|
| Status |
Public on Jan 01, 2021 |
| Title |
CCF 3255_INP |
| Sample type |
SRA |
| |
|
| Source name |
Meningioma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
patient sex: F
tumor grade: 2
tissue/sample type: Meningioma tissue
|
| 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 |
SAMN13168701 |
| SRA |
SRX7079177 |
