|
| Status |
Public on Jul 22, 2012 |
| Title |
cell5_hESC |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic stem cell
|
| 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 using the Epicentre Nextera sample preparation kit, with 5 min tagmentation at 55C with 0.25 ul transposase and 4 ul 5x HMW Nextera reaction buffer, then 35 ul of PB, then 88 ul SPRI XP beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PolyA+ RNA
Single human embryonic stem cell.
|
| 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 |
SRX160224 |
| BioSample |
SAMN01090527 |
