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Sample GSM7025408 Query DataSets for GSM7025408
Status Public on Feb 19, 2024
Title GCB_CK_rep4 [CKDKO_R4]
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
cell type: GCB cell
genotype: CK_het_DKO
Treatment protocol Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before sorting GC B cells.
Extracted molecule genomic DNA
Extraction protocol 60,000 freshly sorted live cells were washed in cold PBS, lysed in 60 ul cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min on ice, followed by addition of 1 ml wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and centrifugation to pellet nuclei.
Bulk ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, nuclei were resuspended in a transposition reaction mix prepared using the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197) and incubated at 37 ÂșC for 30 minutes on thermomixer at 1,000 rpm to allow for transposition-based DNA fragmentation and adapter ligation. Tagged DNA fragments were purified using the Clean & Concentrator-5 Kit (ZYMO, D4014), then subjected to PCR amplification and double-sided bead purification (to remove primer dimers and larger than 1,000 bp fragments) using the AMPure XP beads (Beckman Coulter, A63881).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description CKDKO_R4.mLb.clN.bam
Data processing nfcore atac seq version 1.2.1
Assembly: mm10
Supplementary files format and content: Consensus Peak Counts
 
Submission date Feb 03, 2023
Last update date Feb 19, 2024
Contact name Christopher Russell Chin
E-mail(s) chc2077@med.cornell.edu
Phone 3393640514
Organization name Weill Cornell
Lab Melnick Lab
Street address 413 E 69th Street, Belfer Building, BB-1462
City New York City
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL24247
Series (2)
GSE224512 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas [ATAC-seq]
GSE224513 Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B-cell fate decisions and accelerates development of T-cell depleted lymphomas.
Relations
BioSample SAMN33059405
SRA SRX19279639

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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