|
| Status |
Public on Jan 12, 2022 |
| Title |
Wide type in conventionally raised condition rep2 [WT-CV-2] |
| Sample type |
SRA |
| |
|
| Source name |
Wide type in conventionally raised condition
|
| Organism |
Danio rerio |
| Characteristics |
strain background: AB
age: 7 days post fertilization
genotype: Wilde type
treatment: conventionally raised condition
tissue: larvae intestine
|
| Treatment protocol |
germ free condition was carried out as previously described(Pham et al., 2008).
|
| Growth protocol |
embryos were incubated at 28.5℃ in E3 egg water (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The reads were mapped to danRer10 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample
|
| |
|
| Submission date |
May 12, 2020 |
| Last update date |
Jan 12, 2022 |
| Contact name |
Jong Hwan Kim |
| E-mail(s) |
kkjjhhk@kribb.re.kr
|
| Phone |
0821093299557
|
| Organization name |
Korea Research Institute of Bioscience and Biotechnology
|
| Department |
Genome structure research center
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
ASI|KR|KS015|DAEJEON |
| Country |
South Korea |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE150376 |
mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without gut microbiota. |
|
| Relations |
| BioSample |
SAMN14896674 |
| SRA |
SRX8330119 |
