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Status |
Public on Dec 08, 2024 |
Title |
CD34_Day7_BCL11A_CutRun_2 |
Sample type |
SRA |
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Source name |
Day 7 C34+
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Organism |
Homo sapiens |
Characteristics |
cell type: Day 7 C34+ treatment: BCL11A Cut & Run
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Treatment protocol |
CD34+ Cells were collected at day 7 or day10 cultured in vitro
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Growth protocol |
CD34+ cell were edited by CD33 or BCL11A enhancer gRNAs and then cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1´ penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were collected, dead cells were removed by EasySep Dead Cell Removal (Annexin V) Kit, then process to CUT&RUN process. 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 NovaSeq (100 cycles) Kit.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 1000 |
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Description |
Library name: CD34_Day7_BCL11A_CutRun_2
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Data processing |
CUT&RUN reads were aligned to the hg38 genome using BWA v 0.7.16a11. MACS2 was used for peak calling. Assembly: hg38 Supplementary files format and content: Bed files from peak calling Library strategy: CUT&Run
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Submission date |
Dec 08, 2024 |
Last update date |
Dec 08, 2024 |
Contact name |
Lance Palmer |
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 - Tennessee |
ZIP/Postal code |
38105 |
Country |
USA |
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Platform ID |
GPL30882 |
Series (2) |
GSE283794 |
BCL11A is required for normal erythropoiesis [CUT&Run] |
GSE283797 |
BCL11A is required for normal erythropoiesis |
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Relations |
BioSample |
SAMN45223396 |
SRA |
SRX27006070 |
Supplementary file |
Size |
Download |
File type/resource |
GSM8672407_CD34_day7_BCL11A_rep2.vs.CD34_day7_IgG.rmdup.uq.rmchrM_peaks.rmblck.narrowPeak.gz |
495.9 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
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