|
| Status |
Public on Aug 02, 2021 |
| Title |
RNA-seq in zebrafish ctcf mutant embryos at 48hpf, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: 48 hpf
genotype: ctcf -/-
|
| Treatment protocol |
Injection of tp53 morpholino was performed at 1-cell stage
|
| Growth protocol |
Embryos were grown at 28°C in E3 medium until desired developmental stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIsure (Bioline) and treated with TURBO DNA free kit (Invitrogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
RNA_48h_ctcf_rep2
|
| Data processing |
Reads were aligned against reference genome using STAR software
Read counts per gene were calculated using htseq-count script from HTSeq tools software package
Genome_build: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary_files_format_and_content: Individual counts files (reads per gene)
|
| |
|
| Submission date |
Aug 12, 2020 |
| Last update date |
Aug 02, 2021 |
| Contact name |
José M. Santos-Pereira |
| Organization name |
IBiS, Universidad de Sevilla-CSIC
|
| Street address |
Avda. Manuel Siurot s/n
|
| City |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24776 |
| Series (2) |
| GSE156094 |
CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA-seq] |
| GSE156099 |
CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression |
|
| Relations |
| BioSample |
SAMN15802235 |
| SRA |
SRX8931587 |
