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| Status |
Public on Jul 05, 2016 |
| Title |
Shox2-palate E12.5 |
| Sample type |
SRA |
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| Source name |
embryonic palate
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| Organism |
Mus musculus |
| Characteristics |
sample type: Shox2-HA
age: E12.5
antibody: anti-HA(Abcam, Cat.Ab9110, Lot. GR146572-6)
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| Growth protocol |
fresh dissected tissue
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP, following manufracture protocol provided by Active Motif ChIP-IT high sensitivity protocol
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Standard mapping using bowtie for illumina
Peaks calling using MACS/MACS2 with default setting in Galaxy main/Cistrome instance
mm9
bedgraph files are generated by MACS
Bedgraph was converted to bigwig using Bedgraph to bigwig tool in Galaxy main instance
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-signal filtered against Non tagged control by MACS2
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| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yiping Chen |
| E-mail(s) |
ychen@tulane.edu
|
| Organization name |
Tulane University
|
| Department |
CMB
|
| Street address |
6400 Freret
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| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70118 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
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| Relations |
| BioSample |
SAMN05000973 |
| SRA |
SRX1764534 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2177163_Shox2-Palate_E12.5.bed.gz |
120.8 Kb |
(ftp)(http) |
BED |
| GSM2177163_Shox2_Palate_E12.5_filtered.bigwig |
701.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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