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Sample GSM7221986 Query DataSets for GSM7221986
Status Public on Jan 30, 2024
Title RIP_GPATCH4-His-Flag_A
Sample type SRA
Source name Flp-In T-Rex HEK293
Organism Homo sapiens
Characteristics cell line: Flp-In T-Rex HEK293
genotype: WT
Treatment protocol Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking. Cells were UV crosslinked using light at 254 nm as previously described (Sloan et al., 2015; Memet et al., 2017).
Growth protocol HEK293 Flp-In T-Rex cell lines expressing GPATCH4-His-FLAG or the His-FLAG tag alone were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum .
Extracted molecule total RNA
Extraction protocol Crosslinked RNA-protein complexes were purified and RNAs associated with His-FLAG-tagged proteins were recovered.
Small RNAs <200 nt were enriched and libraries were constructed using the QIAseq miRNA Library Kit Catalog no.331502 according to the maufacturer's instructions.
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing 3' Adaptor seuquences (AACTGTAGGCACCATCAAT) were Clipped using Flexbar (version 3.5.0) with the following arguments -qf i1.8 -qt 13 -u 0 -m 15 -n 8 -at RIGHT -z GZ -o -ao 2 -ae 0.1 -as AACTGTAGGCACCATCAAT
Clipped reads were aligned to the human genome using STAR (Version 2.7.10a) with the following arguments --alignEndsType EndToEnd --outFilterMismatchNmax 10 --outFilterMultimapScoreRange 10 --quantMode TranscriptomeSAM GeneCounts --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 30 --outSAMunmapped Within --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM --readFilesCommand zcat
Bedgraphs were generated using bedtools (version 2.27.1) with the following arguments genomecov -ibam .bg
Assembly: Homo_sapiens.GRCh38.108
Supplementary files format and content: Aligned reads in bedgraph format
Submission date Apr 24, 2023
Last update date Jan 30, 2024
Contact name Katherine Bohnsack
Organization name University Medical Centre Göttingen
Street address Humboldtallee 23
City Göttingen
ZIP/Postal code 37073
Country Germany
Platform ID GPL20301
Series (2)
GSE230432 GPATCH4 regulates rRNA and snRNA 2’-O-methylation in both DHX15-dependent and -independent manners [small RNA-seq]
GSE230433 GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and -independent manners
BioSample SAMN34353378
SRA SRX20083834

Supplementary file Size Download File type/resource
GSM7221986_RIP_GPATCH4-His-Flag_A.bedgraph.gz 3.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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