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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 14, 2017 |
| Title |
NSCinput |
| Sample type |
SRA |
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| Source name |
Emrbyonic neural stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
age: E14.5
cell type: Embryonic neural stem cells
chip antibody: none
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| Treatment protocol |
none
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| Growth protocol |
NSCs were grown as neurospheres in presence of EGF and bFGF
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of 5µg of anti-Foxp1 (ab16645, Abcam) coupled to A/G sepharose beads (Santa Cruz Biotechnology).
Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
input ChIP-seq
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| Data processing |
ChIP-sequencing reads were mapped with Bowtie 2.1.0 against the reference genome (mm10) using default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER software using the input as a control (Fold over local region=8, Fold over input=2) (Heinz et al., 2010).
Mapped fragments were extended according to the average fragment size and converted to TDF files, visualized with IGV tools v2.3.36 and represented as coverage normalized tracks (Robinson et al., 2011). SAMtools was used for manipulation of SAM and BAM files; manipulation of BED file format was performed with BEDtools (Li et al., 2009; Quinlan and Hall, 2010).
Motif discovery, peak annotation and generation of histograms were performed using HOMER software. For motif discovery the 200 bp sequence surrounding each peak was examined and motifs with length of 8, 10 and 12 nt were searched. Motifs were identified through de novo motif discovery.
For functional annotation of peaks the software GREAT was used, where genes that presented peaks within 1kb with Forkhead motif were selected (McLean et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Jul 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul J Coffer |
| E-mail(s) |
p.j.coffer@umcutrecht.nl
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| Organization name |
UMC Utrecht
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| Department |
Regenerative Medicine Center
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| Lab |
Coffer Lab
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| Street address |
Uppsalalaan 6
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| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE101632 |
Foxp1 binding profiling in mouse embryonic neural stem cells (NSCs) |
| GSE101633 |
Role of Foxp1 in mouse embryonic neural stem cells (NSCs) |
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| Relations |
| BioSample |
SAMN07369155 |
| SRA |
SRX3015773 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2711173_NSCsinput.bw |
16.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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