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Sample GSM7230176 Query DataSets for GSM7230176
Status Public on Jan 30, 2024
Title GPATCH4-His-Flag_Input
Sample type SRA
 
Source name Flp-In T-Rex HEK293
Organism Homo sapiens
Characteristics cell line: Flp-In T-Rex HEK293
genotype: WT with Flp-In locus modified fro expression of GPATCH4-His-FLAG
chip antibody: none
Treatment protocol Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking with 1.5 mM EGS for 10 min at room temperature and 1% PFA for 45 min at 4°C.
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 genomic DNA
Extraction protocol ChIP was performed usign the ChIP-IT High Seneitivity kit (Active Motif 53040). Chromatin shearing to 200-500 bp fragments was performed by sonication. 30 µg of sheared chromatin was subjected to immunoprecipitations using anti-FLAG M2 beads (Sigma-Aldrich M8823). Eluates were treated with Proteinase K.
Libraries were constructed using the TruSeq ChIP Library Preparation Kit (Illumina) according to the maufacturer's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing Raw data were quality checked using FastQC (v0.11.9). The average Phred score is 35.
Single-end reads were aligned to the human rDNA using default bowtie2 (v2.3.5.1) arguments.
Duplicated reads were marked with Picard (v3.0.0) using the following arguments: MarkDuplicates VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=FALSE
Using samtools (v1.10), .bam files were filtered to remove duplicated, unmapped, not primary alignment, and low-quality reads with the following arguments: view -F 1804 -q 30
Bedgraph files were generated using bedtools (version 2.27.1) with the following arguments genomecov -ibam .bg -scale RPM. Bedgraph files were then converted to bigwig files using bedGraphToBigWig (v4)
Assembly: Human ribosomal DNA (accesion number U13369.1)
Supplementary files format and content: Aligned reads in bigwig format
 
Submission date Apr 26, 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)
GSE230433 GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and -independent manners
GSE230637 GPATCH4 regulates rRNA and snRNA 2’-O-methylation in both DHX15-dependent and -independent manners [ChIP-Seq]
Relations
BioSample SAMN34381870
SRA SRX20108496

Supplementary file Size Download File type/resource
GSM7230176_GPATCH4-His-Flag_Input.bw 99.5 Kb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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