sORFs.org: repository of small ORFs identified by ribosome profiling

sORFs.org datasets. This section provides detailed information about the datasets used. For more information about the dataset processing please consult the INFO page. navigate through the datasets on the left to acquire more information about the corresponding dataset.

lee_2012      

HEK293 Human embryonic kidney cells 293, also often referred to as HEK 293, HEK-293, 293 cells, or less precisely as HEK cells, are a specific cell line originally derived from human embryonic kidney cells grown in tissue culture
References Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
Authors Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB.
GEO accession SRA056377
treatment type pre-lysis cycloheximide treatment nuclease used: RNase I
total number of reads (CHX/EM sample) reads mapped to rRNA (CHX/EM sample) reads mapped to tRNA (CHX/EM sample) reads mapped to snRNA/snoRNA (CHX/EM sample) reads mapped to genomix(% total number of reads)
54339118 32762206 70788 1222645 12353438 (22.73%)
Total number of reads (HARR/LTM sample) reads mapped to rRNA (HARR/LTM sample) reads mapped to tRNA (HARR/LTM sample) reads mapped to snRNA/snoRNA (HARR/LTM sample) reads mapped to genomix(% total number of reads)
43885186 29002331 40377 1470910 6462878 (14.73%)
FastQC quality control CHX/EM data (no rRNA/tRNA/snRNA/snoRNA) FastQC provides quality control checks on raw sequence data coming from high throughput sequencing pipelines. FastQC provides a modular set of analyses which can be used to give a quick impression on the quality and potential problems of the data. Prior to the FastQC analysis, rRNA, tRNA, snRNA & snoRNA were removed from the data.

source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FastQC quality control CHX/EM
FastQC quality control HARR/LTM data (no rRNA/tRNA/snRNA/snoRNA) FastQC provides quality control checks on raw sequence data coming from high throughput sequencing pipelines. FastQC provides a modular set of analyses which can be used to give a quick impression on the quality and potential problems of the data. Prior to the FastQC analysis, rRNA, tRNA, snRNA & snoRNA were removed from the data.

source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FastQC quality control CHX/EM