|
| Status |
Public on Apr 18, 2024 |
| Title |
HK1_sgFLI1-2 |
| Sample type |
SRA |
| |
|
| Source name |
nasopharynx
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: nasopharynx
cell line: HK1
cell type: Nasopharyngeal carcinoma cells
genotype: FLI1 knockout
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed with the AllPrep RNA/DNA Mini Kit (Qiagen) according to manufacturer’s instructions.
The NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) was employed for generating sequencing libraries, following the manufacturer's guidelines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-Seq data underwent adaptor trimming, and data quality assessment was performed using fastp software (v 0.23.2) prior to any data filtering steps.
The reads were aligned to the human reference genome (GRCh38.p12 assembly) using HISAT2 software (v 2.0.4).
The aligned reads were then assembled into transcripts or genes using StringTie software (v 1.3.4d) and the genome annotation file (hg38_ucsc.annotated.gtf).
For quantification purposes, the relative abundance of the transcripts/genes was determined using a normalized metric called FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: hg38
Supplementary files format and content: excel file includes raw counts for each Sample
Supplementary files format and content: excel file includes RPKM values for each Sample
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Apr 18, 2024 |
| Contact name |
wuguo deng |
| E-mail(s) |
dengwg@sysucc.org.cn
|
| Phone |
15627863020
|
| Organization name |
Sun yat-sen university
|
| Street address |
651 Dongfengdongroad, Guangzhou, Guangdog
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE247897 |
FLI1 promotes IFN-γ-induced kynurenine production to impair anti-tumor immunity (RNA-Seq) |
| GSE247898 |
FLI1 promotes IFN-γ-induced kynurenine production to impair anti-tumor immunity |
|
| Relations |
| BioSample |
SAMN38268997 |
| SRA |
SRX22537795 |
