|
| Status |
Public on Jun 12, 2024 |
| Title |
C3H anti-GFP mCherry reporter, Day 2, No ligand, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
c3h/10t1/2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: c3h/10t1/2
genotype: SFFV_myc- LaG17_synNotch_TetRVP64 , TRE_mCherry
treatment: No ligand
|
| Treatment protocol |
All cells were droplet seeded onto Fibronectin treated PDMS coverslips microcontact printed either with or without its activating ligand (GFP or mCherry). Cells were allowed to culture for 2 days before total RNA extraction. Droplet seeding was performed as follows: 6x10^4 cells were seeded in a 50uL droplet on top of the patterns, allowed to attach for 30 minutes, prior to adding additional media.
|
| Growth protocol |
All cell types were maintained in high glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extraction using miRNeasy kit (Qiagen), RNA cleanup and concentrator (Zymo), before being sequenced by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads by Novogene.
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 |
Induc-mCherry2
|
| Data processing |
Fastqc files were trimmed with trimmomatic v0.39 using default settings. Trimmed fastQ files were aligned to GRCm38 reference genome supplemented with custom transgenic sequences using STAR v2.7.10b with default parameters. Transcriptome alignments were quantified using featureCount using the custom gene annotation file combining GENCODE annotation file and transgenes.
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
|
| |
|
| Submission date |
Jun 07, 2024 |
| Last update date |
Jun 12, 2024 |
| 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) |
| GSE269373 |
Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs [RNA-seq] |
| GSE269404 |
Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs |
|
| Relations |
| BioSample |
SAMN41748899 |
| SRA |
SRX24839817 |
