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Sample GSM1666997 Query DataSets for GSM1666997
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 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]
BioSample SAMN03568973
SRA SRX1011027

Supplementary file Size Download File type/resource 82.1 Mb (ftp)(http) BW
GSM1666997_RFX2_WT_exp2_vs_GRCm38.70_peaks.bed.gz 289.5 Kb (ftp)(http) BED
GSM1666997_RFX2_WT_vs_GRCm38.70_peaks.bed.gz 68.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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