|
Status |
Public on Feb 03, 2024 |
Title |
1143 |
Sample type |
SRA |
|
|
Source name |
anterior mouse forelimb
|
Organism |
Mus musculus |
Characteristics |
tissue: anterior mouse forelimb genotype: Gli3Xt-J ; Gli3+/+ cell type: Anterior forelimb pair (~2-400K cells) Stage: E11.5 (43s)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
2-400K cells from anterior, posterior or whole forelimbs from wild-type embryos incubated with anti-SMARCC1 or anti-Rabbit IGG antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC. Samples were library prepped and run on a BioAnalyzer to assess quality prior to sequencing. Libraries prepared using the NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S), PCR amplified for 14 cycles and cleaned up using SparQ PureMag beads (QuantaBio 95196-060) at a ratio of 0.8x beads. NEBNext Ultra II DNA library prep kit (New England Biolabs E7645S)
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
2-400K cells from anterior forelimbs from wild-type embryos incubated with anti-SMARCC1 antibody overnight at 4degC, and then treated with p-AG-Mnase (Epicypher) for 2H at 4degC.
|
Data processing |
Base calling was done using Illumina bcl2fastq version 2.20.0 Raw sequencing reads are mapped to mouse mm10 genome using Bowtie2 (version 2.3.5). Peak calling was done using MACS2
|
|
|
Submission date |
Feb 03, 2023 |
Last update date |
Feb 03, 2024 |
Contact name |
Steven A. Vokes |
E-mail(s) |
svokes@austin.utexas.edu
|
Organization name |
University of Texas at Austin
|
Department |
Molecular Biosciences
|
Street address |
2500 Speedway, STOP A5000
|
City |
Austin |
State/province |
Texas |
ZIP/Postal code |
78757 |
Country |
USA |
|
|
Platform ID |
GPL24247 |
Series (2) |
GSE224508 |
The BAF complex does not mediate GLI repression (Gli3 null Cut&RUN) |
GSE224510 |
The BAF complex does not mediate GLI repression |
|
Relations |
BioSample |
SAMN33059266 |
SRA |
SRX19278078 |