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Sample GSM1268951 Query DataSets for GSM1268951
Status Public on Dec 02, 2013
Title 3P-seqs in kidney wild type
Sample type SRA
Source name Kidney
Organism Mus musculus
Characteristics data type: 3P-seq fastq
tissue: Kidney
genotype: willd type
genetic background: 129S5/SvEvBrd
Extracted molecule total RNA
Extraction protocol RNA from wild type and miR-22D (Gurha et al., 2012) mouse tissues was isolated by adding a steel bead and 1 mL TRI Reagent to tissues and then vortexing for two minutes in a TissueLyser II (Qiagen) at 30 Hz, twice. The homogenate was centrifuged for 8 min at 12,000xg and the supernatant was purified according to manufacturer’s protocol with an additional phenol/chloroform extraction after phase separation.
3P-Seq libraries were prepared from 75 μg of isolated RNA (mouse tissues, mESC, NIH3T3) as described previously (Jan et al., 2011) with modifications (see Supplemental Information).
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Data processing Basecalls performed using CASAVA version 1.7
Reads are reverse-complemented first and mapped reads with at least one untemplated adenylate residue using Bowtie with option (bowtie -p 4 -q --phred33-quals -5 3 -l 25 -n 1 -e 240 --best --strata -m 1).
We considered as a cluster those 3P-tags ending 31 nucleotides within the most frequently implicated cleavage position, which was then regarded as a candidate poly(A) cleavage site.
To control for PCR amplification bias, we only used those clusters with at least two identifiably independent reads in our downstream analysis (e.g. tags with different ends, different number 3’-terminal adenylates, and/or from two different libraries).
Genome_build: mm9
Supplementary_files_format_and_content: bed files including 3P-seq clusters
Submission date Nov 19, 2013
Last update date May 15, 2019
Contact name Jin-Wu Nam
Organization name Hanyang University
Street address 222 Wangsimni Seongdong-gu
City Seoul
ZIP/Postal code 133-791
Country South Korea
Platform ID GPL13112
Series (2)
GSE52528 Global analyses of the effect of different cellular contexts on microRNA targeting (3P-Seq Mouse)
GSE52531 Global analyses of the effect of different cellular contexts on microRNA targeting
BioSample SAMN02412866
SRA SRX380422

Supplementary file Size Download File type/resource
GSM1268951_kidney_wt_pA.15.sumCM.bed.gz 1010.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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