|
| Status |
Public on Nov 18, 2018 |
| Title |
H3K4me3_FF_ChIPSeq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
GSCs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: germline stem cells (GSCs)
genotype: Kmt2bF/F
chip antibody: H3K4me3 (Abcam, ab8580)
|
| Treatment protocol |
Kmt2b knockout in GSCs was done by adding 4-OHT at a final concentration of 1 μM to the media. For control, Kmt2bF/F; Rosa26-CreERT2 GSCs was mock-treated with 100% ethanol in parallel with the knockout.
|
| Growth protocol |
GSCs were grown on fibroblast feeder cells in GS media for 6 days after 4-OHT treatment prior to harvesting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked and chromatin was prepared according to a previous report (Nat. Protoc. 3, 1032–1045) with modifications. For RNA-seq, total RNA was purified using Isogen (Nippon Gene), and treated with DNaseI to digest genomic DNA.
ChIP-seq and RNA-seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), respectively, according to manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Reads were quality- and adaptor-trimmed using Trim Galore! version 0.4.0.
ChIP-seq reads were aligned to mouse genome using Bowtie version 1.1.1 with the parameters -n 2 -l 30 --best --strata -m 1.
RNA-seq reads were aligned to mouse genome using TopHat version 2.0.14 with default parameters except that a gtf reference file was used.
ChIP-seq and RNA-seq read count was done using SeqMonk version 0.30.2, correcting for total count per million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated using SeqMonk contain corrected RNA-seq read count for all genes and corrected ChIP-seq read count for TSSs ±0.5 kb.
|
| |
|
| Submission date |
Dec 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shin-ichi Tomizawa |
| Organization name |
Yokohama City University
|
| Department |
School of Medicine
|
| Lab |
Histology
|
| Street address |
3-9 Fukuura, Kanazawa-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
236-0004 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE92677 |
Kmt2b conveys monovalent and bivalent H3K4me3 in spermatogonial stem cells at germline and embryonic promoters |
|
| Relations |
| BioSample |
SAMN06169791 |
| SRA |
SRX2438157 |
