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Sample GSM967517 Query DataSets for GSM967517
Status Public on Jul 22, 2012
Title LNCaP s_2_1c
Sample type SRA
 
Source name LNCaP cell
Organism Homo sapiens
Characteristics cell line: LNCaP
Extracted molecule total RNA
Extraction protocol cDNA was generated as described in the manual for "SMARTer Ultra Low RNA Kit for Illumina sequencing" marketed by Clontech. Then, a sequencing library was generated as described in Illumina's "Ultra Low Input mRNA-Seq Guide".
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description PolyA+ RNA
Single cell from the prostate cancer cell line LNCaP, spiked into blood and picked by EPCAM marker.
Data processing Alignment by Bowtie (version 0.12.7, option –best) to genome and exon-exon junctions.
Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
Conversion by samtools to bam format.
Conversion by bedtools to bed format.
Generation of RPKM (reads per kilobase and million mapped reads) values by rpkmforgenes.py available at http://sandberg.cmb.ki.se/rnaseq/.
Genome_build: mm9 for mouse; hg19 for human.
Supplementary_files_format_and_content: Bed12 format with uniquely aligned reads.
Supplementary_files_format_and_content: Tab-delimited plain text format with gene expression values in RPKM.
 
Submission date Jul 16, 2012
Last update date May 15, 2019
Contact name Daniel Ramsköld
E-mail(s) daniel.ramskold@ki.se
Organization name Karolinska Institutet
Lab Rickard Sandberg's group (rickard.sandberg@ki.se) (2008-2014, 2018-); Rheumatology unit (2014-2018)
Street address Nobels väg 3
City Stockholm
ZIP/Postal code 17177
Country Sweden
 
Platform ID GPL10999
Series (1)
GSE38495 Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Relations
SRA SRX160229
BioSample SAMN01090532

Supplementary file Size Download File type/resource
GSM967517_s_2_1c.bed.gz 376.1 Mb (ftp)(http) BED
GSM967517_s_2_1c_RPKM.txt.gz 351.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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