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Sample GSM4875815 Query DataSets for GSM4875815
Status Public on Feb 23, 2022
Title Differentiating megakaryocytes on D6
Sample type SRA
 
Source name A1ATD1 induced pluripotent stem cells
Organism Homo sapiens
Characteristics cell line: A1ATD1
day of differentiation: 6
cell type: Differentiating megakaryocytes
sequencing run: Run 1
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 cDNA
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 was 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 genes detected in fewer than 3 cells were discarded from count matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw.mtx: MatrixMarket of raw expression levels for cells.
Supplementary_files_format_and_content: cell-meta.csv: Metadata for cells.
 
Submission date Nov 01, 2020
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)
GSE160604 Identifying novel surface markers for megakaryocyte progenitor cells [10x timecourse]
GSE168291 Identifying novel surface markers for megakaryocyte progenitor cells
Relations
BioSample SAMN16621757
SRA SRX9415799

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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