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| Status |
Public on Dec 14, 2020 |
| Title |
T74_P003 |
| Sample type |
SRA |
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| Source name |
T74
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| Organism |
Homo sapiens |
| Characteristics |
cell_number: 18
tissue: TONSIL
Sex: M
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
May 07, 2020 |
| Last update date |
Dec 15, 2020 |
| Contact name |
Luca Mazzurana |
| E-mail(s) |
luca.mazzurana@ki.se
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| Organization name |
Karolinska Institutet
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| Street address |
Alfred Nobels Aleè 8
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| City |
Huddinge |
| ZIP/Postal code |
14152 |
| Country |
Sweden |
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| 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 |
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| Relations |
| Reanalysis of |
GSM1810550 |
| Reanalysis of |
GSM1810551 |
| Reanalysis of |
GSM1810552 |
| Reanalysis of |
GSM1810553 |
| Reanalysis of |
GSM1810554 |
| Reanalysis of |
GSM1810555 |
| Reanalysis of |
GSM1810556 |
| Reanalysis of |
GSM1810557 |
| Reanalysis of |
GSM1810558 |
| Reanalysis of |
GSM1810559 |
| Reanalysis of |
GSM1810560 |
| Reanalysis of |
GSM1810561 |
| Reanalysis of |
GSM1810562 |
| Reanalysis of |
GSM1810563 |
| Reanalysis of |
GSM1810564 |
| Reanalysis of |
GSM1810565 |
| Reanalysis of |
GSM1810566 |
| Reanalysis of |
GSM1810567 |
| BioSample |
SAMN14848780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4521378_T74_P003.tar.gz |
772.9 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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