|
| Status |
Public on Aug 31, 2018 |
| Title |
SM22-SmoM2/Tomato |
| Sample type |
SRA |
| |
|
| Source name |
Skin dermis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skin dermis
cell type: Dermal cells of skin
age: 4-5 week old
genotype: SM22rtTA; tetO-Cre; R26-SmoM2/Tomato
|
| Treatment protocol |
The mice were treated with doxycycline (20g/kg) from post-wound 1d to 3d after complete reepithelialization
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Skin wound tissues (3 days after scab detachment) of SM22-Tomato (control) and SM22-SmoM2/Tomato were incubated in 20 mM EDTA solution at 37 oC for 1 hr. After separation of dermis from epidermis, dermal cells were isolated from dermis with collagenase and tomato+dermal cells were collected by FACs.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.
|
| |
|
| Submission date |
Apr 04, 2018 |
| Last update date |
Sep 01, 2018 |
| Contact name |
Chae Ho Lim |
| Organization name |
New York University School of Medicine
|
| Department |
Dermatology
|
| Lab |
Mayumi Ito
|
| Street address |
550 First Ave.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE112671 |
Single cell RNA-seq analysis in dermis of SM22rtTA; tetO-Cre; R26-Tomato (SM22-Tomato, control) and SM22rtTA; tetO-Cre; R26-SmoM2/Tomato (SM22-SmoM2/Tomato, forced Hh activation in wound dermis) at 3 days after complete reepithelialization |
|
| Relations |
| BioSample |
SAMN08863464 |
| SRA |
SRX3881587 |
