|
| Status |
Public on May 28, 2024 |
| Title |
ZRS/hs1516 Hindlimb ZPA, E11.5, replicate 1, ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
FVB (strain)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: FVB (strain)
genotype: ZRS^hs1516/WT
cell type: Hindlimb
genotype: ZRS^hs1516/WT
read size: 100-bp
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Posterior limb bud tissue containing the ZPA region from E11.5 mouse embryos was dissected and manually disassociated followed by snap freezing.
Library construction was performed using the Omni-ATAC-seq protocol (Buenrostro et al., 2013, 2015), with an adjusted lysis step and transposition buffer based on Omni-ATAC protocol (Corces et al., 2017).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
bw file contains data for all replicates.
|
| Data processing |
Fastq files were trimmed and clipped using trim_galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the following options -q 20 --stringency 2 --clip_R1 16 --clip_R2 16. Reads were then aligned to the original mm10 genome assembly as well as to a modified version of the genome containing the corresponding insertion using bedtools getfasta (Quinlan & Hall, 2010).
Assembly: mm10 + custom chr5 (hs1516/ZRS)
|
| |
|
| Submission date |
Sep 20, 2023 |
| Last update date |
May 28, 2024 |
| Contact name |
Evgeny Kvon |
| E-mail(s) |
ekvon@uci.edu
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Street address |
4310 McGaugh Hall
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE243635 |
Conserved Cis-Acting Range Extender Elements Mediate Long-Range Developmental Enhancer Activity in Mammals |
|
| Relations |
| BioSample |
SAMN37482534 |
| SRA |
SRX21838325 |
