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| Status |
Public on Jan 11, 2023 |
| Title |
cold input for BAT H3K27Ac ChIPseq, rep 3 |
| Sample type |
SRA |
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| Source name |
BAT
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| Organism |
Mus musculus |
| Characteristics |
tissue: BAT
chip antibody: none
genotype: WT
treatment: 4h cold stress
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BAT was fixed with 0.8% formaldehyde for 12min (H3K27Ac ChIP) or with 2mM DSG for 25min followed by 0.8% formaldehyde for 12min (other ChIPs). Sonication was done with Diagenode Bioruptor UCD-200, 5" on and 5" off for 3x3min.
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core form 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to uniquely barcoded dual indexes (IDT, Coralville, IA USA).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were trimmed using TrimGalore v0.6.0 (https://github.com/FelixKrueger/TrimGalore) with default settings.
Trimmed reads were aligned to the GRCm38.p6 reference genome from GENCODE vM24 using bwa mem v0.7.17 (Li, 2013). In the case of the C/EBPA and wildtype cold/RT H3K27ac datasets, the reference was concatenated with decoy sequences (Zhang et al., 2021).
Duplicates were marked using SAMBLASTER v 0.1.24 (Faust and Hall, 2014). Alignments were filtered using SAMtools view v1.9 (Li et al., 2009) with the parameters ‘-q 30 -F 2828’ and ‘-f 2’ for paired-end reads.
Peaks were called using macs2 v2.2.7.1 (Zhang et al., 2008) with the parameters ‘-g mm -q 0.05’ and ‘-f BAMPE’ for paired-end reads, using the corresponding input sample as the control.
Bigwig files were generated using deepTools bamCoverage v3.4.3 (Ramirez et al., 2016) with the parameters ‘--binSize 10 --normalizeUsing “CPM” --samFlagExclude 1024’, specifying the ENCODE v2 blacklist using ‘--blackListFileName’; for paired-end reads, the parameters ‘--samFlagInclude 64 --extendReads’ were added.
Assembly: GRCm38.p6
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
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| Submission date |
Sep 18, 2022 |
| Last update date |
Jan 11, 2023 |
| Contact name |
Ning Wu |
| E-mail(s) |
ning@omnispacemail.com
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| Organization name |
Van Andel Institute
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| Street address |
333 Bostwick Ave NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE213600 |
PPARg and C/EBPa response to acute cold stress in brown adipose tissue [ChIP-Seq] |
| GSE213601 |
PPARg and C/EBPa response to acute cold stress in brown adipose tissue |
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| Relations |
| BioSample |
SAMN30918206 |
| SRA |
SRX17622710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6589649_C4input_filt_alns_rmdups.bw |
229.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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