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| Status |
Public on Jun 17, 2021 |
| Title |
U2_EDL |
| Sample type |
SRA |
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| Source name |
hindlimb
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: EDL muscle
protocol: unloading 7 days
lib.sizes: 5495410
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from EDL and Soleus muscles using RNeasy Fibrous Tissue Mini Kit QIAGEN
5 µg of total RNA RIN≥7 processed into cDNA by reverse transcriptase. CAGE libraries prepared according to Murata et al., 2014 (doi: 10.1007/978-1-4939-0805-9_7).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
nAnTi-CAGE
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| Data processing |
Reads were trimmed using fastx_trimmer and removeN scripts from Moirai pipeline (http://fantom.gsc.riken.jp/software/). Adapters were removed by using Trimmomatic-0.38
Trimmed reads mapped on Rnor_6.0 Ensembl genome assembly for Rattus norvegicus using BWA, unmapped reads remapped by Hisat2 and merged into processed BAM files
BAM files used to generate CTSS (CAGE transcription start site) tables in OSC format (https://zenbu-wiki.gsc.riken.jp/zenbu/wiki/index.php/OSCtable) using PromoterPipeline script level1.py (https://github.com/Population-Transcriptomics/C1-CAGE-preview/blob/master/tutorial.md)
OSC files merged into Level2_table.osc by using level2.py from PromoterPipeline.
Genome_build: Rnor_6.0 (GCA_000001895.4)
Supplementary_files_format_and_content: OSC files contain information about position and strand of mapped CAGE reads, column for raw and TPM (tags per million) normalized counts included. Level2_table.osc table contains clustered CAGE signal representing putative promoter regions with expression level within all experiments in raw and TPM normalized counts for these clusters.
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| Submission date |
Dec 11, 2019 |
| Last update date |
Jun 17, 2021 |
| Contact name |
Ruslan Deviatiiarov |
| E-mail(s) |
ruselusalbus@gmail.com
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| Phone |
+79196948678
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| Organization name |
Kazan Federal University
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| Department |
Institute of Fundamental Medicine and Biology
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| Lab |
Extreme Biology
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| Street address |
Paris Commune, 9
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| City |
Kazan |
| State/province |
Tatarstan |
| ZIP/Postal code |
420021 |
| Country |
Russia |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE141827 |
Genome-wide atlas of promoters expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy of skeletal muscles |
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| Relations |
| BioSample |
SAMN13540818 |
| SRA |
SRX7347499 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4213800_Lane3.U2_EDL.TAC.osc.txt.gz |
7.6 Mb |
(ftp)(http) |
TXT |
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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