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| Status |
Public on May 25, 2022 |
| Title |
Fetal_H3K27ac_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: H3K27ac (Thermo, MA5-23516, lot VL3008252)
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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 For phase 2 medium, the interleukin-3 was withdrawn after 9 days of culture.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 |
SAMN20923621 |
| SRA |
SRX11857117 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5530946_3442_hg38.bigwig |
59.1 Mb |
(ftp)(http) |
BIGWIG |
| GSM5530946_3442_peaks_clean.bed.gz |
844.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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