 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 11, 2022 |
| Title |
R636Q_homozygous [Taka12] |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Heart
genotype: R636Q/R636Q
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
iPSC-CMs were homogenized in 1ml of TRizol (Thermo Fisher Scientific). Flash-frozen cardiac samples were homogenized in 1 ml of TRIzol in Precellys Evolution (2 cycles x 30 s at 5000 rpm). RNA as isolated using RNeasy miRNeasy Kit (Qiagen) as per the provider’s instructions.
RNA-seq libraries were prepared using KAPA mRNA HyperPrep (Kapa Biosystems, kk8580) kit following manufacturer’s specifications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include gene read counts for each Sample
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Jiwoong Kim |
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE210783 |
Precise genomic editing of a pathogenic RBM20 mutation rescues dilated cardiomyopathy |
|
| Relations |
| BioSample |
SAMN30201765 |
| SRA |
SRX16990647 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6437601_Taka12.htseq-count.txt.gz |
94.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
