|
| Status |
Public on Apr 23, 2024 |
| Title |
Dark_Adapted_T0_C |
| Sample type |
SRA |
| |
|
| Source name |
Dark_Adapted
|
| Organisms |
Alteromonas macleodii; Prochlorococcus marinus str. NATL2A |
| Characteristics |
strain: MIT1002
cell type: Dark_Adapted
time point: T0
|
| Treatment protocol |
N/A
|
| Growth protocol |
Prochlorococcus and Alteromonas were maintained on Pro99 amended natural seawater in a 13:11 light:dark incubator at 24C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVana microRNA (miRNA) extraction kit (Ambion, USA).
Ribosomal RNA was depleted using RiboZero kit (Illumina) and libraries prepared using the KAPA RNA HyperPrep kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sample_24
|
| Data processing |
Reads were trimmed and adapters were removed with BBDuk (from the BBTools package, V38.16) (parameters: ktrim=r, k=23, mink=11, hdist=1, qtrim=rl, trimq=6)
The trimmed reads were aligned to Prochlorococcus NATL2A (NC_007335.2) and Alteromonas macleodii MIT1002 (NZ_JXRW01000001.1) genomes using bowtie2 (parameters: default)
The number of reads that aligned to each annotated ORF in the “sense” orientation was determined using HTSeq (V0.11.2) (parameters: --nonunique all)
Assembly: NZ_JXRW01000001.1, NC_007335.2
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
|
| |
|
| Submission date |
Apr 18, 2024 |
| Last update date |
Apr 23, 2024 |
| Contact name |
Allison Coe |
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Civil and Environmental Engineering
|
| Lab |
Chisholm Lab
|
| Street address |
15 Vassar St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL34397 |
| Series (1) |
| GSE264347 |
Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus |
|
| Relations |
| BioSample |
SAMN41010168 |
| SRA |
SRX24303983 |
