|
| Status |
Public on Nov 27, 2024 |
| Title |
LDB1_AID_MICRO_C_auxin_rep7 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cell line
cell line: G1E-ER4
cell type: Erythroblast
genotype: LDB1-AID subline
treatment: 4 hour auxin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was digested with Mnase and proximity ligated. Ligated DNA was isolated using phenol:chloroform:isoamyl and ethanol precipitation. Dinucleosomes were isolated by gel extraction. Dinucleosomes weree purified with Zymoclean Geel DNA Recovery kit (D4007)
The NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7635) was used to prepare libraries using unique dual-indexed primers (NEB E6440).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Fastq files were generated with Bclfastq2 v2.15.04
.mcool files were generated using the distiller pipeline (v3.3)
Loops were identified using cooltools (v0.5.3)
Domains were identivied using rGMAP
Assembly: mm9
Supplementary files format and content: mcool:multi-resolution contact map, bedpe: list of Micro-C loop coordinates, bed: list of domain coordinates
Library strategy: Micro-C-seq
|
| |
|
| Submission date |
Jan 28, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Nicholas Aboreden |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Lab |
Blobel Lab
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE254373 |
Ldb1 establishes multi-enhancer networks to regulate gene expression [micro-C-Seq] |
| GSE254378 |
Ldb1 establishes multi-enhancer networks to regulate gene expression |
|
| Relations |
| BioSample |
SAMN39641005 |
| SRA |
SRX23420561 |
