|
| Status |
Public on Dec 15, 2016 |
| Title |
CartWrist_261_AR007_CAGATC |
| Sample type |
SRA |
| |
|
| Source name |
Cartilage from wrist
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: Cartilage from wrist
genotype: wild-type
strain: leucistic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using either Trizol reagent or the Qiagen Rneasy columns.The Illumina TruSeq v2 protocol was used throughout to generate barcoded sequencing libraries. Paired-end, 100-bp sequencing was performed on the Illumina HiSeq 2500 at Harvard Medical School’s Biopolymers facility.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calls were performed using Illumina CASAVA 1.8.2
Trinity version trinityrnaseq_r2013-02-25 was used for de novo transcriptome assembly and analysis as follows. The combined set of 1.3 billion RNA-Seq reads spanning all sampled tissues were combined into a single pair of fastq files, quality trimmed using Trimmomatic (Bolger et al., Bioinformatics, 2014) (parameters LEADING:5 TRAILING:5 MINLEN:36) and subsequently normalized using the in silico normalization step incorporated into Trinity ($TRINTY_HOME/util/normalize_by_kmer_coverage.pl --seqType fq --JM 100G --left ALL_AXOLOTL_READS.left.fq.P.qtrim.fq --right ALL_AXOLOTL_READS.right.fq.P.qtrim.fq --pairs_together --JELLY_CPU 10 --PARALLEL_STATS --max_cov 50). The resulting normalized reads were then assembled using Trinity (Trinity.pl --left left.fq --right right.fq --seqType fq --JM 100G --CPU 10).
Counts of RNA-Seq fragments mapping to transcripts in our assembly were determined for each tissue type using RSEM (Li B and Dewey C.N., BMC Bioinformatics, 2011) (http://deweylab.github.io/RSEM/) with default options.
Genome_build: The axolotl genome has not been fully sequenced; We generated a transcriptome from our RNA-seq data using Trinity and deposited it in TSA (GFBM000000000)
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and TMM-normalized FPKMs for each Sample
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Donald M Bryant |
| Organization name |
Harvard University
|
| Department |
Biological and Biomedical Sciences
|
| Lab |
Whited
|
| Street address |
65 Landsdowne Stree
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL22800 |
| Series (1) |
| GSE92429 |
A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors |
|
| Relations |
| BioSample |
SAMN04228859 |
| SRA |
SRX1406162 |
