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| Status |
Public on Jun 13, 2014 |
| Title |
NT_Input_Ctrl |
| Sample type |
SRA |
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| Source name |
E12.5 Neural Tube
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| Organism |
Mus musculus |
| Characteristics |
strain: ICR
developmental stage: E12.5
antibody: none (input)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Ptf1a and Rbpj E12.5 neural tube mouse embryos 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 liberated by Dounce homogenization and purified by centrifugation through a sucrose gradient (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.25 mM EGTA, 1.25 M sucrose). Nuclei were then fixed in 1% formaldehyde for 10 minutes at 30°C, and fixation was terminated by adding glycine to a final concentration of 0.125 M. After centrifuging through another sucrose gradient, fixed nuclei were lysed in sonication buffer (1% Triton, 0.1% sodium deoxycholate, 150 mM NaCl, 50 mM Tris, 5 mM EDTA). Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30 second on:off cycles.
For Ascl1, ChIP E12.5 mouse neural tubes were dissected into PBS then fixed in 1% formaldehyde for 15 min and lysed in 1% SDS, 10 mM EDTA, and 50 mM Tris. Sonication was performed using a Bioruptor (Diagenode) at high power settings for 45 cycles (30 sec on/30 sec off).
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 |
NT Input control
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| Data processing |
Basecalls performed using CASAVA
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.
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| Submission date |
Mar 12, 2014 |
| 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 (2) |
| GSE55840 |
Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord [ChIP-Seq] |
| GSE55841 |
Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord |
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| Relations |
| Alternative to |
GSM1150340 |
| BioSample |
SAMN02688179 |
| SRA |
SRX485443 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1347010_NT_Input_control.bedGraph.gz |
50.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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