|
| Status |
Public on Jun 10, 2020 |
| Title |
R21_1 |
| Sample type |
SRA |
| |
|
| Source name |
21 DPA, distal amputation
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 10-12 weeks old
tissue: Hind limb digit tip (bone, cartilage, marrow, dermis, epidermis)
treatment: distal amputation
time: 21 DPA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissues were crushed with a pestle and the tissue lysates homogenized. Total RNA was isolated (RNeasy Mini Kit, QIAGEN) following the manufacturer’s protocol, depleted of ribosomal RNA via a hybridization method (Ribo-Zero Gold rRNA Removal Kit, Illumina), and purified with DNase treatment (Ambion DNA-free DNA Removal Kit, Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using 1 µg of total RNA per sample (average RNA integrity number of 8) and standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to mm10 using STAR_2.5.4b with gencode vM15 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Quantified reads were corrected for batch effect using RUVr from the RUVSeq R package (v 1.16.1) according to the protocol described in the vignette using option k=3.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts .txt file
|
| |
|
| Submission date |
May 13, 2019 |
| Last update date |
Jun 10, 2020 |
| Contact name |
Bo Zhang |
| E-mail(s) |
bzhang29@wustl.edu
|
| Phone |
3143624757
|
| Organization name |
Washington University School of Medicine
|
| Department |
Developmental Biology
|
| Lab |
Zhang
|
| Street address |
4515 McKinley Research Bldg 03212
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE131078 |
Transcriptomic analysis of bone and fibrous tissue morphogenesis during digit tip regeneration in the adult mouse |
|
| Relations |
| BioSample |
SAMN11634428 |
| SRA |
SRX5823850 |
