|
| Status |
Public on Jan 25, 2018 |
| Title |
DarkBlue688V |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Taeniopygia guttata |
| Characteristics |
brain region: Ventral striatopallidum
virus group: GFP
barcode: GAGTGG
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from Area X or ventral striatopallidum tissue micropunches using Qiagen Rnease Micro Kits following the manufacturers protocol. We used QIAzol as the lysis reagent. We also performed an additional wash each in RW1 and RPE buffers beyond the manufacturers protocol. Total RNA extracts were provided to the UCLA Neurogenomics Core. PolyA transcripts were selected for as part of the library construction protocol.
Librarires were prepared using the Illumina TruSeq Poly-A prep kit using the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling was done using Sanger/Illumina 1.9 software.
Reads were aligned to taeGut1 whole genome using STAR with the following parameters: --outSAMtype BAM SortedByCoordinate --outSAMattributes MD NH NM --outFilterMultimapNmax 1 --outFilterMismatchNmax 2
TPM (transcripts per million) for each sample were quantified by first counting all of the reads for each sample that mapped to any exon of a gene. Counts in each exon for each gene were then summed so as to produce a single gene-level count within each sample. TPM was calculated for each gene by calculating the number of reads counted for that gene by the gene's length, then dividing this value by the ratio of counts to gene length for all genes. This value is then multiplied by 1 million to generate TPM.
TPM values were log2 transformed and genes with zero variance across samples were removed. We used an iterative process of removing gene expression data from single samples whose expression was greater than 2.5 SD of that gene’s expression across all samples, repeating until no samples remained with expression greater than 2.5 SD away from the gene’s average expression across all samples. Finally, we calculated the intrasample correlation (ISC) and used a hard cutoff of 2 SD away from the group ISC for removal of samples from the study. No sample in any group (Area X or VSP was greater than 2 SD from the group ISC. Finally, data were quantile normalized as the last step before input to WGCNA.
Genome_build: taeGut1
Supplementary_files_format_and_content: .tsv files represent gene symbols and exon counts summed to the gene level for each sample
|
| |
|
| Submission date |
Mar 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zachary Daniel Burkett |
| E-mail(s) |
zburkett@ucla.edu
|
| Phone |
310-267-4017
|
| Organization name |
University of California, Los Angeles
|
| Department |
Integrative Biology & Physiology
|
| Lab |
White Lab
|
| Street address |
610 Charles E Young Drive East Room 1045
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90024 |
| Country |
USA |
| |
|
| Platform ID |
GPL23198 |
| Series (1) |
| GSE96843 |
Weighted gene coexpression analysis of RNA-seq data from 65d juvenile Area X and adjacent non-song ventral striatopallidum (VSP). |
|
| Relations |
| BioSample |
SAMN06622794 |
| SRA |
SRX2658720 |
