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Sample GSM1694995 Query DataSets for GSM1694995
Status Public on Mar 09, 2016
Title liver_H1-sh-hAAT_25nt_rep1
Sample type SRA
Source name liver
Organism Mus musculus
Characteristics tissue: liver
strain: C57Bl/6
Extracted molecule polyA 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.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Description liver_shRNA_FPKM.txt
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
Submission date May 22, 2015
Last update date May 15, 2019
Contact name Paul Valdmanis
Phone 206-221-8059
Organization name University of Washington
Department Medicine
Lab Paul Valdmanis
Street address 1705 NE Pacific St, HSB J-309
City Seattle
State/province WA
ZIP/Postal code 98115-7720
Country USA
Platform ID GPL17021
Series (1)
GSE69186 Small and large RNA sequencing of mouse livers receiving small hairpin RNAs
BioSample SAMN03732583
SRA SRX1037274

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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