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Sample GSM967544 Query DataSets for GSM967544
Status Public on Jul 22, 2012
Title PC3 s4_HCT20630-PC3-14
Sample type SRA
Source name PC3 cell
Organism Homo sapiens
Characteristics cell line: PC3
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 PC3.
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 available at
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
Organization name Karolinska Institutet
Lab Rickard Sandberg's group ( (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
SRA SRX160256
BioSample SAMN01090559

Supplementary file Size Download File type/resource
GSM967544_s4_HCT20630-PC3-14.bed.gz 319.2 Mb (ftp)(http) BED
GSM967544_s4_HCT20630-PC3-14_RPKM.txt.gz 370.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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