title: Snyder_NHR-10_GFP_L4

summary:
modENCODE_submission_4799
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: OP239(official name : OP239 genotype : unc119(ed3);wgIs239(nhr-10::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-10::EGFP fusion protein is expressed in the correct nhr-10 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-10 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs239(nhr-10::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene nhr-10; Strain OP239(official name : OP239 genotype : unc119(ed3);wgIs239(nhr-10::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-10::EGFP fusion protein is expressed in the correct nhr-10 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-10 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_LIN-13_GFP_L1

status: Public on May 11 2013

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

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
modENCODE_submission_4793
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: OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); Developmental Stage: L1 26dC; Genotype: unc119(ed3);wgIs49(lin-13::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L1 26dC; Target gene lin-13; Strain OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); 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: Snyder_LIN-13_GFP_L2

summary:
modENCODE_submission_4794
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: OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs49(lin-13::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene lin-13; Strain OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_NHR-12_GFP_EMB

summary:
modENCODE_submission_4792
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: OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None 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 spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: embryo; Genotype: unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)); Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene nhr-12; Strain OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None 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 spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius


title: Snyder_NHR-21_GFP_L2

summary:
modENCODE_submission_4797
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: OP361(official name : OP361 genotype : unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;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-21::EGFP fusion protein is expressed in the correct nhr-21 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-21 transcription factor. made_by : Unknown ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-21; Strain OP361(official name : OP361 genotype : unc119(ed3);wgIs361(nhr-21::TY1-GFP-3xFLAG;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-21::EGFP fusion protein is expressed in the correct nhr-21 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-21 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Snyder_ZTF-4_GFP_L2

summary:
modENCODE_submission_4796
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: OP322(official name : OP322 genotype : unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)) outcross : 0 mutagen : None 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 spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene ztf-4; Strain OP322(official name : OP322 genotype : unc-119(ed3); wgIs322(ztf-4::TY1 EGFP FLAG; unc119(+)) outcross : 0 mutagen : None 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 spatio-temporal expression pattern of ZTF-4::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-4 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius


title: Snyder_LIN-13_GFP_L4

summary:
modENCODE_submission_4795
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: OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs49(lin-13::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene lin-13; Strain OP49(official name : OP49 genotype : unc119(ed3);wgIs49(lin-13::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-13::EGFP fusion protein is expressed in the correct lin-13 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the LIN-13 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: Whole-transcriptome analysis identifies re-expression of fetal splice variants in cardiac hypertrophy

status: Public on May 14 2013

city: Charlottesville

first: Elizabeth

last: Ames

state: VA

address: Box 800759, Health System

department: Biomedical Engineering

country: USA

institute: University of Virginia

type: Expression profiling by high throughput sequencing

summary: Cardiac hypertrophy has been well-characterized at the level of transcription. During cardiac hypertrophy, genes normally expressed primarily during fetal heart development are re-expressed, and this fetal gene program is believed to be a critical component of the hypertrophic process. Recently, alternative splicing of mRNA transcripts has been shown to be temporally regulated during heart development, leading us to consider whether fetal patterns of splicing also reappear during hypertrophy.We hypothesized that patterns of alternative splicing occurring during heart development are recapitulated during cardiac hypertrophy. Here we present a whole-transcriptome study of isoform expression during pressure-overload cardiac hypertrophy induced by 10 days of transverse aortic constriction (TAC) in rats and in developing fetal rat hearts compared to sham-operated adult rat hearts, using high-throughput sequencing of poly(A) tail mRNA.

overall_design: Quantification of isoform expression in fetal rat hearts, pressure-overloaded rat hearts, and sham-operated rat hearts by Illumina GAIIx in triplicate

middle: G

first: Aaron

middle: J

last: Mackey

first: Jeffrey

middle: W

last: Holmes


title: Snyder_NHR-23_GFP_L2

first: DCC

last: modENCODE

summary:
modENCODE_submission_4634
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: OP43(official name : OP43 genotype : unc-119(ed3); wgIs43(nhr-23::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc-119(ed3); wgIs43(nhr-23::TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene nhr-23; Strain OP43(official name : OP43 genotype : unc-119(ed3); wgIs43(nhr-23::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 and Genetics in Dresden using Tony Hyman's recombineering pipeline.  The resulting plasmid was used for bombardment transformation of an unc-119(ed3) strain. The NHR-23::EGFP fusion protein is expressed in the correct nhr-23 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-223 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

first: Mei

last: Zhong


title: Snyder_NHR-12_GFP_L3

summary:
modENCODE_submission_4790
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: OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None 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 spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene nhr-12; Strain OP318(official name : OP318 genotype : unc-119(ed3); wgIs318(nhr-12::TY1 EGFP FLAG;unc-119(+)) outcross : 3 mutagen : None 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 spatio-temporal expression pattern of NHR-12::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-12 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

first: Mike

last: Snyder

first: Cindie

last: Slightam


title: Snyder_UNC-39_GFP_EMB

summary:
modENCODE_submission_4635
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: OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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 UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ); Developmental Stage: embryo; Genotype: unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119); Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene unc-39; Strain OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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 UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Stuart

last: Kim

first: John

last: Murray


title: Snyder_ELT-3_GFP_EMB

summary:
modENCODE_submission_4789
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: OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::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 ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ); Developmental Stage: embryo; Genotype: unc-119 (ed3) III; wgIs75 [elt-3::TY1::EGFP::FLAG; unc-119 (+)]; Sex: mixed Male and Hermaphrodite population;  EXPERIMENTAL FACTORS: Developmental Stage embryo; Target gene elt-3; Strain OP75(official name : OP75 genotype : unc-119 (ed3) III; wgIs75 [elt-3::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 ELT-3::EGFP fusion protein is expressed in the correct elt-3 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ELT-3 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius

first: Robert

last: Waterston

first: Mark

last: Gerstein


title: Snyder_SKN-1_GFP_L4

summary:
modENCODE_submission_4631
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: OP342(official name : OP342 genotype : unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene skn-1; Strain OP342(official name : OP342 genotype : unc119(ed3);wgIs341(skn-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius

first: Wei

last: Niu

first: Judi

last: Janette


title: Snyder_UNC-39_GFP_L2

summary:
modENCODE_submission_4637
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: OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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 UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene unc-39; Strain OP186(official name : OP186 genotype : unc119(ed3);wgIs186(unc39::TY1 EGFP FLAG C;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 UNC-39::EGFP fusion protein is expressed in the correct unc-39 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the UNC-39 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Debasish

last: Raha

first: Ashish

last: Agarwal


title: Snyder_JUN-1_GFP_L3

summary:
modENCODE_submission_4630
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: OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene jun-1; Strain OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius

first: Valerie

last: Reinke

first: Mihail

last: Sarov


title: Dynamic binding of RBPJ is determined by Notch signalling status

status: Public on May 13 2013

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

summary: Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription factor moiety of Notch (NICD) it regulates the expression of target genes. The prevalent view presumes that RBPJ statically occupies consensus binding sites while exchanging repressors for activators in response to NICD. We present the first specific RBPJ chromatin immunoprecipitation and high-throughput sequencing study in mammalian cells. To dissect the mode of transcriptional regulation by RBPJ and identify its direct targets, whole genome binding profiles were generated for RBPJ, its coactivator p300, NICD and the histone H3 modifications H3K4me3, H3K4me1 and H3K27ac in myogenic cells under active or inhibitory Notch signalling conditions. Our results demonstrate dynamic binding of RBPJ in response to Notch activation at essentially all sites co-occupied by NICD. Additionally, we identify a distinct set of sites where RBPJ recruits neither NICD nor p300, and binds DNA statically, irrespective of Notch activity. These findings significantly modify our views on how RBPJ and Notch signalling mediate their activities and consequently impact on cell fate decisions.

overall_design: ChIP (chromatin immunoprecipitation) is followed by deep sequencing to generate genome-wide patterns of RBP-J binding in mouse C2C12 cells under various conditions. Cells were either Notch activated by exposure to immobilized ligand or by overexpression of NICDGFP, or Notch inhibited by treatment with DAPT. Notch activation and inhibition treatments were applied for 6h and 24h. In addition to RBP-J, p300 and NICDGFP were profiled by ChIP-Seq and gene expression was assessed by RNA-Seq.

first: David

last: Castel

first: Philippos

last: Mourikis

first: Stefanie

last: Bartels

first: Arie

middle: B

first: Shahragim

last: Tajbakhsh

first: Hendrik

last: Stunnenberg


title: Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae

city: Newark

first: Vidhyavathi

last: Raman

state: DE

address: 531 S college Ave

department: Plant and Soil Sciences

institute: University of Delaware

type: Non-coding RNA profiling by high throughput sequencing

summary: The rice blast fungus, Magnaporthe oryzae is a destructive pathogen of rice and other related crops, causing significant yield losses worldwide. Endogenous small RNAs (sRNAs), including small interfering RNAs (siRNAs) and microRNAs (miRNAs) are critical components of gene regulation in many eukaryotic organisms. Recently several new species of sRNAs have been identified in fungi. This fact along with the availability of genome sequence makes M. oryzae a compelling target for sRNA profiling. We have examined sRNA species and their biosynthetic genes in M. oryzae, and the degree to which these elements regulate fungal stress responses. To this end, we have characterized sRNAs under different physiological stress conditions, which had not yet been examined in this fungus. The resulting libraries are composed of more than 37 million total genome matched reads mapping to intergenic regions, coding sequences, retrotransposons, inverted, tandem, and other repeated regions of the genome with more than half of the small RNAs arising from intergenic regions. The 24 nucleotide (nt) size class of sRNAs was predominant. A comparison to transcriptional data of M. oryzae undergoing the same physiological stresses indicates that sRNAs play a role in transcriptional regulation for a small subset of genes. Support for this idea comes from generation and characterization of mutants putatively involved in sRNAs biogenesis; our results indicate that the deletion of Dicer-like genes and an RNA-Dependent RNA Polymerase gene increases the transcriptional regulation of this subset of genes, including one involved in virulence. Various physiological stressors and in planta conditions alter the small RNA profile of the rice blast fungus. Characterization of sRNA biosynthetic mutants helps to clarify the role of sRNAs in transcriptional control.

sample_organism:
Oryza sativa
Pyricularia oryzae

platform_organism:
Oryza sativa
Pyricularia oryzae

overall_design: Examination of small RNA populations of eight mycelial as well as In planta tissues of M. oryzae strain 70-15. Mycelia grown in complete medium (CM), minimal medium (MM), carbon starved medium (CS: MM lacking carbon source), nitrogen starved medium (NS: MM lacking nitrogen source) and a reactive oxygen species-rich environment generated by amendment of Paraquat (PQ) to the CM. In planta tissues include mock inoculated rice leaves (LMg0), 72 hours post-inoculation in rice leaves (LMg72) and 96 hours post-inoculation in rice leaves (LMg96).

first: Stacey

middle: A

last: Simon

first: Amanda

last: Romag

first: Feray

last: Demirci

first: Sandra

middle: M

last: Mathioni

first: Jixian

last: Zhai

first: Blake

middle: C

last: Meyers

first: Nicole

last: Donofrio


title: Snyder_JUN-1_GFP_L1

first: DCC

last: modENCODE

summary:
modENCODE_submission_4629
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: OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); Developmental Stage: L1 26dC; Genotype: unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L1 26dC; Target gene jun-1; Strain OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); 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

first: Anthony

last: Hyman


title: Snyder_NHR-76_GFP_L4

summary:
modENCODE_submission_4628
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: OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::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 NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ); Developmental Stage: L4; Genotype: unc-119(ed3); wgIs203(nhr-76::TY1 EGFP FLAG; unc-119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene nhr-76; Strain OP203(official name : OP203 genotype : unc-119(ed3); wgIs203(nhr-76::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 NHR-76::EGFP fusion protein is expressed in the correct nhr-76 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NHR-76 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius

last: Reinke

first: Mihail

last: Sarov


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

summary:
modENCODE_submission_4625
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: OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs234(T24H10.7:TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene jun-1; Strain OP234(official name : OP234 genotype : unc119(ed3);wgIs234(T24H10.7: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 JUN-1::EGFP fusion protein is expressed in the correct jun-1 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the JUN-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: [E-MTAB-1505] GENCODE PCR-Seq Batch IX

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

summary:
Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (GENCODE PCR-Seq Batch IX)
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. In batch IX, a set of de novo transcript models was tested aiming to incorporate new long non-coding RNA models into the GENCODE annotation. The original set was built with Cufflinks from ENCODE RNAseq data derived from 15 cell lines by the Gingeras (CSHL) and Wold (CalTech) labs. A subset of multiexonic transcripts not overlapping the GENCODE v10 annotation was selected for this experiment.

ArrayExpress Release Date: 2012-10-01

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

Person Roles: investigator
Person Last Name: Guigo
Person First Name: Roderic
Person Mid Initials:
Person Email: roderic.guigo@crg.cat
Person Phone:
Person Address: Barcelona, Spain
Person Affiliation: Centre for Genomic Regulation (CRG)

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:
Experimental Design: organism_part_comparison_design
Experimental Design: reference_design
Experimental Design: co-expression_design
Experimental Factor Name: organism part
Experimental Factor Type: organism part


title: Snyder_ZTF-11_GFP_L3

summary:
modENCODE_submission_4626
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: OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-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 ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ); Developmental Stage: L3; Genotype: unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene ztf-11; Strain OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-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 ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: [E-MTAB-1226] GENCODE Batch VIII b: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing

summary:
Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII b)
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Centre for Genomic Regulation (CRG), Barcelona, Spain.

ArrayExpress Release Date:  2012-08-31

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

Person Roles: investigator
Person Last Name: Guigo
Person First Name: Roderic
Person Mid Initials:
Person Email: roderic.guigo@crg.cat
Person Phone:
Person Address: Barcelona, Spain
Person Affiliation: Centre for Genomic Regulation (CRG)

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


title: [E-MTAB-1309] GENCODE PCR-Seq Batch IX


title: [E-MTAB-1310] GENCODE PCR-Seq Batch X

summary:
Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues (GENCODE PCR-Seq Batch X)
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification of at least one of their unique splice junctions followed by sequencing. Batch X targets manually annotated transcripts from GENCODE v11 (released Feb 2012) with novel or putative status, non-pseudogene biotype and unique splice junctions not validated previously.

ArrayExpress Release Date: 2012-10-01

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

Person Roles: investigator
Person Last Name: Guigo
Person First Name: Roderic
Person Mid Initials:
Person Email: roderic.guigo@crg.cat
Person Phone:
Person Address: Barcelona, Spain
Person Affiliation: Centre for Genomic Regulation (CRG)

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


title: [E-MTAB-1222] GENCODE Batch VIII a: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing

summary:
Transcriptional profiling by high throughput sequencing of RACE-PCR-amplified human brain and testis samples to determine lncRNA transcript 5' and 3'-ends (GENCODE Batch VIII a)
As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Andalusian Human Genome Sequencing Centre (CASEGH), Seville, Spain.

ArrayExpress Release Date: 2012-08-31

Person Roles: submitter
Person Last Name: Gonzalez
Person First Name: Jose
Person Mid Initials: M
Person Email: jmg@sanger.ac.uk
Person Phone: -498006
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Hubbard
Person First Name: Tim
Person Mid Initials:
Person Email: th@sanger.ac.uk
Person Phone: -498055
Person Address: Wellcome Trust Genome Campus, Hinxton, UK
Person Affiliation: Wellcome Trust Sanger Institute

Person Roles: investigator
Person Last Name: Reymond
Person First Name: Alexandre
Person Mid Initials:
Person Email: Alexandre.Reymond@unil.ch
Person Phone:
Person Address: Lausanne, Switzerland
Person Affiliation: University of Lausanne

Person Roles: investigator
Person Last Name: Guigo
Person First Name: Roderic
Person Mid Initials:
Person Email: roderic.guigo@crg.cat
Person Phone:
Person Address: Barcelona, Spain
Person Affiliation: Centre for Genomic Regulation (CRG)

Person Roles: investigator
Person Last Name: Santoyo
Person First Name: Javier
Person Mid Initials:
Person Email: jsantoyo@bioinfomgp.org
Person Phone:
Person Address: Seville, Spain
Person Affiliation: Andalusian Human Genome Sequencing Centre (CASEGH)

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


title: The genetic framework of the Drosophila piRNA pathway

status: Public on May 10 2013

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: The animal piRNA pathway is a small RNA silencing system that acts in gonads and protects the genome against the deleterious influence of transposons. A major bottleneck in the field is the lack of comprehensive knowledge of the factors and molecular processes that constitute this pathway. We conducted an RNAi screen in Drosophila and identified ~50 genes that strongly impact the ovarian somatic piRNA pathway. Many identified genes fall into functional categories that indicate essential roles for mitochondrial metabolism, RNA export, the nuclear pore, transcription elongation and chromatin regulation in the pathway. Follow-up studies on two factors demonstrate the identification of components acting at distinct hierarchical levels of the pathway. Finally, we define CG2183/Gasz as a novel primary piRNA biogenesis factor in somatic and germline cells. Based on the similarities between insect and vertebrate piRNA pathways our results have far-reaching implications for the understanding of this conserved genome defense system.

overall_design: Steady-state RNA levels in wild-type ovarian somatic cells (OSC) and RNAi knock-downs of the piRNA pathway components.

first: Julius

last: Brennecke


title: Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: We report the application of FAIRE seq in Human Mammary Epithelial Cells for identifying the breast cancer risk functional SNPs in enhancer region.

overall_design: Examination of FAIRE assay in HMEC

first: Gerhard

last: Coetzee


title: Genome-wide Analysis of Functional Sirtuin Chromatin Targets in Yeast

first: Kunal

last: Poorey

address: 1340 Jefferson Park Avenue

department: Biomedical Sciences: Biochemistry, Molecular Biology & Genetics

institute: University of Virginia Health System

summary: Sir2 and the homologous proteins, Hst1, Hst2, Hst3, and Hst4 from Saccharomyces cerevisiae are NAD+-dependent histone deacetylases of the sirtuin protein family. Sir2 functions in transcriptional silencing at the silent mating-type loci, telomeres, and rDNA locus, but also promotes replicative lifespan. To gain a better understanding of the chromatin-regulatory roles carried out by Sir2 and the Hst proteins, we performed ChIP-sequencing analysis on all five sirtuins and Sum1, the DNA binding partner for Hst1. Sir2, Hst1, and Sum1 were abundantly, and functionally co-enriched at several major targets, including the telomeric repeats, where they were required for maintaining proper telomere repeat length. At tRNA target genes they were required for efficient cohesin and condensin deposition. Across the open reading frames of glycolytic and ribosomal protein genes, Sir2 and Hst1 functioned in NAD+-dependent transcriptional repression at the diauxic shift, directly linking Sir2 to glucose metabolism, which could have implications for longevity.

overall_design: Six factors and Input ChIP-seq samples were analyzed in Saccharomyces eerevisiae.

first: Mingguang

last: Li

first: Veena

last: Valsakumar

first: Stefan

last: Bekiranov

first: Jeffrey

middle: S

last: Smith


title: A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Nucleotide-resolution, genome-wide, 5'-end maps of the transcriptome of Propionibacterium acnes (cultured with and without potassium downshift)

city: Leeds

first: David

last: Romero A.

state: West Yorkshire

address: Woodhouse lane

institute: University of Leeds

summary: The differential RNA-seq data contained within this entry is complemented by global RNA-seq and microarray data, which is also deposited in GEO.

overall_design: Duplicate cultures of Propionibacterium acnes strain KPA171202 were grown exponentially in batch culture under anaerobic growth. Samples were taken following subculture with and without potassium downshift (i.e. removal from medium). This produced 4 samples; 2 replicates x 2 conditions.  Aliquots of each of the 4 samples were then incubated with or without incubation TAP (tobacco acid pyrophosphatase) before library construction.  Thus, 8 libraries were analysed.  TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.

first: Yu-fei

last: Lin

last: Romero

first: Kenneth

last: McDowall


title: A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila

status: Public on May 09 2013

city: Cold Spring Harbor

first: Felix

last: Muerdter

state: New York

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratories

summary: A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and novel components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. We identified and validated 87 genes necessary for transposon silencing. Among these were several novel piRNA biogenesis factors. We also found CG3893 (asterix) to be essential for transposon silencing, most likely by contributing to the effector step of transcriptional repression. Asterix loss leads to decreases in H3K9me3 marks on certain transposons but has no effect on piRNA levels.

overall_design: We sequenced small RNAs, RNA-seq and ChIP-seq from either tj-Gal4 driven hpRNA knockdown flies or P-element insertion flies

first: Paloma

last: Guzzardo

first: Jesse

last: Gillis

first: Yicheng

last: Luo

first: Yang

last: Yu

first: Caifu

last: Chen

first: Richard

last: Fekete

first: Gregory

last: Hannon


title: Snyder_ELT-1_GFP_L2

first: DCC

last: modENCODE

summary:
modENCODE_submission_4632
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: OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); Developmental Stage: L2; Genotype: unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene elt-1; Strain OP354(official name : OP354 genotype : unc119(ed3);wgIs354(elt-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None 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 bombardment transformation of an unc-119(ed3) strain. made_by : Bob Waterston's lab from UW ); 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: Snyder_ZTF-11_GFP_L4

summary:
modENCODE_submission_4627
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: OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-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 ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ); Developmental Stage: L4; Genotype: unc119(ed3);wgIs236(elk-2::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite;  EXPERIMENTAL FACTORS: Developmental Stage L4; Target gene ztf-11; Strain OP236(official name : OP236 genotype : unc119(ed3);wgIs236(elk-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 ZTF-11::EGFP fusion protein is expressed in the correct ztf-11 spatio-temporal expression pattern.  This strain was used for ChIP-seq experiments to map the in vivo binding sites for the ZTF-11 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius


title: AID stabilizes a stem cell phenotype by removing epigenetic memory of secondary pluripotency network genes

status: Public on May 08 2013

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: The activation-induced cytidine deaminase enzyme (AID) is required in germinal center (GC) B cells for somatic hyper-mutation and class switch recombination at the immunoglobulin locus. In GC-B cells, AID is highly expressed, with inherent mutator activity that helps generate antibody diversity. However, AID may also regulate gene expression epigenetically, irrespective of mutator activity, by directly deaminating 5-methylcytosine (5mC) in concert with base excision repair glycosylases to exchange unmethylated cytosine. This pathway promotes gene demethylation, thereby removing epigenetic memory. For example, AID promotes active demethylation of the genome in primordial germ cells. However, the range and mechanism by which AID promotes pluripotency is not known. Different studies have suggested either a requirement or a lack of function for promoting pluripotency in somatic nuclei following fusion with embryonic stem cells (ESC). Here we tested directly whether AID regulates epigenetic memory, by comparing the relative ability of cells lacking AID to reprogram from a differentiated cell type to an induced pluripotent stem cell (iPSC). We show that loss of AID impacts two distinct steps of reprogramming: First, AID-null cells are transiently hyper-responsive to the reprogramming process. Second, although they initiate expression of pluripotency genes, they fail to stabilize the pluripotent state. The genome of AID-null cells remains hypermethylated in reprogramming cells, and hypermethylated genes associated with pluripotency fail to be stably up-regulated. MYC target genes are highly enriched in the set of genes hypermethylated and under-expressed in reprogramming cells lacking AID. Recent studies identified a distinctive late step of reprogramming associated with methylation status. AID appears to regulate this step to stabilize the pluripotent state, removing epigenetic memory to promote expression of secondary pluripotency network genes.

overall_design: Transcriptome sequencing of AID-null tail fibroblasts, wildtype tail fibroblasts, AID-null and wildtype tail fibroblasts reprogrammed for three weeks by ectopic expression of  transcription factors Oct4, Sox2, KLf4 and cMyc. Methylation profiling by reduced representation bisulphite seuencing of AID-null tail fibroblasts, wildtype tail fibroblasts, AID-null and wildtype tail fibroblasts reprogrammed for three weeks and AID-null and wildtype clones after three weeks of reprogramming (Picked at two weeks)

first: Ritu

last: Kumar

first: Jayanta

last: Choudhuri

first: Todd

last: Evans


title: GRO-seq of Drosophila embryos at 2-2.5 hours and 3-3.5 hours after egg laying (AEL)

status: Public on May 28 2013

city: Manchester

first: Abbie

last: Saunders

address: D.1401 Michael Smith Building, Oxford Road

department: Faculty of Life Sciences

institute: University of Manchester

summary: The transition in developmental control from maternal to zygotic gene products marks a critical step in early embryogenesis. Here, we use GRO-seq analysis to map the genome-wide RNA polymerase distribution during the Drosophila maternal to zygotic transition. This analysis unambiguously identifies the zygotic transcriptome, and provides insight into its mechanisms of regulation.

overall_design: Two replicates of GRO-seq at each time point.

first: Hilary

middle: L

last: Ashe

first: Leighton

last: Core

middle: T

last: Lis


title: Multiple roles for Grainyhead-like transcription factors in the establishment and maintenance of human mucociliary airway epithelium (ChIP-Seq)

status: Public on May 07 2013

city: Durham

first: Timothy

middle: E

last: Reddy

state: NC

address: 2347 CIEMAS, 101 Science Drive

department: Department of Biostatistics & Bioinformatics

institute: Duke University

summary: The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated p63+ Krt5+ basal cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in co-ordinating the expression of numerous proteins required for epithelial morphogenesis, differentiation, remodeling and repair. However, little is known about their function in the adult lung. Here, we focus on the role of GRHL2 in primary human bronchial epithelial (HBE) cells, using either shRNA or a dominant negative protein (DN-GRHL2) to inhibit its function. We follow changes in epithelial phenotype, and in gene transcription using RNA-seq or microarray analysis, both in undifferentiated basal cells and in cells differentiating in air-liquid interface culture into a mucociliary epithelium with transepithelial electrical resistance. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2. Using ChIP-seq to map sites of GRHL2 binding in the basal cells we identify 7,687 potential primary targets, and confirm that GRHL2 binding is strongly enriched near GRHL-regulated genes. Different subsets of the large cohort of potential GRHL2 targets appear to be active in basal and differentiated cells. Taken together, the results strongly support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell adhesion, polarity and morphogenesis.

overall_design: Frozen primary human bronchial epithelial (HBE) cells were obtained from three donors and grown to confluence in standard culture conditions. Cells were crosslinked with formaldehyde and collected in aliquots of ~20M cells per donor. ChIP-seq for GRHL2 (Antibody: Sigma HPA004820) was then performed relative to an input control for each donor.

first: Xia

last: Gao

first: Christopher

last: Vockley

first: Florencia

last: Pauli

first: Kimberly

last: Newberry

first: Yan

last: Xue

first: Scott

middle: H

last: Randell

first: Brigid

last: Hogan


title: Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

city: Basel

first: Andreas

middle: R

last: Gruber

address: Klingelbergstrasse 50-70

department: Biozentrum

country: Switzerland

institute: University of Basel

summary:
Background: In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequenced long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins.
Results: Analysis of these data sets revealed that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently catalogued. We further found that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs revealed that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein.
Conclusions: We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.

overall_design: PAR-CLIP profiling for snoRNP core proteins NOP56, NOP58, Fibrillarin, and Dyskerin in HEK293 cells. Small RNA profiling using RNA-seq in HEK293 and HeLa cells, small RNA profiling using IP-seq of Ago2 associated small RNAs.

first: Shivendra

last: Kishore

first: Dominik

last: Jedlinski

first: Hadi

last: Jorjani

first: Afzal

middle: P

last: Syed

first: Mihaela

last: Zavolan


title: Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERα binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERα binding sites. The raw data used in this study is from GSE27463 but sequenced to a greater depth.

overall_design: Using GRO-seq over a time course (0, 10, 40 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.


title: A Snapshot of the Hepatic Transcriptome: Ad Libitum Alcohol Intake Suppresses Expression of Cholesterol Synthesis Genes in Alcohol-Preferring (P) Rats

city: West Lafayette

first: Amy

last: Lossie

state: IN

address: 125 S. Russell St.

institute: Purdue University

summary:
Introduction: Though heavy alcohol drinking has been well characterized as causing a variety of injuries, recent epidemiological evidence in humans suggests moderate consumption may provide beneficial effects. For example, there exists a J- or U-shaped relationship between the level of alcohol intake and cardiovascular disease risk. We investigated the underlying mechanisms of these positive consequences by identifying which genes are responsive to moderate alcohol intake in the liver, the primary site for alcohol metabolism.
Methods: Twelve female, inbred, alcohol-preferring (iP10a) rats were split equally between chronic water exposure and voluntary chronic ethanol exposure. Hepatic cholesterol and triglyceride levels were analyzed both histologically and biochemically. Hepatic transcriptomes were paired-end sequenced on the Illumina HiScanSQ system. Reads were analyzed and mapped using CLCbio Genomics Workbench 4.9. We confirmed altered expression of a subset of genes using TaqMan-based qRT-PCR. To quantify DNA methylation, we first digested DNA with methylation sensitive restriction enzymes and then performed qPCR using TaqMan assays surrounding the digest sites. Calculating ΔCt between a mock digest and digest determines the percent methylation in that locus.
Results: Voluntary alcohol consumption in iP10a rats modeled moderate consumption in humans. These levels did not result in intrahepatic fat accumulation. Sequencing produced ~1.2 Gb of sequence per sample, and 65% of reads mapped uniquely. Using a FDR corrected p value of 0.05 we found 250 altered transcripts. Ontology analysis of genes with a fold change ≥1.3 identified many cholesterol synthesis genes and cytoskeleton subunit genes, all of which were down-regulated. Of the 28 genes reanalyzed by qRT-PCR, altered expression was confirmed in 24 genes including the majority of the cholesterol synthesis and cytoskeleton subunit genes. Lastly, we profiled methylation throughout the promoter and gene body of four genes elicited in the RNA-Seq experiment. We found that alcohol caused demethylation at all loci; however this loss happened in a site-specific, tightly regulated manner.
Conclusion: Voluntary consumption in the iP10a animals models moderate consumption in humans, does not produce intrahepatic fat accumulation, and causes down-regulation of a majority of cholesterol synthesis genes. Moderate alcohol also results in a tightly-regulated demethylation effect. Our results explain, at least in part, the J- or U-shaped relationship between level of alcohol intake and cardiovascular disease risk.

overall_design: We sequenced 12 female iP10a rat hepatic transcriptomes providing 6 biological replicates for water control and 6 for ethanol treatment.

first: Jonathon

middle: D

last: Klein


title: Multiple roles for Grainyheadlike transcription factors in the establishment and maintenance of human mucociliary airway epithelium

first: Timothy

last: Reddy

overall_design: Frozen primary human bronchial epithelial (HBE) cells were obtained from three donors. Passage 2 cells at 40% confluence were infected with H2B-GFP or DN-GRHL2 lentivirus and 1 mg/ml puromycin added 48 h later. At confluence, Doxycycline 0.5 mg/ml was added for 24 h. RNA-seq was performed on all six samples, as well as samples from two donors that were not infected.


title: Transcriptome sequencing of neonatal thymic epithelial cells.

city: Montreal

first: Charles

last: St-Pierre

state: Quebec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

institute: Montreal University

summary:
Purpose: In all vertebrates, the thymus is necessary and sufficient for production of classic adaptive T cells. The key components of the thymus are cortical and medullary thymic epithelial cells (cTECs and mTECs). Despite the capital role of TECs, our understanding of TEC biology is quite rudimentary. For instance, we ignore what might be the extent of divergence in the functional program of these two TECs populations. It also remains unclear why the number of TECs decreases rapidly with age, thereby leading to progressive thymic insufficiency.
Methods: Systems level understanding of cell function begins with gene expression profiling, and the transcriptome is currently the only '-ome' that can be reliably tackled in its entirety in freshly harvested primary cells. In order to gain novel insights into TEC biology, we therefore decided to analyse the whole transcriptome of cTECs, mTECs and skin epithelial cells. We elected to analyse gene expression using RNA-seq rather microarrays because RNA-seq has higher sensitivity and dynamic range coupled to lower technical variations.
Results: Our deep sequencing approach provides a unique perspective into the transcriptome of TECs. Consistent with their ability to express ectopic genes, we found that mTECs expressed more genes than other cell populations. Out of a total of 15,069 genes expressed in TECs, 25% were differentially expressed by at least 5-fold in cTECs vs. mTECs. Genes expressed at higher levels in cTECs than mTECs regulate numerous cell functions including cell differentiation, cell movement and microtubule dynamics. Almost all positive regulators of the cell cycle were overexpressed in skin ECs relative to TECs.
Conclusions: Our RNA-seq data provide novel insights into the transcriptional landscape of TECs, highlight substantial divergences in the transcriptome of TEC subsets and suggest that cell cycle progression is differentially regulated in TECS and skinECs. We believe that our work will therefore represent a valuable resource and will be of great interest to readers working in biological sciences, particularly in the areas of immunology and systems biology.

overall_design: The mRNA profiles of cTEC, mTEC (from 14 thymi of 7-days old C57BL/6 mice) and skinEC (from the trunk and dorsum of seven newborn mice) were generated by RNA-sequencing using Illumina HiSeq2000.

first: Sylvie

last: Brochu

first: Claude

last: Perreault


title: Identification of differentially expressed transcripts and pathways one week and six months following implant of left ventricular devices

status: Public on May 06 2013

city: Excelsior

first: Rod

middle: A.

last: Staggs

state: MN

address: 20040 Cottagewood Ave

institute: Minnesota Informatics

summary: A specific set of genes involved in regulating cellular immune response, antigen presentation, and T cell activation and survival were down-regulated 7 days after LVAD placement. 6 months following LVAD placement, the expression levels of these genes were significantly increased; yet importantly, remained significantly lower than age and sex-matched samples from healthy controls.

overall_design: Examination of the effect of LVAD implant on peripheral blood transcriptome.  Blood was drawn before LVAD placement, 7 days post implant, and 180 days post implant.  RNA sequencing was performaed on all samples.

first: Adam

last: Mitchell

first: Jennifer

last: Hall


title: Whole genome transcriptome analysis (RNAseq) identifies genes upregulated during ciliogenesis in Chlamydomonas reinhardtii

city: Saint Louis

first: Huawen

last: Lin

address: 4566 Scott Ave

department: Genetics

institute: Washington University in St Louis

summary: We used pH shock to deflagellate Chlamydomonas and collected samples before pH shock (pre), 3, 10, 30, and 60 min post-deflagellation to look at the genes that are upregulated as Chlamydomonas regrows its flagella.  We aligned our data to v5.3 of the Chlamydomonas genome and compared transcript levels post-deflagellation to the pre-deflagellation levels.  A gene was considered expressed if the FPKMM value was at least 3.  If transcript level increased 2.5 fold following deflagellation, we considered the gene to be upregulated.  If the transcript levels decreased 2.5 fold following deflagellation, we considered the gene to be downregulated.  In all, we found 10,815 genes to be expressed during our experiment.  There were 1875 genes upregulated following deflagellation, 4,392 genes downregulated, and 4,548 genes that did not alter their expression

overall_design: We analyzed mRNA from 5 samples before and after deflagellation.

first: Alison

last: Albee

first: Alan

last: Kwan

first: Susan

last: Dutcher


title: G-Quadruplex structures are stable and detectable in human genomic DNA.

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

summary: The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA.

overall_design: Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

first: Enid

middle: Y

last: Lam

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

city: La Jolla

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: RNAP II is frequently paused near gene promoters in mammals and its transition to productive elongation requires active recruitment of P-TEFb, a cyclin-dependent kinase for RNAP II and other key transcription elongation factors. A fraction of P-TEFb is sequestered in an inhibitory complex containing the 7SK noncoding RNA, but it has been unclear how P-TEFb is switched from the 7SK complex to RNAP II during transcription activation. We report that SRSF2 (also known as SC35, an SR splicing factor) is part of the 7SK complex assembled at gene promoters and plays a direct role in transcription pause release. We demonstrate RNA-dependent, coordinated release of SRSF2 and P-TEFb from the 7SK complex and transcription activation via SRSF2 binding to promoter-associated nascent RNA. These findings reveal an unanticipated SR protein function, a role for promoter-proximal nascent RNA in gene activation, and an analogous mechanism to HIV Tat/TAR for activating cellular genes.

overall_design: SR ChIP-seq, Pol II ChIP-seq, and Gro-seq

first: Xiong

last: Ji

first: Yu

last: Zhou

first: Shatakshi

last: Pandit

first: Jie

last: Huang

first: Hairi

last: Li

first: Rui

last: Xiao

first: Christopher

last: Burge


title: Genome-scale DNA methylation maps of mouse chromaffin cells with or without Sdhb knock-out.

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

country: France

institute: Ligue Contre Le Cancer

summary: We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype.

overall_design: Reduced representation bisulfite sequencing of 4 mouse chromaffin cell samples (2 Sdhb wild-type and 2 Sdhb knock-out).

first: Anne-Paule

last: Gimenez-Roqueplo

first: Judith

last: Favier


title: Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

summary: Several organisms belonging to diverse animal groups have retained Dnmt2 as their only bona fide DNA methyltransferase gene. However, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which prompted us to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Using whole-genome bisulfite sequencing we show here that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in a Dnmt2-deficient fly strain. Furthermore, genetically modified mouse embryonic stem cells that had retained Dnmt2 as their only bona fide DNA methyltransferase gene, did not show any detectable DNA methylation patterns. Our results thus uncover fundamental differences among animal methylomes and suggest that Dnmt2-only organisms lack biologically relevant DNA methylation patterns.

overall_design: Whole methylome analysis of Mus musculus. One sample was analyzed containing DNA from Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/- mice.

first: F

last: Lyko

first: W

last: Reik


title: Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Schistosoma mansoni]

summary: Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation.

overall_design: Whole genome methylation analysis of S. mansoni. One sample was analyzed, containing DNA from adult male worms.

first: M

last: Fantappie


title: Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

overall_design: Whole genome methylation analysis of D. melanogaster. Two samples were analyzed, one sample containing DNA from WT embryos, one sample containing DNA from Dnmt2-/- embryos.

first: G

last: Hannon


title: Saccharomyces cerevisiae Transcript Isoform mapping

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

summary: Extensive transcriptional heterogeneity revealed by isoform profiling

overall_design: Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5' capped mRNA transcription start site and the 3' polyadenylation site in different conditions: WT cells grown in glucose media [ypd, 2 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)], WT cells grown in galactose media [ypgal, 4 biological replicates (bio) and 3 independent library preparations, technical replicates(lib)]. A modified protocol designed to enrich in long mRNA molecules was performed for WT cells grown in glucose media [ypd, 2 biological replicates (bio)] and in galactose media [ypgal, 2 biological replicates (bio)] conditions. Finally, control samples performed with a modified protocol designed to identify non-capped but polyadenylated molecules was performed in WT cells grown both in glucose (nypd) and galactose (nypgal) media.

first: Vicent

last: Pelechano

first: Lars

last: Steinmetz