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Sample GSM4812175 Query DataSets for GSM4812175
Status Public on Dec 07, 2020
Title tomo-seq zebrafish replicate1
Sample type SRA
 
Source name one-cell stage embryo
Organism Danio rerio
Characteristics strain: AB wildtype
treatment: untreated
extraction protocol: Fresh frozen, cryo-sectioned embryo.
Extracted molecule polyA RNA
Extraction protocol none provided by the submitter
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 3' biased spatially barcoded sub-single cell transcriptome. R1 contains biological information, R2 contains 6 nt UMI and 8 nt section barcode.
Data processing zebrafish tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode
Genome_build: GRCz10 - release 90
Supplementary_files_format_and_content: csv file containing gene counts per section
xenopus tomo-seq
demultiplexing with bcl2fastq v2.18.0.12
mapping with STAR v2.5.3a
split counts by section barcode and translate gene identifier to gene names
Genome_build: X. tropicalis v9.1 genome assembly, X.laevis v9.2 genome assembly
Supplementary_files_format_and_content: csv file containing gene counts per section
scSLAM-seq zebrafish
demultiplexing using cellranger mkfastq v3.0.2
mapping and whitelisting of cells with cellranger v3.0.2
splitting labeled reads (>1 T-C mutation) from unlabeled into separate fastq files (submitted to this GEO entry)
mapping with STARsolo v2.7.0f_0328
single cell analysis in seurat v3.1.2
Genome_build: GRCz11
Supplementary_files_format_and_content: _barcodes.tsv list of barcodes, _genes.tsv list of genes, and _matrix.tsv count matrix
 
Submission date Sep 30, 2020
Last update date Dec 08, 2020
Contact name Jan Philipp Junker
E-mail(s) JanPhilipp.Junker@mdc-berlin.de
Organization name MDC
Department BIMSB
Lab Junker
Street address Hannoversche Str. 28
City Berlin
ZIP/Postal code 10115
Country Germany
 
Platform ID GPL20828
Series (1)
GSE158849 Spatio-temporal mRNA tracking in the early zebrafish embryo
Relations
BioSample SAMN16320333
SRA SRX9221548

Supplementary file Size Download File type/resource
GSM4812175_tomoseq.zebrafish.rep1.csv.gz 1012.1 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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