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| Status |
Public on Aug 26, 2022 |
| Title |
5‘_end_sequencing_Control_1.fastq.gz |
| Sample type |
SRA |
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| Source name |
HeLa cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: Control for 5' end sequencing
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| Growth protocol |
HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.
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| Extracted molecule |
total RNA |
| Extraction protocol |
20 μg of total RNA was polyA selected and then was treated with E.coli purified AlkB for demethylation of the RNA as previously describe (Zheng et al., 2015). Next, we construction uncapped 5′-specific sequencing libraries as previously describe (Pelechano et al., 2016).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
5' end RNA-sequencing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13).TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12) witth “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Aligned Reads on exons were counted using HTSEQ (0.5.4p3).
HTSEQ was used to count reads at exons of genes. Normalization was done using DESEQ.
Genome_build: hg19 for human data, mm10 for mouse data
Supplementary_files_format_and_content: Processed data file 5prime_htseq_readcounts.txt is a tab delimited .txt files containing raw read counts obtained from HTSEQ (0.5.4p3) at exons of genes. also included is 5‘_end_sequencing_Control_1.bw as bigwig file
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| Submission date |
Apr 23, 2020 |
| Last update date |
Aug 26, 2022 |
| Contact name |
Pierre-Rene Körner |
| Organization name |
Netherlands Cancer Institute (NKI)
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| Department |
Oncogenomics
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE149204 |
Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential |
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| Relations |
| BioSample |
SAMN14678265 |
| SRA |
SRX8163577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4492180_fiveprime_end_sequencing_Control_1.bw |
49.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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