|
| Status |
Public on May 14, 2023 |
| Title |
MN_D9_chrRNA_rep1_Prom |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived motor neuron progenitors
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPSC-derived motor neuron progenitors
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Qiazol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002) or targeted PCR amplification of gene interest and DNA nanopore sequencing (SQK-LSK109)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_splicing_status_per_read.txt: text files containing the overall splicing status of each read
Supplementary files format and content: *_hg38_multi_introns_isoforms_counts.txt or hg38_multi_introns_counts.txt: text files containing the per-intron splicing status for each intron in each read
Supplementary files format and content: *_hg38_multi_exons_isoforms_counts.txt: text files containing the per-exon splicing status for each exon in each read
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
May 14, 2023 |
| Contact name |
Karine Choquet |
| E-mail(s) |
[email protected]
|
| Organization name |
Université de Sherbrooke
|
| Department |
Biochemistry and Functional Genomics
|
| Street address |
3201 rue Jean-Mignault
|
| City |
Sherbrooke |
| State/province |
Québec |
| ZIP/Postal code |
J1E 4K8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE208259 |
pre-mRNA splicing order is defined and maintains splicing fidelity across multi-intronic transcripts [II] |
| GSE232455 |
pre-mRNA splicing order is defined and maintains splicing fidelity across multi-intronic transcripts |
|
| Relations |
| BioSample |
SAMN32876990 |
| SRA |
SRX19142691 |
