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Sample GSM1968483 Query DataSets for GSM1968483
Status Public on May 13, 2016
Title UHRR smartseq E
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 SRX1471841
BioSample SAMN04326827

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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