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| Status |
Public on Dec 02, 2013 |
| Title |
3P-seqs in HEK293 cells |
| Sample type |
SRA |
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| Source name |
HEK293 cells
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| Organism |
Homo sapiens |
| Characteristics |
data type: 3P-seq fastq
cell line: HEK293 cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from cell lines 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 (HeLa, HEK293, Huh7, IMR90 cells) as described previously (Jan et al., 2011) with modifications (see Supplemental Information).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
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| 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: hg19
Supplementary_files_format_and_content: bed files including 3P-seq clusters
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| Submission date |
Nov 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin-Wu Nam |
| E-mail(s) |
coya75@gmail.com
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| Organization name |
Hanyang University
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| Street address |
222 Wangsimni Seongdong-gu
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| City |
Seoul |
| ZIP/Postal code |
133-791 |
| Country |
South Korea |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE52527 |
Global analyses of the effect of different cellular contexts on microRNA targeting (3P-Seq Human) |
| GSE52531 |
Global analyses of the effect of different cellular contexts on microRNA targeting |
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| Relations |
| BioSample |
SAMN02412854 |
| SRA |
SRX380414 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1268943_hek293.15.sumCM.bed.gz |
751.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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