|
| Status |
Public on Aug 09, 2018 |
| Title |
Forebrain_SA_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Forebrain_SA
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
animal_number: 32
hibernation_stage: SA
Sex: M
tb at sac'ing: 37
tissue: Forebrain
|
| Growth protocol |
Animal housing and sample collection were performed as described previously (Grabek K. et al. eLife 2015).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted as described previously (Grabek K. et al. eLife 2015).
Illumina TruSeq mRNA Strand Specific
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
transcriptome.gtf
gatk_sites_annotation.txt.gz
gatk_sites_proportions.txt.gz
gatk_sites_raw_counts.txt.gz
hyperedited_sites.bed.gz
hyperedited_sites_annotation.txt.gz
hyperedited_sites_proportions.txt.gz
hyperedited_sites_raw_counts.txt.gz
B32_14_CCGTCC_L002_R1_001
|
| Data processing |
RNA-Seq libraries were trimmed with bcl2fastq (illumina 4000 libraries) or cutadapt (illumina 2500) to remove illumina adapters. Reads were then aligned with STAR in two-pass mode against the spetri2 genome supplemented with a custom transcriptome built with all the brain and additionally neonate and testes RNA-Seq libraries. PCR duplicates were marked using picard, and intron junctions were split and trimmed using GATK SplitNTrim. HaplotypeCaller was used to identify variants, followed by base recalibration with variants identified from Haplotype Caller. This process was repeated another two times to establish properly recalibrated quality scores. Variant calls from all samples were merged and filtered to identify variants with a minimum variant allele frequency > 0.05 and < 0.95. Variants were annotated with SNPeff using ensembl85 annotations. For each variant the read count for each allele was enumerated. RNA editing events were called from A-to-G variants with significant (FDR <0.01) variant allele frequencies associated with hibernation state in an ANOVA-like analysis.
Hyperedited reads were identified following the approach described in Porath et al. Nature Communications 2014. Hyperedited sites supported by less than two reads were excluded.
A novel transcriptome assembly was generated using Stringtie and TACO on Hisat2 alignments from brain, testes, and neonatal RNA-Seq libraries. Only genomic contigs of at least 10kbp were used for HISAT2 alignments and generating the transcriptome
Genome_build: spetri2
Supplementary_files_format_and_content: Processed data format and content is described in supplied readme.txt
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kent Augustus Riemondy |
| Organization name |
University of Colorado School of Medicine
|
| Department |
Biochemistry and Molecular Genetics
|
| Street address |
12801 E 17th Ave
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL22929 |
| Series (1) |
| GSE106947 |
Dynamic Temperature-Sensitive A-to-I RNA editing in the Brain of a Heterothermic Mammal during Hibernation |
|
| Relations |
| BioSample |
SAMN08028587 |
| SRA |
SRX3395053 |
