|
| Status |
Public on Oct 13, 2023 |
| Title |
CD34, day 13, Don001, H3K4me3 |
| 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
antibody: Merck Millipore, 07-473
|
| Treatment protocol |
Cells were grown, treated and processed as described in the Methods section of the paper.
|
| Growth protocol |
Cells were grown, treated and processed as described in the Methods section of the paper.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown, treated and processed as described in the Methods section of the paper.
The NEBNext Ultra II DNA Library Prep Kit (New England Biolabs: NEB: 7645S/L) was used to prepare indexed sequencing libraries following the manufacturer supplied protocol. PCR amplification was performed for 7-11 cycles (depending on input DNA concentration) using NEBNext Mulitplex Oligos (New England Biolabs: E7335S/L and E7500S/L). Indexed sample concentration was quantified using the KAPA Library Quantification Complete Kit (Universal)(Roche: KK4824). Samples were pooled as a 2 nM or 4 nM library and sequenced with a high-Output v2 75 cycle kits on the Illumina NextSeq 500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Erythroid_day_13_CD34+_don001_H3K4me3_ChIP-seq
|
| 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) |
| GSE244925 |
Active regulatory elements recruit cohesin to establish cell-specific chromatin domains [ChIP-seq] |
| GSE244929 |
Active regulatory elements recruit cohesin to establish cell-specific chromatin domains. |
|
| Relations |
| BioSample |
SAMN37736514 |
| SRA |
SRX22037085 |
