|
| Status |
Public on May 14, 2024 |
| Title |
wildtype OP50 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
entire body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: entire body
strain: Bristol strain N2
genotype: wildtype
treatment: S basal medium with E. coli OP50
|
| Treatment protocol |
The animals were transferred to S-basal medium with OP50 or L. paracasei subsp. paracasei 2004 for 3day.
|
| Growth protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen) from C. elegans Bristol strain N2 cultured in S basal medium with E. coli OP50 or L. paracasei subsp. paracasei 2004 for three days from three days after hatching.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were collected with TRIzol following manufacture's protocol.
RNA-seq library preparation and RNA sequencing were performed at Macrogen Inc. using Illumina HiSeq 2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
N2_OP50_rep2
|
| Data processing |
fastqc 0.11.8
catadapt 2.7
trim_galore 0.6.4_dev
hisat2 2.1.0
samtools 1.7
stringtie 2.1.1
Assembly: WBcel235
Supplementary files format and content: csv file contains CPM values for each sample
|
| |
|
| Submission date |
Aug 22, 2023 |
| Last update date |
May 14, 2024 |
| Contact name |
Masaharu Uno |
| Organization name |
RIKEN
|
| Department |
BDR
|
| Lab |
Molecular Biology of Aging
|
| Street address |
2-2-3, Minatojima-minamimachi, Chuo-ku
|
| City |
Kobe |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE241495 |
Effect of lactic acid bacterium 2004 on transcription profile in wildtype animals and daf-16 mutants. |
|
| Relations |
| BioSample |
SAMN37116198 |
| SRA |
SRX21457597 |
