|
| Status |
Public on Apr 03, 2013 |
| Title |
CHIP-seq:IgG control |
| Sample type |
SRA |
| |
|
| Source name |
CD71+Ter119+ cells facs sorted cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: CD71+Ter119+ cells (facs sorted)
age: 8- to 12-wk-old
genotype/variation: KAP1 WT
strain: mix strain
chip antibody: IgG (control IP)
|
| Treatment protocol |
HEL were activated in presence of hemin at a final concentration of 50 micromolar during five days
|
| Growth protocol |
no growth protocol for CD71+Ter119+ cells. HEL are cultured in RPMI 10%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked by 1% formaldehyde and sonicated, and chromatin was immunoprecipitated by using an affinity-purified rabbit polyclonal antibody raised against KAP1 aa 20-418, RBCC (F. R. Santoni de Sio et al.,. Blood 119, 4675 (2012)). Detailed protocols for ChIP are described in D. C. Schultz,. Genes Dev 15, 428 (2001).
Reverse cross-linking was performed overnight in the presence of proteinase K and RNase, followed by DNA extraction using the MinElute PCR purification kit (Quiagen) according to manufacturer protocol.
10 ng were used to prepare libraries for sequencing, following the ChIP Seq library preparation protocol (including End Repair for blunted end fragments, addition of "A" base to the 3' end and ligation of adapters to DNA fragments (kit IP-102-1001). Ligation products were then purified on 2% E Gels Size Select (Invitrogen, fragments of 200 bp recovered), followed by enrichment of DNA fragments by PCR (18 cycles).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sorted cells from bone marrow of 8- to 12-wk-old Kap-flox/stopfloxYFP
Processed data file:
Chipseq_KAP1_BMsortedTer119CD71_no_repeats_peaks.bed
|
| Data processing |
Raw reads were mapped to the mouse genome and human transcriptome using Bowtie
Peaks were called using MACS
RPKM values were calculated using R/Bioconductor
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .bed file contains the peaks called (linked as supplementary file on Series record)
|
| |
|
| Submission date |
Feb 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Adamandia Kapopoulou |
| E-mail(s) |
adamandia.kapopoulou@epfl.ch
|
| Phone |
0041216930940
|
| Organization name |
EPFL
|
| Department |
Sciences de la Vie
|
| Lab |
Trono
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE44061 |
KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy [Seq] |
| GSE44065 |
KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy |
|
| Relations |
| SRA |
SRX225201 |
| BioSample |
SAMN01911260 |
