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Status |
Public on Jan 08, 2016 |
Title |
E11.5_WT1 |
Sample type |
SRA |
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Source name |
5-HT neuron
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: 5-HT neuron developmental stage: E11.5 genotype: wild type
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Growth protocol |
Animals were reared in standard housing conditions.
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Extracted molecule |
total RNA |
Extraction protocol |
EYFP+ 5-HT neurons were sorted using a BD FACSAria into Trizol reagent and extracted RNA was Dnase I treated and purified using the RNA Clean & Concentrator-5 kit (Zymo). Purified total RNA was amplified with the SMARTer Ultra-low mRNA-Seq kit (Clontech) or Ovation RNA-Seq System V2 (NuGEN). Dissected YFP+ tissue between the mid-hindbrain boundary and rhombomere 4 of E12.5 to E15.5 hindbrains from Pet-1-/-; ePet-mycPet-1; ePet-EYFP embryos was quickly flash frozen on dry ice. Chromatin was isolated and immunoprecipitated using a ChIP grade, goat anti-Myc antibody (Abcam ab9132, Cambridge, MA, validation report at abcam.com) with proprietary protocols (Active Motif, Carlsbad, CA). RNA libraries were prepared for sequencing using either Clontech SMARTer RNA-seq (E11.5, E15.5C_WT, E15.5C_KO, PN) or NuGen Ovation RNA-Seq v2 (E15.5N_WT, E15.5N_KO). ChIP-seq libraries were prepared using standard Illumina ChIP-seq methods.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
Illumina Casava1.8.2 software used for basecalling. Sequenced reads were filtered for low-quality sequence, then mapped to mm9 whole genome using tophat2. Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks. Reads were mapped to the Mus musculus genome (UCSC mm10) using the Burroughs-Wheeler Aligner (BWA) and were filtered to select reads that map to a single location (Li and Durbin, 2009). Peak calling was performed with MACS v1.4.2 modified to accept a custom scaling factor of 0.8195945 derived from the Normalization ChIPseq software (NCIS) (Zhang et al., 2008; Liang and Keleş, 2012). MycPet-1 ChIP peaks were associated to genes using the GREAT web service v3.0 (mm10) with 5kb intervals upstream and downstream of the TSS and TTS of each gene model along with peaks that overlap the gene body. Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample in the time-series gene expression trajectory (E11.5, E15.5, PN; Gene_expression_trajectories_E11.5_E15.5_PN.matrix.txt) and WT vs. Pet-1-/- (E15.5_WT vs E15.5_KO) generated by cufflinks. For ChIP-seq, a BED file of mycPet-1 ChIP peaks is provided.
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Submission date |
Oct 23, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Evan Deneris |
E-mail(s) |
esd@case.edu
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Organization name |
Case Western Reserve University
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Department |
Neurosciences
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Street address |
2109 Adelbert Rd.
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City |
Cleveland |
State/province |
OH |
ZIP/Postal code |
44106 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE74315 |
Pet-1 Switches Transcriptional Targets Postnatally to Regulate Maturation of Serotonin Neuron Excitability. |
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Relations |
BioSample |
SAMN04210158 |
SRA |
SRX1371357 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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