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| Status |
Public on Apr 08, 2014 |
| Title |
knl2_pellet_(20120223_8) |
| Sample type |
SRA |
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| Source name |
insoluble chromatin
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: embryo
genetic background: N2
genotype: WT
knockdown: knl2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
KNL-2 depleted (knl-2(RNAi),knl2) embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction, insoluble chromatin was retained. KNL-2 was depleted by RNAi by feeding N2 worms on bacteria expressing dsRNA, so the depletion is entirely post-transcriptional.
see MNase_ChIP_Seq_protocol
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
insoluble chromatin
age:embryos, strain:N2, mutant:WT, RNAi:knl2
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| Data processing |
1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.
Genome_build: WS220
Supplementary_files_format_and_content: bam, wig, and bed
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| Submission date |
Feb 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platform ID |
GPL13657 |
| Series (1) |
| GSE44412 |
Holocentromeres are dispersed point centromeres localized at transcription factor hotspots |
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| Relations |
| SRA |
SRX246040 |
| BioSample |
SAMN01931895 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1089280_knl2_pellet_20120223_8.bam |
789.8 Mb |
(ftp)(http) |
BAM |
| GSM1089280_knl2_pellet_20120223_8.bed.gz |
69.5 Mb |
(ftp)(http) |
BED |
| GSM1089280_knl2_pellet_20120223_8.wig.gz |
76.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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