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.

crappe_2014      

HCT116 One of 3 strains of malignant cells isolated from a male with colonic carcinoma.
References PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Authors Jeroen Crappé, Elvis Ndah, Alexander Koch, Sandra Steyaert, Daria Gawron, Sarah De Keulenaer, Ellen De Meester, Tim De Meyer, Wim Van Criekinge, Petra Van Damme, Gerben Menschaert
GEO accession GSM1403307
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)
155006923 105778679 73964 1261228 30240537 (19.51%)
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)
158957695 99422691 121322 2115684 40379644 (25.40%)
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