|
| Status |
Public on May 07, 2019 |
| Title |
H3_SF1_F_2 |
| Sample type |
SRA |
| |
|
| Source name |
H3_SF1_F
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6 x CD1
genotype/variation: SF1-eGFP
embryonic stage: E10.5
Sex: female
cell type: FACS-sorted gonadal progenitor cells
chip antibody: H3 Active Motif 39763
chip protocol: Van Galen et al, 2016
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS). For ChIP-seq, 30K-100K cells were collected per replicate.
ChIP-seq libraries were prepared with no modifications according to Van Galen et al., 2016.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
HOMER was used for calling peaks with the findPeaks function and settings “--style histone”, with a size of 5000 for H3K27me3 and 1000 for H3K4me3. The setting “-C 0” was used in MNase ChIP to disable fold enrichment limit of expected unique tag positions. H3K27me3 and H3K4me3 were used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser. For optimal visualization, ChIP-seq replicates were concatenated to increase number of reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser of concatenated replicates. bed files contain coordinates of called peaks.
|
| |
|
| Submission date |
May 06, 2019 |
| Last update date |
May 07, 2019 |
| Contact name |
Sara A. Garcia-Moreno |
| E-mail(s) |
sara.garciamoreno@duke.edu
|
| Phone |
2066878614
|
| Organization name |
Duke University
|
| Lab |
Sara A. Garcia-Moreno
|
| Street address |
Nanaline Bldg. Research Drive
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
60657 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE130749 |
CBX2 is required to stabilize the testis pathway by repressing Wnt signaling |
|
| Relations |
| BioSample |
SAMN11581226 |
| SRA |
SRX5795454 |
