|
| Status |
Public on Jul 07, 2023 |
| Title |
Syn3A cells, colony A3_S, endpoint evolution |
| Sample type |
SRA |
| |
|
| Source name |
synthetic bacterium
|
| Organism |
synthetic bacterium JCVI-Syn3A |
| Characteristics |
cell line: synthetic bacterium
cell type: synthetic
treatment: evolution endpoint
|
| Growth protocol |
ALE experiments were conducted with automated devices that serially propagated batch cultures of JCVI-syn3A between growth tubes with 15 mL of SP4-KO medium (containing 17% v/v KnockOut™ Serum Replacement [GIBCO] in lieu of fetal bovine serum in SP4), well aerated through mixing and kept at 37°C. Ten replicate lineages were started from the JCVI-syn3A ancestor and for each lineage 150 ul of culture was passed to a fresh tube once daily (6.6 generations/day), switching to 30 ul passage volume (9 generations/day) after 200 generations and continuing for a total of 400 generations
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA was isolated using bead agitation in 96-well plates
Total RNA isolation, rRNA removal, and sequencing library preparation was performed as previously described (Chen et al. 2021) removal, and sequencing library preparation was performed as previously described (Chen et al. 2021)
Libraries were run on an Illumina NextSeq, raw sequencing reads were mapped using Bowtie
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
GenBank ID: CP016816.2
|
| Data processing |
Reads counted using HTSeq
Libarires normalized using transciptos per million (TPM)
Assembly: GenBank ID: CP016816.2
Supplementary files format and content: csv
Supplementary files format and content: comma seperated value containing log TPM values of each gene expression levels
|
| |
|
| Submission date |
May 27, 2022 |
| Last update date |
Jul 07, 2023 |
| Contact name |
Christopher Dalldorf |
| E-mail(s) |
cdalldor@eng.ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
SBRG, Palsson
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL32299 |
| Series (1) |
| GSE205017 |
Adaptive Evolution of a Minimal Organism with a Synthetic Genome |
|
| Relations |
| BioSample |
SAMN28700717 |
| SRA |
SRX15485295 |
