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| Status |
Public on May 22, 2018 |
| Title |
RatID_7_CX_TRM_MBD-seq |
| Sample type |
SRA |
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| Source name |
Perilesional cortex, TBI
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| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague-Dawley
gender: Male
age: Adult
tissue: perilesional cortex
treatment: TBI
rat_id: 7
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| Treatment protocol |
TBI was inducted with lateral fluid precussion (LFP) as described by McIntosh et al. (1989) and Kharatishvili et al. (2006). Animals were anesthetized with an intraperitoneal (i.p.) injection of a solution (6 ml/kg) containing sodium pentobarbital (58 mg/kg), chloral hydrate (60 mg/kg), magnesium sulphate (127.2 mg/kg), propylene glycol (42.8%) and absolute ethanol (11.6%) and placed in a Kopf stereotactic frame (David Kopf Instruments, Tujunga, CA, USA). The skull was exposed with a midline skin incision followed by extraction of the periosteum. The left temporal muscle was detached from the lateral ridge and then a circular craniectomy (diameter 5mm) was performed over the left parietal lobe midway between lambda and bregma keeping the dura mater intact. The edges of craniectomy were sealed with a modified LuerLock cap that was filled with saline while the calvaria was covered with dental acrylate (Selectaplus CN, Dentsply DeTrey GmbH, Dreieich, Germany). Lateral FPI was induced 90 min after the administration of anaesthesia by connecting the rat to a fluid-precussion device (AmScien Instruments, Richmond, VA, USA) via a female Luer-Lock fitting. In this study, the main of the impact was 3.32 +/- 0.01 atm. Control animals received anaesthesia and all surgical procedures but without lateral FPI.
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| Growth protocol |
Adult male rats (Sprague-Dawley, Harlan, Netherlands) weight 330-371g at a time of traumatic brain injury were housed in a controlled environment (21-23 °C, 12h dark/light cycle, 50-60% relative humidity) with drinking and feeding ad libitum.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was collected 3 months after TBI. For tissue collection, rats were anesthetized with isoflurane and decapitated. The brain was removed from skull, flushed with 0.9% cold sodium chloride, and two 2-mm-thick coronal slices (between -2.2 to -6.2 from the bregma) were cut with a slicing matrix. Perilesional cortex, thalamus, and dentate gyrus (including CA3c-b) were dissected under the magnifying glass on top of the light table. Samples were stored at -80oC until RNA extraction.
DNA extraction was done by using the DNeasy Blood & Tissue kit (Qiagen #69504) enrichment (Invitrogen). Sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (New England Biolabs). Libraries were quantified on MultiNA system and sequenced at a concentration of 13 pM on the Genome Analyzer IIx (Illumina Inc, CA, USA) using the TruSeq version 5 cluster kit (cBot) and SBS kit (36 cycles).
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Processed data file: Cortex_Repitools_gene_body_counts.txt
Processed data file: Cortex_Repitools_exon_counts.txt
Processed data file: Cortex_Repitools_promoter_counts.txt
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| Data processing |
Base calling was performed with OLBv1.8 software.
Reads were aligned to the rat genome (Rnor_5.0) using Spliced Transcripts Alignment to a Reference (STAR) (version 2.3.0e_r291).
Differentially methylated gene promoter, exons, and gene bodies were identified with Repitools R-package (R version 3.1.0).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include count matrix.
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| Submission date |
Dec 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anssi Lipponen |
| Organization name |
University of Eastern Finland
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| Department |
A. I. Virtanen Institute for Molecular Sciences
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| Lab |
Epilepsy Research Laboratory
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| Street address |
Neulaniementie 2
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| City |
Kuopio |
| ZIP/Postal code |
70150 |
| Country |
Finland |
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| Platform ID |
GPL10669 |
| Series (1) |
| GSE107837 |
Transcriptomics but not DNA methylomics find Tp73, Cebpd, Pax6 and Spi1 transcription factors as treatment targets for traumatic brain injury |
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| Relations |
| BioSample |
SAMN08148001 |
| SRA |
SRX3456248 |
| 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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