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| Status |
Public on May 01, 2024 |
| Title |
HUDEP-2 WT DNase-I 60U/mL |
| Sample type |
SRA |
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| Source name |
HUDEP-2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2
cell type: human erythroid progenitors
genotype: WT
treatment: untreated
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| Growth protocol |
HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from 100,000-200,000 cells were extracted in the presence of 0.04% de-ionized IGEPAL CA-630 incubated at 4 ºC for 10 min. Nuclei were treated with a gradient of DNase I solution (40 IU to 100 IU of DNase I) for 3 min at 37 ºC. DNase I digestion was quenched by adding an equal volume of 5X Stop buffer and 20μL RNase A (Sigma, R4642) followed by incubation at 37 ºC for 60min. After incubation, 1μL of Proteinase K (Sigma, P4850) was added and the reactions were incubated at 50 ºC for 60min. Digested genomic DNA was visualized on 1.2% agarose gen and the fragment size profile was generated using the Fragment Analyzer (Advanced Analytical). Prior to genomic library generation, fragments were subjected to size selection with large fragment depletion by magnetic bead separation. Fragment size distribution and concentration of the fractionated sample was measured with Fragment Analyzer (Advanced Analytical).
Illumina compatible, double-stranded DNA library libraries from the size fractionated samples were constructed using the ThruPLEX DNA-seq Kit (Takara Bio) according to manufacturer’s instructions.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalling, RTA v3.4.4
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.3
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Assembly: GRCh38
Supplementary files format and content: Normalized DNaseI density bigWig files
Library strategy: DNaseI-seq
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| Submission date |
Dec 27, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Jeff Vierstra |
| E-mail(s) |
jvierstra@altius.org
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| Organization name |
Altius Institute for Biomedical Sciences
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| Street address |
2211 Elliot Ave
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE252160 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [DNaseI-seq] |
| GSE252163 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors |
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| Relations |
| BioSample |
SAMN39152163 |
| SRA |
SRX23045033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7995348_LN46730.75_20.normalized.GRCh38_no_alts.bw |
86.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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