|
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 |