|
| Status |
Public on Nov 11, 2022 |
| Title |
bc1003_5p--bc1003_3p: Stellate g. & Visceral g. - Isoseq |
| Sample type |
SRA |
| |
|
| Source name |
Stellate g. & Visceral g.
|
| Organism |
Octopus vulgaris |
| Characteristics |
tissue: Stellate g. & Visceral g.
extract_protocol: Iso-seq Express 2.0
strategy: FL cDNA
basecalling: SMRT Link
downstream analysis: lima, isoseq3 cluster, TAMA collapse
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Adult specimens of O. vulgaris (body weight 800 g ± 50 g, mean ± SD) were collected from the Bay of Naples (Italy) and transferred to the Department of Biology, University of Naples Federico II (Italy). Samples (N=8) were anesthetized by isoflurane insufflation (Polese et al. 2014), and tissues were dissected under sterile conditions following institutional guidelines. The collected samples were snap frozen in liquid nitrogen and immediately put in Trizol, then stored at −80 °C. The RNA has been extracted from the tissues using Direct-zolTM RNA Miniprep (Zymo Research), following the manufacturer’s protocol. RNA has been stored at -80 C prior to sequencing, and it was transported using dry ice. The quality of RNA has been accessed with Bioanalyzer and only samples with intact RNA have been kept for library preparation.
Library construction protocols are listed in the columns of SAMPLES section above
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Sequel |
| |
|
| Data processing |
bcl2fastq software has been used for basecalling for PolyA, total RNA and Small RNA libraries. For FLAMseq and Isoseq FLAMAnalysis and isoseq3 pipelines have been used to obtain full-length non-chimeric ( FLNC) reads.
PolyA and totalRNA sequencing data have been mapped to the genome using STAR aligner (Dobin et al. 2013) using default parameters
Iso-seq and FLAMseq FLNCs have been mapped to the genome with minimap2 (v 2.17-r941) using the parameters "--cs -ax splice:hq -uf --secondary=no -C5"
MicroRNA counts file has been generated using quantifier.pl script from miRDeep2 package and the sequences of microRNAs predicted in this study
*_clean_genomic_tail_length.txt.gz files for FLAMseq have been generated by FLAMAnalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis).
Genome_build: GCF_006345805.1_ASM634580v1
Supplementary_files_format_and_content: miRNAs_expressed_all_samples_mirgenedb.csv.gz contains raw and normalized counts for each microRNA in every tissue in the dataset
Supplementary_files_format_and_content: totalRNA_fc_221221.txt.gz, polyARNA_fc_221221.txt.gz - tab-separated file with read counts for individual genes in the genome produced with featureCounts
Supplementary_files_format_and_content: *bed files for Isoseq have been obtained by collapsing reads into individual libraries into the sets of putative isoforms using TAMA collapse (https://github.com/GenomeRIK/tama)
Supplementary_files_format_and_content: *_clean_genomic_tail_length.txt.gz files contain the poly(A) tail length, sequence and a read_ID for every read in the dataset
|
| |
|
| Submission date |
Dec 23, 2021 |
| Last update date |
Nov 11, 2022 |
| Contact name |
Grygoriy Zolotarov |
| E-mail(s) |
[email protected]
|
| Phone |
+420777072165
|
| Organization name |
Max Delbruck Center for Molecular Medicine
|
| Department |
Berlin Institute of Medical Systems Biology
|
| Lab |
Systems Biology of Gene Regulatory Elements
|
| Street address |
Hannoversche Strasse 28
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL31141 |
| Series (1) |
| GSE192550 |
Mapping and understanding the function of RNA in octopus brain |
|
| Relations |
| BioSample |
SAMN24368968 |
| SRA |
SRX13497404 |
