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Sample GSM5928806 Query DataSets for GSM5928806
Status Public on Sep 13, 2023
Title Pot1afl/fl BM cells rep3
Sample type SRA
 
Source name Whole bone marrow cells
Organism Mus musculus
Characteristics strain: C57BL/6
age: 2-3 weeks old
genotype: NG2-cre/Pot1afl/fl
Extracted molecule total RNA
Extraction protocol After pre-run setup, the pump of the cells, then the beads, and finally the oil were started. After assessment of droplet quality and bead droplets, the beads were in the whiter layer on top. Through the breakage treatment, the white beads were gathered and washed with 5X RT buffer. cDNA strands were generated on the RNA hybridized to the bead primer with reverse transcription mix. After exonuclease Ⅰ treatment by incubating at 37°C for 45 minutes with rotation, PCR program was exceeded by 95°C 3 minutes—4 cycles of 98°C 20 seconds, 65°C 45 seconds, 72°C 3 minutes—9 cycles of 98°C 20 seconds, 67°C 20 seconds, 72°C 3 minutes—72°C 5 minutes; 4°C hold. The purified cDNA by AMPure XP beads was measured by Bioanalyzer.
Pooled libraries were sequenced on the NextSeq 500 system using a 75-cycle kit. The sequencing reads were aligned to the reference mouse genome (mm10) and an expression matrix of read counts for each gene and cell was prepared using the Drop-seq software available from McCarroll Lab.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing The sequencing reads were aligned to the reference mouse genome by STAR embeddfd in the Drop-seq software available from McCarroll Lab (Macosko et al., 2015).
The expression matrix of read counts for each gene and cell was prepared using the said software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts.
 
Submission date Mar 01, 2022
Last update date Sep 13, 2023
Contact name Yuichiro Semba
E-mail(s) semba.yuichiro.208@m.kyushu-u.ac.jp
Organization name Kyushu University
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL21103
Series (1)
GSE197721 Genome-wide maps of hematopoietic stem and progenitor cells in mice bone marrow.
Relations
BioSample SAMN26345523
SRA SRX14333283

Supplementary file Size Download File type/resource
GSM5928806_KO3_counts.txt.gz 127.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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