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Status |
Public on Dec 15, 2016 |
Title |
Bone_255_AR005_ACAGTG |
Sample type |
SRA |
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Source name |
Bone
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Organism |
Ambystoma mexicanum |
Characteristics |
tissue: Bone genotype: wild-type strain: leucistic
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Dec 15, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Donald M Bryant |
Organization name |
Harvard University
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Department |
Biological and Biomedical Sciences
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Lab |
Whited
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Street address |
65 Landsdowne Stree
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL22800 |
Series (1) |
GSE92429 |
A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors |
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Relations |
BioSample |
SAMN04228853 |
SRA |
SRX1406084 |
Supplementary data files not provided |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data are available on Series record |
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