|
| Status |
Public on Mar 23, 2020 |
| Title |
Mouse 1534 Igheavy chain Variable family 558 amplicon |
| Sample type |
SRA |
| |
|
| Source name |
mouse proB cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: primary proB cells
timepoint: 8 weeks
treatment: no treatment
genetic alteration: KO
pcr primer: Vh558
seqbatch: 185891a
|
| Treatment protocol |
no treatment
|
| Growth protocol |
proB cells were sorted from bone marrow of 8 week old mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using the Invitrogen PureLink Genomic DNA Kit and PCR was conducted. A 500bp fragment corresponding to Variable gene to JH4 Product was gel extracted with Qiagen gel extraction kit.
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA). platform (Illumina, San Diego, CA) with 150bp, paired-end reads.
Sequencing was done using the Illumina MiSeq, utilizing V2 chemistry.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
1534_V558
kept.cdr3s.csv
SRR9107707 corresponds to processed data file 1534_1534_296841w_NE4.clones.txt.
SRR9107708 corresponds to processed data file 1534_1534_298140w_BB3.clones.txt.
|
| Data processing |
MiXCR Version: 2.1.11; built=Fri Jun 15 06:30:50 CST 2018; rev=45d8571; lib=repseqio.v1.5
Command line arguments: align -s mmu -p rna-seq -OallowPartialAlignments=true -OvParameters.parameters.maxHits=1 -OdParameters.maxHits=1 -OjParameters.parameters.maxHits=1 -OvParameters.geneFeatureToAlign=VGeneWithP -OdParameters.geneFeatureToAlign=DRegionWithP -OjParameters.geneFeatureToAlign=JRegionWithP --report filname.log -f filename.r1.fq filename.r2.fq alignments.vdjca
Command line arguments: assemblePartial --report filename.log -f alignments.vdjca alignments_rescued_1.vdjca
Command line arguments: assemblePartial --report filename.log -f alignments_rescued_1.vdjca alignments_rescued_2.vdjca
Command line arguments: assemble --report filename.log -f alignments_rescued_2.vdjca clones.clns
Genome_build: None
Supplementary_files_format_and_content: [kept.cdr3s.csv] CSV of MiXCR output for all unique detected CDR3 clones, heavy chain locus, alignment scores
Supplementary_files_format_and_content: [clones.txt] TXT of detected clones per sample
Supplementary_files_format_and_content: https://mixcr.readthedocs.io/en/master/export.html#available-fields
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Mar 23, 2020 |
| Contact name |
Charlie Hatton |
| E-mail(s) |
Charles_Hatton@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Scott Armstrong/CPCT
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE131608 |
H3K36 methyltransferase SETD2 regulates lymphoid and neural development [MIXCR] |
| GSE131690 |
H3K36 methyltransferase SETD2 regulates NHEJ during lymphoid and neural development |
|
| Relations |
| BioSample |
SAMN11812324 |
| SRA |
SRX5882342 |
