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Sample GSM3432576 Query DataSets for GSM3432576
Status Public on Aug 14, 2019
Title O1_TA_Hi_23 [scRNA-seq]
Sample type SRA
 
Source name Tibialis anterior muscles
Organism Mus musculus
Characteristics strain: MGI: 5308730
cell type: Muscle stem cells
age: 24 months
mouse id: O1
Treatment protocol Muscles were chopped and put into a 15 ml Falcon tube containing 10 ml of DMEM, 0.08% collagenase D (Sigma, 11 088 882 001), 0.1% trypsin (ThermoFisher, 15090), 10 µg/ml DNaseI (Sigma, 11284932) at 37°C under gentle agitation for 25 min. The digestion was repeated 3 times until complete digestion of the muscle. The supernatants were filtered through a 70-µm cell strainer (Miltenyi, 130-098-462). Cells were spun for 15 min at 515g at 4°C and the pellets were resuspended in 1 ml freezing medium (10% DMSO (Sigma, D2438) in foetal calf serum (FCS, Invitrogen)) for long term storage in liquid nitrogen. Before FACS isolation, samples were thawed in 50 ml of cold DMEM, spun for 15 min at 515g at 4°C. Pellets were resuspended in 300 µl of DMEM 2% FCS 1 µg/mL propidium iodide (Calbiochem, 537060) and filtered through a 40-µm cell strainer (BD Falcon, 352235). Viable cells were isolated based on size, granulosity and GFP expression level (top 10% nGFPHi cells) using a MoFlo Astrios cell sorter (Beckmann Coulter). Single cells were collected in 2.5 µL cold RLT Plus buffer (Qiagen, 1053393) containing 1U/µL RNase inhibitor (Ambion, AM2694) in 96 well-plates (LoBind Eppendorf, 0030129504), flash-frozen on dry ice and stored at -80°C.
Extracted molecule total RNA
Extraction protocol We prepared scM&T-seq libraries by isolating mRNA on magnetic beads and separating from the single-cell lysate prior to reverse transcription and amplification using Smartseq2 but with 25 PCR cycles.
scM&T-seq (C. Angermueller et al., 2016)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description mRNA
processed data file: Table_raw_counts_RNA_QSC.txt
Data processing Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Genome_build: GRCm38
Supplementary_files_format_and_content: Table_raw_counts_RNA_QSC.txt file contains the raw counts per gene quantified over the exons using the RNA-seq quantitation pipeline in Seqmonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) in the format: <gene name> <chromosome> <start> <counts cell1> <counts cell 2> .... < counts celln>
 
Submission date Oct 16, 2018
Last update date Aug 14, 2019
Contact name Felix Krueger
E-mail(s) fkrueger@altoslabs.com
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE121364 Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells [scRNA-seq]
GSE121437 Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells
Relations
BioSample SAMN10249417
SRA SRX4895209

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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