|
| Status |
Public on Jun 18, 2024 |
| Title |
H2023 Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
NCI-H2023
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCI-H2023
cell type: Non-small cell lung cancer
genotype: PTPRH Endogenous
treatment: FBS stimulation
|
| Treatment protocol |
Cells were serum starved for 24 hours, followed by FBS stimulation (5% or 10% in complete media for NCI-H2023 and NCI-H23 derived cells, respectively) for 16 hours prior to collection of total RNA.
|
| Growth protocol |
Each cell line was seeded in 6-wells plates (n=3/group) and the total RNA was extracted when cells reached ~80% confluency.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen #74104) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Paired-end RNA sequencing (Illumina PE150) were conducted using NovaSeq X Plus Series (Illumina) with a minimum coverage of 30M reads per sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
MC2
|
| Data processing |
The quality of the raw reads was assessed through FastQC 0.11.7 and trimmed using Trimmomatic 0.39. Trimmed reads were aligned against the human genome (grch38) using Hisat2 2.1.0 and a count matrix of raw reads to be used as input for DESeq2 was generated by StringTie 2.1.3 as described in the StringTie documentation.
Assembly: Trimmed reads were aligned against the human genome (grch38) using Hisat2 2.1.0
Supplementary files format and content: gene_count_matrix.csv includes matrix of raw counts for each sample.
Supplementary files format and content: phenodata.csv included phenodata information for each sample.
|
| |
|
| Submission date |
Jun 18, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Mylena M.O. Ortiz |
| E-mail(s) |
[email protected]
|
| Organization name |
Michigan State University
|
| Department |
Genetics and Genomics Sciences
|
| Lab |
Eran Andrechek
|
| Street address |
567 Wilson Road
|
| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE270167 |
Effects of the receptor-like protein tyrosine phosphatase PTPRH overexpression on gene expression in non-small cell lung cancer cell lines |
|
| Relations |
| SRA |
SRX24967207 |
| BioSample |
SAMN41896188 |
