|
| Status |
Public on Nov 27, 2024 |
| Title |
LDB1_AID_untreated_YY1_rep2 |
| 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: Untreated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from lysed cells was sonicated using the Bioruptor Pico, immunoprecipitated, and then extracted using the QIAquick PCR Purification kit (Qiagen 28106).
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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
LDB1_AID_untreated_YY1_merged_rpm.bw
LDB1_AID_YY1_untreated_consensus_peaks.bed
|
| Data processing |
Fastq files were generated with Bclfastq2 v2.15.04
Reads were aligned using bowtie2 with default settings, de-duplicated, and filtered for MAPQ>20
bigwig files were generated using deeptools (v3.5.1) bamCoverage (binSize=20, normalizeUsing=BPM). Pol2 bigwig files were normalized using RPKM.
Macs2 (v2.2.9.1) was used to identify peaks using matched input and p = 1e-5
Assembly: mm9
Supplementary files format and content: bed:peak calls, bw: tracks of ChIP-seq signals
|
| |
|
| 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) |
| GSE254377 |
Ldb1 establishes multi-enhancer networks to regulate gene expression [ChIP-Seq] |
| GSE254378 |
Ldb1 establishes multi-enhancer networks to regulate gene expression |
|
| Relations |
| BioSample |
SAMN39642214 |
| SRA |
SRX23421468 |
