|
| Status |
Public on Jul 11, 2023 |
| Title |
donor2_biorepl1_spikein_10pRNA_W1 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood monocytes / whole organism
|
| Organisms |
Caenorhabditis elegans; Homo sapiens |
| Characteristics |
cell type: peripheral blood monocytes / whole organism
genotype: WT
strain: donor no. 2 / N2 x Hawaii
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen Mini / Trizol
SMART-Seq v4 PLUS kit (Takara)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
donor no. 2 peripheral blood monocytes / N2 and Hawaii strains
Donor no. 2 peripheral blood monocytes, biological replicate 1, with 10 % C.elegans (1:1 N2:Hawaii RNA mix) RNA spike-in
STARA_E3.Human_Roundworm.counts.tsv
|
| Data processing |
Sequence reads were aligned on two alellic pseudogenomes using STAR v2.7.9a (with parameters –outSAMattributes vA vG).
Uniquely aligned reads were assigned towards one of the alleles according to their SNP calls and alignment quality (see https://github.com/gimelbrantlab/fastq2allelictabs).
Allelic gene counts were calculated using featurecounts v2.0.2.
Supplementary files format and content: Tab-delimited text files include allelic gene count values for each sample.
|
| |
|
| Submission date |
Mar 22, 2023 |
| Last update date |
Jul 11, 2023 |
| Contact name |
Asia Mendelevich |
| Organization name |
Altius
|
| Street address |
2211 Elliott Ave
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
| |
|
| Platform ID |
GPL33278 |
| Series (2) |
| GSE228004 |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III] |
| GSE228009 |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale |
|
| Relations |
| BioSample |
SAMN33864477 |
| SRA |
SRX19751467 |
