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| Status |
Public on Apr 04, 2024 |
| Title |
WT M HNF1b |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
genotype: WT
Sex: male
antibody: Invitrogen, 720259
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Snap-frozen kidneys of 12-14 weeks old mice were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. Cells were then lysed using Farnham Lysis Buffer and homogenized on ice. After filtering through a 70um filter, chromatin was sonicated until majority of the fragments were below 1000bp length as assessed by electrophoresis of small aliquots.
Sheared chromatin (>600ug per sample) was incubated with H3K27ac (Active Motif, 39133), H3K4me3 (Millipore, CS200580), and HNF1b (Invitrogen, 720259) antibodies. Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on a NovaSeq 6000 or HiSeq 3000 machine (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
mm10
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| Data processing |
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
next, samples were aligned to mm10 genome with bowtie2 (Langmead et al., Nature methods, 2012)
next, MASC2 was used to visualize peaks (Zhang et al., Genome Biology, 2008)
next, .tdf files were generated using IGV and IGVTools (Robinson et al., Nature Biotechnology 2011)
Assembly: mm10
Supplementary files format and content: .tdf files containing tracks with respective histone modification peak heights and locations
Supplementary files format and content: .bedgraph files containing tracks with respective histone modification peak heights and locations
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| Submission date |
Feb 21, 2024 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Jakub Jankowski |
| E-mail(s) |
jakub.jankowski@nih.gov
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| Organization name |
NIH
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| Department |
NIDDK
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| Lab |
LCMB
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| Street address |
8 Center DR.
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE243944 |
Deletion of Klotho enhancer deepens sexual dimorphism of gene expression without impacting female resistance to kidney injury [ChIP] |
| GSE243946 |
Deletion of Klotho enhancer deepens sexual dimorphism of gene expression without impacting female resistance to kidney injury |
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| Relations |
| BioSample |
SAMN40022966 |
| SRA |
SRX23687684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8093064_WT_M_HNF1b.bedgraph.gz |
154.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM8093064_WT_M_HNF1b.tdf |
77.1 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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