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| Status |
Public on Nov 20, 2017 |
| Title |
mRNA with mir92a MIR after TEX 293 cell rep 2 |
| Sample type |
SRA |
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| Source name |
HEK293
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| Organism |
Homo sapiens |
| Characteristics |
treatment: mRNA with mir92a MIR after TEX 293 cell
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| Growth protocol |
U2OS, HEK293 and HEK293T cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100units/ml penicillin and 100μg/ml streptomycin at 37 °C
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using QIAzol Reagent (Qiagen 79306) and treated with DNase I (NEB-M0303S). 5Μg of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB, E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep kit (NEB, E7420S) or 3‘ mRNA-Seq Library Prep Kit (lexogen 015UG009V0211).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Transfection of miRNA, synthetic mir92a-3p, mirlet7 or negative control dsRNA performed using TransIT-X2TM Dynamic Delivery System according to manufacturer's instructions. Cells were collected for analysis 40h after transfection
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| Data processing |
U2OS samples: Raw reads (fastq files) were inspected for quality issues with FastQC v0.11.2. Reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32
U2OS samples: adapter sequences were removed with Trim Galore v0.3.7, with parameters: -length 15
U2OS samples: filtered to remove very low quality reads, using the fastq_quality_filter program of the FASTX v0.0.14, with a quality threshold of 20 at 90 percent or more of the read's positions
U2OS samples: Sequences were mapped to hg19 using tophat (v2.0.13), with parameters: -N 2 --read-gap-length 5 --read-edit-dist 7 --segment-length 18 --read-realign-edit-dist 3 --no-coverage-search -r 270 --mate-std-dev 100
Remaining reads were re-paired
293 samples: both R1 and R2 reads were quality trimmed at both ends with a threshold of 32
293 samples: adapter sequences were removed with cutadapt v1.7.1
293 samples: reads were filtered by overall quality with a threshold of 20 over 90 percent of the read
293 samples: Remaining reads were re-paired
YMC samples: reads were quality trimmed at both ends with a threshold of 32
YMC samples:adapters were removed with cutadapt
YMC samples: poly-A sequences were trimmed with cutadapt
YMC samples: reads were filtered by overall quality with a threshold of 20 over 90 percent of the read
Genome_build: hg19
Supplementary_files_format_and_content: Supp_Table1_U2OS_TEX_fit_hmm.tsv, Supp_Table2_U2OS_5prime_fit_hmm.tsv, Supp_Table3_U2OS_3prime_fit_hmm.tsv, Supp_Table4_293_TEX_fit_hmm.tsv: These files include HMM predictions of 3'UTR cleavage points, by comparing mRNA-seq data following three different treatments (TEX, 5prime-pulldown and 3prime-pulldown) with the untreated data, for either U2OS or 293 cells.
Supplementary_files_format_and_content: Supp_Table5_3end_RNA-seq_peaks_prox+dist.tsv: Matching proximal and distal peaks in 3'-end RNA-seq data, with and without alpha-amanitin treatments.
Supplementary_files_format_and_content: Supp_Table6_293_Mir92_fit_hmm.tsv, Supp_Table7_293_Let7_fit_hmm.tsv: HMM analysis (as in supp. tables 1-4) for RNA-seq data following miR-92a (table 6) or let-7a (table 7) transfection in 293 cells.
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| Submission date |
Jul 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tommy Kaplan |
| E-mail(s) |
tommy@cs.huji.ac.il
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| Organization name |
Hebrew University
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| Department |
School of Computer Science and Engineering
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| Street address |
Givat Ram Campus
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| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE84068 |
Post-transcriptional 3’UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments |
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| Relations |
| BioSample |
SAMN05361975 |
| SRA |
SRX1898939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2226732_293_mir92a-8_2mis_hg19.bigwig |
200.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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