|
| Status |
Public on Mar 02, 2023 |
| Title |
Active colony ampulla (biol rep 1) |
| Sample type |
SRA |
| |
|
| Source name |
Ampullae cells
|
| Organism |
Botrylloides leachii |
| Characteristics |
cell type: Ampullae cells
physiological state: Active colony
|
| Growth protocol |
Colonies were individually tied onto 5 x 7.5 cm glass slides with fine cotton threads, then cultured in 25 L standing seawater tanks, following Rinkevich and Shapira (1998) and fed daily with a variety of food types (including freeze dried rotifers and commercial powdered plankton).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNeasy mini-Kit (QIAGEN) was used on fresh tissues as per manufacture instructions to isolate RNA.
RNA libraries for RNA-seq were prepared using RNA TruSeq Total RNA Library Prep Kit with Ribo-Zero Gold Sequencing (Epicenter) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
active55ampS14
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/ PCR sequence with Trimmomatic.
Trimmed sequence reads were mapped to B.leachii assembled genome using HiSat2.
Expression quantifications were performed using RSEM.
Functional annotation was done using ANISEED database.
Normalisation of expression and differential expression analysis done with DESeq2.
Assembly: https://www.aniseed.cnrs.fr/aniseed/download/?file=data/boleac/Boleac_SBv3_genome_gff3_fasta.zip&module=aniseed&action=download:index
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 01, 2023 |
| Last update date |
Mar 02, 2023 |
| Contact name |
Julia Panov |
| E-mail(s) |
[email protected]
|
| Organization name |
Tauber Bioinformatics Research Center
|
| Street address |
Aba Hushi Blvd 199 Mount Carmel
|
| City |
Haifa |
| ZIP/Postal code |
3498838 |
| Country |
Israel |
| |
|
| Platform ID |
GPL33202 |
| Series (1) |
| GSE226392 |
Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states |
|
| Relations |
| BioSample |
SAMN33560239 |
| SRA |
SRX19543547 |
