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Sample GSM1917004 Query DataSets for GSM1917004
Status Public on Jan 08, 2016
Title E11.5_WT1
Sample type SRA
 
Source name 5-HT neuron
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: 5-HT neuron
developmental stage: E11.5
genotype: wild type
Growth protocol Animals were reared in standard housing conditions.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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.
 
Submission date Oct 23, 2015
Last update date May 15, 2019
Contact name Evan Deneris
E-mail(s) esd@case.edu
Organization name Case Western Reserve University
Department Neurosciences
Street address 2109 Adelbert Rd.
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL17021
Series (1)
GSE74315 Pet-1 Switches Transcriptional Targets Postnatally to Regulate Maturation of Serotonin Neuron Excitability.
Relations
BioSample SAMN04210158
SRA SRX1371357

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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