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| Status |
Public on Sep 28, 2017 |
| Title |
SORT-Seq zebrafish fin (merged) |
| Sample type |
SRA |
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| Source name |
All cells from caudal fin
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| Organism |
Danio rerio |
| Characteristics |
strain: Wildtype
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were sorted into Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius, after which SORT-Seq (Muraro et al., 2016, with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017) was applied.
As in SORT-Seq protocol (Muraro et al., 2016), with minor modifications as desribed in Supplementary Methods of van den Brink et al., 2017.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads 2 were mapped to the reference transcriptome (created from the genomes downloaded from the UCSC genome browser; ERCC Spike-in sequences and mitochondrial sequences were added) in sense direction using bwa (version 0.6.2-r126) with default parameters. All isoforms of the same gene were merged to a single gene locus and reads mapping to multiple loci in the transcriptome were discarded. Reads 1 contains the cel-specific barcode information (first 8 bases) followed by a UMI-sequence (4bp for unstained satellite cell data; 6bp for MitoTracker Stained satellite cells and zebrafish data) and a polyT-stretch. Reads 1 were thus used to extract the cell-barcode sequences (see “Cel-seq_barcodes_96.csv” file for sequences used for unstained satellite cell data and see "Cel-seq_barcodes_384" for MitoTracker stained satellite cells and zebrafish data) and UMIs; see Supplementary Methods for details.
After mapping, a UMI-correction was applied to the read and barcode counts files to generate unique transcript count tables as described before (see Supplementary Methods section for details). Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).
Genome_build: mus musculus: mm10; danio rerio: Zv9 (Ensembl release 74); both were extended with spike-ins (see "ERCC92.fa")
Supplementary_files_format_and_content: *.coutt.csv, *TranscriptCounts.tsv and *count_table.csv: tab-separated data files listing how many reads of which transcripts were detected in all sequenced cells (after UMI-correction). Column names refer to cells sequenced in this library (numbers refer the the CEL-Seq primer barcode used for that cell). The first column lists official gene symbols followed by the chromosome name, separated by a double underscore. Note that processed files for satellite cell data here still contain ERCC Spike-in molecules, bulk samples (bulk samples are only included in CEL-Seq experiments; see “BulkSamples_BarcodesAndNrOfCellsUsed_perCEL-Seq1-library” file for description of how many cells were used as bulk and which primer barcode sequence was used for bulk sample in each library) and mitochondrial reads (only for MitoTracker stained satellite cells).
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| Submission date |
Sep 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne C van den Brink |
| E-mail(s) |
s.c.vandenbrink@hotmail.com
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| Phone |
+31 (0)30 212 18 00
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| Organization name |
Hubrecht Institute
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| Lab |
Alexander van Oudenaarden
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platform ID |
GPL20828 |
| Series (1) |
| GSE85755 |
Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations |
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| Relations |
| BioSample |
SAMN07647943 |
| SRA |
SRX3187382 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2781033_fin_C_E_count_table.csv.gz |
4.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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