud

first: Pascale

last: Cossart

first: Rotem

last: Sorek


title: Identification of a novel set of DNA methylation markers in bladder cancer using MBD-methylCap/seq and urine DNA screening in a Chinese population

city: shanghai

first: jian

last: yu

address: LN 2200/25, Xietu Road

department: The State-key Laboratory for Oncogenes and Relatead Genes

institute: Shanghai Cancer Institute

summary: The aim of the present study was to identify novel DNA methylation markers in bladder cancer (BCa) through genome-wide profiling of bladder cancer cell lines and subsequent MSP screening in urine samples. Experimental Design: MBD methylCap/seq was carried out to screen differentially methylated CpG islands using two BCa cell lines (5637 and T24) and two normal bladder mucosa (BM) samples. The top one hundred most hypermethylated targets were screened using Methylation Specific PCR (MSP) in small and big cohort of urine samples from BCa patients and normal controls. The diagnostic performance of the gene panel was further evaluated in different clinical scenarios. Results: In total, 1,627 gene promoter regions hypermethylated in BCa cell line were identified in genomic level methylation profiling. The followed screening procedure in clinical urine sample generated eight genes (VAX1, KCNV1, ECEL1, TMEM26, TAL1, PROX1, SLC6A20, and LMX1A) capable of differentiating BCa from normal control. Subsequent validation in a large sample size enabled the optimisation of 5 methylation targets (VAX1, KCNV1, TAL1, PPOX1 and CFTR) for BCa diagnosis with sensitivity and specificity of 86.32% and 87.13%, respectively. In addition, VAX1 and LMX1A methylation could predict the tumour recurrence. Conclusions: Tumor specific biomarkers of BCa could be established by first performing genome level methylation profiling with cell lines and then screening the potential targets in urine samples. The panel of methylated genes identified was promising for the early non-invasive detection and surveillance of BCa.

overall_design: MBD methylCap/seq was carried out to screen differentially methylated CpG islands using two BCa cell lines (5637 and T24), and two normal bladder tissue mix as control.

first: Jian

last: Yu

first: Yang-Xing

last: Zhao

first: Shi-Cheng

last: Guo


title: Replication Timing by Repli-seq from ENCODE/University of Washington

status: Public on Apr 27 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu).

This track is produced as part of the ENCODE Project. This track shows genome-wide assessment of DNA replication timing in cell lines using the sequencing-based "Repli-seq" methodology (see below). Replication timing is known to be an important feature for epigenetic control of gene expression that usually operates at a higher-order level than at the level of specific genes. For each experiment (cell line, replicate), replication timing was ascertained by the isolation and sequencing of newly replicated DNA from six cell cycle fractions: G1/G1b, S1, S2, S3, S4, G2 (six fraction profile). Replication patterns are visualized as a continuous function based on sequencing tag density (Percentage-normalized Signal) and as a wavelet-smoothed transform of the six fraction profile (Wavelet-smoothed Signal). Replication peaks corresponding to replication initiation zones (Peaks) and valleys corresponding to replication termination zones (Valleys) were determined from local maxima and minima, respectively, in the wavelet-smoothed signal data. A measure of relative copy number at each genomic location (Summed Densities) was determined by summing the normalized tag density values of each cell cycle fraction at that location (equals one replicated genome equivalent).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
Cells were grown according to the approved ENCODE cell culture protocols. Repli-seq was performed as described by Hansen et al. (2010). Briefly, newly replicated DNA was labeled in vivo with a pulse of 5-bromo-2-deoxyuridine (BrdU), cells were fractionated into six different parts of the cell cycle by flow cytometry according to DNA content, cell cycle fractionated DNA was sonicated and an anti-BrdU monoclonal antibody was used to isolate the newly replicating DNA. Fragment ends were sequenced using the Illumina Genome Analyzer II or HiSeq platforms (36 bp reads). Some experiments (BJ, K562, BG02ES, GM06990) were originally performed and mapped to an earlier version of the human reference genome NCBI36/hg18 (Hansen et al., 2010) and were remapped to the more recent reference genome GRCh37/hg19.

Uniquely mapping high-quality reads were mapped to the genome minus the Y chromosome. Replication signals within each six cell cycle fraction were derived from the density of sequence tags mapping within a 50 kb sliding window (stepped 1 kb across the genome); these densities were normalized to 4 million tags per genome. To avoid variation due to copy number or sequence bias, cell cycle-specific replication signals at each location were determined as a percentage of the sum of the six normalized tag density signals (Percentage-normalized Signal).

To transform the six fraction replication signals into one track (Wavelet-smoothed Signal), the percentage-normalized signals at each location were used to calculate a weighted average value based on the average DNA content of each fraction according to flow cytometry [higher values correspond to earlier replication; formula=(0.917*G1b)+(0.750*S1)+(0.583*S2)+(0.417*S3)+(0.250*S4)+(0*G2)]. These weighted average data were smoothed by wavelet transformation [J7 level, corresponding to a scale of 128 kb; see Thurman et al. (2007)].

Replication initiation zones were flagged by determining local maxima in the wavelet-smoothed data (Peaks) and, similarly, replication termination zones were flagged by local minima (Valleys).

The sum of the 4 million normalized replication tag densities correspond to replication of one genome and can, therefore, be used as a measure of relative genomic copy number (Summed Densities). This is useful for evaluation of unusual replication patterns, such as "biphasic" ones where replication has both early and late components [as described by Hansen et al. (2010)].

first: Richard

last: Sandstrom