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| Status |
Public on May 29, 2019 |
| Title |
pa6hr-1 |
| Sample type |
SRA |
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| Source name |
6 hr post wounding_oral mucosa
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| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
treatment/timepoint: 6 hr post wounding
tissue: oral mucosa
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| Treatment protocol |
Full thickness incisional wounds were made on the dorsal skin and the anterior of the hard palate of the mice. The wound tissue specimens were harvested at 6h, 24h and 5 days post-wounding.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (including small RNA) was isolated from normal and wound tissue samples stored in RNALater using a miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
small RNA libraries were generated using the Illumina Truseq Small RNA Preparation kit (San Diego, CA)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (NCBI M_musculus/RNA build 01/12/2015), Rfam11, and genomic DNA (UCSC mm10), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: mm10, mirbase v21.0
Supplementary_files_format_and_content: seq read count
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| Submission date |
Oct 30, 2018 |
| Last update date |
May 29, 2019 |
| Contact name |
Xiaofeng Zhou |
| E-mail(s) |
xfzhou@uic.edu
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| Organization name |
University of Illinois at Chicago
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| Street address |
801 S Paulina Street
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| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60612 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE121996 |
miR-Seq on paired skin and oral mucosal wound healing |
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| Relations |
| BioSample |
SAMN10349434 |
| SRA |
SRX4958278 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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