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Sample GSM2521661 Query DataSets for GSM2521661
Status Public on Mar 03, 2018
Title BR_12week
Sample type SRA
 
Source name brain
Organism Petromyzon marinus
Characteristics post-injury time point: 12 week
tissue: brain
Treatment protocol Spinal cord transection
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date Mar 03, 2017
Last update date May 15, 2019
Contact name Mark Evers
Organization name University of Kentucky
Department College of Medicine
Street address 800 Rose Street
City Lexington
State/province Kentucky
ZIP/Postal code 40506
Country USA
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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