|
| Status |
Public on Jan 11, 2020 |
| Title |
ESC-NPC line1 Chr7_APH_ExpA |
| Sample type |
SRA |
| |
|
| Source name |
Induced neural progenitor cells line 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6/129SVE
genotype: Xrcc4-/- p53-/-
treatment: APH
|
| Treatment protocol |
See details in Tena et al.; treatment of samples is indicated in "characteristics: treatment" column
|
| Growth protocol |
embryonic stem cells: DMEM medium (Corning, 10-013-CV) supplemented with 15% FBS
embryonic stem cells-derived neural progenitor cells : N2B27+ 1% B27 (without retinyl acetate) for differentiation and NBBG + 2% B27 (without retinyl acetate) for culture maintainance
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted overnight at 55 degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH 8.0, 0.2 mg/mL proteinase K, prior to DNA fragmentation
HTGTS: LAM-PCR-mediated HTGTS (Frock et al., 2015 and Hu et al., 2016; see manuscript for details)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
HTGTS
ESC-NPC_line1_chr7_APH
|
| Data processing |
Library strategy: LAM-HTGTS
HTGTS Miseq and Nextseq 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.
HTGTS reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
Best-path searching algorithm was used to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
The bait alignment must extend 10 nucleotides past the primer to avoid possible mispriming events and other artifacts
Potential duplicates were removed by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Reads with greater than 30bp gap between bait and prey sequences were filtered out.
Additional stringency was applied to post-filtered HTGTS junctions: reads with shorter than 50bp bait sequences were eliminated from downstream analysis due to potential artifacts; only one unique junctions at each location were preserved for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: HTGTS: tab delimited text files (translocation junctions) 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); cigar for bait sequence (B_Cigar); cigar for prey sequence (Cigar); the entire stitched paired end read sequence (Seq); 10 bp sequence around the junction, 5bp from bait and 5bp from prey (J_seq); barcode used for demultiplex (Barcode); number of unaligned sequences (unaligned); pass (0) or fail (1) the “Bait only” filter (baitonly); pass (0) or fail (1) the “Uncut” filter (uncut); number of nucleotides not aligned to the bait (misprimed); pass (0) or fail (1) the “Frequent cutter” filter (freqcut); number of nucleotides between bait and prey sequences (largegap); pass (0) or fail (1) the “Map quality” filter (mapqual); pass (0) or fail (1) the “Breaksite” filter (breaksite); pass (0) or fail (1) the “Sequential” filter (sequential); pass (0) or fail (1) the “Repeat sequence” filter (repeatseq); number of duplicates in this library (duplicate); and the experiment associated with the read (note).
|
| |
|
| Submission date |
Dec 18, 2019 |
| Last update date |
Jan 11, 2020 |
| Contact name |
Frederick W Alt |
| E-mail(s) |
jianqiao.hu@childrens.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
PCMM
|
| Lab |
Alt
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE142289 |
Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture [HTGTS-Seq] |
| GSE142315 |
Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture |
|
| Relations |
| BioSample |
SAMN13624527 |
| SRA |
SRX7409807 |
