|
| Status |
Public on Jul 18, 2022 |
| Title |
SNXB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCC1954 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC1954
|
| Treatment protocol |
DMSO, 1 µM of SNXB, 1 µM of Lapatinib, and Combination for 24 hours, with three biological repeats
|
| Growth protocol |
HCC1954 cells were cultured in RPMI1640 + 10% FBS + 1% pen/strep/Glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy mini kit
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
Dec 16, 2021 |
| Last update date |
Jul 18, 2022 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE191050 |
RNA-seq on HER2+ cell line upon treatments |
|
| Relations |
| BioSample |
SAMN24118223 |
| SRA |
SRX13426997 |
