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| Status |
Public on Mar 18, 2018 |
| Title |
HEK293T |
| Sample type |
SRA |
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| Source name |
HEK293T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: epithelial
cell source: embryonic kidney cell line
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| Growth protocol |
HEK293T and HeLa cell lines were maintained at 37℃ and 5% CO2 in DMEM media supplemented with 10% fetal bovine serum, 100 I.U./ml Penicillin, 100 μg/ml Streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolated using Trizol
The ribosomal RNA was depleted by using a Ribo-Zero rRNA Removal Kit (Epicentre) and then used as input for the Illumina TruSeq® Stranded Total RNA HT/LT Sample Prep Kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Mapping reads to human genome (version: hg38) using bowtie 2.0 with the parameters: -D 200 -R 3 -N 0 -L 20 -i S,1,0.5 -- score-min=C,-16,0. The aligned reads are discarded and the remaining unmapped RNA-seq reads are used to identify circRNAs.
Mapping unmapped reads to human genome (version hg38) with local model. The unmapped reads were aligned again using bowtie2 with the parameters (-- no-unal -- local -- reorder -k 20 -D 200 -R 3 -N 0 -L 20 -i S,1,0.5) and then converted alignment SAM format into the BAM format sorted by name using samtools program.
Predicting circRNAs from the alignments of unmapped reads using circSeeker program (http://starbase.sysu.edu.cn/circTools.php) with default paramerters (-l 18 -d 300000).
Annotating novel circRNAs using the known gene annotation using circAnno software (http://starbase.sysu.edu.cn/circTools.php) with parameters(-m).We kept only the circRNAs that mapped the precise exon boundaries of known genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include circRNA locations and their read number
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| Submission date |
Apr 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Hua Yang |
| E-mail(s) |
yangjh7@mail.sysu.edu.cn
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| Phone |
86-20-84112517
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| Organization name |
Sun Yat-sen University
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| Department |
School of Life Sciences
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| Street address |
No. 135, Xingang Xi Road
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| City |
Guangzhou |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE97382 |
Discovering the interactions between circRNAs and RNA-binding proteins from RNA-seq and CLIP-seq data |
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| Relations |
| BioSample |
SAMN06681412 |
| SRA |
SRX2705130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2563627_HEK293T_circSeeker_hg38_circRNAs.txt.gz |
131.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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