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| Status |
Public on Jul 18, 2019 |
| Title |
H3K4me3_2 |
| Sample type |
SRA |
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| Source name |
ChIP Sequencing for H3K4me3 in LNCaP cells post 10nM DHT
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| Organism |
Homo sapiens |
| Characteristics |
treatment: 10nM DHT 3 hours
cell line: LNCaP
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| Treatment protocol |
Cells were treated with 10nM DHT for 3 hours before harvesting.
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| Growth protocol |
Cells were grown to 80% confluence on poly-L-lysine coated plates in 5%FBS supplemented RPMI-1640
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
20 million cells/replicate were fixed using 1% formaldehyde for 10 minutes at 24C, quenched for 5 minutes with 0.125M glycine, and stored at -80C until use. Pellets were then thawed on ice and lysed using 1% SDS_lysis buffer, sonicated for 27 cycles (30on/30ff) using a temperature controlled bioruptor, and spun down at max speed for 10 minutes. Clarified chromatin was then incubated with primary antibody overnight, and genomic DNA washed and isolated the next morning.
ChIP sequencing libraries (20ng DNA/sample) were constructed using the KAPA Hyper Prep Kit (Illuminia- Kapa biosystems Cat # KK8502, NimbleGen SeqCap Adapter Kit A- Roche Cat # 07 141 530 001) according to the manufactures instructions. Libraries were assessed for quality, purity, and size using DNA High Sensitivity Bioanalyzer chips, and those passing QC were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems KK4854). Libraries were pooled to a final concentration of 10nM and sequenced using the Illumina HiSeq 4000
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
H3K4me3_peaks.bed
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| Data processing |
Alignment using Bowtie 2 v2.2.9 default parameters
Formatting using Samtools v 1.7, --view BAM file conversion, quality score min of 30 (-q 30), -sort Bamfile sort by chromosome and location, -rmdup duplicate removal, -index Bam file index
Peak calling using MACS2 v2.1.1.20160309, using processed BAM file, input controls, and replicates combined per IP. p<0.00000005, narrow peak calling (broad peaks for H3k27me3),
Signal files using Deeptools v 3.0.0, normalized using RPKM (--normalizeUsing RPKM), binned at 5bp (--bs 5), reads centered (--center reads), extend over half the length of the sequneced library (--extendReads 125), smooth signal (--smooth 250), remove ENCODE blacklist regions (--blackListFileName)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are peak files for each ChIP seqeincing run, combining 2 biological replicates per IP/condition to generate a final peak list. BigWig files are normalized
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| Submission date |
Jul 20, 2018 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Deli Liu |
| E-mail(s) |
del2017@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Street address |
1300 York Ave
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE117430 |
CHD1 functions as a prostate-specific tumor suppressor by modulating nuclear receptor specificity towards distinct transcriptional programs [ChIP-seq] |
| GSE117431 |
Loss of CHD1 facilitates oncogenic hijacking of AR during cancer progression |
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| Relations |
| BioSample |
SAMN09695611 |
| SRA |
SRX4411668 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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