General Information
- Experiment ID
- OEX020247
- Experiment Name
- OEX_weifen_2208091019
- Experiment Type
- Genomic
- Description
- ChIP-seq Analysis
- Protocol
- 0.15 g of PFC tissue was grinded into powder on dry ice and cross-linked in 1% formaldehyde for 10 min at room temperature. Then, the reaction was quenched by adding glycine, and the tissue was further homogenized in a glass douncer. Cell pellets were lysed successively in Farnham Lysis buffer (5mM PIPES pH 8.0, 85mM KCl, 0.5% NP-40) and Lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH8.0) on ice. Nuclei were sonicated for 5 seconds at 15% power of Misonix Q700 for 90 times with 10 seconds refractory period. The supernatant was diluted in Dilution buffer (1.1% Triton X-100, 0.25% sodium deoxycholate, 1.2mM EDTA, 167mM NaCl, 16.7mM Tris-HCl, pH8.0) and transferred to the Protein A/G magnetic beads which were pre-incubated with H3K4me3 (Millipore, 07-473) or H3K27ac (Active Motif, 39133) antibody in PBS with 0.5% BSA at 4 °C for at least 4 h, and rotated overnight at 4 °C. Beads were then washed sequentially with Low salt wash buffer (0.1% SDS, 1% Triton X-100, 0.25% sodium deoxycholate, 1mM EDTA, 150mM NaCl, 50mM Tris-HCl, pH8.0), High salt wash buffer (0.1% SDS, 1% Triton X-100, 0.25% sodium deoxycholate, 1mM EDTA, 500mM NaCl, 50mM Tris-HCl, pH8.0), LiCl wash buffer (500mM LiCl, 1% NP-40, 1% sodium deoxycholate, 100mM Tris-HCl, pH8.0), TE buffer, and eluted with Elution buffer (1% SDS, 0.1M NaHCO3) at 65°C. After adding NaCl to final 200mM, chromatin in the supernatant was reverse crosslinked overnight at 65 °C, and then treated with RNase A (final concentration of 0.1 μg/μl) for 0.5 h at 37 °C and proteinase K (final concentration of 0.4 μg/μl) for 1 h at 55 °C. DNA was extracted with QIAquick MinElute PCR Purification Kit (Qiagen, 28104). Genomic DNA without the immunoprecipitation was used as an input control. Sequencing library was prepared by using Illumina Truseq ChIP Sample Prep Kit (Illumina, USA). The pooled libraries were sequenced on Illumina HiSeq 2000 platform using the 100-bp singled-ended sequencing protocol.
Experiment information
- Attributes
-
library_layout Single mate_pair n/a insertion_size n/a number_of_reads_sequenced n/a library_name n/a library_selection PCR library_strategy ChIP-Seq platform Illumina HiSeq 2000 - Project
-
1
Project ID Project name Create Date OEP003561 Epigenetic regulation of human-specific gene expression in prefrontal cortex 2022-08-07 - Samples
-
9
Sample ID Sample Name Organism Tissue Create Date OES233244 CHerman Pan troglodytes Prefrontal Cortex 2022-08-09 OES233245 CJapie Pan troglodytes Prefrontal Cortex 2022-08-09 OES233246 CSnoy Pan troglodytes Prefrontal Cortex 2022-08-09 OES233241 H602 Homo sapiens Prefrontal Cortex 2022-08-09 OES233242 H879 Homo sapiens Prefrontal Cortex 2022-08-09 OES233243 H933 Homo sapiens Prefrontal Cortex 2022-08-09 OES233247 M135 Macaca mulatta Prefrontal Cortex 2022-08-09 OES233248 M98145 Macaca mulatta Prefrontal Cortex 2022-08-09 OES233249 M99057 Macaca mulatta Prefrontal Cortex 2022-08-09 - Runs
-
9
Run ID Run Name Sample Data Num Create Date OER272077 OER_weifen_2208091303 CHerman 3 2022-08-09 OER272078 OER_weifen_2208091312 CJapie 3 2022-08-09 OER272079 OER_weifen_2208091350 CSnoy 3 2022-08-09 OER272080 OER_weifen_2208091353 H602 3 2022-08-09 OER272081 OER_weifen_2208091356 H879 3 2022-08-09 OER272082 OER_weifen_2208091401 H933 3 2022-08-09 OER272083 OER_weifen_2208091405 M135 3 2022-08-09 OER272084 OER_weifen_2208091407 M98145 3 2022-08-09 OER272085 OER_weifen_2208091409 M99057 3 2022-08-09
Author Information
- Create Date
- 2022-08-09
- Last Modified
- 2023-04-28
- Submission
- weifen sun
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences