|
| Status |
Public on Aug 20, 2018 |
| Title |
MIA PACa-2 siMLL3 2%input |
| Sample type |
SRA |
| |
|
| Source name |
epithelial cells derivef from pancreatic carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MIA PaCa-2 pancreatic cancer cell line
antibody: none
|
| Treatment protocol |
MIA PaCa-2 cells were trypsinized and transfected with 50nΜ siRNA for KMT2D or scramble siRNA. Lipofectamine ® RNAiMAX was used as transfection reagent. RNA-Lipofectamine complexes were made in Opti-MEM (serum free). Cells were plated at a 50% confluence in serum and antibiotic-containing media. 24h later double transfection was performed with the same amounts of siRNAs and cells were incubated for 24h before chromatin isolation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation and final DNA purification was carried out using the SimpleChIP Plus Enzymatic Chromatin IP Kit (9005, Cell Signaling Technology)
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (E6240, New England BioLabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2% input (sequencing control) for the 2 following samples: MK8_MLL11_siMLL2_IP_H3K4me1 and MK9_MLL12_siMLL2_IP_H3K4me3
|
| Data processing |
alignment: Sequencing reads in fastq‐format were aligned to the UCSC hg19 reference genome using BWA (version 0.7.9a bwa mem with default options). Duplicate reads were removed with Picard tools (v. 1.115) MarkDuplicates and were filtered to retain only primary alignments with samtools (v0.1.19, view command with ‐F 0x100 flag).
peak calling: ChIP‐seq peaks were called using HOMER (v4.7) findPeaks using matched input samples with default settings (Poisson pvalue of <= 1E‐4 and fold change >=4.0). For histone marks, the histone option was employed. Further, peaks are annotated using HOMER's annotatePeaks utility using the hg19 annotations database provided with the software.
Genome_build: UCSC hg19 reference genome
Supplementary_files_format_and_content: The processed data files are in bedGraph format and tab-delimited xls format and represent a detailed description of the peak chromosomal coordinates enriched in each sample, peak scores, focus ratio/region size, distance to TSS and detail annotation. Furthermore, all relevant information for the nearest promoter is provided.
|
| |
|
| Submission date |
Aug 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
MARINA KOUTSIOUMPA |
| E-mail(s) |
mkoutsioumpa@gmail.com
|
| Phone |
3104893978
|
| Organization name |
UCLA
|
| Department |
MEDICINE
|
| Lab |
SYSTEMS BIOMEDICINE
|
| Street address |
650 Charles E. Young Dr South, CHS 33-315
|
| City |
LOS ANGELES |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE85886 |
Epigenome Mapping in pancreatic cancer cells |
|
| Relations |
| BioSample |
SAMN05601742 |
| SRA |
SRX2037275 |
