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Status |
Public on May 03, 2012 |
Title |
crt1-4 ChIP H3 |
Sample type |
SRA |
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Source name |
leaf tissue, crt1-4, H3 ChIP
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Organism |
Arabidopsis thaliana |
Characteristics |
genotype: crt1-4 (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 |
SRX145430 |
BioSample |
SAMN00990555 |
Named Annotation |
GSM925661_crt1-4_ChIP-H3_processed.directLinCvg1bpResolution.UCSCwigToAthTAIR8chr12345CM.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM925661_crt1-4_ChIP-H3_processed.directLinCvg1bpResolution.UCSCwigToAthTAIR8chr12345CM.wig.gz |
86.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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