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Status |
Public on May 25, 2022 |
Title |
Fetal_GATA1_r2 |
Sample type |
SRA |
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Source name |
Fetal erythroblasts
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Organism |
Homo sapiens |
Characteristics |
tissue/cell type: CD34+ cells derived from fetal liver cell type: Erythroid cells differentiation: Differentiated day11 chip antibody: GATA1 (Abcam, Ab11852, lot GR3280668-13)
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Growth protocol |
Human CD34+ HSPCs were cultured using a three-phase protocol. For phase 1 medium, IMDM was supplemented with 100 ng/mL of human stem cell factor, 1 ng/mL of interleukin-3, 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 200 μg/mL of holotransferrin, 10 μg/mL of insulin, 5% human male A/B plasma, and 10 mg/mL of heparin. For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture. For phase 3, the cells were cultured with IMDM supplemented with 3 units/mL of erythropoietin, 2% penicillin/streptomycin, 1 mg/mL of holotransferrin, 10 μg/mL of insulin, 5% human A/B plasma, and 10 μg/mL of heparin.
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Extracted molecule |
genomic DNA |
Extraction protocol |
500-800k cells were collected for CUT&RUN. CUT&RUN were performed using the CUT&RUN Assay Kit (Cell Signaling, #86652S) according to the manufacturer’s instructions. Samples were processed for library construction for Illumina sequencing using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to NEB's instructions..
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 2000 |
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Data processing |
library strategy: CUT&RUN Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1 Reads were mapped to reference genome hg38 with Bowtie 1.3.0 using parameters --best --sam --chunkmbs 256 -X 800. Peaks were called using MACS2. Peaks overlapped with blacklist were further filtered out. Genome_build: hg38 Supplementary_files_format_and_content: bigWig files with read coverage; bed files of peaks
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Submission date |
Aug 21, 2021 |
Last update date |
May 27, 2022 |
Contact name |
Peng Huang |
E-mail(s) |
waliays@gmail.com
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Organization name |
Guangzhou Medical University
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Department |
GMU-GIBH Joint School of Life Sciences
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Lab |
Peng Huang
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Street address |
Xinzao, Panyu District
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City |
Guangzhou |
State/province |
Guangdong |
ZIP/Postal code |
511436 |
Country |
China |
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Platform ID |
GPL30173 |
Series (2) |
GSE173587 |
HIC2 represses BCL11A transcription to regulate hemoglobin switching during development |
GSE182530 |
HIC2 represses BCL11A transcription to regulate hemoglobin switching during development [CUT&RUN] |
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Relations |
BioSample |
SAMN20923625 |
SRA |
SRX11857121 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5530950_3437_hg38.bigwig |
56.2 Mb |
(ftp)(http) |
BIGWIG |
GSM5530950_3437_peaks_clean.bed.gz |
608.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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