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| Status |
Public on Feb 23, 2023 |
| Title |
BMMCs_WT_H3K27ac_rep6 |
| Sample type |
SRA |
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| Source name |
Bone-marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone-marrow
strain: Balb/cJ
cell type: mast cell
genotype: wide type
treatment: None
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| Growth protocol |
Bone marrow-derived mast cells (BMMCs) were cultured from bone marrow cells of BALB/c mice in Iscove’s DMEM (10016CV, CorningTM cellgroTM, Manassas, VA) plus 10% FBS,100 units/mL penicillin, 100 μg/mL streptomycin, and 2 mM b-mercaptoethanol in the presence of 20 ng/mL IL-3 for four weeks. Over 99% of BMMCs were mast cells had a mast cell phenotype by FACS analysis (FcεRIα+ c-Kit+).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BMMCs (1 × 105) were treated with concanavalin A-coated beads (Bangs Laboratories, BP531) and incubated with rabbit anti-H3K27ac antibody (Abcam, ab4729) at 4 ℃ overnight. The cells were then incubated with guinea pig anti-rabbit antibody (Antibodies online, ABIN101961) at room temperature for 30 minutes. The cells were washed and incubated with pA-Tn5 adapter complex (Diagenode, C01070001) at room temperature for 1 hour on a rotator. The cell pellet was resuspended in 300 ml tagmentation buffer and incubated at 37 ℃ for 1 hour. The reaction was stopped by adding 10 μL 0.5M EDTA, 3 μL 10% SDS, and 2.5 μL 20 mg/mL Proteinase K, and cells were digested at 37 ℃ overnight. Then, DNA was extracted using phenol chloroform and diluted in 25 ml TE buffer with 1/400 RNAse A.
The tagmented DNA was enriched by PCR amplification using Universal i5 primer and uniquely barcoded i7 primers under the following conditions: 72 °C for 5 min, and 13 cycles: 98 °C for 30 sec, 98 °C for 10 sec, 63 °C for 10 sec, 72°C for 1 min and hold at 8 ℃. The PCR products were cleaned up and size-selected using Ampure XP beads (Beckman Coulter, A63880). The quality and quantity of libraries were analyzed with the Agilent TapeStation 4200 system.
H3K27ac CUT&Tag-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The adaptor sequences in raw reads (two biological replicates for each group) were trimmed using Trimmomatic (version 0.33) (Bolger et al., 2014) and the quality of trimmed sequence data was analyzed by FastQC (version 0.11.9).
The trimmed reads were aligned to the mm10 reference genome using Bowtie2 (version 2.3.5.1) (Langmead and Salzberg, 2012).
Peak calling was performed using MACS2 (version 2.1.2) with default parameters (Zhang et al., 2008).
Supplementary files format and content: mm10
Supplementary files format and content: Tdf and bedgraph files for each sample
Library strategy: CUT&Tag
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| Submission date |
Jan 20, 2023 |
| Last update date |
Feb 23, 2023 |
| Contact name |
HUA HUANG |
| E-mail(s) |
huangh@njhealth.org
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| Phone |
3033981281
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| Organization name |
National Jewish Health
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| Department |
Immunology and Genomic Medicine
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| Lab |
Huang lab
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| Street address |
1400 Jackson street, K511
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE223386 |
The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis [CUT&Tag] |
| GSE223388 |
The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis |
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| Relations |
| BioSample |
SAMN32817911 |
| SRA |
SRX19119172 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6946949_BMMCs_WT_H3K27ac_rep6_treat_pileup.bdg.tdf |
47.8 Mb |
(ftp)(http) |
TDF |
| GSM6946949_BMMCs_WT_H3K27ac_rep6_treat_pileup.bedGraph.gz |
70.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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