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| Status |
Public on Sep 11, 2015 |
| Title |
H3K27ac_chimp1_rep1 |
| Sample type |
SRA |
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| Source name |
Cranial neural crest cells
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| Organism |
Pan troglodytes |
| Characteristics |
individual: 1
cell type: Cranial neural crest cells (CNCCs)
cnccs derived from: 0818 iPSC
culture conditions: +BMP2+ChIRON
chip antibody: anti-H3K27ac (Active Motif, catalog# 39133, lot# 01613007)
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| 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.
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| 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data aligned to hg19
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| 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
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| Submission date |
Jul 10, 2015 |
| Last update date |
Feb 13, 2020 |
| Contact name |
Tomek Swigut |
| E-mail(s) |
swigut@stanford.edu
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| Organization name |
Stanford University
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| Department |
Chemical and Systems Biology
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| Lab |
Wysocka
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| Street address |
265 Campus Dr
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16809 |
| Series (1) |
| GSE70751 |
Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest |
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| Relations |
| BioSample |
SAMN03854148 |
| SRA |
SRX1091522 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1817162_chimp1_K27ac_rep1_normalized.profile.wig.gz |
161.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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