 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 24, 2024 |
| Title |
Nanog |
| Sample type |
SRA |
| |
|
| Source name |
Cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cell
cell line: MEF
cell type: mouse embryonic fibroblast
chip antibody: Flag
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was harvested using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901), 100000 cells per sample was used for sequencing libraries construction
Liarbries were constructed by Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CUT&Tag library construction was performed using Hyperactive InSitu ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, TD901) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202). In brief, around 10000 living cells per sample were obtained and mixed with activated Concanavalin A beads, followed by sequentially incubated with primary and secondary antibodies. The beads were then washed and resuspended in pA(G)-Tn5 buffer supplemented with 10 mM MgCl2 for DNA tagmentation. Next, DNA fragments were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and PCR amplified. After purified by VAHTS DNA Clean Beads (Vazyme, N411), libraries were subjected to Illumina Novaseq instruments for sequencing. Antibodies against Nanog (Abcam, ab214549, 1:50), H3K4me (Abcam, ab313500, 1:50), H3K27ac (Abcam, ab4729, 1:50), flag (Sigma, F1804, 1:50), and Smarca4 (Cell Signaling Technology, 52251, 1:50) were used in this study.
The CUT&Tag reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5). SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. The value were further compressed into a binary format for downstream analysis and data visualization. Replicates were merged using samtools merge and then peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup 1 --nomodel --shiftsize 25. The signals were normalized to one million reads for each sample. Promoters were defined as regions ± 2 kb around transcription start sites (TSSs) of genes.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks&Summits bed
|
| |
|
| Submission date |
Apr 09, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Chengchen Zhao |
| E-mail(s) |
zhaochengchen@westlake.edu.cn
|
| Organization name |
Westlake University
|
| Lab |
Laboratory of Cell Fate Control
|
| Street address |
Dunyu Road No.600, Xihu District
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310030 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE243517 |
Rational cell fate engineering through chromatin dynamics |
| GSE263597 |
Rational cell fate engineering through chromatin dynamics [CUT&TAG II] |
|
| Relations |
| BioSample |
SAMN40904816 |
| SRA |
SRX24201466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8195108_HT-C-61.bw |
128.0 Mb |
(ftp)(http) |
BW |
| GSM8195108_HT-C-61.e5_peaks.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSM8195108_HT-C-61.e5_summits.bed.gz |
762.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
