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| Status |
Public on Oct 01, 2020 |
| Title |
PFC-WT14-20-2 |
| Sample type |
SRA |
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| Source name |
PFC, WT14
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
genotype/variation: WT
developmental stage: Post-natal day 14
tissue: prefrontal cortex
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was carried out using RNeasy lipid tissue kit (QIAGEN, Venlo, The Netherlands)
2.5 μg RNA was used for rRNA depletion using the Ribo‐Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre, Madison, Wisconsin, USA) according to the manufacturer's recommendations. RNA fragmentation reactions were performed using fragmentation buffer (5x; 200 mM Tris‐Ac, 500 mM potassium‐Ac, 150 mM magnesium‐Ac, pH 8.2) in a final concentration of 1x per reaction. Fragmentation reactions were incubated at 95°C for 4 min on a thermal cycler and placed on ice for 10 min. Fragmented rRNA-depleted RNA was purified using ethanol precipitation, First and second strand synthesis was performed as described by Kouwenhoven and colleagues (2015). samples were prepared for sequencing by end repair of 5 ng total DNA as measured by Qubit dsDNA HS (Invitrogen). NEXTflex adaptors (Bioo scientific, Austin, Texas, USA) were ligated to the DNA fragments, followed by post-ligation cleanup using Agencourt AMPure XP beads (Beckman Coulter, Woerden, The Netherlands), library amplification by PCR (10 cycles) and size selection (∼300 bp) using Agencourt AMPure XP beads (Beckman Coulter). Quality control of DNA libraries prepared for sequencing was performed by qPCR and by running the products on a Bioanalyzer (Bio-Rad, Veenendaal, The Netherlands). Cluster generation and sequencing (50 bp, single end reads) was performed with the Illumina HiSeq 2000 sequencer according to standard Illumina protocols. Samples were sequenced to a depth of approximately 29 million reads per sample. Reads were aligned to the rn4 rat genome assembly using the gsnap program
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107381
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| Data processing |
42bp reads were mapped to the rat genome build rn4 using bwa version 0.6.1
BedGraph tracks were generated from BAM files using 'bedtools genomecov', normalized using the '-scale' option
Genome_build: rn4
Supplementary_files_format_and_content: Gzip-compressed bedgraph files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated file with normalized Ensembl gene expression values in Fragments per Kilobase per Million mapped reads (FPKM) for all samples, as calculated by the cufflinks program.
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| Submission date |
Apr 04, 2016 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Jo Huiqing Zhou |
| E-mail(s) |
jo.zhou@radboudumc.nl
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| Organization name |
Radboud University
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| Street address |
Geert Grooteplein 26/28
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| City |
Nijmegen |
| ZIP/Postal code |
6525GA |
| Country |
Netherlands |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE79909 |
Gene expression analysis of serotonin transporter knock-out and wildtype rats during rat postnatal prefrontal cortex development |
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| Relations |
| Reanalysis of |
GSM2107381 |
| BioSample |
SAMN04606256 |
| SRA |
SRX1686522 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2108221_PFC_WT14_20_2_norm.bedgraph.gz |
159.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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