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| Status |
Public on Jun 20, 2024 |
| Title |
Human kidney medulla, Hi-C, rep2 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
kidney region: medulla
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We extracted nuclei from tissues and used the nuclear suspensions for library preparation (1 million nuclei for each Hi-C reaction).
Hi-C library preparation was performed with the Arima Library Prep Kit v2 (A303011, Arima Genomics).
Hi-C and CUT&RUN on the same nuclear suspension pool
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Preprocessing of paired-end raw .fastq files of Hi-C sequencing data were performed with Juicer v1.6, including genome alignment, read sorting, duplicate removal and generation of .hic contact matrices, with resolutions of 5K, 10K, 25K, 50K, 100K, 250K, 500K, 1000K and 2500K bases.
Assembly: Human hg19 (primary assembly of GRCh37) was used as the reference genome.
Supplementary files format and content: .hic Hi-C contact matrices
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| Submission date |
Jan 18, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Benjamin Humphreys |
| Organization name |
Washington University School of Medicine
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| Street address |
660 S Euclid Ave
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE253632 |
Chromatin conformation and histone modification profiling across human kidney anatomic regions [Hi-C] |
| GSE253634 |
Chromatin conformation and histone modification profiling across human kidney anatomic regions |
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| Relations |
| BioSample |
SAMN39487609 |
| SRA |
SRX23305680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8024402_M2_inter_30.hic |
1.6 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
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