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.

fritsch_2012      

THP-1 THP-1 is a human monocytic cell line derived from an acute monocytic leukemia patient. It is used to test leukemia cell lines in immunocytochemical analysis of protein-protein interaction, and immunohistochemistry.
References Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting.
Authors Fritsch C, Herrmann A, Nothnagel M, Szafranski K, Huse K, Schumann F, Schreiber S, Platzer M, Krawczak M, Hampe J, Brosch M
GEO accession GSE39561
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)
296350271 206172475 1279994 1994498 63507158 (21.43%)
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)
283288579 237362129 935369 1831178 24753071 (8.74%)
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