|
| Status |
Public on Oct 10, 2023 |
| Title |
16-301_3 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Dasypus novemcinctus |
| Characteristics |
ind_id: 16-301
quad_id: 16-30
cell type: PBMCs
Sex: Female
infection status: Uninfected
library batch: 4
sequencing flowcell lane: 6
longitudinal sample: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the samples with a Maxwell® 16 Total RNA Purification Kit. Library preparation was done with a poly(A) selection kit (KAPA mRNA HyperPrep) to enrich for mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Multiplexed paired end sequencing (PE76) was done using an Illumina NextSeq500 on multiple flow cells. We blocked for lane batch effects by splitting the quadruplet samples into pairs and ran two pairs of each set per flow cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Nine-banded armadillo
|
| Data processing |
We downloaded the armadillo genome from Ensembl and generated an index file for use within STAR (v2.7).
We mapped reads with STAR (v2.7) and standardized counts to counts per million (CPM) by summing the counts and dividing by 1e6.
We generated personal genomes using g2gtools (v0.2.0). We mapped reads to the personal genomes using STAR. We ran the GATK (v3.6.0) pipeline and IGVtools (v2.3.80) to count reads per SNP.
Genome_build: DasNov3 v95
Supplementary_files_format_and_content: processed_count_data.txt: Count level outputs from STAR per gene.
Supplementary_files_format_and_content: processed_cpm_data.txt: CPMs are converted from the counts.
Supplementary_files_format_and_content: processed_counts_ase_quad_*.txt: ASE level outputs from the GATK pipeline; these counts are per SNP.
|
| |
|
| Submission date |
Dec 12, 2019 |
| Last update date |
Oct 10, 2023 |
| Contact name |
Sara Ballouz |
| Organization name |
UNSW
|
| Street address |
High St
|
| City |
Kensington |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL27905 |
| Series (1) |
| GSE141951 |
Transcriptional legacy in the armadillo |
|
| Relations |
| BioSample |
SAMN13551823 |
| SRA |
SRX7355060 |
