|
| Status |
Public on Oct 27, 2015 |
| Title |
Exp004-2_H3_5000c_Ad_BC02_62-5u |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
experiment: Low_input_K562/Exp004-2
histone modification: H3
cell number: 5000c
mnase units: 62-5u
treatment: none
|
| Treatment protocol |
K562 cells were treated for 48 hours with C646 (25 µM), 48 hours with GSK126 (2 µM), or 96 hours with KDM5-C70 (5 µM). Pfeiffer, SKM-1 and Toledo were treated for 72 hours with GSK126 (1 µM).
|
| Growth protocol |
K562 cells and mouse YAC-1 cells were cultured in RPMI with 10% FCS, penicillin-streptomycin and L-glutamine. Pfeiffer, SKM-1 and Toledo were cultured in RPMI with 20% FCS, penicillin-streptomycin, L-glutamine and β-mercaptoethanol (3.5 µl in 1000 ml).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Mint-ChIP: In vitro transcription, reverse transcription, PCR (see manuscript).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mint-ChIP
|
| Data processing |
Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.
|
| |
|
| Submission date |
Oct 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter van Galen |
| E-mail(s) |
petervangalen@gmail.com, pvangalen@bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital / Broad Institute of MIT and Harvard
|
| Department |
Hematology
|
| Lab |
Van Galen Lab
|
| Street address |
4 Blackfan Circle
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE74359 |
A multiplexed system for quantitative comparisons of chromatin landscapes |
|
| Relations |
| BioSample |
SAMN04215665 |
| SRA |
SRX1383794 |
