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Sample GSM8742710 Query DataSets for GSM8742710
Status Public on Jan 20, 2025
Title TFBS screen, round 2, replicate C
Sample type SRA
 
Source name HAP1
Organism Homo sapiens
Characteristics cell line: HAP1
treatment: TFBS screen, round 2
Growth protocol HAP1 ∆MLH1 cells expressing a doxycycline-inducible prime editor were cultured in IMDM (Invitrogen) with 10% FBS (Invitrogen) and glutamine and penicillin-streptomycin (Invitrogen) at 37 °C and 5% CO2
Extracted molecule genomic DNA
Extraction protocol Between 2 and 4 million cells were collected by centrifugation, and high molecular weight (HMW) genomic DNA was extracted using the Monarch High Molecular Weight DNA Extraction Kit (New England BioLabs).
The R5-2 region of interest was amplified and prepared for Illumina sequencing with index adapters.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description Library name: OTX2_12TFBS_round2_repC.amplicon
Data processing After demultiplexing, paired-end reads were merged using PEAR. Reads containing both forward and reverse PCR primer sequences were identified using the amplicon function of SeqKit. Amplicon sequences were then analyzed to identify and quantify deletions using CRISPResso2.
Supplementary files format and content: .txt, read count for modifications detected within the amplicons.
 
Submission date Jan 17, 2025
Last update date Jan 20, 2025
Contact name Pierre Murat
E-mail(s) pm23@sanger.ac.uk
Organization name Wellcome Sanger Institute
Street address Wellcome Trust Genome Campus
City Hinxton
ZIP/Postal code CB10 1RQ
Country United Kingdom
 
Platform ID GPL15520
Series (1)
GSE287268 Resolution of a human super-enhancer by targeted genome randomisation [Amplicon-seq]
Relations
BioSample SAMN46295337
SRA SRX27389333

Supplementary file Size Download File type/resource
GSM8742710_R2.repC.mod.count.txt.gz 2.6 Kb (ftp)(http) TXT
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Raw data are available in SRA

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