|
| Status |
Public on May 13, 2016 |
| Title |
UHRR smartseq J |
| Sample type |
SRA |
| |
|
| Source name |
Universal Human Reference RNA, Smart-seq2
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference RNA
library preparation: Smart-seq2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stratagene Universal Human Reference RNA (UHRR; catalog #740000).
Library preparations were performed with the Smart-seq2 protocol from UHRR as described in Picelli et al. 2013.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Processed data file: uhrr_smartseq_read_counts.txt
|
| Data processing |
Base-calls were performed with Illumina bcl2fastq.
All cDNA reads were aligned with NextGenMap 0.4.12. Smart-seq2 reads were mapped to genome, whereas UMI-seq reads were mapped to Ensembl GRCh37.74 cDNA.
Smart-seq2 reads were mapped to hg19+ERCC reference and assigned to genes using FeatureCount method in Rsubread package.
UMI-seq reads were tagged with its mate-pair UMI after masking bases below 10 quality score; mapped to Ensembl GRCh37.74 cDNA; total read count and unique read count tables were generated.
Genome_build: GRCh37 (hg19) and ERCC synthetic spike-in reference
Supplementary_files_format_and_content: uhrr_smartseq_read_counts.txt: Tab-delimited text file with raw read counts for the Smart-seq2 method.
Supplementary_files_format_and_content: uhrr_umiseq_read_counts.txt: Tab-delimited text file with raw read counts for the UMI-seq method.
Supplementary_files_format_and_content: uhrr_umiseq_umi_counts.txt: Tab-delimited text file with unique gene-wise counts for the UMI-seq dataset.
|
| |
|
| Submission date |
Dec 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Swati Parekh |
| Organization name |
Ludwig Maximillians University Munich
|
| Department |
Biology II
|
| Lab |
Anthropology & Human genetics
|
| Street address |
Grosshaderner Str. 2
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE75823 |
Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods |
|
| Relations |
| SRA |
SRX1471846 |
| BioSample |
SAMN04326832 |
