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Sample GSM2429648

Query DataSets for GSM2429648

Status

Public on Dec 15, 2016

Title

Bone_255_AR005_ACAGTG

Sample type

SRA

Source name

Bone

Organism

Ambystoma mexicanum

Characteristics

tissue: Bone
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