|
| Status |
Public on Jun 04, 2020 |
| Title |
BI006_marm028_Munchkin_caud_rxn2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult Marmoset Brain
|
| Organism |
Callithrix jacchus |
| Characteristics |
platform: 10X v3
tissue: Striatum; Caudate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single-nucleus gene expression data based on 3' transcript counts
marm.str.int.10X.raw.dge.txt.gz
|
| Data processing |
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 05, 2020 |
| Contact name |
Fenna Marie Krienen |
| E-mail(s) |
fennak@gmail.com, fenna_krienen@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
McCarroll
|
| Street address |
77 Ave Louis Pasteur, NRB 260
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL28240 |
| Series (1) |
| GSE151761 |
Innovations in primate interneuron repertoire |
|
| Relations |
| BioSample |
SAMN15096875 |
| SRA |
SRX8466746 |
