|
| Status |
Public on Aug 21, 2013 |
| Title |
chipseq KO H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
neonatal tail tip fibroblasts, Hotair knockout
|
| Organism |
Mus musculus |
| Characteristics |
strain: backcross to C57BL6 with over 97% similarity
cell type: neonatal tail tip fibroblasts
genotype/variation: Hotair knockout
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extracted DNA was RNase treated and purified using Qiagen column, and sequencing libraries were made following Illumina’s protocol.
For ChIP-seq libraries, chromatin was solubilized and isolated with corresponding antibodies, and the libraries were made following Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq, the processed file is in bedgraph format with for both wildtype, Hotair knockout for H3K27me3 and H3K4me3.
|
| |
|
| Submission date |
Jun 17, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Howard Chang
|
| Street address |
269 Campus Dr. CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE48005 |
Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes [RNA-Seq, ChIP-Seq] |
| GSE48007 |
Targeted disruption of Hotair leads to homeotic transformation and de-repression of imprinted genes |
|
| Relations |
| BioSample |
SAMN02205122 |
| SRA |
SRX306689 |
