|
| Status |
Public on Sep 12, 2020 |
| Title |
Human_blood |
| Sample type |
SRA |
| |
|
| Source name |
Human blood, peripheral leukocytes
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood, peripheral leukocytes
|
| Growth protocol |
HEK293 cells were maintained at ~3×10^6 cells per plate at 37°C in humidified 10% CO2 atmosphere in MEM and 10% FBS, which had been filtered through a 0.2-um PES membrane filter (Nalgene Rapid-flow).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (commercial human total RNAs from Clontech) was enriched for circRNAs by removing rRNAs (RiboMinus Eukaryote Kit) and digesting using RNase R. Reverse transcription was performed with ProtoScript II reverse transcriptase. Circular DNA was precipitated and used as a template for RCA using the TempliPhi 100 Amplification Kit. Debranching was performed by annealing RCA products in a thermocycler using T7 Endonuclease I, followed by isopropanol precipitation. Fragments at 3-50 kb were used for library construction using the Oxford Nanopore Ligation Sequencing Kit (#SQK-LSK109).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
circRNAs
isoCirc_hg19_12Tissues.isocirc.out.gz
|
| Data processing |
Raw ONT long-read data (fast5 format) were base-called using Guppy base-calling software (version 2.1.3). Tandem repeats in each long read were detected by using Tandem Repeats Finder (TRF, version 4.0.9), with recommended settings (TRF /path/to/long_reads 2 7 7 80 10 100 2000 -h -ngs > /path/to/output). The consensus sequence of each tandem repeat was filtered out if length was <30 bp or repeat copy number was <2. Concatemeric copies of consensus sequences were mapped to human reference genome GRCh37/hg19 using minimap2 (version 2.17) with the following settings (minimap2 -ax splice -ub --MD --eqx /path/to/ref_fa /path/to/cons_fa -t 16 > /path/to/output_sam). The minimap2 alignment data were processed by the isoCirc pipeline (https://github.com/Xinglab/isocirc/) to identify high-confidence BSJs and full-length circRNA isoforms. Genome_build was hg19. Supplementary_files_format_and_content: Tab-delimited text files include information of circRNA isoforms identified from each sample.
|
| |
|
| Submission date |
Dec 09, 2019 |
| Last update date |
Sep 12, 2020 |
| Contact name |
Yi Xing |
| E-mail(s) |
[email protected]
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Department of Pathology and Laboratory Medicine
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24106 |
| Series (1) |
| GSE141693 |
isoCirc catalogs full-length circular RNA isoforms in human transcriptomes |
|
| Relations |
| BioSample |
SAMN13514118 |
| SRA |
SRX7291228 |
