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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
Other
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
E-mail(s) sasc@lumc.nl
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]
Relations
BioProject PRJNA703954
SRA SRP307513

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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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