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| Status |
Public on Feb 02, 2024 |
| Title |
Let-7 KD HIC2 ChIP-seq rep2 |
| Sample type |
SRA |
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| Source name |
Human erythroblasts
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Adult peripheral blood
cell type: CD34+ derived erythroblasts
differentiation: Day 11
genotype: Let-7 KD
chip antibody: HIC2 (Proteintech, 22788-1-AP)
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| Growth protocol |
Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Fixed cells were lysised in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysised in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C (Epishear, Active Motif). Chromatin was incubated with antibody and then decrosslink at 65C overnight.
Samples were processed for library construction for Illumina sequencing using NEBNext UltraII for DNA Library Prep Kit (NEB cat# E7645S) according to NEB's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Data processing |
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.
Assembly: hg38
Supplementary files format and content: bigWig files with read coverage
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| Submission date |
Oct 20, 2022 |
| Last update date |
Feb 02, 2024 |
| 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) |
| GSE216195 |
Let-7 miRNAs repress HIC2 to regulate BCL11A transcription and hemoglobin switching [ChIP-Seq] |
| GSE216197 |
Let-7 miRNAs repress HIC2 to regulate BCL11A transcription and hemoglobin switching |
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| Relations |
| BioSample |
SAMN31387076 |
| SRA |
SRX17966415 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6661437_4472_hg38.bigwig |
253.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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