|
| Status |
Public on Feb 28, 2017 |
| Title |
10480X1 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Raphe Nucleus
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: Dorsal Raphe Nucleus
Sex: female
mother id: 10479X1
father id: 10136X7
|
| Growth protocol |
Wake Forest
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold
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 reage
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 reage
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
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).
Make unique transcriptome index for each daughter based on parent genotyping
Novoalign to daughter specific transriptome index
Useq TranscriptomeParser
Count reads with custom pysam based python script
Genome_build: macFas5
Supplementary_files_format_and_content: bam files were generated with novoalign and USeq TranscriptomeParser
|
| |
|
| 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) |
| GSE93786 |
Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain [Primate Daughters] |
| GSE93788 |
Diverse Non-Genetic Allele Specific Expression Effects Shape Genetic Architecture at the Cellular Level in the Mammalian Brain |
|
| Relations |
| BioSample |
SAMN06238206 |
| SRA |
SRX2500752 |
