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| Status |
Public on Mar 10, 2020 |
| Title |
PFC_CS_#10 |
| Sample type |
SRA |
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| Source name |
PFC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: prefrontal cortex
treatment group: cocaine+saline (CS)
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| Treatment protocol |
During the methionine (Sigma, USA) experiments, mice were injected subcutaneously with 1 g/kg (6.6 mmol/kg) L-methionine twice a day for 10 consecutive days using the CPP procedure (including pre-test, training and post-test days). This was found to be the most effective dose and duration for increasing methylation level at certain DNA regions in the brain [25]. During training, mice were injected with methionine 1 h before each behavioral experiment. Animals were divided into 4 groups: (1) saline+saline (SS), (2) MET+saline (MS), (3) MET+cocaine (MC) and (4) cocaine+saline (CS).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Two hours after the (day 10) CPP test, the animals were killed and their mPFCs surgically excised. The tissue was stored in liquid nitrogen immediately after extraction and then transferred to the -80°C freezer. Total RNA was extracted from the frozen tissues using the TIANamp DNA/RNA Isolation Kit (TIANGEN), including additional treatment with RNase-free DNase I (Ambion) for 30 minutes at 37°C to remove contaminating DNA.
18-30nt RNA segments were separated and recovered by PAGE gel. The steps which followed were the same as for generating the mRNA sequencing library from the addition of poly-A. The miRNA DNBs were loaded into the patterned nanoarrays and single-end reads of 50 bp were read through on the BGISEQ-500 platform at Beijing Genomics Institute (BGI; Shenzhen, China).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Reads were aligned against the miRBase (v21) using Bowtie allowing one mismatch. Unaligned sequences were pooled together to identify novel miRNAs using the software package miRDeep (v2.0.0.5) with default parameters. In order to investigate the expression profiles of miRNAs, the frequency of miRNA counts were normalized to TPM (tags per million) using the following formula: normalized expression = actual miRNA read count /total clean read count × 106. Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Mar 09, 2020 |
| Last update date |
Mar 10, 2020 |
| Contact name |
Wang Yan |
| Organization name |
Institute of Psychology
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| Street address |
16# LinCui Road
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| City |
BeiJing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE146631 |
L-methionine counteracts cocaine-conditioned place preference in mice through Glutamatergic plasticity pathways |
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| Relations |
| BioSample |
SAMN14336581 |
| SRA |
SRX7878276 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4399949_10.expr.txt.gz |
19.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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