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Sample GSM2183853 Query DataSets for GSM2183853
Status Public on Jul 22, 2016
Title proB_mouse2_BL6
Sample type SRA
 
Source name proB_mouse2_BL6
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wild-type
bait locus: JH4
growth protocol: No immunization
age: 4-6 weeks
cell type: progenitor B
primer strategy: Individual
dna amount: 2 ug
Treatment protocol No immunization, but the food and water are not germ-free
Growth protocol Mice were bought from Jackson labs and kept in our mouse facility
Extracted molecule genomic DNA
Extraction protocol Tissues were extracted and treated with RBC lysis, resuspended in PBS, and stained for FACS. Bone marrow-derived pro-B (B220+IgM-CD43+) cells were purified from 129SVE or C57BL/6 mice by sorting and after the depletion of erythrocytes. Single cell suspensions were stained with B220-APC, CD43-PE, and IgM-FITC antibodies. Splenic resting B cells were purified using biotin/streptavidin bead methods (B220 positive selection) or EasySep CD43-negative B cell selection. Cells were then processed for genomic DNA extraction.
Libraries were prepared via HTGTS-Rep-seq protocols
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description Sample 2
Barcode: GCCAAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait
Data processing HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends; Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Paire-end sequenced reads were trimmed for barcode and adaptor sequence and joined
The trimmed reads then were searched against VDJ gene databases using igblast1.5 with default parameters and further processed by the HTGTSrep pipeline, or against LAM-HTGTS pipeline with default settings.
For HTGTSrep pipeline, reads can successfully aligned to V, D, J databases are reported and a statistic report including V gene usage and in-frame/non-productive information is created by the pipeline.
Genome_build: mm9, mm9_AJ851868ins (Based on the genome build of mm9, we replaced its chr12 between 114,493,850 and 115,696,909 with the reverse complement sequence of the GeneBank AJ851868.3)
Supplementary_files_format_and_content: tab-delimited text files include aligned V, D, J genes for each read and a V usage report for each sample.
 
Submission date Jun 01, 2016
Last update date May 15, 2019
Contact name Jiazhi Hu
E-mail(s) heartlead@gmail.com
Organization name Children's Hospital Boston
Department PCMM
Lab Frederick Alt
Street address 300 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL16417
Series (1)
GSE82126 A Highly Sensitive and Unbiased Approach for Elucidating Antibody Repertoires
Relations
BioSample SAMN05194899
SRA SRX1814813

Supplementary file Size Download File type/resource
GSM2183853_proB_mouse2_BL6.pass.xls.gz 1.2 Mb (ftp)(http) XLS
GSM2183853_proB_mouse2_BL6_DJ.tlx.txt.gz 777.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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