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| Status |
Public on May 06, 2023 |
| Title |
CapC_HUDEP_KDCon_Rep1 |
| Sample type |
SRA |
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| Source name |
Cord Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cord Blood
cell line: HUDEP-1
cell type: Erythroblasts
genotype: siCon
treatment: differentiation
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
One million cells were used for each reaction. In brief, after fixation with 1% formaldehyde, cells were digested overnight at 37 °C using MboI (NEB, Cat. #R0147). Proximity ligation was carried out overnight at 25 °C with T4 DNA Ligase (NEB, Cat. # M0202M).
After reverse-crosslinking, DNA was purified and sheared to 300-500bp fragments using Covaris M220 sonicator, and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturer’s protocol. Two micrograms indexed and mixed library was use as input for the two rounds downstream hybridization and biotin capture with biotin labeled oligo (Supplementary Table) following with manufacture’s recommendation (Genscript, NGS09612).Two biological replicates per condition were sequenced in a NovaSeq 6000 (S4, PE150, Illumina) by Novogene (Beijing).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Capture-C analysis was performed as described before with capC-MAP (https://github.com/cbrackley/capC-MAP) software. In brief, the raw reads were trimmed with cutadapt, and mapped with hg19 reduced genome that consists of reference genome sequences adjacent to DpnII cut sites by bowtie, The read counts per bin were normalized to the sequencing depth per replicate in CPM. Visualization was performed using average CPM signals per condition at bin size 200 bp with 2 kb/ 4 kb window.
Assembly: hg19
Supplementary files format and content: bedGraph: for GATA-KD sample, viewpoints: SLC4A1, TLCD4, and METTL7A respectively
Supplementary files format and content: bedGraph: for GATABS-KO sample, viewpoin :SLC4A1, only
Library strategy: Capture-C
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| Submission date |
Oct 04, 2022 |
| Last update date |
May 06, 2023 |
| Contact name |
Dong Li |
| E-mail(s) |
lidongpaul@gmail.com
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| Organization name |
Peking University
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| Department |
College of Life Science
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| Lab |
Hsiang-Ying (Sherry) Lee
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| Street address |
No.5 Yiheyuan Road, Haidian District,
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE214806 |
Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis [Cap-C] |
| GSE214811 |
Stage-specific erythroid cell three-dimensional chromatin architecture and transcription factors binding provide insight of human erythropoiesis |
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| Relations |
| BioSample |
SAMN30999245 |
| SRA |
SRX17693483 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6616184_CapC_HUDEP_KDCon_Rep1_VP_METTL7A.bedgraph.gz |
44.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM6616184_CapC_HUDEP_KDCon_Rep1_VP_SLC4A1.bedgraph.gz |
135.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM6616184_CapC_HUDEP_KDCon_Rep1_VP_TLCD4.bedgraph.gz |
183.0 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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