NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7221987 Query DataSets for GSM7221987
Status Public on Jan 30, 2024
Title RIP_GPATCH4-His-Flag_B
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
E-mail(s) katherine.bohnsack@med.uni-goettingen.de
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
Relations
BioSample SAMN34353377
SRA SRX20083835

Supplementary file Size Download File type/resource
GSM7221987_RIP_GPATCH4-His-Flag_B.bedgraph.gz 3.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap