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| Status |
Public on Apr 03, 2019 |
| Title |
Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Difference in RNA content of different cell types introduces bias to gene expression deconvolution methods. If ERCC spike-ins are introduced into samples, predicted proportions of deconvolution methods can be corrected
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| Overall design |
Two cell types of distinctly different sizes and RNA per cell content: HEK cells and Jurkat cells were mixed in different proportions ensuring that each mixture contained total of one million cells. We sequenced RNA of the samples (including ERCC spike-in controls to 382 be able to control for the absolute RNA-concentration).
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| Contributor(s) |
Konstantin Z, Bambouskova M, Swain A, Artyomov MN |
| Citation(s) |
31101809 |
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| Submission date |
Apr 02, 2019 |
| Last update date |
May 29, 2019 |
| Contact name |
Maxim Artyomov |
| E-mail(s) |
martyomov@wustl.edu
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| Organization name |
WASHINGTON UNIVERSITY IN ST LOUIS
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| Department |
Pathology & Immunology
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| Lab |
Artyomov lab
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| Street address |
425 S Euclid Ave
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| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (14)
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| GSM3703351 |
Mixture 4: 80% HEK, 20% Jurkat |
| GSM3703352 |
Mixture 5: 60% HEK, 40% Jurkat |
| GSM3703353 |
Mixture 6: 60% HEK, 40% Jurkat |
| GSM3703354 |
Mixture 7: 50% HEK, 50% Jurkat |
| GSM3703355 |
Mixture 8: 50% HEK, 50% Jurkat |
| GSM3703356 |
Mixture 9: 40% HEK, 60% Jurkat |
| GSM3703357 |
Mixture 10: 40% HEK, 60% Jurkat |
| GSM3703358 |
Mixture 11: 20% HEK, 80% Jurkat |
| GSM3703359 |
Mixture 12: 20% HEK, 80% Jurkat |
| GSM3703360 |
Mixture 13: 0% HEK, 100% Jurkat |
| GSM3703361 |
Mixture 14: 0% HEK, 100% Jurkat |
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| Relations |
| BioProject |
PRJNA530575 |
| SRA |
SRP190212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129240_RAW.tar |
21.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE129240_rsem_expected_counts.tsv.gz |
984.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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