|
| Status |
Public on Jul 17, 2024 |
| Title |
pup-1/-2(om129)_mRNA-seq_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
gender: hermaphrodite
genotype: pup-1/-2(om129)
developmental stage: 1-day adult
|
| Growth protocol |
1 day old adult hermaphrodites raised at 22°C
|
| Extracted molecule |
other |
| Extraction protocol |
RNA was isolated from whole animals using the TRIzol (Invitrogen) method.
Ribosomal-depleted RNA was subjected to the Nano3P-seq protocol (modification of the ONT direct cDNA-seq kit, published by Begik et al. 2023).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
other |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
om129_mRNA_rep4
|
| Data processing |
Basecalled with guppy_basecaller (v4.4.2), demultiplexed with guppy_barcoder (v4.4.2), FASTQ chunks within each genotype/replicate were combined into one FASTQ file using the cat command in Unix, reads were mapped to the transcriptome using minimap2 with the parameters '-ax map-ont --MD -k14' and using the RefSeq GCF 000002985.6 reference. In parallel, the non-basecalled FAST5 files were demultiplexed with the demux_fast5 (v4.1.1) command from the ont_fast5_api software and these were used as input for the find_tails command in the program tailfindr (polyu branch). The resulting tails count table and the SAM file from the mapping step were used as input for the annotate_tails function in tailfinder to produce the final counts table. This was loaded into R to convert to a matrix.
Assembly: RefSeq GCF 000002985.6
Supplementary files format and content: Total counts (not parsed by tail type) in a matrix
|
| |
|
| Submission date |
Jul 05, 2024 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Eleanor Maine |
| E-mail(s) |
emmaine@syr.edu
|
| Organization name |
Syracuse University
|
| Department |
Biology
|
| Street address |
107 College Place
|
| City |
Syracuse |
| State/province |
New York |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL26522 |
| Series (1) |
| GSE271566 |
Sequencing experiments on poly(U) polymerase mutants in C. elegans [mrna] |
|
| Relations |
| BioSample |
SAMN39507849 |
| SRA |
SRX23314879 |
