|
| Status |
Public on Sep 11, 2015 |
| Title |
Blastema |
| Sample type |
SRA |
| |
|
| Source name |
3 day post injury blastma
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
cell type: 3 day post injury blastma
|
| Treatment protocol |
Control and blastema samples were generated by pooling tail tissue from 20 mature axolotls that had either never regenerated or 3 days post injury.
|
| Growth protocol |
All axolotls used in these experiments were bred at the Max Planck CBG (Dresden Germany) or the University of Minnesota in accordance with IACUAC protocol No.1411-32049A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol (Life Technologies) according to the manufacturer’s protocol.
Isolation of the small RNA fraction, generation of libraries and subsequent deep sequencing was carried out by the Functional Genomics Library Construction Core at BC Cancer Agency Genome Sciences Centre, Canada
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Reads were converted from Solexa Format with ShortRead( 1.26.0)
Adapter sequences were removed with ShortRead.
Mapping to miRBase 21 was performed with Bowtie (1.1.2)
Rsamtools (1.18.2) was used to convert and sort reads into binary format and subsequently to enumerate reads for each known miR.
Unmapped reads were tabulated and clustered into families of novel sequences.
Genome_build: NA
Supplementary_files_format_and_content: raw counts and normalized abundance estimates for both samples (Sup_Table_1.csv) and raw counts for unmapped_reads (Sup_Table_2.csv).
|
| |
|
| Submission date |
Aug 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Micah Gearhart |
| E-mail(s) |
gearh006@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Genetics, Cell Biology and Development
|
| Street address |
6-160 Jackson Hall, 321 Church St.
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL20805 |
| Series (1) |
| GSE72057 |
Identification of conserved and novel microRNAs during tail regeneration in the Mexican Axolotl |
|
| Relations |
| BioSample |
SAMN03991373 |
| SRA |
SRX1149363 |
