|
Status |
Public on Oct 13, 2023 |
Title |
EB, day 7, WT, H3K27Ac |
Sample type |
SRA |
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Source name |
Erythroid
|
Organism |
Mus musculus |
Characteristics |
cell type: Erythroid origin cell_line: E14TG2a.IV mouse ES cells strain: 129/Ola differentiation day: Day 7 antibody: abcam, ab4729 antibody lot_#: GB3205523-1
|
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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Embryoid_body_day_7_CD71+_WT_H3K27Ac_ChIP-seq
|
Data processing |
genome build/assembly: mm39 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
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|
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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 |
GPL19057 |
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 |
SAMN37736504 |
SRA |
SRX22037070 |