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| Status |
Public on May 03, 2012 |
| Title |
crh6-3 ChIP H3 |
| Sample type |
SRA |
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| Source name |
leaf tissue, crh6-3, H3 ChIP
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: crh6-3 (eco. Columbia)
tissue: leaf
chip antibody: H3
antibody vendor: Abcam
antibody catalog #: Ab1791
antibody lot#: 774564
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Immunoprecipitated formaldehyde-crosslinked leaf tissue.
Lee et al., Plant Cell 2007 (PMID 17337630).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Genomic DNA immunoprecipitated using H3 antibody.
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| Data processing |
ChIP-Seq PF-passing reads were aligned with Bowtie 0.12.7 to the TAIR8 chr1..5/C/M reference genome, allowing up to 2 and fewest mismatches in the first 28 cycles and up to 100 sum of per-base quality scores at all mismatches, retaining all hits except none if more than 100 hits ('-l 28 -n 2 --nomaqround -e 100 -y -a --best --strata --chunkmbs 1024 -m 100'), filtering to retain only hits with fewest mismatches per read, then retaining only reads with a single hit. Hits were extended in the 3' direction from 50-mers to 220-mers to reflect nominal insert size from library preparation.
Supplementary_files_format_and_content: Each processed file gives the number of 220-mer extended hits covering each genomic basepair (on either strand, unnormalized for variation in genomic mappability or depth of sequencing), presented as a single basepair resolution UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single 'fixedStep start=1 step=1 span=1' header per chromosome in order chr1..5/C/M with exactly one non-negative integer entry associated to each reference chr1..5/C/M basepair).
Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.
Genome_build: TAIR8
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| Submission date |
May 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shawn J. Cokus |
| Organization name |
UCLA
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| Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE37644 |
MORC family ATPases required for heterochromatin condensation and gene silencing |
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| Relations |
| SRA |
SRX145432 |
| BioSample |
SAMN00990557 |
| Named Annotation |
GSM925663_crh6-3_ChIP-H3_processed.directLinCvg1bpResolution.UCSCwigToAthTAIR8chr12345CM.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM925663_crh6-3_ChIP-H3_processed.directLinCvg1bpResolution.UCSCwigToAthTAIR8chr12345CM.wig.gz |
103.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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