 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 01, 2024 |
| Title |
MI-stiff snRNA-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
infarct zone
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: infarct zone
treatment: MI + stiff hydrogel
|
| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitor (N2615; Promega and AM2696; Life Technologies). Heart samples were cut into 2-mm pieces and homogenized using a Dounce homogenizer (885302-0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and they were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-mm cell strainer (43-50040-51; pluriSelect) and then centrifuged at 5003g for 5 minutes at 4°C. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation, the pellet was resuspended in Nuclei Suspension Buffer (1xPBS, 0.07% BSA, and 0.1% RNase inhibitor), filtered through a 20-mm cell strainer (43-50020-50; pluriSelect), and counted.
cDNA libraries were constructed using Chrominum Single-Cell 3’GEM, Library & Gel Bead Kit v3, then sequenced on illumina novaseq 6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The reads were aligned to rat reference genome (rn7; ENSEMBL, version 67) using CellRanger v6.1.1 with default parameters, excluding the option ‘-include-introns’ to obtain intronic reads in nuclei.
Assembly: mRatBN7 (rn7)
Supplementary files format and content: Tab-separated files and matrix files
|
| |
|
| Submission date |
Jan 20, 2024 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Li Shen |
| E-mail(s) |
shenlab@zju.edu.cn
|
| Phone |
86-0571-88981751
|
| Organization name |
Life Sciences Institute, Zhejiang University
|
| Lab |
Shenlab
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE253767 |
Biomechanical basis of intramyocardial hydrogel injection treatment for ischemic cardiomyopathy [snRNA-seq] |
| GSE253768 |
Biomechanical basis of intramyocardial hydrogel injection treatment for ischemic cardiomyopathy |
|
| Relations |
| BioSample |
SAMN39514645 |
| SRA |
SRX23335298 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8027656_MI-stiff1_UMI_mat.csv.gz |
16.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
