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| Status |
Public on May 08, 2021 |
| Title |
Lig4_A1_Cas9_Rep2 |
| Sample type |
SRA |
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| Source name |
v-Abl pro B cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: Emu-Bcl2, Lig4-/-
clone: A1
cell cylce status: G1-arrested
treatment protocol: STI + nucleofection Cas9:c-Myc gRNA
target locus: c-Myc
illumina sequencing: Miseq
number of raw reads used for normalization: 396,387
pipeline used for the analysis: JoinT-seq / LAM-HTGTS / HTGTS-Rep-Rejoin
figure displaying results for this library: 1, S2
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| Treatment protocol |
G1-arrested cells were treated with STI-571 (3µM) for 96h, nucleofection of Cas9:c-Myc gRNA or doxycycline-inducing treatment (2µg/ml) was added to some of the samples
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| Growth protocol |
v-Abl pro-B cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 15% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Nextseq sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Library strategy: JoinT-seq / LAM-HTGTS / HTGTS-Rep-ReOther: Join
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm10 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
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| Submission date |
Dec 01, 2020 |
| Last update date |
May 08, 2021 |
| Contact name |
Marie Le Bouteiller |
| E-mail(s) |
marie.lebouteiller@gmail.com
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| Organization name |
Stanford University
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| Department |
Radiation Oncology
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| Street address |
269 campus drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE162453 |
Ku70 and Ligase IV deficiencies reveal distinct alternative end-joining outcomes in G1-arrested progenitor B cells |
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| Relations |
| BioSample |
SAMN16970779 |
| SRA |
SRX9615411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4952244_VK245_Alt304_HTGTS_Rep_Rejoin.txt.gz |
8.7 Kb |
(ftp)(http) |
TXT |
| GSM4952244_VK245_Alt304_JoinT.txt.gz |
10.0 Kb |
(ftp)(http) |
TXT |
| GSM4952244_VK245_Alt304_LAM_HTGTS.txt.gz |
8.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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