|
| Status |
Public on Dec 07, 2020 |
| Title |
tomo-seq zebrafish replicate2 |
| 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 |
SAMN16320331 |
| SRA |
SRX9221549 |
