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Sample GSM8672407 Query DataSets for GSM8672407
Status Public on Dec 08, 2024
Title CD34_Day7_BCL11A_CutRun_2
Sample type SRA
 
Source name Day 7 C34+
Organism Homo sapiens
Characteristics cell type: Day 7 C34+
treatment: BCL11A Cut & Run
Treatment protocol CD34+ Cells were collected at day 7 or day10 cultured in vitro
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.
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 1000
 
Description Library name: CD34_Day7_BCL11A_CutRun_2
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
 
Submission date Dec 08, 2024
Last update date Dec 08, 2024
Contact name Lance Palmer
Organization name St. Jude Children's Research Hospital
Department Hematology
Street address 262 Danny Thomas Pl
City Memphis
State/province TN - Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL30882
Series (2)
GSE283794 BCL11A is required for normal erythropoiesis [CUT&Run]
GSE283797 BCL11A is required for normal erythropoiesis
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 SelectorHelp
Raw data are available in SRA

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