|
| Status |
Public on Oct 03, 2016 |
| Title |
L5_control_blocked_striatum_MID69405_S55_GTGGCC |
| Sample type |
SRA |
| |
|
| Source name |
striatum, control
|
| Organism |
Mus musculus domesticus |
| Characteristics |
line: L5
tissue: striatum
Sex: male
age: adult
selection: control
wheel_status: blocked
mouse_behavior_id: 69405
sequencing_sample_number: 55
sequencing_index: GTGGCC
running_m_per_24h_before_block: 4099
|
| Treatment protocol |
Starting at 13:00 and ending at 17:00 (1-4 hours after lights shut off) when mice are normally most active on running wheels, mice were removed from their cages and immediately decapitated. All surfaces and instruments were sprayed with RNase away. The brains were immediately placed on an aluminum platform on wet ice with ventral surface exposed. Using the olfactory tubercles and optic chiasm as landmarks, a razor blade was used to cut a coronal section approximately 1.7 mm thick containing the striatum. The section was then flipped horizontally and the entire striatum (dorsal and ventral) was carefully dissected from the cortex, medial septum, and olfactory tubercles. The striatum was then immediately placed in a centrifuge tube on dry ice and subsequently stored at -80° C.
|
| Growth protocol |
The 31 adult male mice from generation 66 used for this experiment were weaned in groups of 2-4 when they were 21 days old, and individually marked, following the usual procedure. When they were 35 days old (+/- 5 days), they were placed individually with access to wheels. Wheel running was monitored continuously for 6 days following the routine phenotyping procedure. Rooms were kept on a shifted light-dark cycle with lights on at 00:00 and off at 12:00. On day 7 at approximately 00:00 hrs, mice were blocked from entering the running wheel by placing a barrier to cover the tunnel connecting the wheel to the cage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized with an RNase-free disposable pellet pestle (Fisher) and RNA was extracted using the commercially available RNeasy® Lipid Tissue Mini Kit (Qiagen). Purification of the isolated RNA included treatment with DNase I (Qiagen), accordingly to the manufacturer's instructions. For assessing total RNA yield, aliquot samples were measured with a Qubit® 2.0 (Life Technologies). Quality and integrity of isolated RNA samples were determined by 28S/18S rRNA analysis with an Agilent 2100 Bioanalyzer (Santa Clara, CA).
RNA-Seq libraries were prepared with Illumina's TruSeq Stranded RNA Sample Prep kit. The libraries were pooled and each pool was quantitated by qPCR before sequencing. Libraries were sequenced in 4 lanes for 101 cycles from each end of the fragments on an Illumina HiSeq 2000 using a TruSeq SBS sequencing kit, version 3.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MID69405
|
| Data processing |
Reads were demultiplexed and fastq files were generated using CASAVA v. 1.8.2.
The fastq files were aligned to the GRCm38 (mm10) genome with Ensembl annotation v. 75 using Tophat2 v. 2.0.10 in paired-end mode with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19.
Aligned reads were sorted using Samtools v. 0.1.19.
Gene tag counts were calculated using htseq-count from HTSeq v. 0.6.1.
Exon bin counts were calculated using a flattend GTF file from Ensembl v. 75 with the dexseq_count.py script from the DEXSeq R package v. 1.9.7.
Genome_build: GRCm38 (Ensembl v. 75 annotation)
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files with output of htseq-count on gene IDs (gene_id.counts) or dexseq-count (DEXSeq.counts).
|
| |
|
| Submission date |
Aug 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael C. Saul |
| E-mail(s) |
michael.saul@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Lab |
Chesler Lab
|
| Street address |
600 Main St
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL17637 |
| Series (1) |
| GSE86076 |
High motivation for exercise is associated with altered chromatin regulators of monoamine receptor gene expression in the striatum of selectively bred mice |
|
| Relations |
| BioSample |
SAMN05661249 |
| SRA |
SRX2054122 |
