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| Status |
Public on Oct 20, 2021 |
| Title |
OA regeneration in cycloheximide, T=120, rep1 |
| Sample type |
SRA |
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| Source name |
Stentor coeruleus cell
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| Organism |
Stentor coeruleus |
| Characteristics |
time: 120 minutes post sucrose shock
treatment: cycloheximide + sucrose shock
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
At each time point, a sample of cells was lysed into RNA-stabilizing buffers specified by the extraction kit, and then stored on ice until the end of the experiment when the RNA purification was performed in parallel on all samples. RNA was extracted at each time point using the Nucleospin RNA XS kit from Clontech (cat. num. 740902.250).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
5-e1_C1-120_S351_L002
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Stentor genome (StentorDB), using tophat2 (-i 9 -I 101 --min-segment-intron 9 --min-coverage-intron 9 --max-segment-intron 101 --max-coverage-intron 101 -p 20). We used Trinity to build a transcriptome (--genome_guided_max_intron 1000). For quantification of transcript abundance, we aligned reads to the transcriptome using Kallisto (-t 15 -b 30). Transcriptome file is included here: SteCoe_Trinity_assembled_transcriptome_for_GEO.fasta
Genome_build: Stentor coeruleus (GCA_001970955.1)
Supplementary_files_format_and_content: For each Sample:
tsv file containing matrix of estimated counts, TPM, effective length for each gene.
HDF5 binary file containing run info, abundance estimates, bootstrap estimates, and transcript length information length.
json file containing information about the run
Trinity generated transcriptome (fasta)
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| Submission date |
Oct 18, 2021 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Wallace Marshall |
| E-mail(s) |
wallace.ucsf@gmail.com
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| Organization name |
UCSF
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| Street address |
600 16th St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL30871 |
| Series (1) |
| GSE186036 |
Modular, Cascade-like Transcriptional Program of Regeneration in Stentor |
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| Relations |
| BioSample |
SAMN22368437 |
| SRA |
SRX12668345 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5629495_5-e1_C1-120_S351_L002_abundance.h5 |
5.4 Mb |
(ftp)(http) |
H5 |
| GSM5629495_5-e1_C1-120_S351_L002_abundance.tsv.gz |
842.5 Kb |
(ftp)(http) |
TSV |
| GSM5629495_5-e1_C1-120_S351_L002_run_info.json.gz |
378 b |
(ftp)(http) |
JSON |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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