|
Status |
Public on Jan 01, 2021 |
Title |
CCF 3622_ChIP |
Sample type |
SRA |
|
|
Source name |
Meningioma tissue
|
Organism |
Homo sapiens |
Characteristics |
patient sex: F tumor grade: 1 tissue/sample type: Meningioma tissue chip antibody: H3K27ac antibody (Active Motif; 39133)
|
Growth protocol |
First-passage arachnoid granulation cells were grown in DMEM supplemented with 7% FBS and 1% penicillin/streptomycin
|
Extracted molecule |
genomic DNA |
Extraction protocol |
5–10 mg of flash-frozen primary meningioma tumors was pulverized, crosslinked using 1.5% formaldehyde and sonicated to fragment sizes of 200-800 bp. Samples were incubated overnight with 5 μg H3K27ac antibody per ChIP experiment (Active Motif; 39133). Enriched DNA was quantified by using PicoGreen (Invitrogen) and ChIP libraries were amplified and barcoded by using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to the manufacturer’s recommendations. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), analyzed using a Bioanalyzer (Agilent Technologies) Samples were sequenced at Genewiz by using Illumina HiSeq 2500 150-bp paired-end reads.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
FASTQ reads were trimmed to remove low quality reads and adaptors with Trim Galore. Uniquely mapped reads were aligned to the human reference genome h19/GRCh37 with the Burrows-Wheeler Aligner to generate BAMs. BAMs were sorted and indexed with SAMtools. PCR duplicates were removed using PicardTools. Peaks were called using the MACS2 callleak function on the ChIP-seq BAM file using the following parameters: BAMPE for paired-end reads, scaling to the larger dataset, the default log2 fold change enrichment of 2 vs. input and a p-value cutoff of 1e-5. Bigwig tracks were generated using the DeepTools (v3.1.2)24 bamCoverage command with RPKM normalization Genome_build: hg19 Supplementary_files_format_and_content: bigwigs
|
|
|
Submission date |
Oct 31, 2019 |
Last update date |
Jan 02, 2021 |
Contact name |
Briana Prager |
E-mail(s) |
briana.prager@gmail.com
|
Organization name |
Cleveland Clinic
|
Street address |
9500 Euclid Ave.
|
City |
Cleveland |
State/province |
OH |
ZIP/Postal code |
44195 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (2) |
GSE139650 |
Enhancer landscape of meningioma [ChIP-seq] |
GSE139652 |
Enhancer landscape of meningioma |
|
Relations |
BioSample |
SAMN13168698 |
SRA |
SRX7079180 |