|
| Status |
Public on Apr 09, 2024 |
| Title |
scCOLORseq_R3 |
| Sample type |
SRA |
| |
|
| Source name |
5TGM1 and Jurkat
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: 5TGM1 and Jurkat
|
| Growth protocol |
Jurkat and 5TGM1 cells were cultured in complete RPMI medium supplemented with 10% Foetal Calf Serum
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
scCOLOR-seq v2 protocol was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
We performed basecalling on the raw pod5 data using Derado in GPU mode from Oxford Nanopore Technologies running on four A100 graphics card. For each read we identify the barcode and UMI sequence by searching for the polyA region and flanking regions before and after the barcode/UMI. Accurately sequenced barcodes were identified based on their dual nucleotide complementarity. Unambiguous barcodes were then used as a guide to error correct the ambiguous barcodes in a second pass correction analysis approach. Fastq data was processed using TallyTrin pipelines (https://github.com/cribbslab/TallyTriN). Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. Mapping settings we as follows: -ax splice -uf MD –sam-hit-only –junc-bed and using the reference transcriptome for human hg38 and mouse mm10. The resulting sam file was sorted and indexed using samtools. The transcript name was then appended to the bam XT flag using the xt_tag_nano script before umi_tools count module was used to count the features using the following settings: --per-gene --gene-tag=XT --per-cell --dual-nucleotide. The umi_tools used to correct for the dimer UMIs is located in the AC-dualoligo in a fork at the repository: https://github.com/Acribbs/UMI-tools.
Assembly: hg38 and mm10
Supplementary files format and content: Tab seperated files and market matrix gz files
Supplementary files format and content: log files: the calculation of polyA positive data that is integral for an up and coming manuscript. The data contained in these files is the output of our analysis workflow.
|
| |
|
| Submission date |
Apr 08, 2024 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Adam Cribbs |
| E-mail(s) |
adam.cribbs@ndorms.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
NDORMS
|
| Street address |
Windmill Road
|
| City |
Oxford |
| ZIP/Postal code |
OX37LD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL32819 |
| Series (1) |
| GSE263458 |
Anchor-Enhanced Bead Design for Reduced Oligonucleotide Synthesis Errors in Single-cell sequencing |
|
| Relations |
| BioSample |
SAMN40874312 |
| SRA |
SRX24189016 |
