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| Status |
Public on Feb 14, 2016 |
| Title |
Kidney normal tissue 1 RNAseq |
| Sample type |
SRA |
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| Source name |
Kidney tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
(Ribosome profiling data only) Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20 -q 5). Reads without adapter sequence were discarded.
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.6) with parameters (--seed 42 --local) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GtRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.7) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25) to hg19 and transcripts defined by GENCODE v19/BASIC.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.
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| Submission date |
Jun 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Koos Rooijers |
| E-mail(s) |
k.rooijers@nki.nl
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| Organization name |
Netherlands Cancer Institute
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| Department |
Gene Regulation
|
| Lab |
Agami Lab
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| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE59820 |
Ribosome profiling on sections taken from a kidney tumor |
| GSE59821 |
Restrictions in amino acid availability revealed by differential ribosome codon reading |
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| Relations |
| BioSample |
SAMN03776741 |
| SRA |
SRX1059892 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1712825_Kidney_normal_tissue_1_RNAseq.normalized.wig.gz |
26.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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