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Sample GSM933348 Query DataSets for GSM933348
Status Public on Sep 13, 2012
Title Chicken_st11-14_NCC_input
Sample type SRA
 
Source name stage11-14_NCC_input
Organism Gallus gallus
Characteristics tissue source: stage 11-14 chicken embryos
cell type: Neural crest cells (NCC)
Treatment protocol Chicken stage 11-14 NCC: Chick embryos were harvested at st.8 and the dorsal neural tube was excised and plated on matrigel coated plates in NCC differentiation media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5x B-27 supplement with Vitamin A (50x stock, Invitrogen), 0.5x N-2 supplement (100x stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 µg/ml bovine insulin (Sigma-Aldrich) and 1x Glutamax-I supplement (100x stock, Invitrogen).
Growth protocol Chicken stage 11-14 NCC: Chick embryos were harvested at st.8 and the dorsal neural tube was excised and plated on matrigel coated plates. After between 48-72 hours cranial neural crest cells began to migrate out of the dorsal neural tube explants and considered to resemble st11-14 NCC from embryos. Cells were then trypsinized an pooled for ChIP assays. Chicken stage 20 NCC: Frontonasal prominences (FNP) NCCs were isolated in cold PBS at St20 according to Hamburger-Hamilton criteria. FNPs were placed in 1.26 U dispase in 1x PBS for 15 minutes at room temperature, then into DMEM with 10% FBS. Surface ectoderm and forebrain neuroectoderm were removed using sharpened tungsten needles leaving only FNP NCCs. Cells were then trypsinized an pooled for ChIP assays.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with 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 size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. 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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Input DNA
Data processing Enrichment analysis was performed using QuEST software with suggested settings for transcription factor binding.
Genome_build: galGal3
Supplementary_files_format_and_content: aligned.bed and calls.bed files including aligned reads and annotated peaks/regions are provided respectively
 
Submission date May 21, 2012
Last update date May 15, 2019
Contact name Alvaro Rada
E-mail(s) alvaror@stanford.edu
Organization name Stanford University
Department Chemical and Systems Biology
Lab Wysocka lab
Street address 269 Campus Drive, CCSR Building
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13797
Series (1)
GSE38066 Epigenomic profiling of enhancers identifies orphan nuclear receptors NR2F1 and NR2F2 as novel regulators of human neural crest.
Relations
SRA SRX148742
BioSample SAMN00996669

Supplementary file Size Download File type/resource
GSM933348_Chicken_st11-14_NCC_input_aligned.bed.gz 64.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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