|
| Status |
Public on Jul 26, 2022 |
| Title |
siSCR rep1 |
| Sample type |
SRA |
| |
|
| Source name |
S18
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: nasopharyngeal carcinoma cell
cell line: S18
|
| Treatment protocol |
S18 cells were treated with circIPO7 siRNA or control siRNA using Lipofectamine 3000 reagent. The cells were harvested after transfection at 48h for assays.
|
| Growth protocol |
S18 cells were maintained in DMEM supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent was used to extract total RNA from S18 cell line.
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end sequence files (fastq) were mapped to the reference genome (hg38) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Genome_build: hg38
|
| |
|
| Submission date |
Nov 23, 2021 |
| Last update date |
Jul 26, 2022 |
| Contact name |
Yingqin Li |
| E-mail(s) |
liyingq@sysucc.org.cn
|
| Organization name |
Sun Yat-sen University Cancer Center
|
| Lab |
State Key Laboratory of Oncology in South China
|
| Street address |
Room 927, Building 2, No. 651 Road Dong Feng East
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE189458 |
The RNA sequencing analysis of nasopharyngeal carcinoma (NPC) cell line S18 upon circIPO7 knockdown |
| GSE189459 |
CircIPO7 Promotes Nasopharyngeal Carcinoma Metastasis and Cisplatin Chemoresistance by Regulating YBX1 Nuclear Localization |
|
| Relations |
| BioSample |
SAMN23413518 |
| SRA |
SRX13212044 |
