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Sample GSM8346757

Query DataSets for GSM8346757

Status

Public on Aug 15, 2024

Title

22RV1 cells, shIMPA1 #2

Sample type

SRA

Source name

22RV1

Organism

Homo sapiens

Characteristics

cell line: 22RV1
cell type: prostate cancer cells
treatment: shIMPA1

Treatment protocol

N/A

Growth protocol

22RV1 cells stably expressing shLuc, shIMPA1 and shIMPDH2 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

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: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2 (KD_RNAseq 123478_processed data.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