 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 19, 2023 |
| Title |
20_kPa_rep2_RNA |
| Sample type |
SRA |
| |
|
| Source name |
Ear
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Ear
cell type: Fibroblast
treatment: 20kPa
|
| Treatment protocol |
A total of 500,000 fibroblasts were cultured on matrices of varying stiffness for 3 days and stored at -80 °C prior to sample processing.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Upon isolating RNA from the samples, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
S202
|
| Data processing |
Raw reads were trimmed with Trim Galore and cutadapt based on quality.
Pair-ended reads were then aligned to mouse reference genome (mm10) with STAR v2.7.10b.
Transcriptome alignments were quantified using featureCount using the gene annotation file from GENCODE.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Dec 13, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Song Li |
| E-mail(s) |
songli@ucla.edu
|
| Organization name |
UCLA
|
| Street address |
404 Westwood Plaza, Eng VI
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE250068 |
Biphasic Regulation of Epigenetic State by Matrix Stiffness during Cell Reprogramming [RNA-seq] |
| GSE250069 |
Biphasic Regulation of Epigenetic State by Matrix Stiffness during Cell Reprogramming |
|
| Relations |
| BioSample |
SAMN38790279 |
| SRA |
SRX22867170 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
