|
| Status |
Public on Sep 01, 2013 |
| Title |
HEK_56 |
| Sample type |
SRA |
| |
|
| Source name |
single cell, HEK293T, SMART-Seq2 (variant 4)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
library prep protocol: SMART-Seq2 (variant 4)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis buffer from the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' (Clontech).
We prepared sequencing libraries according to the optimized Smart-Seq2 protocol, variants of Smart-Seq2 and using the standard Smart-Seq procedure ('SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PolyA+ RNA
|
| Data processing |
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013).
Non-uniquely mapped reads were removed.
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene expression values (tab-delimited text file).
|
| |
|
| Submission date |
Jul 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Rickard Sandberg |
| E-mail(s) |
Rickard.Sandberg@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Cell and Molecular Biology
|
| Street address |
Berzelius vag 35
|
| City |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE49321 |
Improved Smart-Seq for sensitive full-length transcriptome profiling in single cells |
|
| Relations |
| BioSample |
SAMN02296837 |
| SRA |
SRX328719 |
