|
| Status |
Public on Jan 11, 2023 |
| Title |
Vegetative growing cells, 30 min after elutriation, B |
| Sample type |
SRA |
| |
|
| Source name |
CU428
|
| Organism |
Tetrahymena thermophila |
| Characteristics |
cell line: CU428
cell type: vegetative growing cells
genotype: WT
treatment: elutriation synchronized
time: 30 min
|
| Treatment protocol |
Elutriation was used to obtain a synchronized population of cells during vegetative growth. Cells were loaded into the elutriation centrifuge at 850 rpm, 50 ml/min. G1 cells were collected at 60 ml/min (200 ml) and placed in a 2L flask at 30˙C, shaking at 100 rpm. Cells were collected at 30 min time intervals up to 240 min. For each time point, 20 ml of cells were collected, 5 ml prepared for FACs analysis, and 15 ml for isolation of RNA. Cells were centrifuged and cell pellets were washed in 10 mM Tris pH 7.4 before preparation for FACs and RNA isolation.
|
| Growth protocol |
CU428 cells (1.5 L) were grown to ~1x10^5 cells/ml in 2% PPYS/1000 U/ml pen-strep (Sigma Aldrich) at 30˙C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation, cell pellets were resuspended in 1 ml RNAlater and placed at 4˙C overnight. RNAlater was removed and RNA prepared using the Qiagen RNeasy kit with additional DNAse digestion on the column.
10 ug of total RNA were used to make cDNA library was prepared using Illumina RNA-seq Prep Kit (Illumina).
Illumina-HiSeq 2500v4
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
B
|
| Data processing |
After sequencing, adapters and low quality reads were removed by Trimmomatic, paired reads with concordant mappings were aligned to the Tetrahymena genome by HISAT2, the abundance of these transcripts in each sample was computed using StringTie.
Assembly: Tetrahymena genome (SB210, 2021 version, TGD)
Supplementary files format and content: tab-delimited text file includes count values for each Sample
|
| |
|
| Submission date |
Jul 24, 2022 |
| Last update date |
Jan 11, 2023 |
| Contact name |
GEOFFREY KAPLER |
| E-mail(s) |
gkapler@tamu.edu
|
| Organization name |
Texas A&M University
|
| Street address |
4209B Medical Research Education Building II
|
| City |
Bryan |
| State/province |
TX |
| ZIP/Postal code |
77807 |
| Country |
USA |
| |
|
| Platform ID |
GPL23968 |
| Series (1) |
| GSE209619 |
Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles |
|
| Relations |
| BioSample |
SAMN29928020 |
| SRA |
SRX16600522 |
