|
| Status |
Public on Jul 01, 2020 |
| Title |
69947_Igh VDJ-Seq Pro-B cell Igh(+/+) |
| Sample type |
SRA |
| |
|
| Source name |
Pro-B cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Pro-B cell
genotype: Igh(+/+)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ex-vivo FACS sorted from bone marrow
DNA was sheared using the Bioruptor sonicator (Diagenode) and subjected to end-repair and A-tailing, followed by ligation of adapters containing 12 UMI sequences using the NEBNext Ultra II DNA library prep kit for Illumina (NEB). A primer extension step with biotinylated JH-specific primers generated the single-stranded DNA products that were captured using Dynabeads MyOne streptavidin T1 beads (Thermo Fisher Scientific) and PCR-amplified with nested JH-specific and adapter-binding primers. The llumina sequencing adapter primers including the indexes for multiplexing of libraries were added to the PCR products in a final PCR amplification step.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Igh VDJ-Seq Pro-B cell Igh(+/+)
|
| Data processing |
Library strategy: VDJ-seq
The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline:
preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline)
deduplicate.py (default parameters), based on UMI (BabrahamLinkOn pipeline)
assemble_clones.py (default parameters) (BabrahamLinkOn pipeline)
The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
Genome_build: MM10
Supplementary_files_format_and_content: txt (ascii text)
|
| |
|
| Submission date |
Nov 25, 2019 |
| Last update date |
Jul 02, 2020 |
| Contact name |
Meinrad Busslinger |
| E-mail(s) |
meinrad.busslinger@imp.ac.at
|
| Organization name |
IMP
|
| Lab |
Busslinger
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
A-1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE140975 |
Wapl repression by Pax5 promotes loop extrusion and V gene recombination at the Igh locus |
|
| Relations |
| BioSample |
SAMN13384204 |
| SRA |
SRX7213843 |
