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Series GSE167223 Query DataSets for GSE167223
Status Public on Feb 23, 2021
Title Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Using a transcriptome-wide profiling approach to map translation initiation start sites in human beta-cells under standard and inflammatory conditions, we identifies non-canonical start sites and translation initiation within lncRNA.
Overall design EndoC-BH1 cells have been treated 24h with proinflammatory cytokines 1000 U/ml IFNγ and 2 ng/ml IL1β for 24 h. RNA was isolated by TRizol and sequenced by nanopore sequencing to etablish the de novo transcritpome. Upon incubation, cells were treated with 2ug/ml harringtonine for 30 minutes and Cycloheximide (100ug/ml) for ribosome footprint purification.
Contributor(s) Thomaidou S, Boom J, Mei H, Zaldumbide A
Citation(s) 34554924
Submission date Feb 22, 2021
Last update date Dec 14, 2021
Contact name Hailiang Mei
Organization name Leiden University Medical Center
Department Sequencing Analysis Support Core
Street address Einthovenweg 20
City Leiden
ZIP/Postal code 2333 ZC
Country Netherlands
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24106 MinION (Homo sapiens)
Samples (12)
GSM5099830 ENDOC-βH1 cells treated with cytokines rep 1 -ribosome profiling [CYT1]
GSM5099831 ENDOC-βH1 cells treated with cytokines rep 2 -ribosome profiling [CYT2]
GSM5099832 ENDOC-βH1 cells treated with cytokines rep 3 -ribosome profiling [EndoCyto]
BioProject PRJNA703954
SRA SRP307513

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE167223_data_control_rpf_forgeo.txt.gz 17.9 Mb (ftp)(http) TXT
GSE167223_data_cyto_rpf_forgeo.txt.gz 15.2 Mb (ftp)(http) TXT
GSE167223_nanopore_filtered.tsv.gz 510.1 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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