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| Status |
Public on May 24, 2017 |
| Title |
3_P60_C_AMY |
| Sample type |
SRA |
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| Source name |
Brain region
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: AMY
age: P60
Sex: Female
generation: F0
treatment: Control
strain: Sprague-Dawley
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| Growth protocol |
Adolescent female Sprague-Dawley rats from the PRS group underwent a 7-day unpredictable stress procedure, as previously described (Zaidan et al. 2013). Animals from Control and PRS groups were sacrificed two weeks after the end of the stress procedure.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains and Oocytes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. cDNA and primer pools were loaded into the 48.48 Access Array IFC (Fluidigm) and performed target amplification as previously described (Zhang et al. 2014) and was sequenced using NextSeq 500 (Illumina, USA) with 76bp paired-end reads.
RNA libraries were prepared for sequencing using by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped as single-end reads onto a combination of the genome (rn4) and exonic sequences surrounding known splicing junctions using BWA samse.
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: rat genome (rn4, Nov. 2004, Baylor HGSC v. 3.4)
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.
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| Submission date |
May 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hiba Zaidan |
| E-mail(s) |
[email protected]
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| Phone |
972 4 8249320
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| Organization name |
University of Haifa
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| Department |
Psychology
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| Lab |
IGS lab
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| Street address |
199 Aba Khoushy Ave
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| City |
Haifa |
| State/province |
Israel |
| ZIP/Postal code |
3498838 |
| Country |
Israel |
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| Platform ID |
GPL20084 |
| Series (1) |
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| Relations |
| BioSample |
SAMN07158049 |
| SRA |
SRX2845104 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2636121_hiba17sample3_combined_EditLevels.txt.gz |
3.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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