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Sample GSM5081852 Query DataSets for GSM5081852
Status Public on Feb 23, 2022
Title Differentiating megakaryocytes on D7, wPRE
Sample type SRA
Source name A1ATD1 induced pluripotent stem cells
Organism Homo sapiens
Characteristics cell line: A1ATD1
day of differentiation: 7
cell type: Differentiating megakaryocytes
transgene library: wPRE
library batch: Batch 1
Treatment protocol Cells were methanol fixed, as per 10X protocol, and stored at -80 degrees C. They were then rehydrated as per 10X protocol and submitted for library preparation.
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 D7.wPRE
Single cell RNA-Seq
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 were performed using 10x cellranger v3.1.0.
To maintain consistency between sequencing runs, alignment was performed by using only R2 strands, trimmed to 91 nt.
Cells with fewer than 200 unique features and cells with more than 25% of counts from mitochondrial genes were discarded from count matrix.
The processing was performed with regard to the regular gene expression library (GSE160604).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: meta.csv: Comma-separated metadata for cells.
Submission date Feb 12, 2021
Last update date Feb 23, 2022
Contact name Irina Mohorianu
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)
GSE166723 Identifying novel surface markers for megakaryocyte progenitor cells [timecourse transgene]
GSE168291 Identifying novel surface markers for megakaryocyte progenitor cells
BioSample SAMN17904031
SRA SRX10092677

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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