|
| Status |
Public on Jul 11, 2023 |
| Title |
M1W1_50vs50_pRNA_repl2 |
| Sample type |
SRA |
| |
|
| Source name |
v-Abl pro-B clonal cell line Abl.1 / N2 and Hawaii strains
|
| Organisms |
Caenorhabditis elegans; Homo sapiens |
| Characteristics |
cell line: v-Abl pro-B clonal cell line Abl.1 / N2 and Hawaii strains
cell type: pro-B cells / whole organism
genotype: WT
strain: 129S1/SvImJ x Cast/EiJ F1 / N2 x Hawaii
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Agilent Mini / Trizol
NEBNext® Single Cell/Low Input RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Mix of Abl. 1 cell line (129S1xCAST F1) and C.elegans strains mix (N2:Hawaii) RNA, 50:50 proportion, library preparation replicate 2
LOVSON_E1.Mouse_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) |
| GSE228002 |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [I] |
| GSE228009 |
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale |
|
| Relations |
| BioSample |
SAMN33874285 |
| SRA |
SRX19753140 |
