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Sample GSM7995330 Query DataSets for GSM7995330
Status Public on May 01, 2024
Sample type SRA
Source name HUDEP-2
Organism Homo sapiens
Characteristics cell line: HUDEP-2
cell type: human erythroid progenitors
genotype: WT
treatment: GATA1
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.
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.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
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
Submission date Dec 27, 2023
Last update date May 01, 2024
Contact name Jeff Vierstra
Organization name Altius Institute for Biomedical Sciences
Street address 2211 Elliot Ave
City Seattle
State/province WA
ZIP/Postal code 98121
Country USA
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
BioSample SAMN39155043
SRA SRX23045645

Supplementary file Size Download File type/resource 236.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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