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Sample GSM4521376 Query DataSets for GSM4521376
Status Public on Dec 14, 2020
Title T74_P001
Sample type SRA
 
Source name T74
Organism Homo sapiens
Characteristics cell_number: 21
tissue: TONSIL
Sex: M
Extracted molecule total RNA
Extraction protocol Sorted cells were processed using the Smart-seq2 protocol with minor changes (Picelli et al., 2013). Sequencing was done to the average depth of 0.7 million reads per cell with 43bp reads (single end) after demultiplexing. Blood samples were additionally sequenced for V(D)J analysis to and average depth of 0.84 million reads per cell with 150 bp reads (paired end) after demultiplexing.
Smart-Seq2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing The reads were aligned to the human genome (hg19 –GRCh38) and spike-in sequences (from the External RNA Controls Consortium) using STAR v2.5.3a (Dobin et al., 2013), and filtered for uniquely mapping reads. Counts per gene were calculated for each transcript in Ensembl release 92 using rpkmforgenes (Ramsköld et al., 2009). The following rpkmforgenes options were used: -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendsceil
Genome_build: hg19 –GRCh38
Supplementary_files_format_and_content: Tab delimited files include metadata, barcodes and features of each plate. We also included a matrix containing estimated counts.
 
Submission date May 07, 2020
Last update date Dec 15, 2020
Contact name Luca Mazzurana
E-mail(s) luca.mazzurana@ki.se
Organization name Karolinska Institutet
Street address Alfred Nobels Aleè 8
City Huddinge
ZIP/Postal code 14152
Country Sweden
 
Platform ID GPL11154
Series (1)
GSE150050 Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing
Relations
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BioSample SAMN14848782

Supplementary file Size Download File type/resource
GSM4521376_T74_P001.tar.gz 829.5 Kb (ftp)(http) TAR
Processed data provided as supplementary file
Processed data are available on Series record
Raw data not provided for this record

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