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| Status |
Public on May 01, 2024 |
| Title |
HUDEP2 WT GATA1 CUT&RUN |
| 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: GATA1
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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 |
After immobilization of 2x10E5 HUDEP-2 cells with Concannavalin A-coated beads DNA was extracted using phenol-chloroform, iso-amly alcohol precipitation
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 v2.4.19
Assembly: GRCh38
Supplementary files format and content: Normalized H3K27ac CUT&RUN density bigWig file
Supplementary files format and content: Normalized GATA1 CUT&RUN density bigWig file
Library strategy: CUT&RUN
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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) |
| GSE252157 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [CUT&RUN] |
| GSE252163 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors |
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| Relations |
| BioSample |
SAMN39155043 |
| SRA |
SRX23045645 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7995330_LN50853.75_20.normalized.GRCh38_no_alts.bw |
236.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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