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Sample GSM7221981 Query DataSets for GSM7221981
Status Public on Jan 30, 2024
Title 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 hihg glucose DMEM supplemented with 10% foetal calf serum .
Extracted molecule total RNA
Extraction protocol Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-FLAG-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Haag et al., 2017).
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
Data processing Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences NNNNNAGC. Using pyBarcode Filter (pyCRAC version 1.4.5).
3' adaptor sequences (TGGAATTCTCGGGTGCCAAGG) were removed using Flexbar (version 3.5.0). flexbar', '-r', , '-t', '-q', 'TAIL', '-qf', u'i1.8', '-qt', '13', '-u', '0', '-m', '21', '-n', '8', '-at', 'RIGHT', '-z', 'GZ', '-o', '-ao', '2', '-ae', '0.1', '-as'
Identical sequence reads containing the same UMI were collapsed using pyFastqDuplicateRemover (PyCRAC version 1.4.5).
Aligment STAR (version 2.7.0d):params=' --runThreadN 8 --alignEndsType EndToEnd --outFilterMismatchNoverLmax 0.3 --outFilterMultimapScoreRange 10 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 60 --outSAMunmapped Within --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 15 --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.GRCh38.29
Supplementary files format and content: Aligned reads in bedgraph format
Library strategy: CRAC
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)
GSE230431 GPATCH4 regulates rRNA and snRNA 2’-O-methylation in both DHX15-dependent and -independent manners [CRAC]
GSE230433 GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and -independent manners
BioSample SAMN34353588
SRA SRX20084022

Supplementary file Size Download File type/resource
GSM7221981_His-Flag_B.bedgraph.gz 6.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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