|
| Status |
Public on Nov 02, 2015 |
| Title |
RFX2_WT_exp2 |
| Sample type |
SRA |
| |
|
| Source name |
Decapsulated testis
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6|129/Sv|FVB/N Mixed BKG
chip antibody: RFX2 antibody from Santa Cruz Biotechnology – Catalog # sc-10657 – Lot # L0413
tissue: Testis
age: post natal day 29-30
genotype: wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatine was isolated, fragmented by sonication and immunoprecipitated with anti Rfx2 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 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using bowtie 0.12.7 with -m 1
Fragment length was estimated using phantompeakqualtools 2.0
Peaks were called using macs2 2.0.10.20130520 with -p 0.01 –to-large –nomodel and shiftsize set to half the estimated fragment length using inputs as control
Reproducible peaks were obtained by IDR procedure with -p 0.01
Genome_build: GRCm38.70
|
| |
|
| Submission date |
Apr 27, 2015 |
| 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 (2) |
| GSE63130 |
Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes |
| GSE68282 |
Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN03568973 |
| SRA |
SRX1011027 |
