title: JH1_DFL16.1replaceDQ52_JH1bait_rep2

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-replace-DQ52 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DFL16.1-replace-DQ52
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1, Emu-Bcl2


title: JH1_DFL16.1replaceDQ52_JH1bait_rep3

status: Public on Aug 19 2019

type: SRA

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

country: USA

institute: Boston Children's Hospital

description: aligned to modified mm9 genome with DQ52 replaced by DFL16.1

library_source: genomic

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-replace-DQ52 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-replace-DQ52
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

molecule: genomic DNA

organism: Mus musculus

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.

treatment_protocol: RAG2 retrovirally complemented and then 3 uM STI-571 treated for 4 days for RAG2 deficient v-Abl pro-B cells.

tag: cell type

value: v-Abl transformed pro-B cell line

tag: genotype

value: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52inv_replaceDFL16.1_JH1bait_rep1

description: aligned to modified mm9 genome with DFL16.1 replaced by DQ52 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DQ52inv-replace-DFL16.1 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52inv-replace-DFL16.1
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DQ52-del, DFL16.1 replaced by DQ52-inv, Emu-Bcl2, RAG2 deficient


title: JHdel_DQ52RSSDNbait_rep3

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: JH-del, Emu-Bcl2, RAG2 deficient


title: JH1_DFL16.1inv_replaceDQ52_JH1bait_rep2

description: aligned to modified mm9 genome with DQ52 replaced by DFL16.1 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1inv-replace-DQ52 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1inv-replace-DQ52
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DFL16.1-del, DQ52 replaced by DFL16.1 inversion, Emu-Bcl2, RAG2 deficient


title: JHdel_DQ52RSSDNbait_rep1

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JH1_DQ52replaceDFL16.1_JH1bait_rep1

description: aligned to modified mm9 genome with DFL16.1 replaced by DQ52

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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  mm9_DQ52-replace-DFL16.1 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.
We used a best-path searching algorithm 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52-replace-DFL16.1
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DQ52-del, DFL16.1 replaced by DQ52, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52_inv_JH1bait_rep3

description: aligned to modified mm9 genome with DQ52 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DQ52-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DQ52-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, DQ52 inversion, Emu-Bcl2, RAG2 deficient


title: JH1_intervening_DH_inv_JH1bait_rep2

description: aligned to modified mm9 genome with intervening DH inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_intervening-DH-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_intervening-DH-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH1+/-, intervening DH inversion, Emu-Bcl2, RAG2 deficient


title: JH1_intervening_DH_inv_JH1bait_rep1


title: JH1_intervening_DH_inv_JH1bait_rep3


title: JH1_DQ52_inv_JH1bait_rep2

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DQ52-inversion 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.
We used a best-path searching algorithm 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JH1 _JH1bait_set2_rep3

description: aligned to mm9 genome

value: DH-JH1+/-, Emu-Bcl2, RAG2 deficient


title: JH1_DQ52_inv_JH1bait_rep1


title: JH1_DQ52inv_replaceDFL16.1_JH1bait_rep2

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DQ52inv-replace-DFL16.1
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JH1 _JH1bait_set2_rep2

description: aligned to mm9 genome


title: JH1 _JH1bait_set2_rep1

description: aligned to mm9 genome


title: JH1 _JH1bait_set1_rep3

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JH1 _JH1bait_set1_rep2

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: DHJH_DFL16.1_inv_JH1bait_rep3

description: aligned to modified mm9 genome with DFL16.1 inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DFL16.1-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH+/-, DFL16.1 inversion, Emu-Bcl2, RAG2 deficient


title: DHJH_DFL16.1_inv_JH1bait_rep5

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: JH1 _JH1bait_set1_rep1

description: aligned to mm9 genome


title: DHJH_DFL16.1_inv_JH1bait_rep1

data_processing:
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: DHJH_DFL16.1RSSDN_inv_JH1bait_rep2

description: aligned to modified mm9 genome with DFL16.1-RSS-DN inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-RSS-DN-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-RSS-DN-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH+/-, DFL16.1-RSS-DN inversion, Emu-Bcl2, RAG2 deficient


title: DHJH_DFL16.1RSSUP_inv_JH1bait_rep3

description: aligned to modified mm9 genome with DFL16.1-RSS-UP inversion

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-RSS-UP-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-RSS-UP-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH+/-, DFL16.1-RSS-UP inversion, Emu-Bcl2, RAG2 deficient


title: DHJH_JH1bait_set1_rep2

description: aligned to mm9 genome

value: DH-JH+/-, Emu-Bcl2, RAG2 deficient


title: DHJH_JH1bait_set2_rep1

description: aligned to mm9 genome


title: DHJH_DFL16.1_inv_JH1bait_rep4


title: DHJH_JH1bait_set1_rep1

description: aligned to mm9 genome


title: DHJH_JH1bait_set2_rep3

description: aligned to mm9 genome


title: DHJH_DFL16.1RSSDN_inv_JH1bait_rep3

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-RSS-DN-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build:mm9_DFL16.1-RSS-DN-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: DHJH_DFL16.1RSSUP_inv_JH1bait_rep2

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DFL16.1-RSS-UP-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

value: DH-JH+/-, DFL16.1-RSS-UP inversion, Emu-Bcl2


title: DHJH_DFL16.1RSSDN_inv_JH1bait_rep1

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-RSS-DN-inversion 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomolgoy larger than 5 bp.
Genome_build: mm9_DFL16.1-RSS-DN-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: DHJH_DFL16.1RSSUP_inv_JH1bait_rep1

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 mm9_DFL16.1-RSS-UP 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9_DFL16.1-RSS-UP-inversion
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)


title: ino80-8_air_rep2_RNA-seq

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
RNA expression
MZ39_ino80_2
RNA-seq2.tsv

library_source: transcriptomic

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.25
Genome_build: TAIR10

molecule: total RNA

organism: Arabidopsis thaliana

source_name: etiolated seedlings

growth_protocol: etiolated seedlings

extract_protocol:
Qiagen Rneasy Plant Mini kit
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hydrocarbon-free air for three days, 4 hours of ethylene treatmentwhen indicated

tag: tissue

value: etiolated seedlings

tag: treatment

value: air


title: ino80-8_air_rep1_RNA-seq

description:
RNA expression
MZ38_ino80_1
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.24
Genome_build: TAIR10


title: arp5-1_air_rep2_RNA-seq

description:
RNA expression
arp5_2
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.27
Genome_build: TAIR10


title: arp5-1_air_rep1_RNA-seq

description:
RNA expression
arp5_1
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.26
Genome_build: TAIR10


title: een-2_air_rep2_RNA-seq

description:
RNA expression
MZ37_een_2
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.23
Genome_build: TAIR10


title: DHJH_JH1bait_set1_rep3

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq 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 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.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads 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. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
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.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9
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); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.


title: DHJH_JH1bait_set2_rep2

description: aligned to mm9 genome


title: een-2_air_rep1_RNA-seq

description:
RNA expression
MZ36_een_1
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.22
Genome_build: TAIR10


title: DHJH_DFL16.1_inv_JH1bait_rep2


title: Col-0_air_rep2_RNA-seq

description:
RNA expression
MZ33_Col_1
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.21
Genome_build: TAIR10


title: ein2-45_ET_rep2_RNA-seq

description:
RNA expression
RNA_MZ20
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.19
Genome_build: TAIR10

value: 4 hours ET


title: ein2-45_air_rep1_RNA-seq

description:
RNA expression
RNA_MZ17
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.16
Genome_build: TAIR10


title: ein6-1 een-1_ET_rep2_RNA-seq

description:
RNA expression
RNA_MZ16
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.15
Genome_build: TAIR10

value: ein6-1 een-1


title: ein6-1 een-1_air_rep2_RNA-seq

description:
RNA expression
RNA_MZ14
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.13
Genome_build: TAIR10


title: ein6-1 een-1_ET_rep1_RNA-seq

description:
RNA expression
RNA_MZ15
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.14
Genome_build: TAIR10


title: ein6-1 een-1_air_rep1_RNA-seq

description:
RNA expression
RNA_MZ13
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.12
Genome_build: TAIR10


title: een-1_ET_rep1_RNA-seq

description:
RNA expression
RNA_MZ11
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.10
Genome_build: TAIR10


title: Sample 1: Control cy3 vs E. coli challenged cy5 for 3h

status: Public on Aug 20 2019

type: RNA

city: Tsukuba

first: Yuki

last: Nakamura

state: Ibaraki

address: 1-1 Owashi

country: Japan

institute: National Institute of Agrobiololgical Sciences

description: Biological replicate 1 of 3 in 3h.

hyb_protocol: Hybridization was performed with 825 ng of Cy3- and Cy5-labeled cRNA with Hi-RPM Gene Expression Hybridization Kit (Agilent) at 65 ˚C for 17 h at 10 rpm.

scan_protocol: The hybridized arrays were washed with Wash Buffer Kit (Agilent) following manufacturer's instructions. Images were scanned at 5 µm resolution using Agilent DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

organism: Nephotettix cincticeps

source_name: Control

label_protocol: Each 400 ng of total RNA was labeled with Quick Amp Labeling Kit, two colour (Agilent) following manufacturer's instructions. Labeled cRNA was purified with RNeasy Mini kit.

growth_protocol: N. cincticeps Tsukuba strain were reared with rice seedlings in the laboratory at 25-26 degree and 16L-8D.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: One day adult N. cincticeps females were pricked with about 1,500 E. coli cells with a glass needle. Control adults were pricked with sterilized water. Five females were collected up to one sample. Total RNA was extracted after 3 h and 12 h incubation respectively.

tag: strain

value: Tsukuba

tag: age

value: One day adult

source_name: E. coli challenged for 3 hours


title: ein6-1_air_rep2_RNA-seq

description:
RNA expression
RNA_MZ6
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.5
Genome_build: TAIR10


title: een-1_air_rep1_RNA-seq

description:
RNA expression
RNA_MZ9
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.8
Genome_build: TAIR10


title: ein6-1_ET_rep1_RNA-seq

description:
RNA expression
RNA_MZ7
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.6
Genome_build: TAIR10


title: ein6-1_ET_rep2_RNA-seq

description:
RNA expression
RNA_MZ8
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.7
Genome_build: TAIR10


title: ein6-1 een-1_3d_air_MethylC-seq

description:
DNA methylation
bisulfite converted DNA
allc_MZ_S15.tsv

data_processing:
base-calling using RTA 2.7.8; alignment using methpip_se map w/ Bowtie 0.12.7; mC calling using methylpy 1.2.9
Genome_build: TAIR10

extract_protocol:
DNeasy Plant Mini Kit
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment


title: Ler_ET_rep1_RNA-seq

description:
RNA expression
RNA_MZ3
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.2
Genome_build: TAIR10

value: Ler


title: een-1_3d_air_MethylC-seq

description:
DNA methylation
bisulfite converted DNA
allc_MZ_S14.tsv


title: Ler_air_rep1_RNA-seq

description:
RNA expression
RNA_MZ1
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.0
Genome_build: TAIR10


title: 4_LIPUS-3 h: Low-intensity pulsed ultrasound (LIPUS)-3 h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: ST2 cells were with LIPUS for 20 min followed by culturing at 37°C for 3 h

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

label: biotin

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: Mouse ST2 bone marrow stromal cells were used. The cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2.

extract_protocol: Total RNA was extracted from cells using a NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: Low-intensity pulsed ultrasound (LIPUS) was applied by an ultrasound irradiating system, which consists of an irradiator SCI-p1-35 (Medical Ultrasound Co., Ltd., Tokyo Japan) with a ceramic transducer (28 mm dia., 2 mm thickness) and SCI-D100 driving equipment (Medical Ultrasound Co., Ltd.). The cells treated with LIPUS (25 mW/cm2 for 20 min), then cultured at 37°C for 0.5, 1 and 3 h.

value: BALB/c

value: Mouse ST2 bone marrow stromal cells

value: bone marrow

tag: life span

value: infinite

tag: morphology

value: fibroblast-like


title: ein6-1_3d_air_MethylC-seq

description:
DNA methylation
bisulfite converted DNA
allc_MZ_S13.tsv


title: Ler_3d_air_MethylC-seq

description:
DNA methylation
bisulfite converted DNA
allc_MZ_S12.tsv


title: ein2-45_air_rep2_RNA-seq

description:
RNA expression
RNA_MZ18
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.17
Genome_build: TAIR10


title: Col-0_air_rep1_RNA-seq

description:
RNA expression
MZ32_Col_1
RNA-seq2.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.20
Genome_build: TAIR10


title: ein2-45_ET_rep1_RNA-seq

description:
RNA expression
RNA_MZ19
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.18
Genome_build: TAIR10


title: 3_LIPUS-1 h: Low-intensity pulsed ultrasound (LIPUS)-1 h

description: ST2 cells were with LIPUS for 20 min followed by culturing at 37°C for 1 h


title: ein6-1 een-1_3d_air_H3K27me3/H2A.Z_ChIP-reChIP-seq

description:
histone modification/variant
ChIP-seq (Swift BioSciences)
57_38.bw

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare
Genome_build: TAIR10

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared with the Accel-NGS 2S Plus DNA Library Kit (21024, Swift Biosciences).

tag: antibodies

value: H3K27me3 (Active Motif, 39156), H2A.Z (Active Motif, 39647)


title: 2_LIPUS-0.5 h: Low-intensity pulsed ultrasound (LIPUS)-0.5 h

description: ST2 cells were with LIPUS for 20 min followed by culturing at 37°C for 0.5 h

value: Mouse ST2 bone marrow stromal cells9


title: een-1_ET_rep2_RNA-seq

description:
RNA expression
RNA_MZ12
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.11
Genome_build: TAIR10


title: ein6-1 een-1_3d_air_H3K27me3/IgG_ChIP-reChIP-seq

description:
histone modification/control
ChIP-seq (Swift BioSciences)
56_38.bw

value: no

value: H3K27me3 (Active Motif, 39156), mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: 1_Ctr: Control

description: ST2 cells were cultured at 37°C

source_name: ST2 cells were cultured at 37°C


title: ein6-1_air_rep1_RNA-seq

description:
RNA expression
RNA_MZ5
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.4
Genome_build: TAIR10


title: Ler_ET_rep2_RNA-seq

description:
RNA expression
RNA_MZ4
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.3
Genome_build: TAIR10


title: Ler_10d_seedlings_IgG

description: control

data_processing: Genome_build: TAIR10

source_name: de-etiolated seedlings

growth_protocol: etiolated seedlings were grown on Linsmaier and Skoog medium supplemented with 1% sucrose

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hydrocarbon-free air for three days, 4 hours of ethylene treatment when indicated

value: de-etiolated seedlings

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: ein6-1 een-1_3d_shoots_H3K27me3

description:
histone modification
ein6een_shoot_K27_IgG.bw

source_name: shoots from etiolated seedlings

value: shoots from etiolated seedlings

value: H3K27me3 (Active Motif, 39156)


title: ein6-1 een-1_3d_roots_H3K27me3

description:
histone modification
ein6een_root_K27_IgG.bw

source_name: roots from etiolated seedlings

value: roots from etiolated seedlings

value: ein6-1 een-1


title: een-1_air_rep2_RNA-seq

description:
RNA expression
RNA_MZ10
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.9
Genome_build: TAIR10

value: etiolated seedlings

value: air


title: Ler_3d_shoots_H3K27me3

description:
histone modification
Ler_shoot_K27_IgG.bw

value: Ler


title: Ler_3d_roots_H3K27me3

description:
histone modification
Ler_root_K27_IgG.bw


title: ein6-1 een-1_seeds_H3K27me3

description:
histone modification
ein6een_seed_K27_IgG.bw

source_name: dry seeds

value: dry seeds


title: Ler_seeds_H3K27me3

description:
histone modification
Ler_seed_K27_IgG.bw


title: Ler_3d_roots_IgG

description: control


title: Ler 35S:EIN6-FLAG_3d_air_rep2

description:
EIN6
triple_IgG.bw

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; SAMtools merge; bam file comparison using deepTools2.0/bamCompare; data extraction using bigWigAverageOverBed
Genome_build: TAIR10

value: Ler 35S:EIN6-FLAG

value: FLAG (Millipore Sigma, F1804)


title: Ler 35S:EIN6-FLAG_3d_air_rep1

description:
EIN6
triple_IgG.bw


title: Col-0 HTA11:HTA11-GFP_3d_air_GFP

description:
histone variant
60_IgG.bw

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare; data extraction using bigWigAverageOverBed
Genome_build: TAIR10

value: Col-0 HTA11:HTA11-GFP

value: GFP (Millipore Sigma, 11814460001)


title: Ler 35S:EIN6-FLAG_3d_air_rep3

description:
EIN6
triple_IgG.bw


title: Col-0 35S:EEN-FLAG_3d_air_IgG

description: control

value: Col-0 35S:EEN-FLAG


title: Col-0 HTA11:HTA11-GFP_3d_air_H2A.Z

description:
histone variant
61_IgG.bw

value: H2A.Z (Active Motif, 39647)


title: ein6-1 een-1_siliques_H3K27me3

description:
histone modification
ein6een_silique_K27_IgG.bw

source_name: siliques

value: siliques

value: no


title: Ler_flowers_H3K27me3

description:
histone modification
Ler_flower_K27_IgG.bw

source_name: flowers

value: flowers


title: Ler_siliques_H3K27me3

description:
histone modification
Ler_silique_K27_IgG.bw


title: Col-0_3d_air_IgG_(ET)

description: control

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: ein6-1 een-1_flowers_H3K27me3

description:
histone modification
ein6een_flower_K27_IgG.bw

value: H3K27me3 (Active Motif, 39156)


title: Col-0 (pie1-1)_3d_air_H2A.Z

description:
histone variant
Col_pie1_IgG.bw


title: ino80-8_3d_ET_H2A.Z_(ET)

description:
histone variant
09_ino80-8_7_6.bw

value: 4 hours ET


title: Ler_3d_shoots_IgG

description: control

value: shoots from etiolated seedlings


title: ino80-8_3d_air_H2A.Z_(ET)

description:
histone variant
09_ino80-8_7_6.bw

value: etiolated seedlings


title: Col-0 35S:EEN-FLAG_3d_air_rep2

description:
EEN
S_1.bw

value: air


title: Col-0_3d_air_H2A.Z_(ET)

description:
histone variant
09_Col_3_1.bw


title: Ler_3d_air_IgG_rep3

description: control

value: Ler


title: Col-0_3d_ET_H2A.Z_(ET)

description:
histone variant
09_Col_3_1.bw


title: Ler_3d_ET_H3K27me3_rep2

description:
histone modification
12_2_35.bw


title: Ler_3d_ET_H3K27me3_rep3

description:
histone modification
01_5_13.bw


title: Col-0 35S:EEN-FLAG_3d_air_rep1

description:
EEN
3_1.bw


title: Ler_3d_ET_H3K27me3_rep1

description:
histone modification
05_2_11.bw


title: Ler_3d_air_H3K27me3_rep3

description:
histone modification
01_1_13.bw


title: Ler_3d_air_IgG(rep3,rep4,rep5)

description: control


title: Ler_3d_ET_H2A.Z_rep4

description:
histone modification
5_13.bw


title: Ler_3d_ET_H2A.Z_rep5

description:
histone modification
6_13.bw


title: Ler_3d_air_H2A.Z_rep5

description:
histone modification
3_13.bw


title: Ler_3d_ET_H2A.Z_rep3

description:
histone modification
4_13.bw


title: Ler_3d_air_H2A.Z_rep4

description:
histone modification
2_13.bw


title: Ler_3d_air_H2A.Z_rep3

description:
histone modification
1_13.bw


title: pie1-1_3d_air_H2A.Z

description:
histone variant
pie1_IgG.bw


title: een-1_3d_ET_H2A.Z_rep2

description:
histone modification
een_H2AZmerge_ETvsair.bw


title: Ler_3d_ET_H2A.Z_rep2

description:
histone modification
Ler_H2AZmerge_ETvsair.bw


title: Col-0 (pie1-1)_3d_air_IgG

description: control


title: een-1_3d_ET_H2A.Z_rep1


title: Ler_3d_ET_H2A.Z_rep1


title: ref6-1 ino80-1_3d_air_H2A.Z

description:
histone variant
15_IgG.bw


title: ref6-1 arp5-1_3d_air_H2A.Z

description:
histone variant
17_IgG.bw

value: ref6-1 arp5-1


title: ino80-1_3d_air_H2A.Z

description:
histone variant
14_IgG.bw


title: Col-0_3d_air_IgG

description: control


title: arp5-1_3d_air_H2A.Z

description:
histone variant
16_IgG.bw


title: ref6-1 een-2_3d_air_H2A.Z

description:
histone variant
13_IgG.bw

value: ref6-1 een-2


title: ref6-1 arp5-1_3d_air_H3K27me3

description:
histone modification
8_IgG.bw


title: ref6-1_3d_air_H2A.Z

description:
histone variant
11_IgG.bw


title: een-2_3d_air_H2A.Z

description:
histone variant
48_IgG.bw


title: arp5-1_3d_air_H3K27me3

description:
histone modification
7_IgG.bw


title: ref6-1 een-2_3d_air_H3K27me3

description:
histone modification
4_IgG.bw


title: ino80-1_3d_air_H3K27me3

description:
histone modification
5_IgG.bw


title: Col-0_3d_air_H3K27me3

description:
histone modification
1_IgG.bw


title: Ler_IgG_(H3K4me3/H2Aub)

description: control


title: een-1_3d_air_H3K4me3

description:
histone modification
een_H3K4me3.bw

value: H3K4me3 (EMD Millipore, 04-745)


title: Ler_3d_air_H2Aub

description:
histone modification
Ler_H2Aub.bw

value: H2Aub (Cell Signaling Technology, 8240)


title: ein6-1_3d_air_H2Aub

description:
histone modification
ein6_H2Aub.bw


title: een-1_3d_air_H2Aub

description:
histone modification
een_H2Aub.bw


title: ein6-1 een-1_3d_air_H3K4me3

description:
histone modification
ein6een_H3K4me3.bw

value: ein6-1 een-1


title: Ler_3d_air_H3K4me3

description:
histone modification
Ler_H3K4me3.bw


title: ein6-1_3d_air_H3K4me3

description:
histone modification
ein6_H3K4me3.bw


title: Ler_3d_air_IgG_rep2

description: control


title: ein6-1 een-1_3d_air_H2Aub

description:
histone modification
ein6een_H2Aub.bw


title: ein6-1 een-1_3d_air_H2A.Z_rep2

description:
histone variant
ein6een_IgG_H2AZ.bw


title: een-1_3d_air_H2A.Z_rep2

description:
histone variant
een_IgG_H2AZ.bw


title: ein6-1_3d_air_H2A.Z_rep2

description:
histone variant
ein6_IgG_H2AZ.bw


title: Ler_3d_air_H2A.Z_rep2

description:
histone variant
Ler_IgG_H2AZ.bw


title: ein6-1 een-1_3d_air_H3K27me3_rep2

description:
histone modification
ein6een_IgG_merge.bw


title: Ler_3d_air_H3K27me3_rep2

description:
histone modification
Ler_IgG_merge.bw
12_1_35.bw


title: een-1_3d_air_H3K27me3_rep2

description:
histone modification
een_IgG_merge.bw


title: ref6-1 ino80-1_3d_air_H3K27me3

description:
histone modification
6_IgG.bw


title: een-1_3d_air_H2A.Z_rep1

description:
histone variant
een_IgG_H2AZ.bw


title: een-2_3d_air_H3K27me3

description:
histone modification
2_IgG.bw


title: Ler_3d_air_IgG_rep1

description: control


title: ein6-1 een-1_3d_air_H3K27me3_rep1


title: Col-0_3d_air_H2A.Z

description:
histone variant
10_IgG.bw


title: ein6-1_3d_air_H3K27me3_rep2

description:
histone modification
ein6_IgG_merge.bw


title: Ler_3d_air_H2A.Z_rep1

description:
histone variant
Ler_IgG_H2AZ.bw


title: ein6-1_3d_air_H2A.Z_rep1

description:
histone variant
ein6_IgG_H2AZ.bw


title: ein6-1 een-1_3d_air_H2A.Z_rep1

description:
histone variant
ein6een_IgG_H2AZ.bw


title: ref6-1_3d_air_H3K27me3

description:
histone modification
51_IgG.bw


title: een-1_3d_air_H3K27me3_rep1

description:
histone modification
een_IgG_merge.bw


title: ein6-1_3d_air_H3K27me3_rep1

description:
histone modification
ein6_IgG_merge.bw


title: Ler_3d_air_H3K27me3_rep1

description:
histone modification
Ler_IgG_merge.bw
05_1_11.bw


title: Human cadaveric islet TSQ+ PI- 2NBDG Hi (S7)

city: Cambridge

first: Jeffrey

last: Davis

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
.fastq files were transferred to the Harvard Odyssey computing cluster and trimmed using the Trimmomatic method
Trimmed reads were concatenated and aligned using RSEM and the Homo Sapients GRCh38.dna assembly
Aligned reads were normalized and compiled using Trinity's standard RSEM pipeline and DEseq2
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: TSV file of Transcripts per Million (TMM)

organism: Homo sapiens

source_name: Human Islets

growth_protocol: Cells were grown in the same protocol published by Pagliuca et. al. 2014

extract_protocol:
Dissociation in Accutase and Passing through a needle to dissociate was performed for transplanted cells or accutase dissociation only for in vitro cells
Illumina Nextera XT2 prep

tag: genetic background

value: Human Donor

tag: experimental condition

value: in vitro

value: Human Islet Cells


title: Human cadaveric islet TSQ+ PI- 2NBDG Hi (S5)


title: Human cadaveric islet TSQ+ PI- 2NBDG Hi (S10)


title: SC-beta in vivo TSQ+ PI- GFP+ (S24)

source_name: Post-Transplant

value: in vivo

value: iPS Cells

tag: time

value: Post-Transplant


title: Human cadaveric islet TSQ+ PI- 2NBDG Hi (S18)


title: SC-beta in vivo TSQ+ PI- GFP+ (S23)


title: SC-beta in vivo TSQ+ PI- GFP+ (S22)


title: SC-beta in vivo TSQ+ PI- GFP+ (S16)


title: SC-beta in vivo TSQ+ PI- GFP+ (S21)


title: SC-beta in vivo TSQ+ PI- GFP+ (S14)


title: SC-beta in vivo TSQ+ PI- GFP+ (S12)


title: SC-beta in vitro TSQ+ PI- GFP+ (S4)

source_name: Pre-Transplant

value: Pre-Transplant


title: SC-beta in vitro TSQ+ PI- GFP+ (S2)


title: SC-beta in vitro TSQ+ PI- GFP+ (S3)


title: M8

city: Worcester

first: Silvia

last: Corvera

address: 373 Plantation St

institute: University of Massachusetts Medical School

description: processed data file: TPM.txt

data_processing:
The FASTQ files obtained were de-multiplexed using SMART-Seq DE3 Demultiplexing Software by Clontech.
Bowtie was used to align the reads to the human genome assembly hg19.
The aligned reads were then processed by RSEM to generate un-normalized and TPM counts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM.txt: Tab-delimited text file includes TPM values for each sample.

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA extraction was performed using NucleoSpin RNA XS kit (Clontech Laboratories Inc. Cat. No. 740902). Briefly, cells were detached as mentioned in previous section, snap frozen in liquid nitrogen and stored at -80oC overnight. Next day, RNA was prepared from a total of 168 samples across three conditions (C, M and F) according to the manufacturer’s instructions.
cDNA library was prepared using SMART-Seq v4 3’ DE kit according to the manufacturer’s instructions (Clontech Laboratories Inc. Cat. No. 635040). For each clone, 1 ng of total RNA was used as input to synthesize cDNA which was subsequently amplified. Control RNA was provided with the kit. All samples were processed concurrently during library preparation. Prior to purification, the amplified cDNA’s were grouped in fourteen pools of twelve samples each with a unique barcode (Clonetech Oligo dT in-line indexes or IL 1-12) ligated to the 3’end during cDNA synthesis. Pooled and purified libraries were fragmented using Nextera XT DNA Sample Preparation Kit (Illumina, Cat. Nos. FC-131-1024, FC-131- 1096). Illumina sequencing indexes (provided with the SMART-Seq v4 3’ DE kit) were added to the fragmented libraries and indexed libraries were amplified. For intermittent purification steps, Agencourt AMPure XP PCR purification kit (5 ml Beckman Coulter Part No. A63880; 60 ml Beckman Coulter Part No. A63881) was used.

value: Subcutaneous adipose tissue-derived mesenchymal progenitor cells

tag: condition

value: M


title: M78

description: processed data file: TPM.txt


title: SC-beta in vitro TSQ+ PI- GFP+ (S1)


title: M81

description: processed data file: TPM.txt


title: M82

description: processed data file: TPM.txt


title: M75

description: processed data file: TPM.txt


title: M69

description: processed data file: TPM.txt


title: M70

description: processed data file: TPM.txt


title: M71

description: processed data file: TPM.txt


title: M7

description: processed data file: TPM.txt


title: M61

description: processed data file: TPM.txt


title: M6

description: processed data file: TPM.txt


title: M51

description: processed data file: TPM.txt


title: M59

description: processed data file: TPM.txt


title: M56

description: processed data file: TPM.txt


title: SC-beta in vitro TSQ+ PI- GFP+ (S9)


title: M54

description: processed data file: TPM.txt


title: M43

description: processed data file: TPM.txt


title: M50

description: processed data file: TPM.txt


title: M57

description: processed data file: TPM.txt


title: M44

description: processed data file: TPM.txt


title: M40

description: processed data file: TPM.txt


title: M36

description: processed data file: TPM.txt


title: M38

description: processed data file: TPM.txt


title: M5

description: processed data file: TPM.txt


title: M37

description: processed data file: TPM.txt


title: M4

description: processed data file: TPM.txt


title: M39

description: processed data file: TPM.txt


title: M32

description: processed data file: TPM.txt


title: M34

description: processed data file: TPM.txt


title: M30

description: processed data file: TPM.txt


title: M29

description: processed data file: TPM.txt


title: M28

description: processed data file: TPM.txt


title: M26

description: processed data file: TPM.txt


title: M31

description: processed data file: TPM.txt


title: M3

description: processed data file: TPM.txt


title: M27

description: processed data file: TPM.txt


title: M25

description: processed data file: TPM.txt


title: Ler_air_rep2_RNA-seq

description:
RNA expression
RNA_MZ2
RNA-seq1.tsv

data_processing:
base-calling using RTA 2.7.9; alignment using STAR_2.6.0c; transcript quantification (TPM) using RSEM v1.3.1
Genome_build: TAIR10

value: etiolated seedlings


title: M24

description: processed data file: TPM.txt


title: M23

description: processed data file: TPM.txt


title: M22

description: processed data file: TPM.txt


title: M21

description: processed data file: TPM.txt


title: M18

description: processed data file: TPM.txt


title: M17

description: processed data file: TPM.txt


title: M19

description: processed data file: TPM.txt


title: M15

description: processed data file: TPM.txt


title: M14

description: processed data file: TPM.txt


title: M12

description: processed data file: TPM.txt


title: M11

description: processed data file: TPM.txt


title: M13

description: processed data file: TPM.txt


title: M102

description: processed data file: TPM.txt


title: M1

description: processed data file: TPM.txt


title: F82

description: processed data file: TPM.txt

value: F


title: M10

description: processed data file: TPM.txt


title: F81

description: processed data file: TPM.txt


title: F75

description: processed data file: TPM.txt


title: F71

description: processed data file: TPM.txt


title: F8

description: processed data file: TPM.txt


title: F78

description: processed data file: TPM.txt


title: F69

description: processed data file: TPM.txt


title: F61

description: processed data file: TPM.txt


title: F59

description: processed data file: TPM.txt


title: F57

description: processed data file: TPM.txt


title: F54

description: processed data file: TPM.txt


title: F56

description: processed data file: TPM.txt


title: F7

description: processed data file: TPM.txt


title: M20

description: processed data file: TPM.txt


title: F51

description: processed data file: TPM.txt


title: F6

description: processed data file: TPM.txt


title: F50

description: processed data file: TPM.txt


title: F5

description: processed data file: TPM.txt


title: F44

description: processed data file: TPM.txt


title: F70

description: processed data file: TPM.txt


title: F43

description: processed data file: TPM.txt


title: F40

description: processed data file: TPM.txt


title: F39

description: processed data file: TPM.txt


title: F4

description: processed data file: TPM.txt


title: F38

description: processed data file: TPM.txt


title: F36

description: processed data file: TPM.txt


title: F37

description: processed data file: TPM.txt


title: F34

description: processed data file: TPM.txt


title: F32

description: processed data file: TPM.txt


title: F30

description: processed data file: TPM.txt


title: F29

description: processed data file: TPM.txt


title: F28

description: processed data file: TPM.txt


title: F27

description: processed data file: TPM.txt


title: F3

description: processed data file: TPM.txt


title: F26

description: processed data file: TPM.txt


title: F24

description: processed data file: TPM.txt


title: F23

description: processed data file: TPM.txt


title: F25

description: processed data file: TPM.txt


title: F22

description: processed data file: TPM.txt


title: F20

description: processed data file: TPM.txt


title: F21

description: processed data file: TPM.txt


title: F19

description: processed data file: TPM.txt


title: F18

description: processed data file: TPM.txt


title: F15

description: processed data file: TPM.txt


title: F17

description: processed data file: TPM.txt


title: F12

description: processed data file: TPM.txt


title: F13

description: processed data file: TPM.txt


title: F11

description: processed data file: TPM.txt


title: F10

description: processed data file: TPM.txt


title: C82

description: processed data file: TPM.txt

value: C


title: F1

description: processed data file: TPM.txt


title: C61

description: processed data file: TPM.txt


title: C70

description: processed data file: TPM.txt


title: C75

description: processed data file: TPM.txt


title: C71

description: processed data file: TPM.txt


title: C81

description: processed data file: TPM.txt


title: C7

description: processed data file: TPM.txt


title: F31

description: processed data file: TPM.txt


title: C69

description: processed data file: TPM.txt


title: C8

description: processed data file: TPM.txt


title: C78

description: processed data file: TPM.txt


title: C40

description: processed data file: TPM.txt


title: C54

description: processed data file: TPM.txt


title: C51

description: processed data file: TPM.txt


title: C39

description: processed data file: TPM.txt


title: C5

description: processed data file: TPM.txt


title: C59

description: processed data file: TPM.txt


title: C43

description: processed data file: TPM.txt


title: C4

description: processed data file: TPM.txt


title: C56

description: processed data file: TPM.txt


title: F14

description: processed data file: TPM.txt


title: C44

description: processed data file: TPM.txt


title: C50

description: processed data file: TPM.txt


title: C37

description: processed data file: TPM.txt


title: C38

description: processed data file: TPM.txt


title: F102

description: processed data file: TPM.txt


title: C36

description: processed data file: TPM.txt


title: C6

description: processed data file: TPM.txt


title: C57

description: processed data file: TPM.txt


title: C34

description: processed data file: TPM.txt


title: C32

description: processed data file: TPM.txt


title: C31

description: processed data file: TPM.txt


title: C3

description: processed data file: TPM.txt


title: C30

description: processed data file: TPM.txt


title: C27

description: processed data file: TPM.txt


title: C28

description: processed data file: TPM.txt


title: C25

description: processed data file: TPM.txt


title: C24

description: processed data file: TPM.txt


title: C23

description: processed data file: TPM.txt


title: C26

description: processed data file: TPM.txt


title: C22

description: processed data file: TPM.txt


title: C29

description: processed data file: TPM.txt


title: C21

description: processed data file: TPM.txt


title: C20

description: processed data file: TPM.txt


title: C19

description: processed data file: TPM.txt


title: clone_d_rep2

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: 950 Atlantic Drive

institute: Georgia Institute of Technology

description:
Raw_counts_single_cell_clone.csv
Normalized_single_cell_clone.csv

data_processing:
RNA-Seq quality control was initiated with Trim Galore, which was used to trim the 13bp Illumina standard adapter (‘AGATCGGAAGAGC’) by default.
Reads were mapped to hg38 human reference genome by STAR with defalut parameters.
Aligned sequencing reads were counted with intersection-strict mode in HTSeq.
Scale factors of each sample were computed using the trimmed mean of M-value (TMM) algorithm in edgeR.
Raw read counts were normalized by scale factors and then transformed into log2 counts per million reads (CPM). Genes were kept if expressed in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include raw and normalized read counts at the gene level for each sample

molecule: polyA RNA

source_name: HL60 cell line

extract_protocol: Illumina TruSeq Stranded Sample Preparation, Low Sample (LS) Protocol was used for the samples sequenced by Illumina HiSeq 2500. And NEBNext Ultra II Directional 162 RNA Library Prep Kit for Illumina was used for samples sequenced by Illumina NextSeq 550.

tag: differentiation type

value: Parental

tag: clone


title: clone_a_rep2


title: clone3_rep1

source_name: HL60/S4 cell line


title: clone2_rep2


title: clone_b_rep2


title: clone1_rep2


title: HL60_bulk_rep1


title: clone2_rep1


title: clone3_rep2


title: clone_d_rep1


title: HL60_bulk_rep2


title: C18

description: processed data file: TPM.txt


title: HL60/S4_bulk


title: clone_a_rep1


title: clone1_rep1


title: clone_c_rep2


title: clone_b_rep1


title: 3565_shELOVL2.843

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description: ELOVL2_Knockdown_Salmon_Abundance.txt (3565-4965)

data_processing:
FASTQ sequencing reads were trimmed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and transcript quantification was performed using Salmon in the quasi-mapping mode
Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2
Gene set enrichment analysis was performed by selecting differentially expressed genes (FDR-corrected p-value < 0.05), generating a pre-ranked list, and inputting a pre-ranked list into the GSEA desktop application (http://software.broadinstitute.org/gsea/downloads.jsp) (22,23). Pathway enrichment bubble plots were generated using the Bader Lab Enrichment Map Application (24) and Cytoscape (http://www.cytoscape.org).
Genome_build: hg38
Supplementary_files_format_and_content: Text files of Salmon Counts, Abundances, and DESeq2 Differentially expressed genes

source_name: Glioblastoma Stem Cell

growth_protocol:
GSC387 cells from a primary patient derived glioblastoma tumor were injected intracranially into a immunocomprimised NSG mouse and allowed to grow into a tumor.
All GSCs were cultured in Neurobasal media (Invitrogen) supplemented with B27 without vitamin A (Invitrogen), EGF, and bFGF (10 ng/ml each; R&D Systems), sodium pyruvate, and glutamax.

extract_protocol:
Cells were dissociated from the tumor and cultured as described in the methods
Cellular RNA was extracted using the Qiagen miRNeasy Mini Kit (catalog number 217004) according to the manufacturers instructions.

treatment_protocol: Cells were treated with a non-targeting control shRNA (shCONT) or shRNAs targeting ELOVL2

tag: cell line

tag: transfection

tag: tumor type

value: Glioblastoma


title: C15

description: processed data file: TPM.txt

tag: cell type


title: C17

description: processed data file: TPM.txt


title: C14

description: processed data file: TPM.txt


title: 3565_shELOVL2.308

description: ELOVL2_Knockdown_Salmon_Abundance.txt (3565-314664)


title: 3565_shCONT

description: ELOVL2_Knockdown_Salmon_Abundance.txt (3565-NT)

value: shCONT


title: 387_shELOVL2.843

description: ELOVL2_Knockdown_Salmon_Abundance.txt (387-4965)