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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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