 |
 |
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |