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Status |
Public on Mar 03, 2018 |
Title |
BR_12week |
Sample type |
SRA |
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Source name |
brain
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Organism |
Petromyzon marinus |
Characteristics |
post-injury time point: 12 week tissue: brain
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Treatment protocol |
Spinal cord transection
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Extracted molecule |
polyA RNA |
Extraction protocol |
Brains (whole brains without the olfactory lobes) and spinal cords (1cm surrounding the lesion), were harvested from uninjured lampreys, and at 10 time points from 6 hours to 12 weeks post injury. Tissue was stored in RNALater and then homogenized, pooled by time point (n=6 animals per time point), and total RNA (RIN >9) extracted using Trizol. RNA-Seq libraries (~250bp) were created using TruSeq RNA Sample Prep Kit v2 (Illumina Inc.; San Diego, CA), + Ribo-Zero Gold (Epicentre).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Align to reference gene models (Ensembl; Pmarinus_7.0) using RSEM Calculate raw transcript expression for each time point using RSEM Calculate expression fold change and probability of differential expression using EBseq Genome_build: RNA-Seq reads were mapped against gene models from the publicly available lamprey genome (Ensembl; Pmarinus_7.0) Supplementary_files_format_and_content: "genes.results" files contain transcript abundance generated by RSEM in the standard RSEM output format. ".appended" files contain differential expression estimates generated by Ebseq in the standard EBseq output format.
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Submission date |
Mar 03, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Mark Evers |
Organization name |
University of Kentucky
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Department |
College of Medicine
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Street address |
800 Rose Street
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City |
Lexington |
State/province |
Kentucky |
ZIP/Postal code |
40506 |
Country |
USA |
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Platform ID |
GPL20963 |
Series (1) |
GSE95686 |
RNA-Seq analysis after spinal cord injury in lamprey reveals distinct transcriptional responses during functional recovery in spinal cord and brain |
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Relations |
BioSample |
SAMN06477677 |
SRA |
SRX2612220 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2521661_BR_12w.ebseq.noqs.appended.txt.gz |
825.5 Kb |
(ftp)(http) |
TXT |
GSM2521661_BR_12wk_Comb.genes.results.txt.gz |
382.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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