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Sample GSM5081941 Query DataSets for GSM5081941
Status Public on Feb 23, 2022
Title D27 megakaryocyte culture sorted for progenitor cells
Sample type SRA
 
Source name A1ATD induced pluripotent stem cells
Organism Homo sapiens
Characteristics cell line: A1ATD1
day of differentiation: 27
cell type: Induced pluripotent stem cell-derived megakaryocytes
sorted for: MICBhi, PVRhii, CD42lo
Treatment protocol Cells were stained with antibodies against MICB, PVR and CD42 and sorted using FACS Aria III, selecting viable cells by DAPI staining. These were directly prepared for 10X sequencing.
Growth protocol Moreau et al., 2016. Megakaryocyte forward programming by lentiviral transduction with 3 transcription factors and two cytokine combinations.
Extracted molecule total RNA
Extraction protocol 10X library preparation.
10X VDJ protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description D27
Single cell RNA-Seq
cDNA
Data processing Quality of fastq files was assessed with Fastqc v0.11.3 and summarised with MultiQC v1.8.
Alignment and protein-coding gene quantification was performed using 10x cellranger v3.1.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
 
Submission date Feb 13, 2021
Last update date Feb 23, 2022
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24676
Series (2)
GSE166726 Identifying novel surface markers for megakaryocyte progenitor cells [10x D27]
GSE168291 Identifying novel surface markers for megakaryocyte progenitor cells
Relations
BioSample SAMN17910189
SRA SRX10094798

Supplementary file Size Download File type/resource
GSM5081941_SIGAE11-barcodes.tsv.gz 10.6 Kb (ftp)(http) TSV
GSM5081941_SIGAE11-features.tsv.gz 297.6 Kb (ftp)(http) TSV
GSM5081941_counts.mtx.gz 20.9 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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