|
| Status |
Public on Apr 03, 2014 |
| Title |
input (ChIP) |
| Sample type |
SRA |
| |
|
| Source name |
facial mesenchyme
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL6/j
genotype/variation: wt
embryonic stage: 11.5
chip antibody: none
|
| Treatment protocol |
None
|
| Growth protocol |
Mouse facial mesenchyme: dissected from bronchial arch to forebrain boundary
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from drbris of nuclei and DNA-wrapped histones were Immunoprecipitated with specific antibody.
Libraries were prepared with NEB Next ChIP-seq Sample Prep Master Mix Set I (Cat.No.E6240S, NEB) and NEB Next Multiplex Oligos for Illumina (Cat.No: E7335S, NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3_ChIP-seq
|
| Data processing |
ChIP-seq reads were aligned to the reference genome mm9 with bowtie2 allowing for max 1 mismatch.
Duplicted reads and reads mapping multiple locations were removed. In the end bam files containing 10 - 20 e6 useful reads were subjected to MACS14 for peak calling with default parameters.
Tracks were made using genomeCoverageBed and wigToBigWig softwares.
genome build: mm9
processed data files format and content: .txt files report Base pair coverage was calculated and normalized to 1X ~11e6 reads, then the coverage was summed within bins of 50bp
processed data files format and content: .bed MACS14 Peak calling file. MACS was run with default parameters
processed data files format and content: .bw Tracks of the coverage file. (Not normalized to input)
|
| |
|
| Submission date |
Dec 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Massimo Petretich |
| E-mail(s) |
petretic@embl.de
|
| Phone |
0049-(0)62213878569
|
| Organization name |
EMBL
|
| Department |
Developmental biology
|
| Lab |
Spitz
|
| Street address |
Meyerhofstraße 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE52974 |
The 8q24 cleft lip susceptibility locus is a remote Myc enhancer required for normal face morphology |
|
| Relations |
| BioSample |
SAMN02435486 |
| SRA |
SRX387017 |
