|
| Status |
Public on Feb 10, 2024 |
| Title |
ZC3H14_iCLIP_R1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293 cells
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ZC3H14_iCLIP_crosslinked_nucleotide.txt.gz
|
| Data processing |
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 10, 2024 |
| Contact name |
Xiaolin Wang |
| E-mail(s) |
wxl20089@mail.ustc.edu.cn
|
| Phone |
15155979787
|
| Organization name |
USTC
|
| Street address |
Huangshan Road
|
| City |
Hefei |
| ZIP/Postal code |
230026 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE254916 |
Conserved regulation of ZC3H14/Nab2 in circRNA biogenesis |
|
| Relations |
| BioSample |
SAMN39748430 |
| SRA |
SRX23508644 |
