|
| Status |
Public on Feb 05, 2024 |
| Title |
Nanog, bioChIP |
| Sample type |
SRA |
| |
|
| Source name |
pre-implantation embryo
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pre-implantation embryo
cell line: J1 ES cells
cell type: mouse embryonic stem cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
bioChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Chromatin IP against biotinylated protein
|
| Data processing |
The FASTQ files of bioChIP-seq and ATAC-seq were trimmed with Trim Galore v0.6.7
The reads were mapped to the mm10 mouse reference genome using bowtie2 v2.4.4 with default parameters.
All alignments were further sorted by Picard Tools v2.27.2 and filtered by Samtools v1.14 with MAPQ >= 10.
The PCR duplicates were removed using Picard Tools v2.27.2.
Peaks were identified using MACS2 v2.2.7.1 with a cutoff of FDR<0.05
Assembly: RPGC normalized bigwig files were generated using deeptools bamcoverage v3.5.0.
Supplementary files format and content: Bigwig files normalized by 1x depth (reads per genome coverage, RPGC)
|
| |
|
| Submission date |
Dec 12, 2022 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Qingqing Guo |
| E-mail(s) |
qg778@utexas.edu
|
| Organization name |
The University of Texas at Austin
|
| Street address |
2506 Speedway
|
| City |
AUSTIN |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE220724 |
Systematic mapping of TF-mediated cell fate changes by a pooled inductioncoupled with scRNA-seq and multi-omics approaches |
|
| Relations |
| BioSample |
SAMN32168059 |
| SRA |
SRX18646251 |
