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SRX2671645: GSM2549944: Tbx16_input; Danio rerio; ChIP-Seq
1 ILLUMINA (Illumina Genome Analyzer IIx) run: 12M spots, 432.6M bases, 262.6Mb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide profiling of Ta, Tbx16 and Mixl1 binding in early zebrafish embryos
show Abstracthide Abstract
Identification of Ta and Tbx16 binding sites during gastrulation, and Mixl1 binding sites during endoderm specification Overall design: Replicate ChIP samples for Ta, Tbx16 and Mixl1 with matched input samples - 6x ChIP samples (2 per factor); 3x input samples
Sample: Tbx16_input
SAMN06642297 • SRS2071024 • All experiments • All runs
Organism: Danio rerio
Library:
Instrument: Illumina Genome Analyzer IIx
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Sequential cytoplasmic and nuclear lysis, followed by sonication and centrifugal clarification from was used to obtain chromatin of appropriate fragment size. Desired protein-DNA complexes were isolated using antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Experiment attributes:
GEO Accession: GSM2549944
Links:
Runs: 1 run, 12M spots, 432.6M bases, 262.6Mb
Run# of Spots# of BasesSizePublished
SRR537629112,016,254432.6M262.6Mb2017-06-12

ID:
3856685

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