|
| Status |
Public on May 07, 2024 |
| Title |
Hypsibius exemplaris 03h hours after exposure to 100µM BML, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Hypsibius exemplaris 03h hours after exposure to 100µM BML
|
| Organism |
Hypsibius exemplaris |
| Characteristics |
treatment: BML
time: 03h hours
tissue: Whole body
|
| Treatment protocol |
Fifty individuals per sample were placed in 96 well flat bottom plates and was exposed to 200µL 100µM Bleomycin (melted in Volvic water) for 24 hours (N=5). A control series exposed to Volvic water was also set. After 24 hours, the control specimens and T0 specimens were collected and placed in a microtube with the least amount of water possible and frozen at -80˚C. The remining samples were washed with 300µL Volvic water twice to remove bleomycin and were placed on 45mm agar plates with 2mL volvic water supplied with 10µL Chlorella to feed on. These specimens were incubated at 18˚C until sampling. After 1,3, 6, 9, 12, 24 hours, each sample were collected as stated above and frozen at -80˚C.
|
| Growth protocol |
H. exemplaris was cultured following our previous studies. Briefly, specimens were placed on 2% agar gels using Volvic water, supplied with Volvic water containing Chlorella vulgaris. Individuals were collected and moved to a new agar plate every 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were submitted to transcriptome sequencing (N=3). The total RNA was extracted with Direct-Zol Micro Kit and quantified with Qubit RNA HS.
An Illumina sequencing library was constructed from 30ng of total RNA with NEB Next Ultra RNA following the manufacture’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bleomycin-03h-1
|
| Data processing |
The quality of RNA-Seq reads were validated with FastQC v0.11.3
The sequenced reads were mapped to CDS and quantified with RSEM v1.2.26 {Li, 2011 #3027} and bowtie2 v2.2.9 {Langmead, 2012 #233} using the Trinity align_and_estimate_abundance.pl utility {Grabherr, 2011 #312}. Differential expression was tested with DESeq2 v1.22.2 {Love, 2014 #870} using the Trinity run_DE_analysis.pl, and transcripts with adjusted p-values below 0.05 and fold change over 1.5 or below 2/3 were designated as differentially expressed genes.
Genome_build: GCA_002082055.1_nHd_3.1
Supplementary_files_format_and_content: RSEM quantified TPM values
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
May 07, 2024 |
| Contact name |
Yuki Yoshida |
| Organization name |
NARO
|
| Department |
NIAS
|
| Street address |
1-2 Owashi
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8634 |
| Country |
Japan |
| |
|
| Platform ID |
GPL29853 |
| Series (1) |
| GSE168917 |
Transcriptome analysis of the extremophile tardigrade Hypsibius exemplaris exposed to the DNA-damaging agent bleomycin |
|
| Relations |
| BioSample |
SAMN18312849 |
| SRA |
SRX10341757 |
