|
| Status |
Public on Jun 08, 2023 |
| Title |
Erythroblasts_ATACseq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HD3
|
| Organism |
Gallus gallus |
| Characteristics |
cell line: HD3
cell type: Chicken erythroblasts
genotype: WT
|
| Growth protocol |
Primary fibroblasts and HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei extraction of 150,000 cells was treated with the Tn5 enzyme (Illumina) for 30 min. Following tagmentation, DNA was extracted using MinElute columns (Qiagen).
ATAC-seq libraries were amplified for 10 PCR cycles using the Nextera barcode system (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ATAC-seq reads were mapped to the GRCg6a genome using Bowtie2 (v2.3.5). Duplicates and reads longer than 150 bp were removed with Samtools (v1.9).
Peaks were called with MACS2 (v2.1.2) with a significance level of 0.01 and the peaks conserved between two biological replicates were used for analysis
Assembly: GRCg6a
Supplementary files format and content: NarrowPeak file with the consensus accessible peaks shared between 2 biological replicates per cell type.
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Mayra Furlan-Magaril |
| E-mail(s) |
mfurlan@ifc.unam.mx
|
| Phone |
525512291890
|
| Organization name |
IFC-UNAM
|
| Department |
Molecular Genetics
|
| Lab |
Genome Topology
|
| Street address |
Circuito exterior s/n
|
| City |
Mexico City |
| State/province |
Mexico City |
| ZIP/Postal code |
04510 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL19005 |
| Series (2) |
| GSE206191 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ATAC-seq] |
| GSE206194 |
RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes |
|
| Relations |
| BioSample |
SAMN29095169 |
| SRA |
SRX15713139 |
