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Sample GSM7156026 Query DataSets for GSM7156026
Status Public on May 05, 2023
Title CHO_SAHK2_H3K18la_rep2
Sample type SRA
 
Source name MI5-4 (CHO)
Organism Cricetulus griseus
Characteristics cell line: MI5-4 (CHO)
antibody: H3K18la
Growth protocol MI5-4 CHO cells were cultured in Minimum Essential Medium alpha containing 1,000 mg/L glucose supplemented with 10% fetal bovine serum and 1% penicillin‒streptomycin at 37 °C in a humidified atmosphere with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol MI5-4 CHO cells were incubated with NE1 buffer on ice for 10 min. After collecting nuclear pellets, concanavalin A-coated magnetic beads were mixed and incubated for 10 min at RT. Next, the unbound supernatant was removed, and the bead-bound cells were resuspended in antibody buffer. Anti-H3K18la (PTM-1406, PTM Biolabs), anti-H3K18ac (ab1191, Abcam), and anti-IgG negative control (13-0042, EpiCypher) antibodies were added, and incubated on a nutator overnight at 4 °C. The primary antibodies were removed, and incubation with 0.5 ug of secondary antibody was performed on a nutator for 1 h at RT followed by incubation with pAG-Tn5 in 300-wash buffer for 1 h at RT. The bead/nucleus pellet was resuspended in tagmentation buffer, and the mixture was incubated for 1 h at 37 °C. Next, the bead/nucleus pellet was resuspended in TAPS buffer. The bead/nucleus pellet was then resuspended in SDS release buffer and incubated for 1 h at 58 °C. Next, SDS quenching buffer was added.
To amplify the libraries, 2 ul of a universal i5 and a uniquely barcoded i7 primer (10 uM stocks) were added. A volume of 25 ul of NEBNext High-Fidelity 2x PCR Master mix was added and mixed. The samples were placed in athermocycler with aheated lid using the following cycling conditions: 58 °C for 5 min; 72 °C for 5 min; 98 °C for 45 sec; 14 cycles of 98 °C for 15 sec and 60 °C for 10 sec; final extension at 72 °C for 1 min; and hold at 8 °C. Post-PCR clean-up was performed by adding 1.3x AMPure XP beads, and the libraries were incubated with the beads for 10 min at RT, washed twice gently in 80% ethanol, and eluted in 15 ul of 10 mM Tris pH 8.0. The tubes were placed on a magnetic stand, and the liquid was withdrawn into a fresh tube.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Quality check was done using FastQC v0.11.8
Sequenced reads were mapped to CHOK1GS (Ensembl) using Bowtie2 v2.4.2
Mapped reads with a MAPQ lower than 2 were filtered and sorted by samtools v1.10
Conversion of sorted bam files into bedgraph files was done using bedtools v2.30
Peaks were called using SEACR v1.3
Bigwig files were generated using deepTools v2.0
Assembly: CHOK1GS
Supplementary files format and content: bigwig files RPKM normalized by deepTools
 
Submission date Apr 06, 2023
Last update date May 05, 2023
Contact name Nissim Hay
E-mail(s) [email protected]
Organization name University of Illinois Chicago
Department BMG
Street address 900 South Ashland Ave
City Chicago
State/province IL
ZIP/Postal code 60607
Country USA
 
Platform ID GPL27425
Series (2)
GSE229151 Hexokinase 2 and lactate mediated gene expression via histone H3 lysine 18 lactylation (CHO CUT&Tag)
GSE229156 Hexokinase 2 and lactate
Relations
SRA SRX19900023
BioSample SAMN34105213

Supplementary file Size Download File type/resource
GSM7156026_CHO_SAHK2_H3K18la_rep2_RPKM.bw 2.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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