|
| Status |
Public on Apr 11, 2019 |
| Title |
MULTI-seq: Universal sample multiplexing for single-cell RNA sequencing using lipid-tagged indices |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We report the development of MULTI-seq: a scRNA-seq and snRNA-seq sample multiplexing approach using lipid- or cholesterol-modified oligonucleotides. We demonstrate MULTI-seq utility in the following scRNA-seq and snRNA-seq contexts: (1) Live HEKs and HMECs with and without stimulation with TGF-β, (2) Purified nuclei from HEKs, MEFs, and Jurkats stimulated for 0-24 hrs with ionomycin and PMA, (3) 96 unique HMEC cultures (with one technical replicate), and (4) human metastases and mouse immune cells isolated from cryopreserved primary tissue samples dissected from a patient-derived xenograft mouse model of triple-negative breast cancer at progressive stages of metastasis to the lung.
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| |
|
| Overall design |
Single-cell or single-nucleus gene expression profiles for (1) HEKs and HMECs, (2) HEKs, MEFs, and Jurkats, (3) HMECs in distinct culture conditions, and (4) Human metastases and mouse immune cells from PDX mice.
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| |
|
| Contributor(s) |
McGinnis CS, Gartner ZJ |
| Citation(s) |
31209384 |
| |
| Submission date |
Apr 10, 2019 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Christopher S McGinnis |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, San Francisco
|
| Department |
Pharmaceutical Chemistry
|
| Lab |
Zev Gartner
|
| Street address |
600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL25431 |
Illumina HiSeq 4000 (Homo sapiens; Mus musculus) |
| GPL25526 |
Illumina NovaSeq 6000 (Homo sapiens; Mus musculus) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA531855 |
| SRA |
SRP192397 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129578_HMEC1_techrep_matrix.mtx.gz |
39.1 Mb |
(ftp)(http) |
MTX |
| GSE129578_HMEC2_techrep_matrix.mtx.gz |
34.6 Mb |
(ftp)(http) |
MTX |
| GSE129578_HMEC3_techrep_matrix.mtx.gz |
36.3 Mb |
(ftp)(http) |
MTX |
| GSE129578_HMEC4_techrep_matrix.mtx.gz |
50.5 Mb |
(ftp)(http) |
MTX |
| GSE129578_HMEC_orig_matrix.mtx.gz |
608.9 Mb |
(ftp)(http) |
MTX |
| GSE129578_PDX_hs_matrix.mtx.gz |
5.9 Mb |
(ftp)(http) |
MTX |
| GSE129578_PDX_mm_matrix.mtx.gz |
47.3 Mb |
(ftp)(http) |
MTX |
| GSE129578_POC_matrix.mtx.gz |
269.3 Mb |
(ftp)(http) |
MTX |
| GSE129578_POC_nuc_matrix.mtx.gz |
70.7 Mb |
(ftp)(http) |
MTX |
| GSE129578_processed_data_files.csv.tar.gz |
3.7 Mb |
(ftp)(http) |
TAR |
| GSE129578_processed_data_files.tsv.tar.gz |
32.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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