|
| Status |
Public on Feb 28, 2017 |
| Title |
Mother 7231 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Raphe Nucleus
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Dorsal Raphe Nucleus
Sex: female
|
| Treatment protocol |
None
|
| Growth protocol |
Wake Forest
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq DNA PCR-Free Sample Prep (550 bp mean insert size)
DNA samples (2 ug) were sheared using a Covaris S2 Focused-ultrasonicator and libraries were prepared using the Illumina TruSeq DNA PCR-Free Sample Preparation Kit (cat# FC-121-3001 and FC-121-3002) with an average insert size of 550 bp. Adapter-ligated molecules were analyzed by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824) and the molarity of individual libraries were normalized to 10 nM in preparation for Illumina sequence analysis.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
10136X5
|
| Data processing |
Library strategy: wgs
HiSeq 101 Cycle Paired-End Sequencing v4 Sequencing libraries (25 pM) were chemically denatured are applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001). Following transfer of the flowcell to an Illumina HiSeq instrument, a 101 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).
Realign with GATK
Genotyped with GATK
Genome_build: macFas5
Supplementary_files_format_and_content: bam files were generated with novoalign and GATK
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher Gregg |
| E-mail(s) |
chris.gregg@neuro.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Neurobiology and Anatomy
|
| Street address |
323 Wintrobe Bldg 530, 20 North 1900 East
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84132-3401 |
| Country |
USA |
| |
|
| Platform ID |
GPL18648 |
| Series (2) |
| GSE93785 |
Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain [Primate Parents] |
| GSE93788 |
Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain |
|
| Relations |
| BioSample |
SAMN06238199 |
| SRA |
SRX2500417 |
