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| Status |
Public on Jan 18, 2023 |
| Title |
UB cells,Mutant,E16.5,CUTTAG,biol rep 2 [K4me3_cko_5] |
| Sample type |
SRA |
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| Source name |
ureteric bud,FACS-sorted,E16.5
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| Organism |
Mus musculus |
| Characteristics |
tissue: ureteric bud,FACS-sorted,E16.5
cell type: intermediate mesoderm epithelial cells
age: E16.5
genotype: Hoxb7Cre-GFP+,Ash2l F/F
chip antibody: H3K4me3 (Invitrogen,MA5-11199)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
E16.5 embryonic kidneys were dissected and cut into small pieces, trypsinized for 30 min at 37℃, and trypsinization was terminated by adding DMEM/F12 supplemented with 10% FBS. After centrifugation, cells were resuspended in DMEM/F12 supplemented with 2% FBS and filtered 2 times through 70µm cell-strainer cap (Biosharp, BS-70-XBS). The single cell suspension was transferred into a polypropylene tube (Falcon, 352063) and kept on ice until FACS. The GFP+ cells were isolated into DMEM/F12 supplemented with 10% FBS using Sony MA900 Cell Sorter.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
CUT&Tag-seq, For library preparation, the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit was purchased from Novoprotein, and libraries were generated according to the manufacturer’s instructions.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
libraries were sequenced on Illumina® platform, raw reads were filtered and mapped to the mouse genome (GRCm39) using bowtie2 (v2.2.9). Peak calling was accomplished using SEACR (v1.3), and peaks were annotated using ChIPseeker (v 1.12.1).
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag
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| Submission date |
Oct 22, 2022 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Ziyi Zhao |
| E-mail(s) |
nephox@sjtu.edu.cn
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| Organization name |
Shanghai jiaotong university school of medicine
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE208273 |
ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity [CUT&Tag] |
| GSE208275 |
ASH2L controls ureteric bud morphogenesis via regulation of RET/GFRA1 signaling activity |
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| Relations |
| BioSample |
SAMN31413881 |
| SRA |
SRX17995373 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6670890_K4me3_cko_5.bigwig |
6.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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