title: Chro(Chriz)BR.Clone_8 ChIP-chip

summary:
modENCODE_submission_276
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determe the locations of 125 chromosomal proteins and histone modifications across the Drosophila melanogaster genome. The proteins and modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+; Antibody Chro(Chriz)BR


title: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (64-cell stage)

status: Public on Mar 09 2010

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

country: Japan

institute: Kyoto University

type: Genome binding/occupancy profiling by genome tiling array

summary: A genomic overview of in vivo binding of a transcription factor FoxD-a/b in the ascidian 64-cell stage embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged FoxD-a/b. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.

first: Yutaka

last: Satou


title: Neurogenin ChIP-chip on Ciona intestinalis embryo (64-cell stage)

summary: A genomic overview of in vivo binding of a transcription factor Neurogenin in the ascidian 64-cell stage embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged Neurogenin. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: Otx ChIP-chip on Ciona intestinalis embryo (early gastrula)

summary: A genomic overview of in vivo binding of a transcription factor Otx in the ascidian early gastrula embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged Otx. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: FoxD-a/b ChIP-chip on Ciona intestinalis embryo (32-cell stage)

summary: A genomic overview of in vivo binding of a transcription factor FoxD-a/b in the ascidian 32-cell stage embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged FoxD-a/b. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis. Two independent experiments were performed to reduce experimental errors.


title: FoxA-a ChIP-chip on Ciona intestinalis embryo (64-cell stage)

summary: A genomic overview of in vivo binding of a transcription factor FoxA-a in the ascidian 64-cell stage embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged FoxA-a. After fixation, Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: Snail ChIP-chip on Ciona intestinalis embryo (early gastrula)

summary: A genomic overview of in vivo binding of a transcription factor Snail in the ascidian early gastrula embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged Snail. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula)

summary: A genomic overview of in vivo binding of a transcription factor SoxC in the ascidian early gastrula embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged SoxC. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: Illumina HapMap (Hap650Yv3)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina Inc.

summary: HapMap samples

overall_design: 120 samples from Hap650Yv3_Final_Report.txt


title: Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula)

summary: A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.

overall_design: Fertilized eggs were electroporated with a construct encoding GFP-tagged Tbx6b. After fixation, chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE (Whole Cell Extract) DNA were amplified by LM-PCR for the Chip analysis.  Two independent experiments were performed to reduce experimental errors.


title: FGF Receptor and Wnt-1 Signaling Cooperate in Mammary Tumorigenesis

status: Public on Mar 01 2010

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: The fibroblast growth factor pathway is known to cooperate with the highly oncogenic Wnt/beta-catenin pathway in mouse models of breast cancer.  To investigate the mechanisms involved in this cooperativity, we utilized MMTV-driven transgenic mouse lines expressing a drug-inducible model for FGF Receptor signaling (iFGFR) crossed with the previously characterized MMTV-Wnt-1 mouse model.  In these bigenic mice, both iFGFR1 and iFGFR2 activation resulted in a dramatic enhancement of mammary tumorigenesis.  Tumor microarray analysis identified no transcriptional enhancement of Wnt/beta-catenin targets, however, identified a protein translational gene signature that also correlated with elevated FGFR1 and FGFR2 expression in several human breast cancer data sets.  Additionally, iFGFR1 activation resulted in enhanced polysome recruitment and a marked increase in protein expression of several different Wnt/beta-catenin target oncogenes.  Rapid FGFR-induced ERK activation and phosphorylation of key translation regulators was observed both in vivo in the transgenic mouse model, and in human breast cancer cell lines treated with exogenous FGF.  These studies suggest that translational regulation is a key rate-limiting step required for oncogenic cooperativity between the Wnt and FGF pathways.

overall_design: reference X sample

first: Adam

middle: C

last: Pond

first: Jason

middle: I

last: Herschkowitz

middle: M


title: B. subtilis: temporal expression response to amino acid treatment

status: Public on Sep 09 2009

city: Shanghai

first: Hui

last: Yu

address: No.100, Rd. Qinzhou

country: China

institute: Shanghai Center for Bioinformation Technology

summary: Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pool. In this study, an Agilent customized microarray representing approximately 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses. Amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to pulses of valine, glutamate, and glutamine, respectively, and Val-, Glu and Gln-specific genes were further distinguished from them. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, hierarchical clustering and enrichment of functional categories. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Three amino acids (Glutamate, Glutamine, and Valine) were adopted to perturb the culture of subtilis. Four time-points were investigated for each perturbation. There are two replicates for the first time-point of Valine-treatment experiment.

first: Bang-Ce

last: Ye

first: Yan

last: Zhang


title: Dm_y[1]cn[1] bw[1] sp[1]_pupa_WhitePrePupaep3day_TotalRNA_p200_350-352-354_38bp

status: Public on Jun 02 2009

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: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary:
modENCODE_submission_542

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Pupae, WPP + 3 days

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Pupae, WPP + 3 days

first: Tom

last: Gingeras

first: Chris

last: Zaleski

first: Susan

last: Celniker


title: Dm_OregonR_embryo_2-4h_poly-Ap_p200_127-128-129_38bp

summary:
modENCODE_submission_513

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Oregon-R; Developmental Stage: Embryo 2-4h, OregonR

GENOTYPE: TBA

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 2-4h, OregonR


title: Dm_ML-DmBG2-c2_TotalRNA_p200_470-472-474_38bp

summary:
modENCODE_submission_337

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmBG2-c2

TISSUE: CNS-derived cell-line

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmBG2-c2


title: Chro(Chriz)BR.BG3 ChIP-chip

status: Public on Mar 12 2010

summary:
modENCODE_submission_275
This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We aim to determe the locations of 125 chromosomal proteins and histone modifications across the Drosophila melanogaster genome. The proteins and modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Keywords: CHIP-chip

overall_design: EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown;  NUMBER OF REPLICATES: 4;  EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2; Antibody Chro(Chriz)BR

first: Gary

last: Karpen

first: Sarah

last: Elgin

first: Andrey

last: Gortchakov

first: Greg

last: Shanower

first: Michael

last: Tolstorukov

first: Peter

last: Kharchenko

first: Mitzi

last: Kuroda

first: Vincenzo

last: Pirrotta

last: Park

first: Aki

last: Minoda

first: Nicole

last: Riddle

first: Yuri

last: Schwartz

first: Art

last: Alekseyenko

first: Cameron

last: Kennedy


title: Dm_y[1]cn[1] bw[1] sp[1]_pupa_WhitePrePupaep4day_TotalRNA_p200_356-358-360_38bp

first: DCC

last: modENCODE

summary:
modENCODE_submission_543

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Pupae, WPP + 4 days

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Pupae, WPP + 4 days

last: Gingeras


title: Dm_mbn2_TotalRNA_p200_044-046-048_38bp

summary:
modENCODE_submission_139

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: Mbn2

TISSUE: embryonic/larval hemocyte

GENOTYPE: l(2)malignant blood neoplasm

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line Mbn2

first: Tom

first: Aarron

last: Willingham

last: Celniker


title: Dm_y[1]cn[1] bw[1] sp[1]_pupa_WhitePrePupaep1day_TotalRNA_p200_338-340-342_38bp

summary:
modENCODE_submission_545

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: WPP + 24 hr

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage WPP + 24 hr

first: Chris

last: Zaleski

first: Susan


title: Dm_Kc167_nuclearRNA_p200_475-476-477_38bp

summary:
modENCODE_submission_267

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: Kc167

TISSUE: embryo-derived cell-line

GENOTYPE: se/e

SEX: Female

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line Kc167


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_4-6h_TotalRNA_p200_224-226-228_38bp

summary:
modENCODE_submission_120

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 4-6h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 4-6h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_2-4h_poly-Ap_p200_406-407-408_38bp

summary:
modENCODE_submission_119

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 2-4h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 2-4h


title: Dm_OregonR_embryo_14-16h_poly-Ap_p200_130-131-132_38bp

summary:
modENCODE_submission_514

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Oregon-R; Developmental Stage: Embryo 14-16h

GENOTYPE: TBA

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 14-16h


title: Dm_Kc167_polyApRNA_p200_145-146-147_38bp

summary:
modENCODE_submission_268

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: ChIP-chip analysis of the Ciona intestinalis embryo

first: Atsushi

last: Kubo

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

overall_design: Refer to individual Series


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_2-4h_TotalRNA_p200_218-220-222_38bp

summary:
modENCODE_submission_118

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_22-24h_TotalRNA_p200_278-280-282_38bp

summary:
modENCODE_submission_117

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 22-24hSC

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 22-24hSC


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_6-8h_poly-Ap_p200_412-413-414_38bp

summary:
modENCODE_submission_122

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 6-8h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 6-8h


title: Dm_CME_W2_TotalRNA_p200_460-462-464_38bp

summary:
modENCODE_submission_140

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: CME W2

TISSUE: dorsal mesothoracic disc

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line CME W2


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_20-22h_TotalRNA_p200_272-274-276_38bp

summary:
modENCODE_submission_116

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 20-22h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 2; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 20-22h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_20-22h_poly-Ap_p200_433-434-435_38bp

summary:
modENCODE_submission_115

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 20-22h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 20-22h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_18-20h_TotalRNA_p200_266-268-270_38bp

summary:
modENCODE_submission_113

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 18-20h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 18-20h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_18-20h_poly-Ap_p200_430-431-432_38bp

summary:
modENCODE_submission_114

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 18-20h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 2; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 18-20h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_14-16h_poly-Ap_p200_424-425-426_38bp

summary:
modENCODE_submission_110

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 14-16h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 2; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 14-16h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_16-18h_poly-Ap_p200_427-428-429_38bp

summary:
modENCODE_submission_112

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 16-18h

GENOTYPE: w[1] cn[1] bw[1] sp[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 16-18h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_16-18h_TotalRNA_p200_260-262-264_38bp

summary:
modENCODE_submission_111

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 16-18h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 16-18h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_14-16h_TotalRNA_p200_254-256-258_38bp

summary:
modENCODE_submission_109

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 14-16h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 14-16h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_12-14h_poly-Ap_p200_421-422-423_38bp

summary:
modENCODE_submission_108

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 12-14h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 12-14h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_12-14h_TotalRNA_p200_248-250-252_38bp

summary:
modENCODE_submission_107

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_10-12h_poly-Ap_p200_418-419-420_38bp

summary:
modENCODE_submission_106

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 10-12h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 10-12h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_10-12h_TotalRNA_p200_242-244-246_38bp

summary:
modENCODE_submission_105

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_8-10h_poly-Ap_p200_415-416-417_38bp

summary:
modENCODE_submission_104

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 8-10h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 8-10h


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_0-2h_poly-Ap_p200_403-404-405_38bp

summary:
modENCODE_submission_102

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Embryo 0-2h

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 0-2h


title: Dm_y[1]cn[1] bw[1] sp[1]_larval_L3_gut_stage1_TotalRNA_p200_440-442-444_38bp

summary:
modENCODE_submission_100

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L3 stage larvae, Dark Blue Gut

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage L3 stage larvae, Dark Blue Gut


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_0-2h_TotalRNA_p200_212-214-216_38bp

summary:
modENCODE_submission_101

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_8-10h_TotalRNA_p200_236-238-240_38bp

summary:
modENCODE_submission_103

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis


title: Dm_y[1]cn[1] bw[1] sp[1]_adult_Male_5dayPostEclosion_TotalRNA_p200_380-382-384_38bp

summary:
modENCODE_submission_99

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult male, eclosion + 5 days

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Adult male, eclosion + 5 days


title: Dm_y[1]cn[1] bw[1] sp[1]_adult_Female_1dayPostEclosion_TotalRNA_p200_374-376-378_38bp

summary:
modENCODE_submission_96

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Developmental Stage: Adult female, eclosion + 1 day

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Female

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Adult female, eclosion + 1 day


title: Dm_y[1]cn[1] bw[1] sp[1]_adult_Male_1dayPostEclosion_TotalRNA_p200_368-370-372_38bp

summary:
modENCODE_submission_98

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult male, eclosion + 1 day

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Adult male, eclosion + 1 day


title: Dm_y[1]cn[1] bw[1] sp[1]_larval_L2_TotalRNA_p200_290-292-294_38bp

summary:
modENCODE_submission_94

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L2 stage larvae

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage L2 stage larvae


title: Dm_y[1]cn[1] bw[1] sp[1]_prepupa_WhitePrePupae_TotalRNA_p200_326-328-330_38bp

summary:
modENCODE_submission_95

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: White prepupae (WPP)

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage White prepupae (WPP)


title: Dm_y[1]cn[1] bw[1] sp[1]_larval_L1_TotalRNA_p200_284-286-288_38bp

summary:
modENCODE_submission_93

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: L1 stage larvae

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage L1 stage larvae


title: Dm_y[1]cn[1] bw[1] sp[1]_adult_Female_5dayPostEclosion_TotalRNA_p200_386-388-390_38bp

summary:
modENCODE_submission_97

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Strain: Y cn bw sp; Developmental Stage: Adult female, eclosion + 5 days

GENOTYPE: y[1] oc[R3.2]; Gr22b[1] Gr22d[1] cn[1] CG33964[R4.2] bw[1] sp[1]; LysC[1] lab[R4.2] MstProx[1] GstD5[1] Rh6[1]

SEX: Female

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Adult female, eclosion + 5 days


title: Dm_S2-DRSC_TotalRNA_p200_014-016-018_38bp

summary:
modENCODE_submission_64

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: S2-DRSC

TISSUE: embryo-derived cell-line

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line S2-DRSC


title: Dm_Sg4_TotalRNA_p200_200-202-204_38bp

summary:
modENCODE_submission_67

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: Sg4

TISSUE: embryo-derived cell-line

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line Sg4


title: Dm_S2R+_TotalRNA_p200_020-022-024_38bp

summary:
modENCODE_submission_65

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: S2R+

TISSUE: embryo-derived cell-line

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line S2R+


title: Dm_y[1]cn[1] bw[1] sp[1]_embryo_6-8h_TotalRNA_p200_230-232-234_38bp

summary:
modENCODE_submission_92

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Developmental Stage: Embryo 6-8h

GENOTYPE: w[1] cn[1] bw[1] sp[1]

SEX: Unknown

NUMBER OF REPLICATES: 2; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Developmental Stage Embryo 6-8h


title: Dm_DmD8_TotalRNA_p200_206-208-210_38bp

summary:
modENCODE_submission_61

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD8

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD8


title: Dm_DmD32_TotalRNA_p200_164-166-168_38bp

summary:
modENCODE_submission_59

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD32

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD32


title: Dm_S3_TotalRNA_p200_104-106-108_38bp

summary:
modENCODE_submission_66

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: S3

TISSUE: embryo-derived cell-line

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line S3


title: Dm_DmD4-c1_TotalRNA_p200_140-142-144_38bp

summary:
modENCODE_submission_60

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD4-c1

TISSUE: imaginal disc-derived cell-line

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD4-c1


title: Dm_DmD20-c2_TotalRNA_p200_182-184-186_38bp

summary:
modENCODE_submission_56

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD20-c2

TISSUE: antenna disc-derived cell-line

GENOTYPE: y v f mal

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD20-c2


title: Dm_S1_TotalRNA_p200_026-028-030_38bp

summary:
modENCODE_submission_63

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: S1

TISSUE: embryo-derived cell-line

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line S1


title: Dm_DmD20-c5_TotalRNA_p200_188-190-192_38bp

summary:
modENCODE_submission_57

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD20-c5

TISSUE: antenna disc-derived cell-line

GENOTYPE: y v f mal

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD20-c5


title: Dm_DmD21_TotalRNA_p200_050-052-054_38bp

summary:
modENCODE_submission_58

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD21

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD21


title: Dm_DmD16-c3_TotalRNA_p200_138-136-138_38bp

summary:
modENCODE_submission_69

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD16-c3

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

SEX: Female

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD16-c3


title: Dm_ML-DmD11_TotalRNA_p200_170-172-174_38bp

summary:
modENCODE_submission_54

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD11

TISSUE: eye-antenna disc-derived cell-line

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD11


title: Dm_DmD17-c3_TotalRNA_p200_194-196-198_38bp

summary:
modENCODE_submission_55

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD17-c3

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD17-c3


title: Dm_ML-DmBG1-c2_TotalRNA_p200_116-118-120_38bp

summary:
modENCODE_submission_52

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmBG1-c1

TISSUE: CNS-derived cell-line

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmBG1-c1


title: Dm_Kc167_TotalRNA_p200_002-004-006_38bp

summary:
modENCODE_submission_51

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: Kc167

TISSUE: embryo-derived cell-line

GENOTYPE: se/e

SEX: Female

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line Kc167


title: Dm_DmD9_TotalRNA_p200_072-074-076_38bp

summary:
modENCODE_submission_62

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmD9

TISSUE: dorsal mesothoracic disc

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmD9


title: Genomewide analysis of Insulator protein binding sites in Drosophila embryos at E0-12

status: Public on May 29 2009

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary:
Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries.  A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation.  We studied by ChIP-chip the genome-wide binding sites of 6 insulator-associated proteins – dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4) and GAF – to obtain the first comprehensive map of insulator elements in Drosophila embryos. We identify over 14,000 putative insulators, including all previously known insulators.  We find two major classes of insulators defined by dCTCF/CP190/BEAF-32 and Su(Hw) respectively. Distributional analyses of insulators revealed that particular sub-classes of insulator elements are excluded between cis-regulatory elements and their target promoters, divide differentially expressed, alternative, and divergent promoters, act as chromatin boundaries, are associated with chromosomal breakpoints among species, and are embedded within active chromatin domains. Together, these results provide a map demarcating the boundaries of gene regulatory units, and a framework for understanding insulator function during the development and evolution of Drosophila.

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: ChIP-chip experiments were performed in Triplicate on Affymetrix arrays and compared to Input samples for the following datasets: E-0-12H: CTCF-C, CTCF-N, CP-190, BEAF-32, Su(Hw)-1, Su(Hw)-2, Mod(mdg4), GAF, H3K4me3, H3K27me3 and PolII. In addition ChIP experiments in S2 cells and Kc cells have been performed for H3K4me3 and CTCF. In addition, total RNA extracts have been performed in Embryos 0-12h and hybridized on Affymetrix Tiling arrays.

first: Nicolas

last: Negre

first: Christopher

middle: D

last: Brown

first: Carolyn

middle: A

last: Morrison

first: Parantu

middle: K

last: Shah

middle: P


title: Dm_1182-4H_TotalRNA_p200_038-040-042_38bp

summary:
modENCODE_submission_40

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: 1182-4H

TISSUE: embryo-derived cell-line

GENOTYPE: mh

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line 1182-4H


title: Dm_GM2_TotalRNA_p200_008-010-012_38bp

summary:
modENCODE_submission_50

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: GM2

TISSUE: embryo-derived cell-line

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line GM2


title: Dm_CME-L1_TotalRNA_p200_086-088-090_38bp

summary:
modENCODE_submission_48

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: CME-L1

TISSUE: ventral prothoracic disc

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line CME-L1


title: Dm_CME-W1-Cl.8p_TotalRNA_p200_060-062-064_38bp

summary:
modENCODE_submission_49

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+

TISSUE: dorsal mesothoracic disc

SEX: Male

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line CME-W1-Cl.8+


title: Dm_ML-DmBG3-c2_TotalRNA_p200_122-124-126_38bp

summary:
modENCODE_submission_53

This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648

Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs.

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

Keywords: Transcript tiling array analysis

overall_design:
EXPERIMENT TYPE: Transcript tiling array analysis

BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2

TISSUE: CNS-derived cell-line

GENOTYPE: y v f mal

SEX: Unknown

NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap.

EXPERIMENTAL FACTORS: Cell Line ML-DmBG3-c2


title: ChIP-chip of gsbnpurif in Drosophila embryos at E7-24h time point.

status: Public on May 13 2009

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Affymetrix Drosophila Tiling 2.0R arrays for multiple transcription factor antibodies at various time-points of Drosophila development.

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: For each combination of time-point and antibody, ChIP experiments have been performed and hybridized on Affymetrix Drosophila Tiling 2.0R arrays. At least 3 biological replicates for the ChIP sample have been hybridized.

first: Nick

last: Bild


title: ChIP-chip of brm in Drosophila embryos at pupae time point.

status: Public on May 12 2009


title: ChIP-chip of UBX2 in Drosophila embryos at E3-8h time point.


title: ChIP-chip of UBX7701 in Drosophila embryos at E3-8h time point.


title: ChIP-chip of end300 in Drosophila embryos at E7-24h time point.


title: ChIP-chip of UBX1 in Drosophila embryos at E3-8h time point.


title: ChIP-chip of GROAviva in Drosophila embryos at E0-12h time point.


title: ChIP-chip of TTK in Drosophila embryos at E0-12h time point.


title: ChIP-chip of snr1 in Drosohila embryos at Pupae time point.


title: ChIP-chip of Stat92E in Drosophila embryos at E0-12h time point.


title: ChIP-chip of RUN7659 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of KN in Drosophila embryos at E0-12h time point.


title: ChIP-chip of INVGFP in Drosophila embryos at E0-12h time point.


title: ChIP-chip of H3K9me3 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of UBX7701 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of INV7657 in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of H3K4me3 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of ZFH1 in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of H3K36me3 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of Gro3 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of dll in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of FTZ-F1 in Drosophila embryos at E0-12h time point.


title: ChIP-chip of ENserum in Drosophila embryos at E0-12h time point.


title: ChIP-chip of D in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of bks in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of chinmo in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of bab1 in Drosophila embryos at 0-12 hours of development


title: ChIP-chip of CNC in Drosophila embryos at E-0-12h time point.


title: ChIP-chip of dCtBP7667 in Drosophila embryos at E-0-12h time point.


title: ETV6-NTRK3 fusion oncogene initiates breast cancer from committed alveolar progenitors via activation of AP1 complex

status: Public on Apr 07 2008

first: Charles

last: Perou

summary:
For the largest class of human tumors, those of epithelial origin, little is known about their initiating genetic hits or cells of origin.  Whether tissue stem cells or more committed progenitors are targets for transformation is also uncertain. Experience in hematopoietic malignancies and sarcomas teaches that recurrent chromosomal translocations represent initiating oncogenic events. To develop a system in which epithelial tumorigenesis can be assessed from the initial event to frank malignancy, we have generated mice that conditionally express the Etv6-NTRK3 (EN) fusion oncoprotein, the product of the t(12;15)(p13;q25) translocation characteristic of one form of human breast cancer. Activation of EN expression in mammary tissues by Whey acidic protein (Wap) promoter-driven Cre leads to fully penetrant, multifocal malignant breast cancer with short latency. We provide genetic evidence that committed, bipotent or CD61+ luminal alveolar progenitors, can be targets of tumorigenesis. Furthermore, EN transforms these otherwise transient progenitors through the AP1 complex. Our model supports the existence of an epithelial cell hierarchy in both normal mammary glands and malignancy. To our knowledge, this is the first murine model of human epithelial cancer based on a recurrent chromosomal translocation. Given increasing relevance of chromosomal translocations in epithelial cancers, such mice serve as a paradigm for the study of their genetic pathogenesis and cellular origins, and generation of novel preclinical models.
Keywords: Reference X Sample

overall_design: Reference X Sample

first: Zhe

last: Li

first: Christina

last: Togon

first: Frank

last: Godinho

first: Laura

last: Yasaitis

first: Hanno

last: Hock

first: Jason

last: Herschkowitz

last: lannon

first: Eunah

last: Cho

first: Seong-Jim

last: Kim

first: Roderick

last: Bronson

first: Poul

last: Sorensen

first: Stuart

last: Orkin


title: In Vitro and In Vivo Analysis of B-Myb in Basal-Like Breast Cancer

status: Public on Jan 07 2009

summary:
The basal-like breast cancer subtype portends a poor clinical prognosis, and a defining feature of this subtype is the high expression of genes in the “proliferation signature”.  B-Myb, a member of the MYB protein family of transcription factors, is highly expressed in the proliferation signature and is amplified and overexpressed in a variety of tumor types, including breast.  In this report we demonstrated that B-Myb is highly expressed in basal-like breast cancer relative to the other subtypes, and B-Myb expression alone is prognostic. We also identified an association between a nonsynonymous B-Myb germline variant (S427G, rs2070235) and an increased risk of having a basal-like breast cancer among patients with breast cancer.  The expression of B-Myb, or the S427G variant, was manipulated in vitro and we observed that in hTERT-immortalized normal Human Mammary Epithelial Cells, but not basal-like tumor-derived lines, cells ectopically expressing B-Myb showed increased sensitivity to DNA topoisomerase II inhibitors, but not other chemotherapeutics; in addition, microarray analyses of B-Myb overexpressing cells identified many G2/M targets as being preferentially induced.  These results again suggest that B-Myb is involved in G2/M cell cycle control and that dysregulation of B-Myb may contribute to an increased sensitivity to a specific class of chemotherapeutic agents in vitro, and potentially in vivo. These data provide insight into the influence of B-Myb in human breast cancer, which is of potential clinical importance for determining disease risk and for guiding treatment.
Keywords: MYB protein family of transcription factors in Breast Cancer subtype study

overall_design: Reference VS. Samples

first: Aaron

middle: R

last: Thorner

first: Katherine

last: Hoadley

first: Joel

last: Parker

first: Robert

last: Millikan