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Sample GSM7832133 Query DataSets for GSM7832133
Status Public on Oct 13, 2023
Title EB, day 7, R2-only, RAD21
Sample type SRA
 
Source name Erythroid
Organism Mus musculus
Characteristics cell type: Erythroid
origin cell_line: CD34+ human erythroid
differentiation day: Day 13
antibody: abcam, ab1546769
antibody lot_#: 1035529-4
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 Embryoid_body_day_7_CD71+_R2-only_RAD21_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
 
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 SAMN37736505
SRA SRX22037069

Supplementary file Size Download File type/resource
GSM7832133_R2only_CD71-EB_RAD21-ChIP_merged.bw 256.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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