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Sample GSM8124885 Query DataSets for GSM8124885
Status Public on Mar 05, 2024
Title day235_CapIGseq_BCL2+CK_rep3
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell line: N.A.
cell type: Germinal center B cell
genotype: BCL2+CK
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the PureLink genomic DNA mini kit (Invitrogen, cat# K182002) following the manual.
Briefly, 250 ng of DNA per sample was sheared to 250 bp segments using the Covaris LE220 and then subject to DNA library construction using the KAPA HyperPrep kit (Roche, cat# KK8502). We next followed the IDT xGen hybridization capture of DNA libraries protocol to capture the BCR VDJ fragments from the library using a custom probe set designed through the IDT xGen Hyb Panel design tool.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description MBM-00-BCK3-T0-D-DNA-capBCR
Data processing Raw data was processed following the MiXCR pipeline (DOI: 10.1038/nmeth.3364). the diversity of BCR repertoire, we used the iNEXT (version 3.0.0) R package.
Assembly: mm10
Supplementary files format and content: csv file including unique clone number, Shannon diversity score/group, Simpson clonality score/group for each sample
Library strategy: CapIG-seq (aka, B cell receptor sequencing)
 
Submission date Mar 04, 2024
Last update date Mar 05, 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)
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.
GSE260810 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 [CapIG-seq]
Relations
BioSample SAMN40255058
SRA SRX23831380

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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