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Sample GSM6689313 Query DataSets for GSM6689313
Status Public on Mar 27, 2024
Title 22Rv1, Control, rep1
Sample type SRA
 
Source name Cell line
Organism Homo sapiens
Characteristics tissue: Cell line
cell line: 22Rv1
cell type: Prostate cancer cell line
genotype: Wilde Type
Growth protocol The medium for this cell lines is RPMI-1640 Medium supplumented with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol  Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 22Rv1sgGFP-1
Data processing RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). 
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: 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 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.
Supplementary files format and content: 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.
 
Submission date Oct 27, 2022
Last update date Mar 27, 2024
Contact name Yasutaka Yamada
E-mail(s) yasutaka_yamada@dfci.harvard.edu
Phone 8574988355
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Beltran
Street address 44 Binney street
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24676
Series (2)
GSE216054 DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3
GSE216712 DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [22Rv1sgCD276]
Relations
BioSample SAMN31489036
SRA SRX18046666

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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