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| Status |
Public on May 11, 2023 |
| Title |
MEF, KO, ctrl, H3K27ac |
| Sample type |
SRA |
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| Source name |
mouse embryonic fibroblast
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast
genotype: LKB1 knockout
treatment: control
antibody: H3K27ac
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were trimmed with TrimGalore v0.6.0
Trimmed reads were aligned with bwa mem v0.7.17 and duplicates were marked using SAMBLASTER v0.1.24.
BigWig files were generated using bamCoverage in DeepTools v with the parameters, '--binSize 10 --extendReads --normalizeUsing "CPM" --samFlagExclude 1024 --samFlagInclude 64' and '--blackListFileName' to specify the ENCODE blacklist v2.
Assembly: mm10
Supplementary files format and content: Bigwig
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| Submission date |
Oct 04, 2022 |
| Last update date |
May 11, 2023 |
| Contact name |
Russell Jones |
| E-mail(s) |
russell.jones@vai.org
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| Phone |
6166001610
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| Organization name |
Van Andel Institute
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE214822 |
Genome wide screen of H3K27ac enrichment in WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts |
| GSE214824 |
WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts |
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| Relations |
| BioSample |
SAMN31155865 |
| SRA |
SRX17797885 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6616324_SC9.bw |
58.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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