|
Status |
Public on Jan 12, 2022 |
Title |
tp53 mutant in conventionally raised condition rep2 [P53-CV-2] |
Sample type |
SRA |
|
|
Source name |
tp53 mutant in conventionally raised condition
|
Organism |
Danio rerio |
Characteristics |
strain background: AB age: 7 days post fertilization genotype: tp53e7/e7 mutant 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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|
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
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|
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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 |
SAMN14896678 |
SRA |
SRX8330115 |