ChIP-seq tracks Track Settings
 
ChIP-seq tracks

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256-cell
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Oblong
Sphere
Dome
30%-epiboly
50%-epiboly
Shield
75%-epiboly
Bud
5-9 somites
26+ somites
Prim-5
Long-pec
Protruding-mouth
90 Days-2 Years
nan
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ChIP-seq target
















ChIP-seq target
nanog-like   nanog-like
Rad21   Rad21
sox10   sox10
H3K27ac   H3K27ac
Cdx4   Cdx4
H3K4me3   H3K4me3
H3K4me1   H3K4me1
Smad2   Smad2
Eomesa   Eomesa
Mixl1   Mixl1
Mxtx2   Mxtx2
Pol II 8WG16   Pol II 8WG16
H3K27me3   H3K27me3
Sox2   Sox2
zgata1   zgata1
H2AFV   H2AFV
H3K36me3   H3K36me3
Pol II 4H8   Pol II 4H8
Sall4   Sall4
Zic3   Zic3
Pou5f3   Pou5f3
H3K14ac   H3K14ac
CTCF   CTCF
ChIP-seq target
















ChIP-seq target
 All
Developmental stage
256-cell
512-cell
Oblong
Sphere
Dome
30%-epiboly
50%-epiboly
Shield
75%-epiboly
Bud
5-9 somites
26+ somites
Prim-5
Long-pec
Protruding-mouth
90 Days-2 Years
nan
Developmental stage
All 
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ChIP-seq tracks

The whole ChIP-seq dataset including raw data and metadata annotation can be found in the DANIO-CODE Data Coordination Center (https://danio-code.zfin.org/dataExport/?view=table&selected_facet=ChIP-seq-assay_type)

This is a ChIP-seq super track that groups together signal (bigWig format) and narrow peaks (bigNarrowPeak format) of ChIP-seq data. regions (bigBed format).

The ChIP-seq pipeline used to generate these tracks are described https://gitlab.com/danio-code/DANIO-CODE_ChIP-seq.

Briefly, the pipeline consists of:
  1. Aligning reads (bwa): Aligning raw reads to the reference genome.
  2. Filtering of aligned reads: Filtering the ba file for unaligned reads and and duplicates with samtools and sambamba.
  3. Optical duplicates detection: Detect optical duplicates with Picard tools.
  4. Duplicates removal: Second round of filtering with samtools and sambamba.
  5. Cross-correlation analysis.

Track definition: ChIP-seq tracks consist of 2 different types: #. ChIP-seq signals. #. ChIP-seq narrow peaks.

For more information on how the data were processed, please refer https://gitlab.com/danio-code/ADANIO-CODE_RNA-seq.