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Sample GSM5527607

Query DataSets for GSM5527607

Status

Public on Sep 30, 2021

Title

91CC

Sample type

SRA

Source name

Brain

Organism

Rattus norvegicus

Characteristics

strain: Sprague-Daley
Sex: Male
age: Adult
tissue: Brain
hemisphere: CONTRA
treatment: SHAM
animal id: 91

Treatment protocol

Penetrating Ballistic Brain Injury (PBBI). Following a recovery period of approximately 2–3 days after EEG/implantation, animals received a right unilateral frontal PBBI injury. This penetrating injury was a model of a shockwave with a ballistic component that created a brain cavity. A computer-controlled simulated ballistic injury device with an attached custom-designed 20 G stainless steel tubular probe. Along one end of this probe were fixed holes covered by airtight elastic tubing. Following unilateral (right) frontal pole craniectomy (+4.5mm anteroposterior, +2mm medio-lateral from bregma), the probe was inserted at an angle of 50° from the vertical axis and 25° counter-clockwise from the anterior-posterior axis to a distance of 1.2 cm from the dural surface of the brain. An automated pulse-generator was used to quickly (< 40 ms) inflate/deflate the elastic tubing into an elliptical balloon to a size roughly equal to 10% brain volume. Sham animals were subjected to identical procedures but without probe insertion.
Sleep-Wake Assessment. Twenty-four hour continuous EEG/EMG data were collected (n=11). EG electrodes were implanted using a flexible shielded cable and multipin connector equipped with multichannel gold contact swivel commutator (Dragonfly Inc., Ridgeley, WV). All EEG/EMG/ECG signals were continuously monitored at a sampling frequency of 400 Hz using a computerized Grass Technologies LTM Monitoring amplifier and data acquisition system (Natus Neurology Incorporated - Grass Products, Warwick, RI). EEG and EMG signals were used to objectively classify 1-second epochs into vigilance states (wakefulness, slow-wave sleep, and REM sleep) using a computerized algorithm based on EEG and EMG amplitudes and frequencies as well as the probability that the subject will transition from a given stage to another (Neuroscore 3.0 software, Data Sciences International, St Paul, MN). The sleep score for a given 10-second period was based on the summary of 1-second epochs. Epochs were assigned to a specific vigilance state when < 50% of the epoch fulfilled the criteria for a sleep stage.
The time spent in vigilance states (minutes/hour) was calculated for the entire 12-hour period. All 10-second epochs were summed into 60-minute bins and group-averaged to examine the amount of time spent in wake, SWS, and REM sleep. Polysomnograms of each hemisphere (contralateral and ipsilateral to injury) were scored separately. Sleep-wake parameters used in these analyses included latency (onset) to SWS or REM sleep (defined as the time interval to the first six consecutive SWS or REM 10-second epochs), and duration of sleep/wake states.

Growth protocol

11 adult male Sprague-Daley rats (275–320 g) were maintained on a 12:12 light:dark cycle for at least two weeks, then were randomized to PBBI (n=6) or sham (n=5) groups.

Extracted molecule

total RNA

Extraction protocol

Brains were harvested, underwent sectioning and cortical tissue samples were stored. RNA were isolated from tissue samples.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Alignment of sequenced reads was done with STAR 2.4.2a. STAR index was created using splice junction annotation database for guidance and both genome sequence and annotation files of Ensembl Rnor 6.0.
Quantification of gene expression was achieved through featureCounts 1.4.3-p1 with Ensembl Rnor 6.0 annotation.
Genome_build: Ensembl rnor 6.0 (Rnor_6.0)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file includes raw counts.

Submission date

Aug 18, 2021

Last update date

Sep 30, 2021

Contact name

Fatemeh Haghighi

E-mail(s)

fatemeh.haghighi@mssm.edu

Organization name

Icahn School of Medicine at Mount Sinai

Department

Neuroscience