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| Status |
Public on Apr 28, 2023 |
| Title |
HUDEP2_175_LMO2 |
| Sample type |
SRA |
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| Source name |
HUDEP2_175_LMO2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP2
antibody: TAL1
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| Treatment protocol |
HUDEP2 cells were eletroporated with NT or -175 sgRNA RNP complex.
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| Growth protocol |
HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin. Erythroid differentiation of CD34+ cells was performed using a three-phase culture protocol. For phase 1 (days 0-7), cells were maintained at a density of 1-4 × 105 /mL in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin-streptomycin, 3 IU/mL heparin, 10 μg/mL insulin, 200 μg/mL holo-transferrin, 1 IU erythropoietin, 10 ng/mL SCF, and 1 ng/mL interleukin-3 (IL-3). For phase 2 (days 8-12), IL-3 was omitted from the medium. Cells were maintained at a density of 0.2-0.8 × 106/mL. For phase 3 (days 12-18), IL-3 and SCF were omitted, the holo-transferrin concentration was increased to 1 mg/mL, and the cells were maintained at a density of 1-2 × 106/mL.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction for DNA sequencing was performed using a NEBNext UltraII DNA Library Prep Kit from NEB (E7645S). Indexed samples were analyzed by paired-end NGS using an Illumina NextSeq Mid-Output (150 cycles) Kit.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
CUT&RUN
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| Data processing |
BWA mem mapping to hg19
normalized signal (bw file) was generated using s3norm_pipeline.py -r mean
Assembly: hg19
Supplementary files format and content: bigwiggle and bedgraph
Library strategy: CUT&RUN
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| Submission date |
Apr 03, 2023 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Jonanthan Yen |
| E-mail(s) |
thiyagarajibms@gmail.com
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Hematology
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE228819 |
Potent and uniform fetal hemoglobin induction via base editing [Cut & Run] |
| GSE228822 |
Potent and uniform fetal hemoglobin induction via base editing |
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| Relations |
| BioSample |
SAMN34052544 |
| SRA |
SRX19851037 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7139612_HUDEP2_175_LMO2.bedGraph.gz |
17.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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