|
| Status |
Public on Oct 13, 2023 |
| Title |
Erythroid_day_13_CD34+_don001_ATAC-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Erythroid
|
| Organism |
Homo sapiens |
| Characteristics |
donor id: Don001
cell type: Erythroid
origin cell_line: CD34+ human erythroid
differentiation day: Day 13
selection antibody: CD34 microbead, Miltenyi Biotec #130-046-702
|
| Growth protocol |
CD34+ cells were isolated from fresh blood as previously described (Truch, 2022) and subject to a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 75,000 cells were used per biological replicate.
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CD34, day 13, don001, rep1
|
| Data processing |
genome build/assembly: hg38
All data was processed using the CATCH-up pipeline (https://github.com/Hughes-Genome-Group/UpStreamPipeline/tree/main/genetics/catch-up)
aligner_algorithm: bowtie2 (bowtie2 v2.4.5)
samtools_sort_extra: -m 4G (samtools v1.15.1)
filtering_extra: -bShuF 4 -f 3 -q 30 (samtools v1.15.1)
bam_coverage: --binSize 1 --normalizeUsingRPKM --extendReads (deepTools v3.5.1)
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Oct 09, 2023 |
| Last update date |
Oct 13, 2023 |
| Contact name |
Emily Georgiades |
| Organization name |
Weatherall Institute of Molecular Medicine
|
| Street address |
John Radcliffe Hospital/Headley Way
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE244927 |
Active regulatory elements recruit cohesin to establish cell-specific chromatin domains [ATAC-seq] |
| GSE244929 |
Active regulatory elements recruit cohesin to establish cell-specific chromatin domains. |
|
| Relations |
| BioSample |
SAMN37736539 |
| SRA |
SRX22036894 |
