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| Status |
Public on Feb 12, 2016 |
| Title |
LNCaP_rep1 |
| Sample type |
SRA |
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| Source name |
prostate cancer cell (LNCaP)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP cell
passages: Primary PC
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| Growth protocol |
Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were flash frozen on dry ice, and RNA was harvested using Rneasy Plus Mini Ki t(Qiagen). Ribo-zero rRNA remove Kit was used. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
LNCaP_rep1.txt
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| Data processing |
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with parameters "-p 4 --keep-fasta-order --keep-tmp -z0 --no-coverage-search --bowtie1 --library-type fr-unstranded --max-multihits 20".
Raw count and RPKM were calcualted using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--' -r hg19.refseq.bed12"
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed files are Tab separated plain text files. Each file contains 10 columns:Chromosome, transcript start position, transcript end position, RefSeq accession number, score (0), transcript strand, read count calculated from reads mapped to forward strand, read count calculated from reads mapped to reverse strand, RPKM calculated from reads mapped to forward strand, RPKM calculated from reads mapped to reverse strand.
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| Submission date |
Feb 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
LIGUO WANG |
| E-mail(s) |
wang.liguo@mayo.edu
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| Organization name |
Mayo Clinic
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| Department |
Division of Computational Biology
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| Street address |
200 1st St SW
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE55030 |
Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs [RNA-Seq] |
| GSE55032 |
Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs |
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| Relations |
| BioSample |
SAMN02641985 |
| SRA |
SRX471199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1328161_C4-2_rep1_count.txt.gz |
725.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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