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Sample GSM8192576 Query DataSets for GSM8192576
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 WIMM
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
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

Supplementary file Size Download File type/resource
GSM8192576_mtx_positional.tar.gz 9.5 Mb (ftp)(http) TAR
GSM8192576_mtx_spacer.tar.gz 8.0 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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