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| Status |
Public on Aug 15, 2013 |
| Title |
ChIPseq_Rbpj_NT_1 |
| Sample type |
SRA |
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| Source name |
E12.5 Neural Tube
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E12.5
strain: ICR
antibody: Lab generated rabbit anti-Rbpj(Tx857)
tissue: Neural Tube
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neural tube (caudel to midbrain), telencephalon, or limb tissues from E12.5 mouse embryos, or pancreata from E17.5 embryos were dissected and placed in Buffer A (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose) on ice. Nuclei were liberat
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Rbpj NT #1
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| Data processing |
Basecalls performed using CASAVA (NT Ptf1a v1.6.0,Pancreas Ptf1a v1.3.0,All other samples v1.7.0)
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
Peak calling was performed by HOMER using an FDR cutoff of 0.001. Putative peaks were required to have 4-fold enrichment over the control/input sample and a cumulative Poisson p-value of <0.0001
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome. Each ChIPseq bedgraph file name describes the transcription factor used for ChIP in the respective tissue type.
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| Submission date |
May 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jane E Johnson |
| E-mail(s) |
jane.johnson@utsouthwestern.edu
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| Organization name |
UT Southwestern Medical Center
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| Department |
Neuroscience
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE47459 |
Program specificity for Ptf1a in Pancreas versus Neural Tube Development correlates with distinct collaborating cofactors and chromatin accessibility |
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| Relations |
| Alternative to |
GSM1347009 |
| BioSample |
SAMN02182690 |
| SRA |
SRX287018 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1150327_ChIPseq_RbpJ_NT_1.bedGraph.gz |
50.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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