|
| Status |
Public on Jun 01, 2023 |
| Title |
30cycle_dropseq |
| Sample type |
SRA |
| |
|
| Source name |
JJN3 and 5TGMG1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JJN3 and 5TGMG1
cell type: Myeloma cell lines (500 cells)
treatment: 30cycles
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were processed using either 10X chromium or the Drop-seq DolomiteBio Nadia encapsulator system.
10X library preperation or scCOLOR-seq protocol was used.
For nanopore sequencing, cDNA was amplified with 30 or 35 PCR reactions and sequencing libraries were prepared using the Oxford Nanopore LSK-114 library preperation kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r104_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a A100 graphics card.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Mar 13, 2023 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Adam Cribbs |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
NDORMS
|
| Street address |
Windmill Road
|
| City |
Oxford |
| ZIP/Postal code |
OX37LD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26167 |
| Series (2) |
| GSE218901 |
Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq] |
| GSE218903 |
Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules |
|
| Relations |
| BioSample |
SAMN33743859 |
| SRA |
SRX19662561 |
