|
| Status |
Public on Nov 27, 2024 |
| Title |
LDB1_AID_TRI_C_auxin_biorep4 |
| 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: auxin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was digested with NLAIII and proximity ligated. Oligonucleotide capture was performed using a biotinylated probe to enrich for the Myc promoter using KAPA HyperCapture Reagents (Roch, 9075810001).
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
Capcruncher was used to identify multiway contacts.
Cooler was used to genereate cool files (binned at 5kb).
Assembly: mm9
Supplementary files format and content: cool: contact map for multiway interactions with Myc promoter. All reads in cool file contain one fragment mapping to capture region (Myc promoter), and at least two additional fragments separated by NLAIII recognition site.
Library strategy: Tri-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) |
| GSE254372 |
Ldb1 establishes multi-enhancer networks to regulate gene expression [Tri-C-Seq] |
| GSE254378 |
Ldb1 establishes multi-enhancer networks to regulate gene expression |
|
| Relations |
| BioSample |
SAMN39639201 |
| SRA |
SRX23419979 |
