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Sample GSM1817223 Query DataSets for GSM1817223
Status Public on Sep 11, 2015
Title Input_chimp_rep1
Sample type SRA
 
Source name Cranial neural crest cells
Organism Pan troglodytes
Characteristics cell type: Cranial neural crest cells (CNCCs)
cnccs derived from: 0818 iPSC
chip antibody: none (input)
Growth protocol hESCs/iPSCs were incubated with 2mg/ml collagenase. Once detached, clusters of 100-200 cells were plated in CNCC differentiation medium: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml bovine insulin (Sigma-Aldrich) and 1× Glutamax-I supplement (100× stock, Invitrogen). Medium was changed every other day. After seven days of differentiation, neuroepithelial spheres attached to the dish and gave rise to migratory CNCC. Three-four days after the appearance of the first CNCC, cells were dissociated with accutase until single cells and passaged onto fibronectin-coated plates. CNCCs were then transitioned to CNCC early maintenance media: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 1 mg/ml bovine serum albumin, serum replacement grade (Gemini Bio-Products # 700-104P) and 1× Glutamax-I supplement (100× stock, Invitrogen). CNCCs were passaged onto fibronectin-coated plates 1:3 every three days, and after 1-2 passages, transitioned to CNCC long term maintenance media, which is composed of CNCC early maintenance media plus 3uM ChIRON 99021 (Selleck, CHIR-99021) and 50ng/ml BMP2 (Peprotech). Cells were maintained on fibronectin with passaging every ~ 3days, and collected at passage 4 for all ChIPs and downstream assays.
Extracted molecule genomic DNA
Extraction protocol ChIPs were performed using approximately 0.5-1 x 10^7 CNCCs fixed with 1% formaldehyde for 10 min at room temp. RNA was extracted using Trizol.
Sequencing libraries were prepared starting from ~30ng of ChIP DNA or oligo-dT purified mRNA using the NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description processed data aligned to hg19
Data processing Reads aligned to hg19 (regardless of species of origin) using default settings with Bowtie2.2.4
Wig files were generated with QuEST2.4
RNA-seq were aligned to hg19 and quantified against human ENSEMBL 78 (GRCh37) gene models using htseq-count. Variance-stabilizing transformation (VST) was applied across samples for processed data.
Genome_build: Alignments done using hg19 as reference
Supplementary_files_format_and_content: [ChIP-seq, ATAC-seq] wig
Supplementary_files_format_and_content: [RNA-seq] txt
 
Submission date Jul 10, 2015
Last update date May 15, 2019
Contact name Joanna Wysocka
Organization name Stanford University
Street address 265 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13802
Series (1)
GSE70751 Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest
Relations
BioSample SAMN03854170
SRA SRX1091574

Supplementary file Size Download File type/resource
GSM1817223_chimp1_input_normalized.profile.wig.gz 3.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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