|
| Status |
Public on Mar 27, 2024 |
| Title |
mBC replicate 1 scRNA |
| Sample type |
SRA |
| |
|
| Source name |
Mouse brain cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse brain cortex
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
GAGE-seq protocol
Hi-C and scRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexing using custom scripts
Alignment by BWA (version 0.7.17-r1188) for genomic DNA and by STAR (version 2.7.8a) for RNA
Deduplication using custom scripts
Contact calling by pairtools (version 0.3.1-dev.1)
RNA read count extraction by featureCounts (version 2.0.1)
Assembly: hg38; mm10
Supplementary files format and content: Tab-delimited text files include chromatin contact pairs for single cells
Supplementary files format and content: Tab-delimited text files include RNA reads and mapped genes for single cells
|
| |
|
| Submission date |
Jul 21, 2023 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Jian Ma |
| E-mail(s) |
jianma@cs.cmu.edu
|
| Organization name |
Carnegie Mellon University
|
| Street address |
5000 Forbes Ave
|
| City |
Pittsburgh |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE238001 |
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells |
|
| Relations |
| BioSample |
SAMN36678063 |
| SRA |
SRX21126325 |
