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| Status |
Public on Mar 09, 2016 |
| Title |
H1_sh_hAAT_25nt_rep3_Ago2IP |
| Sample type |
SRA |
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| Source name |
liver - Ago2 IP
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57Bl/6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Large RNA samples were homogenized and extracted by Trizol; mRNAs were enriched through poly-A purification from a poly-A spin kit (NEB); small RNA samples were extracted using a miRvana microRNA isolation kit (samples 13-50) or total Trizol-extracted RNA (samples 51-93)
RNAseq library samples 1-6 were prepared using an Illumina TruSeq kit. RNAseq library samples 7-12 were prepared using a ScriptSeq v2 kit (Epicentre).
3ug of miRvana extracted or 5ug of Trizol extracted small RNAs were ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to barcoded adapters. Dual-ligated RNA was reverse transcribed, PCR amplified and size selected on 4% NuSieve (Lonza) agarose. Small RNA sequencing was performed on the Illumina GAII (samples 13-50) and miSeq (samples 51-93) platforms.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Ago2IP_smallRNA_RPM.txt
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| Data processing |
RNAseq reads were aligned to the mm9 genome through a standardized pipeline generated by the Stanford Center for Genomics and Personalized Medicine
FPKM values were calculated by use of Cufflinks v2.2.1 with the following parameters: “--library-norm-method quartile” and removing ribosomal, snoRNA and mitochondrial sequences.
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker-1 clipped and aligned to mouse hairpins from mirBase release 15 using bowtie (version 0.12.7) with 2 mismatches and command -- best
small RNA sequences from 293 cells were aligned to the miR-122 plasmid that was transfected and raw counts for each small RNA that was generated were tabulated
Genome_build: mm9, mirBase release 15
Supplementary_files_format_and_content: File of FPKM values for RNAseq samples, of reads per million (RPM) mapped microRNA hits for mouse small RNA sequencing samples, and alignment to a transfected plasmid in human cell line samples, all in tab delimited text format
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| Submission date |
May 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Valdmanis |
| E-mail(s) |
paulnv@uw.edu
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| Phone |
206-221-8059
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| Organization name |
University of Washington
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| Department |
Medicine
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| Lab |
Paul Valdmanis
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| Street address |
1705 NE Pacific St, HSB J-309
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98115-7720 |
| Country |
USA |
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| Platform ID |
GPL9250 |
| Series (1) |
| GSE69186 |
Small and large RNA sequencing of mouse livers receiving small hairpin RNAs |
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| Relations |
| BioSample |
SAMN03732608 |
| SRA |
SRX1037299 |
| 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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