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Series GSE252510 Query DataSets for GSE252510
Status Public on Feb 14, 2024
Title Mouse Smartseq3 Data from Mold et al. Clonally Heritable Gene Expression Imparts a Layer of Diversity in Cell Types
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Mouse cells harvested from the central nervous system of two different mice injected at post-coital day 9.5 with lentivirus encoding barcodes that allow for clonal tracking and gene expression in single cell RNAseq measurements (TREX, Ratz et al 2022). Cells are isolated from the cortex 14 days after birth and profiled by scRNA-seq using the Smartseq3 method.
 
Overall design Smartseq3 libraries were prepared on single cells isolated from the mouse cortex and FACS sorted based on GFP expression (indicating lentiviral expression of clonal barcodes) according to the standard protocol (https://www.protocols.io/view/smart-seq3-protocol-36wgq5rjxgk5/v3).

Please note that Series supplementary files include an example of how the .yaml file for the zumis-run looks like, the expected barcodes and the .fa file for lentiviral barcodes within the samples, which are needed to accurately regenerate the entire pipeline.
 
Contributor(s) Mold JE, Erickson C, Ratz M, Frisén J
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Submission date Jan 04, 2024
Last update date Feb 14, 2024
Contact name Carl-Johan Wilheard Torkel Eriksson
Organization name Karolinska Institute
Department CMB
Lab Jonas Frisén
Street address Solnavägen 9
City Solna
State/province Stockholm
ZIP/Postal code 17145
Country Sweden
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (1)
GSM8002350 barcoded_ss3_cortex
Relations
BioProject PRJNA1061057

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE252510_EGFP_30N_2.fa.fai.txt.gz 74 b (ftp)(http) TXT
GSE252510_EGFP_30N_2.fa.gz 918 b (ftp)(http) FA
GSE252510_RAW.tar 3.8 Gb (http)(custom) TAR (of RDS)
GSE252510_Smartseq3_example.run.yaml.gz 657 b (ftp)(http) YAML
GSE252510_expected_barcodes.txt.gz 21.8 Kb (ftp)(http) TXT
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Raw data are available in SRA

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