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| Status |
Public on Oct 31, 2019 |
| Title |
c31-input (ChIP-seq) |
| Sample type |
SRA |
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| Source name |
brain prefrontal cortex region tissues
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| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
age: 80
Sex: male
braak: -
chip antibody: none
tissue: brain prefrontal cortex region tissues
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| Treatment protocol |
NA
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| Growth protocol |
NA
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sonicated by Bioruptor (Diagenode, Belgium) under the condition as follows: 20 cycles of 30 s on, 60 s off. The sonicated chromatin was spun down at 12,000 rpm for 10 min at 4 °C to collect the chromatin. Add antibody (10 μg) to the soluble chromatin (80 μg), and incubate at 4 °C with rotation overnight. Protein A/G Dynabeads (10 μl of beads per 1 μg of antibody, Life Tech, 10004D) were washed three times with Low Salt Wash Buffer. The washed Dynabeads were added to the soluble chromatin and antibodies, incubated at 4°C for 4 h with rotation. The magnetic Dynabeads were pelleted by placing the tubes in a magnetic rack and were sequentially washed once with Low Salt Wash Buffer, once with High-salt Wash Buffer, once with LiCl Wash Buffer. Wash the beads three times with TE buffer. Remove any supernatant remaining after the last washing. The beads were resuspended in 150 μl of Elution Buffer (50 mM Tris•Cl pH 8.0, 10 mM EDTA, 1% SDS), followed by incubation for 15 min at 65 °C. Repeat step 7 again, combine the elution, then you have 300 μl of the eluted DNA solution. Add 1 μl of high concentration RNase A (10 mg/ml) to the eluted DNA solution and the Input samples (500 μl), respectively. Incubate them at 37 ℃ for 1 h. Reverse formaldehyde crosslinks by respectively adding 12.5 μl or 55 μl of 5 M NaCl to the eluted DNA solution and the Input samples to a final concentration of 0.2 M. Incubate samples at 65 ℃ (650 rpm) for more than 8 h (less than 16 h). Add both 80.5 μl of ddH2O and 5 μl of 20 mg/ml Proteinase K to the eluted DNA solution, and just 5 μl of Proteinase K to the Inputs. Incubate at 56 ℃ for 2 h. Extract once with 400 μl of phenol/chloroform/isoamyl alcohol, and once with 400 μl of chloroform/isoamyl alcohol (optional). Transfer 355 μl of supernatant to a new tube. Add 55 μl or 40 μl of 3 M NaAc (pH 5.2, 0.3 M final) to the Input samples and eluted DNA solution, 5 μl of glycogen each sample and mix well. Add 800 μl (two-fold volume) of absolute ethanol. Precipitate at -20 ℃ overnight or at -80 ℃ for 4 h. Centrifuge at 14000 rmp for 20 min at 4 ℃. Wash once with 75% ethanol and store at -20 ℃.
The library is constructed under the protocol of Iillumina
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The adaptors were cut using Ngmerge
Pair-end reads were aligned to hg38 genome using bowtie2 under default parameter setting
The TF binding sites were detected by macs2
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak
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| Submission date |
Mar 29, 2019 |
| Last update date |
Oct 31, 2019 |
| Contact name |
Guofeng Meng |
| E-mail(s) |
menggf@gmail.com
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| Phone |
0862161590480
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| Organization name |
Shanghai University of Traditional Chinese Medicine
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| Street address |
Jinke 3528
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| City |
Shanghai |
| ZIP/Postal code |
20000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE129039 |
ChIP-seq studies to ATF4, OLIG2, THRA binding sites of AD brain samples |
| GSE129041 |
Transcriptional regulation loss disturbs the brain function and indicates detrimental clinical outcomes of Alzheimer's disease |
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| Relations |
| BioSample |
SAMN11287760 |
| SRA |
SRX5600910 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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