|
Status |
Public on Mar 05, 2024 |
Title |
day235_CapIGseq_BCL2+CK_rep4 |
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-BCK4-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 |
SAMN40255057 |
SRA |
SRX23831381 |