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| Status |
Public on Jul 05, 2024 |
| Title |
B16, HP, replicate 1, H3K27ac |
| Sample type |
SRA |
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| Source name |
B16 F10
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| Organism |
Mus musculus |
| Characteristics |
cell type: Melanocytes
cell line: B16 F10
chip antibody: H3K27ac (Abcam #ab4729)
condition: high pigment
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| Growth protocol |
B16 F10 cells were cultured at a very low density of 100 cells/cm2 in DMEM high glucose supplemented with 10% fetal bovin serum at 37 °C, 5% CO2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
B16 F10 cells were trypsinized at day 5, spun down at 400g, then washed and resuspended in 1x DPBS. Low and high pigmented cells were sorted using the side scatter intensity of a flow cytometer. Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a bath sonicator (Diagenode Bioruptor).
ChIP-seq libraries were prepared using the NEB Ultra II DNA library prep kit (E7103S) complemented with NEBNext Multiplex Oligos for Illumina (E6440S). Equal ammount of DNA was used as starting material for all samples in each replicate set. Libraries were amplified using 5-7 cycles on the thermocycler. Post amplification cleanup was performed using NEBNext beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
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| Description |
10x Genomics
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| Data processing |
Basecalls were performed using bcl2fastq v2.20 for NextSeq output.
ChIP-seq reads were trimmed using a sliding window of 4 bases and average quality score of >15 using Trimmomatic v0.33, discarding reads left with < 50 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie 2 version 2.5.1.
Peaks were called uing MACS3 with the significance cut-off q-value <=0.05
bigWig files were generated using the ucsc bedgraphtobigwig tool converting the SPMR normalized bedgraph files generated by MACS3. narrowPeak files were generated using MACS3 with default parameters and retaining all duplicate reads
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
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| Submission date |
May 22, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Vivek T Natarajan |
| E-mail(s) |
tnvivek@igib.in
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| Organization name |
CSIR-IGIB
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| Lab |
Pigment Cell Biology Lab
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| Street address |
Mathura Road
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| City |
Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110025 |
| Country |
India |
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| Platform ID |
GPL30172 |
| Series (2) |
| GSE233135 |
H3K27ac ChIP sequencing of low and high pigment B16 cells [B16_D5_LP_HP_ChIPSeq] |
| GSE233198 |
Differential programs of melanocyte cell states |
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| Relations |
| BioSample |
SAMN35309342 |
| SRA |
SRX20465742 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7401920_HP_1_mm10_peaks.narrowPeak.gz |
1.3 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM7401920_HP_1_mm10_treat_pileup.bw |
65.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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