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| Status |
Public on Dec 05, 2019 |
| Title |
Massively multiplex chemical transcriptomics at single cell resolution |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Single-cell RNA-seq libraries were generated using two and three level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of untreated or small molecule inhibitor exposed HEK293T, NIH3T3, A549, MCF7 and K562 cells. Different cells and different treatment were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing well-specific oligos that are specific to a given cell type, replicate or treatment condition.
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| Overall design |
Single-cell RNA-seq libraries were generated using two and three level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of untreated or small molecule inhibitor exposed HEK293T, NIH3T3, A549, MCF7 and K562 cells. Different cells and different treatment were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing well-specific oligos that are specific to a given cell type, replicate or treatment condition.
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| Contributor(s) |
Srivatsan S, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson D, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C |
| Citation(s) |
31806696 |
| Submission date |
Nov 05, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
José L McFaline-Figueroa |
| E-mail(s) |
jm5200@columbia.edu, joselmc@uw.edu
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| Organization name |
Columbia University
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| Department |
Biomedical Engineering
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| Street address |
500W 120th st.
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10033 |
| Country |
USA |
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| Platforms (3) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
| GPL24625 |
NextSeq 550 (Homo sapiens; Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA587707 |
| SRA |
SRP228591 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE139944_RAW.tar |
9.2 Gb |
(http)(custom) |
TAR (of MATRIX, RDS, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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