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Sample GSM1347009 Query DataSets for GSM1347009
Status Public on Jun 13, 2014
Title ChIP-seq_Rbpj_NT_1
Sample type SRA
Source name E12.5 Neural Tube
Organism Mus musculus
Characteristics strain: ICR
developmental stage: E12.5
antibody: Lab generated rabbit anti-Rbpj
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
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Rbpj NT
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.
Submission date Mar 12, 2014
Last update date May 15, 2019
Contact name Jane E Johnson
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
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
Alternative to GSM1150327
BioSample SAMN02688196
SRA SRX485442

Supplementary file Size Download File type/resource
GSM1347009_ChIPseq_RbpJ_NT_1.bedGraph.gz 50.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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