|
| Status |
Public on Feb 09, 2023 |
| Title |
Scalable co-sequencing of RNA and DNA from individual nuclei |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
We present DEFND-seq (DNA and Expression From Nucleosome Depletion), a scalable method for co-sequencing RNA and DNA from single nuclei. In DEFND-seq we treat nuclei with lithium diiodosalicylate to disrupt chromatin and expose genoimc DNA. The nuclei are then tagmented with Tn5 transposase, which fragments and tags gDNA. Tagmented nuclei are loaded into a microfluidic droplet generator which combines nuclei, beads containing transcriptomic and genomic barcodes, and reverse transcription reagents into single droplets. Ultimately two libraries are created, one for nuclear mRNA and one for genomic DNA, with each library containing barcodes linking it to its nuclei of origin, thus allowing simultaneous analysis of single nuclei transcriptomes and genomes. Once nuclei have been depleted of nucleosomes, all steps can be performed using a 10x Chromium Controller and 10x Multiome Kit without further experimental modification.
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| |
|
| Overall design |
DEFND-seq (snRNA/DNA-seq), snATAC-seq, snDNA-seq
|
| |
|
| Contributor(s) |
Olsen T, Sims PA |
| Citation(s) |
36798358 |
| |
| Submission date |
Jan 31, 2023 |
| Last update date |
May 20, 2024 |
| Contact name |
Peter A Sims |
| E-mail(s) |
pas2182@columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
3960 Broadway, Lasker 203AC
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platforms (5)
|
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
| GPL24625 |
NextSeq 550 (Homo sapiens; Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL34474 |
Element AVITI (Homo sapiens; Mus musculus) |
|
| Samples (13)
|
| GSM7016412 |
snDNA-seq of LAND-treated BJ nuclei with 10x scATAC-seq kit |
| GSM7016413 |
snDNA-seq of xSDS-treated BJ nuclei with 10x scATAC-seq kit |
| GSM7016414 |
snATAC-seq of BJ nuclei with 10x scATAC-seq |
| GSM7016415 |
snRNA-seq of LAND-treated BJ nuclei with 10x Multiome (DEFND-seq RNA library) |
| GSM7016416 |
snDNA-seq of LAND-treated BJ nuclei with 10x Multiome (DEFND-seq DNA library) |
| GSM7016417 |
snRNA-seq of LAND-treated U87 and 3T3 nuclei with 10x Multiome (DEFND-seq RNA library) |
| GSM7016418 |
snDNA-seq of LAND-treated U87 and 3T3 nuclei with 10x Multiome (DEFND-seq DNA library) |
| GSM7016419 |
snRNA-seq of LAND-treated glioblastoma nuclei with 10x Multiome (DEFND-seq RNA library) |
| GSM7817780 |
snRNA-seq of LAND-treated glioblastoma nuclei with 10x Multiome (DEFND-seq RNA library) - PTO037 |
| GSM8265289 |
snRNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq RNA library - first reaction) |
| GSM8265290 |
snRNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq RNA library - second reaction) |
| GSM8265291 |
snDNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq DNA library - first reaction) |
| GSM8265292 |
snDNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq DNA library - second reaction) |
|
| Relations |
| BioProject |
PRJNA929977 |
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