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| Status |
Public on Sep 24, 2019 |
| Title |
Control_1 |
| Sample type |
SRA |
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| Source name |
Brainstem
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| Organism |
Petromyzon marinus |
| Characteristics |
treatment: Control
ecotype: Spain: river Ulla
age: 5-7 years
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The brainstems of control and treated larvae were dissected out and immediately put in RNAlater (Ambion Inc., TX, USA). RNA extraction was performed using the RNeasy mini kit (Qiagen) with DNase treatment following the manufacturer’s instructions. Isolated RNAs were eluted in nuclease free water.
mRNA sequencing libraries were prepared from poly dT selected mRNA using the Illumina TrueSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
RNA-Seq of Petromyzon marinus: control-treated brainstem after spinal injury
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| Data processing |
Raw paired-end FASTQ files were quality filtered using Fastp to remove leading or trailing bases with Phred quality scores < 15 (-q 15), reads with length < 30 base pairs (-l 30), polyG tails (--trim_poly_g) and trim adaptor sequences (detected by per-read overlap, default).
Genome alignment: The resulting trimmed FASTQ files were aligned against the latest lamprey genome assembly (Pmar_germline 1.0) using STAR in 2-pass mapping mode (--twopassMode Basic) with the following parameters: 10 maximum multiple alignments allowed per read (--outFilterMultimapNmax 10), 10 maximum mismatches per read pair (--outFilterMismatchNmax 10), minimum and maximum intron lengths of 20 and 1M bp respectively (--alignIntronMin 20; --alignIntronMax 1000000), maximum distance of 1 Mb between mate reads (--alignMatesGapMax 1000000) and detection of chimerica sequences with a minimum mapped length of 20 bp (--chimSegmentMin 20; --chimScoreMin 1).
Transcriptome reconstruction: StringTie with default parameters (fr-firststrand, --rf) was used to construct the lamprey transcriptome for our samples using the genome alignment files.
Generation of read counts per gene: FeatureCounts was used to quantify gene expression at the gene level with the following parameters: fragments (paired-end reads) were counted instead of individual reads ('-p'), only fragments with both ends mapper were considered ('-B'), chimeric fragments were not considered ('-C'), and strand specified as reversely stranded ('-s 2').
Genome_build: Pmar_germline 1.0
Supplementary_files_format_and_content: Tab delimited text with raw read counts for each gene in the genome-guided de novo transcriptome (TSA submission GHVE00000000). The first six columns of the file correspond to gene ID, chromosome, start and end positions, strand and length of the gene
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| Submission date |
Sep 23, 2019 |
| Last update date |
Sep 24, 2019 |
| Contact name |
Diego Robledo |
| E-mail(s) |
diego.robledo@usc.es
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| Organization name |
University of Santiago de Compostela
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| Department |
Genetics
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| Street address |
Rúa Lope Gómez de Marzoa s/n CIBUS building
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| City |
Santiago de Compostela |
| ZIP/Postal code |
15782 |
| Country |
Spain |
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| Platform ID |
GPL27509 |
| Series (2) |
| GSE137859 |
RNA sequencing analysis of the sea lamprey brainstem after spinal cord injury and GABA or baclofen treatments [GABA] |
| GSE137860 |
RNA sequencing analysis of the sea lamprey brainstem after spinal cord injury and GABA or baclofen treatments |
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| Relations |
| BioSample |
SAMN12607220 |
| SRA |
SRX6736551 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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