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Sample GSM4734348 Query DataSets for GSM4734348
Status Public on Dec 04, 2020
Title AFX6.63
Sample type SRA
Source name Primed pluripotent stem cells
Organism Mus musculus
Characteristics cell line: AFX6
cell type: Pluripotent stem cells
condition: Primed
Treatment protocol N/A
Growth protocol FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX.
Extracted molecule total RNA
Extraction protocol Cells were directly sorted into each well of 96-well plate filled with 2.3 µl of lysis buffer (1 unit/µl of SUPERaseIN RNase inhibitor (Invitrogen), 0.2% Triton X) by BD FACSAria Fusion (BD Biosciences).
Libraries were prepared by Smart-seq2 (Illumina) followed by previously described (Picelli et al., 2014).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description Sample 255
Smart-seq2 scRNA-seq, PE, 101bp reads.
Data processing The quality of the data was assessed using FastQC and MultiQC.
The reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate).
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters), only uniquely mapped reads were used.
Cells with fewer than 3m reads total were discarded from further analysis.
Raw expression levels were normalized with sctransform.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw.csv contains raw gene counts.
Supplementary_files_format_and_content: normalized.csv contains cells sctransform-normalized expression levels of cells that passed QC.
Submission date Aug 20, 2020
Last update date Dec 04, 2020
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 GPL21103
Series (2)
GSE156588 Capture of mouse and human stem cells with features of formative pluripotency [scRNA-seq]
GSE156589 Capture of mouse and human stem cells with features of formative pluripotency
BioSample SAMN15869651
SRA SRX8980071

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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