|
| Status |
Public on Jun 15, 2024 |
| Title |
ESC, DMSO, H2BK5Ac, ChIP, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E14TG2a
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14TG2a
cell type: Embryonic stem cells
spike-in reference_organism: Drosophila melanogaster
spike-in cell_line: SG4
chip antibody: H2BK5Ac (Active Motif 39123)
treatment: DMSO 6 hour
|
| Treatment protocol |
ESCs were first treated with 1uM 4-hydroxytamoxifen for 5 days to remove endogenous HDAC1/2, these cells were then treated with 100 nM dTAGV-1 for 2/6/24 hours or with an equivlaent volume of DMSO.
|
| Growth protocol |
ESCs were grown on tissue culture plates pre-treated with 0.1% gelatine in KO DMEM supplemented with 15% FBS, pen-strep glutamine, 2-Mercaptoethanol and leukemia inhibitory factor in humidified atmosphere at 37 C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following cell lysis chromatin was fragmented by 5 minutes of MNase digestion.
Libraries were prepared for ChIP and matched input samples using the NEBNext Ultra II DNA library kit and indexed using NEBNext Multiplex Oligos.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed using trimmomatic
Trimmed reads were aligned to the mm10 genome sequence using Bowtie 2 using –no-mixed and –no-discordant options
SAM files were converted to BAM files, then sorted using samtools before duplicates were removed using sambamba
BAM files were merged using samtools merge
Merged BAM files were converted to bigWigs using deeptools bamCoverage and input files were subtracted from ChIP files. bigWig files were then viewed on the genome browser
Assembly: mm10
Supplementary files format and content: bigWig - dense, contiuous data for display as a graph on the genome browser
|
| |
|
| Submission date |
Jun 09, 2024 |
| Last update date |
Jun 15, 2024 |
| Contact name |
Shaun Cowley |
| E-mail(s) |
smc57@le.ac.uk, cowleylabprimers@gmail.com
|
| Organization name |
University of Leicester
|
| Department |
Molecular and Cell Biology
|
| Lab |
3/37
|
| Street address |
Henry Wellcome Building, Lancaster Road
|
| City |
Leicester |
| ZIP/Postal code |
LE1 7RH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE269433 |
Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq] |
| GSE269448 |
Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites |
|
| Relations |
| BioSample |
SAMN41769132 |
| SRA |
SRX24855060 |
