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Sample GSM2283583 Query DataSets for GSM2283583
Status Public on Sep 28, 2017
Title SORT-Seq; 2h-collagenase-treated; library2
Sample type SRA
 
Source name Satellite cells from Tibialis Anterior muscle
Organism Mus musculus
Characteristics tissue: Satellite cells from Tibialis Anterior muscle
strain: Pax7nGFP
gender: male
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description mice kindly provided by Dr. S. Tajbakhsh, Pasteur Institute Paris, France
SvdB-6e2h-pl3-lib2-Diss2h_AHVCTTBGXX_S17
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).
 
Submission date Aug 17, 2016
Last update date May 15, 2019
Contact name Susanne C van den Brink
E-mail(s) s.c.vandenbrink@hotmail.com
Phone +31 (0)30 212 18 00
Organization name Hubrecht Institute
Lab Alexander van Oudenaarden
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platform ID GPL19057
Series (1)
GSE85755 Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations
Relations
BioSample SAMN05583861
SRA SRX2033532

Supplementary file Size Download File type/resource
GSM2283583_CEL-Seq2_2h-collagenase-treated_library2_unique_transcript_counts.coutt.txt.gz 281.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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