|
| Status |
Public on Jul 29, 2021 |
| Title |
ATAC HH24 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
wing bud
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: wing buds
developmental stage: HH24
strain: White Leghorn
|
| Growth protocol |
Fertilized chicken White Leghorn eggs were purchased from a local supplier, incubated at 38ºC and staged according to Hamburger and Hamilton (1951).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Per biological replicate, dissected left and right wing buds from one embryo at the desired stage were pooled and dissociated in PBS (Gibco 14040-117) at 4ºC using a 2ml glass tissue grinder (Sigma-Aldrich D8938; 20 strokes with pestle A followed by 20 strokes with pestle B).
75'000 cells were processed per sample for ATAC-Seq as described in Buenrostro et al., 2015. Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi:10.1002/0471142727.mb2129s109
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Samples were mapped to the chicken genome (UCSC version galGal4) with the qAlign function of the R/Bioconductor package QuasR (version 1.8.2) using options '-m 1 --best --strata --maxins 2000'.
Coverage tracks per sample were generated by tiling the genome in 10 bp windows, counting the number of 5'-ends per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Supplementary_files_format_and_content: bigWig files with scores representing RPKM values (within 10 bp windows)
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
Nov 18, 2021 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
|
| Organization name |
University of Basel
|
| Department |
Departement of Biomedicine
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE151467 |
cis-regulation of Grem1 expression during limb development [ATAC HH24] |
| GSE151488 |
cis-regulation of Grem1 expression during limb development |
|
| Relations |
| BioSample |
SAMN15060517 |
| SRA |
SRX8428110 |
