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| Status |
Public on May 12, 2022 |
| Title |
16D LTenza FUCRW 3 |
| Sample type |
SRA |
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| Source name |
16D
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 16D
cell type: Prostate cancer
genotype: WT
treatment: LTenza FUCRW
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| Growth protocol |
16D cells were maintained in RPMI + 10% FBS + 1% Penn/Strep
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated by RNeasy Mini Kit from Qiagen. The integrity of total RNA was examined by the Agilent 4200 TapeStation System.
Libraries for RNA-Seq were constructed with Nugen Universal plus mRNA-Seq Kit to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final libraries. Amplified libraries were quantified by Qubit dsDNA HS (High Sensitivity) Assay Kit, and quality-checked by the Agilent 4200 TapeStation System. Different index adaptors were used for multiplexing samples in one sequencing lane. Sequencing was performed with HiSeq3000 sequencer to produce 50 base-pair single-end reads (1 x 50 bp).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
6_FUCRW_enza_3_S6
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| Data processing |
The Partek flow was used for the data analysis. The alignment was performed using STAR and RSEM with assembly as hg38 and the aligner index as whole genome. The hg38 – Ensembl GRch38 was used for gene feature annotation. For normalization of transcripts counts, the normalization method, TPM, was used.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
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| Submission date |
May 12, 2022 |
| Last update date |
May 12, 2022 |
| Contact name |
Andrew Scott Goldstein |
| Organization name |
UCLA
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| Department |
Urology
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| Lab |
Goldstein
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| Street address |
610 Charles E Young Dr East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE202897 |
RNA sequencing of 16D LTenza cells transduced with cMyc, shRb1, shTp53, shRb1_shTp53 |
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| Relations |
| BioSample |
SAMN28208799 |
| SRA |
SRX15244335 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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