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| Status |
Public on Sep 25, 2024 |
| Title |
Ct-Grp7-R6 |
| Sample type |
SRA |
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| Source name |
Dorsal striatum
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Long Evans
tissue: Dorsal striatum
age: adult
genotype: wild type
treatment: Control
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| Treatment protocol |
Training: Rats were randomly segregated into two groups of saline (n = 12) or METH (0.1 mg/kg /infusion) (n = 36). On each training day, rats were trained to lever press on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 22 days.
1st Footshock phase: Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the initial footshock at 0.18 mA and increased the foot-shock intensity by 0.06 mA up to a final current of 0.36 mA (with a total of 8 punishment days). After 8 days of foot-shock we identified two phenotypes. Some rats continued to take METH in presence of aversive stimuli (foot-shock 0.18 to 0.36 mA) we termed those rats shock-resistant (SR), whereas some rats decrease their reinforced lever responding and we called them shock-sensitive (SS)
The animals were withdrawal (force abstinent) from METH for 15 days, during which they are tested for METH seeking behavior on WD1 and WD15.
Rats were again allowed to self-administer METH-HCl and saline on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 12 days.
2nd Footshock phase: Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the foot-shock intensity to 0.30 mA, with a total of 3 punishment days. After 3 days of foot-shock we identified three phenotypes. We observed some SS rats from 1st punishment phase showed compulsive METH intake in presence of aversive stimuli (foot-shock, 0.30 mA), we called these rats resurgence shock-resistant (RSR), while remaining SS rats decrease their METH intake in presence of aversive stimuli. SR rats continued to self-administered METH during 2nd punishment phase.
The animals were withdrawal (force abstinent) from METH for 15 days, during which they are tested for METH seeking behavior on WD1 and WD15. The animals were euthanized 15 days later, the brain region was dissected, snap frozen on dry ice and then stored in the -70C freezer.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
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| Submission date |
Dec 13, 2022 |
| Last update date |
Sep 25, 2024 |
| Contact name |
Atul Daiwile |
| E-mail(s) |
atul.daiwile@nih.gov
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| Organization name |
NIDA
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| Department |
MNRB
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| Street address |
251 Bayview Blvd,
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL22396 |
| Series (1) |
| GSE220896 |
Compulsive methamphetamine taking is associated with differential expression of HDAC2-regulated genes in the rat dorsal striatum |
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| Relations |
| BioSample |
SAMN32206750 |
| SRA |
SRX18677544 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6825607_Ct-Grp7-R6.counts.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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