|
| Status |
Public on Aug 15, 2024 |
| Title |
ALDH low LNCaP cells, No2_2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP cells
cell type: prostate cancer cells
group: ALDH low
|
| Treatment protocol |
N/A
|
| Growth protocol |
LNCaP ALDH high and ALDH low cells were cultured in RPMI-1640 supplied with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
mRNA sequencing via polyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Description |
LNALNegNo2
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Supplementary files format and content: csv
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Aug 15, 2024 |
| Contact name |
Che-Chia Hsu |
| E-mail(s) |
che-chia.hsu@duke.edu
|
| Phone |
9196682177
|
| Organization name |
Duke University
|
| Department |
Pathology
|
| Street address |
210 Research Drive, GSRB2, Rm#4014
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE270565 |
Characterization of gene profile between ALDH high LNCaP cells and ALDH low LNCaP cells |
|
| Relations |
| BioSample |
SAMN42048718 |
| SRA |
SRX25059297 |
