|
| Status |
Public on Feb 27, 2015 |
| Title |
C_WT |
| Sample type |
SRA |
| |
|
| Source name |
WT T-cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6 (H2b) background
cell type: T-cells
genotype/variation: WT
chip antibody: Rabbit polyclonal anti-mouse NLRC5 (aa 1–139) custom antibody generated by Adipogen
|
| Growth protocol |
Sex and age-matched 6 to 12 week-old mice were used. Five mice were pooled for each genotype.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatine was isolated, fragmented by sonication and immunoprecipitated it with anti Nlrc5 antibody
Libraries were prepared according to Illumina's instructions using the Truseq ChIP-seq protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 3
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome (GRCm38.70) using bowtie 0.12.7 with -m 1
Sample 9 "WT" was used to generate the 5 pseudo-replicates of WT (i.e., samples "A_WT" to "E_WT") by random sub-sampling. However, sample 9 was not directly used for the analysis.
Peaks were called using macs2 2.0.10.20130520 with -p 0.001 using NLRC5 as control
Genome_build: GRCm38.70
Supplementary_files_format_and_content: bigwig and bed files report peaks
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sylvain LEMEILLE |
| Organization name |
University of Geneva Medical School
|
| Department |
Department of Pathology and Immunology
|
| Street address |
1 rue Michel-Servet
|
| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE59092 |
NLRC5 specifically transactivates MHC class I and related genes through a distinctive SXY module |
|
| Relations |
| BioSample |
SAMN02902870 |
| SRA |
SRX646162 |
