|
| Status |
Public on Sep 09, 2020 |
| Title |
Scalable Dual-omic Profiling with Single-nucleus Chromatin Accessibility and mRNA Expression Sequencing 2 (SNARE-seq2) |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
We perform benchmark experiments using cell lines to develop and assess the performance of a scalable method for generating matched RNA and chromatin accessibility profiles
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| |
|
| Overall design |
3T3 cells amd A549 cells were fixed with 1% formaldehyde and cryopreserved in 1x PBS with 10% (vol/vol) DMSO and 0.1% (wt/vol) BSA for three weeks. GM12878 cells were freshly fixed with 1% formaldeyhyde and ran in two separate experiments. GM12878 nuclei were lysed in cell lysis buffer with RNase Inhibitors (10 mM Tris pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v NP-40, Superase RNase Inhibitors, Enzymatics RNase Inhibitors) then fixed with 1% formaldehyde. Fixed samples were processed with SNARE-seq2 protocol.
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| |
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| Contributor(s) |
Plongthongkum N, Diep D, Zhang K |
| Citation(s) |
34650278 |
| |
| Submission date |
Sep 08, 2020 |
| Last update date |
Jun 23, 2022 |
| Contact name |
Kun Zhang |
| E-mail(s) |
k4zhang@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Bioengineering
|
| Lab |
Integrative Genomics Laboratory
|
| Street address |
9500 Gilman Dr Mailcode: 0412
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (12)
|
| GSM4772950 |
3T3 cells processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772951 |
A549 cells processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772952 |
GM12878 cells exp1 processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772953 |
GM12878 nuclei exp2 processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772954 |
GM12878 cells exp3 1 processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772955 |
GM12878 cells exp3 2 processed with SNARE-seq2 protocol (ATACseq) |
| GSM4772956 |
3T3 cells processed with SNARE-seq2 protocol (RNAseq) |
| GSM4772957 |
A549 cells processed with SNARE-seq2 protocol (RNAseq) |
| GSM4772958 |
GM12878 cells exp1 processed with SNARE-seq2 protocol (RNAseq) |
| GSM4772959 |
GM12878 nuclei exp2 processed with SNARE-seq2 protocol (RNAseq) |
| GSM4772960 |
GM12878 cells exp3 1 processed with SNARE-seq2 protocol (RNAseq) |
| GSM4772961 |
GM12878 cells exp3 2 processed with SNARE-seq2 protocol (RNAseq) |
|
| Relations |
| BioProject |
PRJNA662341 |
| SRA |
SRP281423 |
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