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| Status |
Public on Oct 22, 2018 |
| Title |
VL3-3M2 dEb H3K9me2 |
| Sample type |
SRA |
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| Source name |
VL3-3M2 cell line (dEb)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
sample type: Cell line
cell type/line: VL3-3M2
age: NA
genotype/variation: dEb
antibody: H3K9me2 (abcam ab1220)
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| Treatment protocol |
Derivative VL3-3M2 cell lines were obtained by CRISPR/Cas9-mediated deletion of regulatory elements (usRC or Eb)
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| Growth protocol |
VL3-3M2 cells were maintained in RPMI 1640 with L-glutamine supplemented with 10% fetal bovine serum, 50 U/mL penicillin-streptomycin and 55 uM 2-mercaptoethanol.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleosomes were obtained by micrococcal nuclease digestion and antibody added. Pulldown was performed using protein A-agarose and bound DNA was purified by phenol-chloroform extraction
Library preparation and high-throughput sequencing were performed by the Duke Center for Genomic and Computational Biology Core Facility
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Demultiplexed .fastq files were trimmed using the fastqFilter command in the R dada2 (1.8.0) package with the parameters “truncLen = 0, trimLeft = 0, maxN = 0, minQ = 0, rm.phix = TRUE”
The trimmed files were aligned to the mm9 genome using the qAlign command in the R QuasR (1.20.0) package with the parameters “aligner = “Rbowtie”, maxHits = 1, paired = NULL”.
Duplicate and replicate .bam files were merged using the mergeBam command in the R Rsamtools (1.32.0) package.
Reads were placed into 200 bp bins using the constructBins command in the R mosaics (2.18.0) package with the parameters “fragLen = 150, binSize = 200, capping = 50, PET = FALSE”. Reads that corresponded to chromosome Y, chromosome M or unmapped parts of the chromosome were excluded.
Bins were assembled into tracks in the .bedgraph format.
H3K27ac tracks were normalized to reads per million.
H3K9me2 tracks were normalized for read count relative to the input sample and a value of 1 was added to bins with no reads. Log2 ratios of the H3K9me2 sample over input were then plotted.
Genome_build: mm9
Supplementary_files_format_and_content: .bedgraph in 200bp bins. Bins with a value of 0 were deleted to reduce file size.
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| Submission date |
Jun 11, 2018 |
| Last update date |
Oct 23, 2018 |
| Contact name |
Michael S Krangel |
| Organization name |
Duke University
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| Department |
Immunology
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| Street address |
207 Research Drive, Jones Building, Room 316
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE115582 |
A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus [ChIP-seq] |
| GSE116954 |
A lamina-associated domain border governs nuclear lamina interactions, transcription and recombination of the Tcrb locus. |
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| Relations |
| BioSample |
SAMN09390619 |
| SRA |
SRX4192519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3184384_Eb_H3K9me2.bedgraph.gz |
87.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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