title: Strawberry_ripe_RNA-seq_2

description:
Fruit_ripe_rep2
sequencing instrument(s): HiSeq X Ten


title: Cs_leaf_H3K27me3

status: Public on Jul 04 2018

type: SRA

city: Hong Hong

first: Silin

last: Zhong

address: Shatin, N.T.

department: School of Life Sciences

country: China

institute: CUHK

description:
Cs_leaf
sequencing instrument(s): HiSeq X Ten

library_source: genomic

data_processing:
Most of the sequencing and base-calling services were provide by CloudHealth Genomics, Ltd. (Shanghai).
For RNA-Seq dataset, raw data was aligned to a home maintained rDNA database using Bowtie2 (version 2.1.0) with default parameters to filter out any rRNA sequence. Retained reads were then mapped to genome reference using TopHat2 (v2.1.1) with parameters: --read-realign-edit-dist 0 --max-intron-length 10000 --max-segment-intron 10000 --prefilter-multihits. FPKM value of each gene was calculated using StringTie (v1.3.1c) with parameters: -e -j 3 -f 0.2 -A. Raw read counts of genes were calculated using HTSeq (version 0.9.1) with parameters: --nonunique all.
For DNase-Seq and ChIP-Seq dataset, raw reads were mapped to the genome reference using Bowtie2 (version 2.1.0) with option: -3 100.  For DNase-Seq and transcription factor ChIP-Seq datasets, peaks were called using MACS (ver 2.1.1.20160309), with the parameters: --nomodel -q 0.01 and -q 0.01, respectively. For H3K27me3 ChIP-Seq dataset, peaks were called using SICER (version 1.1) with the settings: window size 150, gap size 300, FDR 0.01. H3K27me3 candidate peaks were filtered further by their length, fold of enrichment and FDR: 1. peaks shorter than 300 bp was discarded; 2. for peaks shorter than 1kb, fold of enrichment and FDR requirement cutoff were setted as 5 and 1e-50, respectively for apple and tomato datasets,  4 and 1e-50 repectively for banana, grape and pear datasets, 3 and 1e-5  for datasets of other species; 3. for peaks longer than 1kb, fold of enrichment cutoff were setted as 4 for apple and tomato datasets, 3 for banana, grape and pear datasets, 2 for datasets of other species; Alignments with mapping score less than 10 and PCR duplicates were discarded using samtools before peak calling. bedgraph file generated by MACS with --SPMR enabled was converted to bw file using bedGraphToBigWig.
For Bisulfite-Seq dataset, raw data was mapped to genome reference using BSMAP (version 2.90) with the parameters: -A AGATCGGAAGAGC -w 100 -r 0 -q 10. Methylation ratio of each cytosine was calculated using methratio.py with the parameters: -z -r. The result file was compressed using bgzip and index using tabix.
Genome_build: Arabidopsis thaliana: genome release 9 (assembly), TAIR10 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Athaliana
Genome_build: Apple: GDDH13 Version 1.1 (assembly), GDDH13 Version 1.1 (annotation), https://iris.angers.inra.fr/gddh13/
Genome_build: Banana: DH-Pahang v2 (assembly), DH-Pahang v2 (annotation), http://banana-genome.cirad.fr/content/download-dh-pahang
Genome_build: Cucumber: Chinese long v2 (assembly), Chinese long v2 (annotation), ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/
Genome_build: Grape: Genoscope (12X) (assembly), CRIBI V2.1 (annotation), http://genomes.cribi.unipd.it/DATA/V2/V2.1/
Genome_build: Melon: v3.5 (assembly), v3.5 (annotation), https://melonomics.net/files/Genome/Melon_genome_v3.5_Garcia-Mas_et_al_2012/
Genome_build: Papaya: ASGPBv0.4 (assembly), ASGPBv0.4 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Cpapaya
Genome_build: Peach: v1.0 (assembly), v1.0 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ppersica
Genome_build: Pear: Pbr_v1.0 (assembly), NCBI Annotation Release 101 (annotation), https://www.ncbi.nlm.nih.gov/genome/12793
Genome_build: Strawberry: v1.1 (assembly), v1.1 (annotation), http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Fvesca
Genome_build: Watermelon: v1 (assembly), v1 (annotation), ftp://www.icugi.org/pub/genome/watermelon/97103/v1/
Genome_build: Tomato: v2.5 (assembly), ITAG2.4 (annotation), ftp://ftp.solgenomics.net/tomato_genome/assembly/build_2.50/
Genome_build: Rice: Os-Nipponbare-Reference-IRGSP-1.0 (assembly), MSU release 7.0 (annotation), https://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Osativa
Supplementary_files_format_and_content: For RNA-Seq dataset, tab delimited abundance file gives FPKM of each gene, tab delimited count file gives read counts of each gene
Supplementary_files_format_and_content: For Dnase-Seq dataset, bw file shows the read density across the entile genome, tab delimited file in narrowPeak format shows peak calling information generated by MACS2
Supplementary_files_format_and_content: For Bisulfite-Seq dataset, bgzip compressed tab delimited file gives all and mC counts of each genomic cytosine across the entile genome. Index file are also provided, so one can fast retrieve the data randomly using tabix.
Supplementary_files_format_and_content: For ChIP-Seq dataset, bw file shows the read density across the entile genome. For transcription factor ChIP-Seq dataset, tab delimited file in narrowPeak format shows peak calling information generated by MACS2. For H3K27me3 ChIP-Seq dataset, tab delimited file shows peak calling information generated by SICER.

molecule: genomic DNA

organism: Cucumis sativus

source_name: leaf

extract_protocol:
conventional TruSeq protocol or more recent Tn5-based ChIP-Seq library construction protocol
histone-DNA complexes were isolated with H3K27me3 antibody (RevMAb and Millipore).

tag: cultivar

value: Chinese Long (line9930)

tag: tissue

value: leaf

tag: developmental stage

value: not collected


title: PS_fruit_20DPA_RNA-seq_1

description:
PS_fruit_20DPA_rep1
sequencing instrument(s): HiSeq X Ten

library_source: transcriptomic

molecule: polyA RNA

organism: Cucumis melo

source_name: 20DPA fruit flesh

extract_protocol:
Standard non-stranded illumina RNA-Seq libraries protocol
mRNA was extracted from tissue using standard protocol

value: Piel de Sapo

value: fruit flesh and peel

value: 20 days post anthesis


title: PS_fruit_10DPA_RNA-seq_2

description:
PS_fruit_10DPA_rep2
sequencing instrument(s): HiSeq X Ten

source_name: 10DPA fruit flesh

value: 10 days post anthesis


title: Cs_leaf_BS-seq

extract_protocol:
Whole-genome bisulfite sequencing was carried out as previously described in Zhong, S. et al., Nat. Biotechnol., 2013. The sonicated genomic DNA was end-repaired, dA-tailed and ligated to a fully methylated Y-shape adapter.
Genomic DNA was extracted from different tissues using the DNeasy Plant Kit (Qiagen)


title: Strawberry_immature_RNA-seq_2

description:
Fruit_immature_rep2
sequencing instrument(s): HiSeq X Ten

organism: Fragaria vesca

source_name: immature receptacle

value: receptacle without seed

value: immature


title: Strawberry_immature_RNA-seq_3

description:
Fruit_immature_rep3
sequencing instrument(s): HiSeq X Ten


title: Cs_10DPA_BS-seq

description:
Cs_10DPA
sequencing instrument(s): HiSeq X Ten

value: fruit flesh

value: 10 days post anthesis (immature)


title: Strawberry_leaf_RNA-seq_2

description:
Leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: PS_leaf_RNA-seq_2

description:
PS_leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: Cs_40DPA_BS-seq

description:
Cs_40DPA
sequencing instrument(s): HiSeq X Ten

source_name: 40DPA fruit flesh

value: 40 days post anthesis (ripe)


title: PS_leaf_RNA-seq_1

description:
PS_leaf_rep1
sequencing instrument(s): HiSeq X Ten

extract_protocol:
Strand specific RNA library protocol described in Zhong, S. et al., Cold Spring Harb. Protoc, 2011. Second stranded.
mRNA was extracted from tissue using standard protocol


title: PbW_mature_H3K27me3

description:
PbW_mature
sequencing instrument(s): HiSeq X Ten

organism: Pyrus x bretschneideri

source_name: ripe fruit flesh

value: Williams

value: ripe


title: PI_40DPA_RNA-seq_2

description:
PI_fruit_40DPA_rep2
sequencing instrument(s): HiSeq X Ten

value: 40 days post anthesis


title: Strawberry_leaf_RNA-seq_1

description:
Leaf_rep1
sequencing instrument(s): HiSeq X Ten

extract_protocol:
Strand specific RNA library protocol described in Zhong, S. et al., Cold Spring Harb. Protoc, 2011. First stranded.
mRNA was extracted from tissue using standard protocol


title: Cucumber_40DPA_ethylene_RNA-seq_1

description:
Fruit_ripe_Eth1.5_rep1
sequencing instrument(s): HiSeq X Ten


title: Cucumber_40DPA_ethylene_RNA-seq_2

description:
Fruit_ripe_Eth1.5_rep2
sequencing instrument(s): HiSeq X Ten


title: PbW_before_turning_H3K27me3

description:
PbW_before_turning
sequencing instrument(s): HiSeq X Ten

source_name: mature green fruit flesh

value: before turning


title: Cs_leaf_DNase-seq

extract_protocol: DNase-Seq was performed as described in 1. Grøntved, L. et al., Epigenetics Chromatin 5, 10 (2012). The purified nuclei were suspended in 500 ul of nuclease digestion buffer (30 mM Tris-HCl pH 8.0, 14 mM MgCl2, 0.5% NP-40, 0.2% BSA) containing different concentration of DNase (Cyanase, RiboSolutions). After a short incubation at 37°C for 3 min, the digestion was immediately terminated by adding EDTA and SDS. RNase A was then added to digest the RNA. The DNA was purified by Phenol/Chloroform extraction and ethanol precipitation. The purified total DNA was run on a 2% agarose gel and the small fragments released by the DNase digestion were purified and converted to Illumina TruSeq libraries as described in He, H.H. et al., Nat. Methods, 2014.


title: PI_fruit_20DPA_RNA-seq_2

description:
PI_fruit_20DPA_rep2
sequencing instrument(s): HiSeq X Ten


title: PI_fruit_20DPA_RNA-seq_1

description:
PI_fruit_20DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: PI_fruit_10DPA_RNA-seq_2

description:
PI_fruit_10DPA_rep2
sequencing instrument(s): HiSeq X Ten


title: PbW_leaf_H3K27me3

description:
PbW_leaf
sequencing instrument(s): HiSeq X Ten


title: PbD_mature_H3K27me3

description:
PbD_mature
sequencing instrument(s): HiSeq X Ten

value: Dangshanshuli


title: PbD_immature_H3K27me3

description:
PbD_immature
sequencing instrument(s): HiSeq X Ten

source_name: immature fruit flesh


title: PbD_leaf_H3K27me3

description:
PbD_leaf
sequencing instrument(s): HiSeq X Ten


title: Cucumber_40DPA_RNA-seq_2

description:
Fruit_40DPA_rep2
sequencing instrument(s): HiSeq X Ten

value: Chinese Long (line9930)


title: PS_10DPA_RNA-seq_1

description:
PS_fruit_10DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: Cs_10DPA_DNase-seq

description:
Cs_10DPA
sequencing instrument(s): HiSeq X Ten


title: PI_10DPA_RNA-seq_1

description:
PI_fruit_10DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: PI_leaf_RNA-seq_2

description:
PI_leaf_rep2
sequencing instrument(s): HiSeq X Ten

value: leaf


title: PI_leaf_RNA-seq_1

description:
PI_leaf_rep1
sequencing instrument(s): HiSeq X Ten

value: not collected


title: PbW_ripe_BS-seq

description:
PbW_ripe
sequencing instrument(s): HiSeq X Ten


title: Cucumber_20DPA_RNA-seq_1

description:
Fruit_20DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: Cucumber_30DPA_RNA-seq_1

description:
Fruit_30DPA_rep1
sequencing instrument(s): HiSeq X Ten

source_name: 30DPA fruit flesh

value: 30 days post anthesis


title: PI_40DPA_RNA-seq_1

description:
PI_fruit_40DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: fruit flesh and peel


title: PbW_leaf_BS-seq

source_name: young leaf

value: young


title: PbD_ripe_BS-seq

description:
PbD_ripe
sequencing instrument(s): HiSeq X Ten


title: Cucumber_10DPA_RNA-seq_2

description:
Fruit_10DPA_rep2
sequencing instrument(s): HiSeq X Ten

value: 10 days post anthesis


title: Ma_leaf.old_2_H3K27me3

description:
Ma_leaf.old_2
sequencing instrument(s): HiSeq X Ten

organism: Musa acuminata AAA Group

source_name: old leaf

value: Cavendish, cv Baxi

value: old stage


title: Cucumber_10DPA_RNA-seq_1

description:
Fruit_10DPA_rep1
sequencing instrument(s): HiSeq X Ten

value: fruit flesh


title: Cucumber_40DPA_RNA-seq_1

description:
Fruit_40DPA_rep1
sequencing instrument(s): HiSeq X Ten


title: PbD_leaf_BS-seq


title: PbW_ripe_DNase-seq


title: Ma_leaf.young_2_H3K27me3

description:
Ma_leaf.young_2
sequencing instrument(s): HiSeq X Ten

value: young stage


title: Cucumber_leaf_RNA-seq_2

description:
Leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: Cucumber_leaf_RNA-seq_1

description:
Leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: Cucumber_30DPA_RNA-seq_2

description:
Fruit_30DPA_rep2
sequencing instrument(s): HiSeq X Ten


title: Ma_stage4.peel_H3K27me3

description:
Ma_stage4.peel
sequencing instrument(s): HiSeq X Ten

source_name: stage 4 fruit peel

value: Cavendish

value: peel

value: stage 4 of 4 (from immature to ripe)


title: PbD_ripe_DNase-seq

value: ripe


title: Ma_stage1.peel_H3K27me3

description:
Ma_stage1.peel
sequencing instrument(s): HiSeq X Ten

source_name: stage 1 fruit peel

value: stage 1 of 4 (from immature to ripe)


title: Cucumber_20DPA_RNA-seq_2

description:
Fruit_20DPA_rep2
sequencing instrument(s): HiSeq X Ten

value: 20 days post anthesis


title: Vv_mature_H3K27me3

description:
Vv_mature
sequencing instrument(s): HiSeq X Ten

organism: Vitis vinifera

source_name: ripe fruit

value: Grapevine PN40024


title: PbD_leaf_DNase-seq

description:
PbD_leaf
sequencing instrument(s): HiSeq X Ten

value: Dangshanshuli

value: leaf


title: Ma_stage4.pulp_H3K27me3

description:
Ma_stage4.pulp
sequencing instrument(s): HiSeq X Ten

source_name: stage 4 fruit pulp

value: pulp


title: Vv_immature_2_H3K27me3

description:
Vv_immature_2
sequencing instrument(s): HiSeq X Ten

source_name: immature fruit

value: before veraison


title: atr8-mutant-replicate 3

type: RNA

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi, South Campus

description: Gene expression data of mutant atr8 10 day old seedling dipped in air purged water for 6 hours (hypoxic stress treatment), then recovered on 1/2 MS agar medium for 22 hours

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300

data_processing: First-order analysis was performed using Affymetrix® GeneChip® Command Console® 3.0. Normalization of data and differential expression analysis was done using CLC Genomics workbench

label: Biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedling

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA

growth_protocol: Seedlings were grown on 1/2 MS medium with 2% sucrose, 0.5 µg/ml thiamine-HCl, and 0.24% gellan gum under 16 h light (~60 µmol/m^2s) and 8 h dark cycle at 20°C.

extract_protocol: Tripure Isolation Reagent extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 10-day-old seedling after germination dipped in air purged water for 6 h and recovered on 1/2 MS agar medium for 22 h.

tag: genotype

value: atr8 mutant

tag: ecotype

value: Wassilevskija (WS)

value: Seedling (10 days after germination)


title: Vv_leaf_H3K27me3

description:
Vv_leaf
sequencing instrument(s): HiSeq X Ten

source_name: leaf

value: not collected


title: Pear_D_fruit_RNA-seq_1

description:
Dangshanshuli_fruit_ripe_rep1
sequencing instrument(s): HiSeq X Ten

value: fruit flesh


title: Ma_leaf_H3K27me3

description:
Ma_leaf
sequencing instrument(s): HiSeq X Ten


title: Pear_D_fruit_ripe_RNA-seq_2

description:
Dangshanshuli_fruit_ripe_rep2
sequencing instrument(s): HiSeq X Ten


title: Ma_leaf.mature_H3K27me3

description:
Ma_leaf.mature
sequencing instrument(s): HiSeq X Ten

source_name: adult leaf

value: Cavendish, cv Baxi

value: adult stage


title: Ma_pulp_ripe_BS-seq

description:
Ma_pulp_ripe
sequencing instrument(s): HiSeq X Ten

value: Cavendish cv. Baxi


title: PbW_leaf_DNase-seq

description:
PbW_leaf
sequencing instrument(s): HiSeq X Ten

value: Williams


title: Vv_ripe_BS-seq

description:
Vv_ripe
sequencing instrument(s): HiSeq X Ten

value: Pinot Noir

value: ripe


title: Cs_40DPA_DNase-seq

description:
Cs_40DPA
sequencing instrument(s): Illumina HiSeq 4000,HiSeq X Ten

value: Chinese Long (line9930)

value: 40 days post anthesis


title: atr8-mutant-replicate 1


title: Md_mature_H3K27me3

description:
Md_mature
sequencing instrument(s): HiSeq X Ten

organism: Malus domestica

value: Golden Delicious


title: atr8-mutant-replicate 2


title: Md_immature_H3K27me3

description:
Md_immature
sequencing instrument(s): HiSeq X Ten

value: immature


title: Vv_immature_BS-seq

description:
Vv_immature
sequencing instrument(s): HiSeq X Ten


title: Vv_leaf_BS-seq

value: leaf


title: Pear_D_immature_2

description:
Dangshanshuli_fruit_immature_2
sequencing instrument(s): HiSeq X Ten

value: Dangshanshuli

value: fruit flesh and peel


title: Ma_pulp_immature_BS-seq

description:
Ma_pulp_immature
sequencing instrument(s): HiSeq X Ten

source_name: stage 1 fruit pulp

value: stage 1 of 4 (from immature to ripe)


title: WT-control-replicate 3

description: Gene expression data of wild type 10 day old seedling dipped in air purged water for 6 hours (hypoxic stress treatment), then recovered on 1/2 MS agar medium for 22 hours

value: wild type

value: Wassilevskija (WS)

value: Seedling (10 days after germination)


title: Pear_D_fruit_RNA-seq_2

description:
Dangshanshuli_peel_ripe_rep1
sequencing instrument(s): HiSeq X Ten

source_name: ripe fruit peel

value: fruit peel


title: Ma_leaf_BS-seq

value: not collected


title: Pear_D_immature_1

description:
Dangshanshuli_fruit_immature_1
sequencing instrument(s): HiSeq X Ten


title: Ma_stage4_DNase-seq

description:
Ma_stage4
sequencing instrument(s): HiSeq X Ten

value: Cavendish

value: pulp

value: stage 4 of 4 (from immature to ripe)


title: Vv_ripe_2_DNase-seq

description:
Vv_ripe_2
sequencing instrument(s): HiSeq X Ten

value: Grapevine PN40024

value: fruit flesh

value: ripe


title: Ma_stage1.pulp_H3K27me3

description:
Ma_stage1.pulp
sequencing instrument(s): HiSeq X Ten


title: Md_leaf_H3K27me3

description:
Md_leaf
sequencing instrument(s): HiSeq X Ten

value: Golden Delicious


title: Pear_D_peel_ripe_RNA-seq_2

description:
Dangshanshuli_peel_ripe_rep2
sequencing instrument(s): HiSeq X Ten


title: WT-control-replicate 1


title: WT-control-replicate 2


title: Ma_stage1_DNase-seq

description:
Ma_stage1
sequencing instrument(s): HiSeq X Ten


title: Md_ripe_BS-seq

description:
Md_ripe
sequencing instrument(s): HiSeq X Ten


title: Md_immature_BS-seq

value: immature


title: Pear_D_leaf_RNA-seq_2

description:
Dangshanshuli_leaf_rep2
sequencing instrument(s): HiSeq X Ten

value: leaf


title: Pear_D_leaf_RNA-seq_1

description:
Dangshanshuli_leaf_rep1
sequencing instrument(s): HiSeq X Ten

value: Dangshanshuli


title: Banana_pulp_S4_RNA-seq_2

description:
Pulp_stage4_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 4 pulp


title: Grape_Friut_ripe_RNA-seq_2

description:
Friut_mature_rep2
sequencing instrument(s): HiSeq X Ten


title: Md_leaf_BS-seq

value: young


title: Ma_leaf_DNase-seq

description:
Ma_leaf
sequencing instrument(s): HiSeq X Ten


title: Md_ripe_DNase-seq

source_name: ripe fruit flesh


title: Banana_pulp_S4_RNA-seq_1

description:
Pulp_stage4_rep1
sequencing instrument(s): HiSeq X Ten


title: Pear_W_ripe_RNA-seq_2

description:
Williams_fruit_ripe_rep2
sequencing instrument(s): HiSeq X Ten

value: Williams


title: Grape_ripe_RNA-seq_1

description:
Friut_mature_rep1
sequencing instrument(s): HiSeq X Ten


title: Banana_pulp_S3_RNA-seq_1

description:
Pulp_stage3_rep1
sequencing instrument(s): HiSeq X Ten

source_name: stage 3 pulp

value: stage 3 of 4 (from immature to ripe)


title: Grape_immature_RNA-seq_1

description:
Friut_break_rep1
sequencing instrument(s): HiSeq X Ten

source_name: before veraison fruit

value: before veraison


title: Pear_W_fruit_RNA-seq_2

description:
Williams_fruit_ripe_rep1
sequencing instrument(s): HiSeq X Ten


title: Md_immature_DNase-seq

description:
Md_immature
sequencing instrument(s): HiSeq X Ten

source_name: immature fruit flesh


title: Grape_immature_RNA-seq_2

description:
Friut_break_rep2
sequencing instrument(s): HiSeq X Ten


title: Vv_leaf_DNase-seq

description:
Vv_leaf
sequencing instrument(s): HiSeq X Ten


title: Banana_pulp_S3_RNA-seq_2

description:
Pulp_stage3_rep2
sequencing instrument(s): HiSeq X Ten


title: Pear_W_fruit_RNA-seq_1

description:
Williams_fruit_beforeturning
sequencing instrument(s): HiSeq X Ten

source_name: mature green fruit flesh

value: before turning


title: NAC_ripe_2_ChIP-seq

description:
NAC_ripe_2
sequencing instrument(s): HiSeq X Ten

organism: Prunus persica

extract_protocol:
conventional TruSeq protocol or more recent Tn5-based ChIP-Seq library construction protocol
TF-DNA complexes were isolated using anti-NAC rabbit serum.

value: babygold


title: Grape_Friut_green_RNA-seq_2

description:
Friut_green_rep2
sequencing instrument(s): HiSeq X Ten


title: Pear_D_leaf_RNA-seq_3

description:
Dangshanshuli_leaf_rep3
sequencing instrument(s): HiSeq X Ten

source_name: young leaf

value: not collected


title: Apple_ripe_RNA-seq_1

description:
Peel_ripe_rep1
sequencing instrument(s): HiSeq X Ten

value: fruit peel


title: Pear_W_leaf_RNA-seq_1

description:
Williams_leaf
sequencing instrument(s): HiSeq X Ten


title: Grape_Friut_break_RNA-seq_2

description:
Friut_green_rep1
sequencing instrument(s): HiSeq X Ten


title: Banana_pulp_S2_RNA-seq_2

description:
Pulp_stage2_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 2 pulp

value: Cavendish

value: pulp

value: stage 2 of 4 (from immature to ripe)


title: Grape_leaf_RNA-seq_3

description:
Leaf_rep3
sequencing instrument(s): HiSeq X Ten

value: Grapevine PN40024


title: Apple_peel_ripe_RNA-seq_2

description:
Peel_ripe_rep2
sequencing instrument(s): HiSeq X Ten

value: ripe


title: Pp_mature_H3K27me3

description:
Pp_mature
sequencing instrument(s): HiSeq X Ten

value: fruit flesh


title: Apple_flesh_ripe_RNA-seq_2

description:
Flesh_ripe_rep2
sequencing instrument(s): HiSeq X Ten

value: Golden Delicious


title: Md_leaf_DNase-seq

description:
Md_leaf
sequencing instrument(s): HiSeq X Ten

value: leaf


title: Grape_leaf_RNA-seq_2

description:
Leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: Banana_pulp_S1_RNA-seq_1

description:
Pulp_stage1_rep1
sequencing instrument(s): HiSeq X Ten

source_name: stage 1 pulp

value: stage 1 of 4 (from immature to ripe)


title: Pp_leaf1_H3K27me3

description:
Pp_leaf1
sequencing instrument(s): HiSeq X Ten


title: Pp_immature_2.Maotao_H3K27me3

description:
Pp_immature_2.Maotao
sequencing instrument(s): HiSeq X Ten

value: NJC 83

value: immature


title: Apple_immature_RNA-seq_2

description:
Fruit_immature_rep2
sequencing instrument(s): HiSeq X Ten


title: Strawberry_ripe_RNA-seq_1

description:
Fruit_ripe_rep1
sequencing instrument(s): Illumina HiSeq 4000

source_name: ripe receptacle

value: receptacle without seed


title: Apple_ripe_RNA-seq_2

description:
Flesh_ripe_rep1
sequencing instrument(s): HiSeq X Ten


title: Banana_peel_S4_RNA-seq_2

description:
Peel_stage4_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 4 peel

value: peel

value: stage 4 of 4 (from immature to ripe)


title: Strawberry_immature_RNA-seq_1

description:
Fruit_immature_rep1
sequencing instrument(s): Illumina HiSeq 4000

source_name: immature receptacle


title: Banana_pulp_S1_RNA-seq_2

description:
Pulp_stage1_rep2
sequencing instrument(s): HiSeq X Ten


title: Banana_peel_S4_RNA-seq_1

description:
Peel_stage4_rep1
sequencing instrument(s): HiSeq X Ten


title: Apple_immature_RNA-seq_1

description:
Fruit_immature_rep1
sequencing instrument(s): HiSeq X Ten

source_name: immature fruit


title: Pp_19DPA_BS-seq

description:
Pp_19DPA
sequencing instrument(s): HiSeq X Ten

source_name: 19DPA fruit flesh

value: babygold

value: 127 days post anthesis (ripe)


title: Banana_peel_S3_RNA-seq_2

description:
Peel_stage3_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 3 peel

value: stage 3 of 4 (from immature to ripe)


title: Cp_mature_H3K27me3

description:
Cp_mature
sequencing instrument(s): HiSeq X Ten

organism: Carica papaya


title: Banana_pulp_S2_RNA-seq_1

description:
Pulp_stage2_rep1
sequencing instrument(s): HiSeq X Ten

value: Cavendish


title: Apple_leaf_RNA-seq_2

source_name: Leaf

value: not collected


title: Pp_leaf_BS-seq

description:
Pp_leaf
sequencing instrument(s): HiSeq X Ten

source_name: leaf


title: Banana_peel_S3_RNA-seq_1

description:
Peel_stage3_rep1
sequencing instrument(s): HiSeq X Ten


title: Pp_ripe_2_DNase-seq

description:
Pp_ripe_2
sequencing instrument(s): HiSeq X Ten


title: Cp_leaf_H3K27me3

description:
Cp_leaf
sequencing instrument(s): HiSeq X Ten


title: Apple_leaf_RNA-seq_1

description:
Leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: Banana_peel_S2_RNA-seq_2

description:
Peel_stage2_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 2 peel

value: stage 2 of 4 (from immature to ripe)


title: Apple_immature_RNA-seq_3

description:
Fruit_immature_rep3
sequencing instrument(s): HiSeq X Ten


title: Cp_ripe_BS-seq

description:
Cp_ripe
sequencing instrument(s): HiSeq X Ten

source_name: ripe fruit flesh

value: stage4 of 4 (from immature to ripe)


title: Cp_immature_H3K27me3

description:
Cp_immature
sequencing instrument(s): HiSeq X Ten


title: Grape_leaf_RNA-seq_1

value: Grapevine PN40024


title: Banana_peel_S2_RNA-seq_1

description:
Peel_stage2_rep1
sequencing instrument(s): HiSeq X Ten


title: Pp_127DPA_BS-seq

description:
Pp_127DPA
sequencing instrument(s): HiSeq X Ten

source_name: 127DPA fruit flesh

value: fruit flesh

value: 19 days post anthesis (immature)


title: Cp_immature_BS-seq

value: stage1 of 4 (from immature to ripe)


title: Peach_ripe_RNA-seq_2

description:
Fruit_ripe_rep2
sequencing instrument(s): HiSeq X Ten

value: ripe


title: Pp_leaf_2_DNase-seq

description:
Pp_leaf_2
sequencing instrument(s): HiSeq X Ten

value: leaf


title: Banana_peel_S1_RNA-seq_2

description:
Peel_stage1_rep2
sequencing instrument(s): HiSeq X Ten

source_name: stage 1 peel

value: stage 1 of 4 (from immature to ripe)


title: Banana_peel_S1_RNA-seq_1

description:
Peel_stage1_rep1
sequencing instrument(s): HiSeq X Ten


title: healthy volunteer, rep3 [circRNA]

city: Harbin

first: Zhibo

last: Guo

state: Heilongjiang

address: No.23 Street

institute: Harbin Medical University

description:
C3
circRNA expression of healthy volunteer, replicate 3.

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 4 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.
When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes>=2.0 and p-values<=0.05 are selected as the significantly differentially expressed.

organism: Homo sapiens

source_name: bone marrow mononuclear cells, healthy

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Freshly drawn bone marrow from EMI, non-EMI AML patients and healthy volunteers were separated, then total RNA was extracted based on standard protocol.

tag: disease state

value: healthy

tag: cell type

value: bone marrow mononuclear cells

tag: gender

value: female


title: Cp_leaf_DNase-seq


title: Peach_ripe_RNA-seq_1

description:
Fruit_ripe_rep1
sequencing instrument(s): HiSeq X Ten

value: babygold


title: Papaya_S4_RNA-seq_2

description:
Tainong1_fruit_stage4 (ripe)_rep2
sequencing instrument(s): HiSeq X Ten


title: healthy volunteer, rep1 [circRNA]

description:
C1
circRNA expression of healthy volunteer, replicate 1.


title: Banana_leaf_RNA-seq_1

source_name: mature leaf


title: healthy volunteer, rep2 [circRNA]

description:
C2
circRNA expression of healthy volunteer, replicate 2.

value: male


title: Peach_immature_RNA-seq_1

description:
Fruit_immature_rep1
sequencing instrument(s): HiSeq X Ten

source_name: immature fruit flesh

value: immature


title: non-extramedullary infiltration, rep4 [circRNA]

description:
T2.4
circRNA expression of AML patient without extramedullary infiltration, replicate 4.

source_name: bone marrow mononuclear cells, AML without EMI

value: AML without EMI


title: Banana_leaf_old_RNA-seq_2

description:
Leaf_old_rep2
sequencing instrument(s): HiSeq X Ten

source_name: old leaf

value: Cavendish

value: old


title: Pp_immature_DNase-seq

description:
Pp_immature
sequencing instrument(s): HiSeq X Ten


title: Papaya_S4_RNA-seq_1

description:
Tainong1_fruit_stage4 (ripe)_rep1
sequencing instrument(s): HiSeq X Ten

value: stage4 of 4 (from immature to ripe)


title: non-extramedullary infiltration, rep3 [circRNA]

description:
T2.3
circRNA expression of AML patient without extramedullary infiltration, replicate 3.


title: Peach_leaf_RNA-seq_2

description:
Leaf_rep2
sequencing instrument(s): HiSeq X Ten

value: not collected


title: Papaya_S3_RNA-seq_1

description:
Tainong1_fruit_stage3
sequencing instrument(s): HiSeq X Ten

source_name: stage 3 fruit flesh

value: fruit flesh

value: stage3 of 4 (from immature to ripe)


title: Banana_leaf_old_RNA-seq_1

description:
Leaf_old_rep1
sequencing instrument(s): HiSeq X Ten


title: Peach_leaf_RNA-seq_1

description:
Leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: Papaya_S2_RNA-seq_1

description:
Tainong1_fruit_stage2
sequencing instrument(s): HiSeq X Ten

source_name: stage 2 fruit flesh

value: stage2 of 4 (from immature to ripe)


title: Cp_leaf_BS-seq

description:
Cp_leaf
sequencing instrument(s): HiSeq X Ten


title: Banana_leaf_adult_RNA-seq_2

description:
Leaf_mature_rep2
sequencing instrument(s): HiSeq X Ten

value: adult


title: Cp_ripe_DNase-seq

description:
Cp_ripe
sequencing instrument(s): Illumina HiSeq 4000,HiSeq X Ten

value: ripe


title: healthy volunteer, rep4 [circRNA]

description:
C4
circRNA expression of healthy volunteer, replicate 4.


title: non-extramedullary infiltration, rep2 [circRNA]

description:
T2.2
circRNA expression of AML patient without extramedullary infiltration, replicate 2.


title: Banana_leaf_RNA-seq_2

value: leaf


title: Peach_immature_RNA-seq_2

description:
Fruit_immature_rep2
sequencing instrument(s): HiSeq X Ten


title: non-extramedullary infiltration, rep1 [circRNA]

description:
T2.1
circRNA expression of AML patient without extramedullary infiltration, replicate 1.


title: Banana_leaf_young_RNA-seq_2

description:
Leaf_young_rep2
sequencing instrument(s): HiSeq X Ten

source_name: young leaf

value: young


title: extramedullary infiltration, rep4 [circRNA]

description:
T1.4
circRNA expression of AML patient with extramedullary infiltration, replicate 4.

source_name: bone marrow mononuclear cells, AML with EMI

value: AML with EMI

value: bone marrow mononuclear cells


title: Papaya_S1_RNA-seq_1

description:
Tainong1_fruit_stage1 (immature)_rep1
sequencing instrument(s): HiSeq X Ten

value: stage1 of 4 (from immature to ripe)


title: Papaya_150DPA_RNA-seq_1

description:
Golden_fruit_150DPA
sequencing instrument(s): Illumina HiSeq 4000

source_name: 150DPA fruit flesh

value: 150 days post anthesis


title: Papaya_leaf_RNA-seq_2

description:
Tainong1_leaf_rep2
sequencing instrument(s): HiSeq X Ten


title: extramedullary infiltration, rep2 [circRNA]

description:
T1.2
circRNA expression of AML patient with extramedullary infiltration, replicate 2.

value: female


title: Papaya_leaf_RNA-seq_1

description:
Tainong1_leaf_rep1
sequencing instrument(s): HiSeq X Ten


title: Papaya_30DPA_RNA-seq_1

description:
Golden_fruit_30DPA
sequencing instrument(s): Illumina HiSeq 4000

source_name: 30DPA fruit flesh

value: 30 days post anthesis


title: Banana_leaf_young_RNA-seq_1

description:
Leaf_young_rep1
sequencing instrument(s): HiSeq X Ten

value: Cavendish


title: Papaya_S1_RNA-seq_2

description:
Tainong1_fruit_stage1 (immature)_rep2
sequencing instrument(s): HiSeq X Ten


title: History-dependence BAR-Seq [24]

status: Public on Jul 03 2018

city: Leuven

first: Abbas

last: Jariani

address: Gaston Geenslaan 1, box 2471

department: KU Leuven - VIB Centre for Microbiology

country: Belgium

institute: KU Leuven - VIB

description:
sample name:
24
DNA barcode of deleted cassette

data_processing:
Library strategy: BAR-seq
Blast the barcodes against the sequencing reads and get the number of counts allowing for 2 mismatches and 3 gaps
Genome_build: not-applicable
Supplementary_files_format_and_content: CSV format with the count of barcodes of each gene deletion in each condition. The results for the up-tag and down-tag of the deletion cassette are separated. Please see the FASTA files on the series record for barcode sequences and the "Readme_barcodePositions.pdf" file for explanation of the Yeast Deletion Collection used in this study.

organism: Saccharomyces cerevisiae

source_name: Amplified barcodes from pooled Yeast Deletion collection

growth_protocol: Yeast deletion collection pooled together and grown in YP-glu5% or YP-mal10%

extract_protocol:
DNA was extracted using a Zymolyase-based protocol, and the genomic DNA extracts were equalized  based on the cell density of the samples.  BAR-seq; PMID: 24192834
PCR barcode amplification of the UP and DN barcodes was  done using primer sets (UP-tag: U1 and p69; DN-tag: D1 and D2) that generate respectively 168bp and  190bp fragments containing these barcodes at one of their ends. Ex-Taq polymerase (TaKaRa) was  used using standard cycling conditions, including 30s of elongation time and an annealing temperature  of 55°C. A limited number of amplification cycles (16) was done to avoid issues associated with over-  amplification.

tag: background strain

value: BY4730, NatR:MAL63::MAL13, MAL12:yEcitrine:LEU2, MAL11:mCherry:URA3

tag: condition

value: End of maltose growth after 8h glucose


title: History-dependence BAR-Seq [25]

description:
sample name:
25
DNA barcode of deleted cassette

value: End of maltose growth after 10h glucose


title: History-dependence BAR-Seq [28]

description:
sample name:
28
DNA barcode of deleted cassette

value: End of maltose growth after 12h glucose


title: History-dependence BAR-Seq [23]

description:
sample name:
23
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [30]

description:
sample name:
30
DNA barcode of deleted cassette

value: Initial YDC pool


title: History-dependence BAR-Seq [29]

description:
sample name:
29
DNA barcode of deleted cassette


title: Banana_leaf_adult_RNA-seq_1

description:
Leaf_mature_rep1
sequencing instrument(s): HiSeq X Ten


title: History-dependence BAR-Seq [21]

description:
sample name:
21
DNA barcode of deleted cassette

value: End of maltose growth after 6h glucose


title: extramedullary infiltration, rep1 [circRNA]

description:
T1.1
circRNA expression of AML patient with extramedullary infiltration, replicate 1.


title: History-dependence BAR-Seq [20]

description:
sample name:
20
DNA barcode of deleted cassette

value: End of maltose growth after 4h glucose


title: History-dependence BAR-Seq [27]

description:
sample name:
27
DNA barcode of deleted cassette


title: Cp_immature_DNase-seq

description:
Cp_immature
sequencing instrument(s): Illumina HiSeq 4000,HiSeq X Ten

value: fruit flesh

value: immature


title: History-dependence BAR-Seq [19]

description:
sample name:
19
DNA barcode of deleted cassette


title: extramedullary infiltration, rep3 [circRNA]

description:
T1.3
circRNA expression of AML patient with extramedullary infiltration, replicate 3.

value: male


title: History-dependence BAR-Seq [18]

description:
sample name:
18
DNA barcode of deleted cassette

value: End of maltose growth after 2h glucose


title: History-dependence BAR-Seq [22]

description:
sample name:
22
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [16]

description:
sample name:
16
DNA barcode of deleted cassette

value: End of maltose growth after 0h glucose


title: History-dependence BAR-Seq [14]

description:
sample name:
14
DNA barcode of deleted cassette

value: 12h in glucose


title: History-dependence BAR-Seq [17]

description:
sample name:
17
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [12]

description:
sample name:
12
DNA barcode of deleted cassette

value: 10h in glucose


title: History-dependence BAR-Seq [10]

description:
sample name:
10
DNA barcode of deleted cassette

value: 8h in glucose


title: History-dependence BAR-Seq [15]

description:
sample name:
15
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [13]

description:
sample name:
13
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [9]

description:
sample name:
9
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [11]

description:
sample name:
11
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [6]

description:
sample name:
6
DNA barcode of deleted cassette

value: 4h in glucose


title: History-dependence BAR-Seq [7]

description:
sample name:
7
DNA barcode of deleted cassette

value: 6h in glucose


title: History-dependence BAR-Seq [4]

description:
sample name:
4
DNA barcode of deleted cassette

value: BY4730, NatR:MAL63::MAL13, MAL12:yEcitrine:LEU2, MAL11:mCherry:URA3

value: 2h in glucose


title: History-dependence BAR-Seq [2]

description:
sample name:
2
DNA barcode of deleted cassette

value: End of maltose pregrowth


title: History-dependence BAR-Seq [5]

description:
sample name:
5
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [1]

description:
sample name:
1
DNA barcode of deleted cassette


title: History-dependence BAR-Seq [3]

description:
sample name:
3
DNA barcode of deleted cassette


title: Knockdown RVT1(siRNA-RVT1)#b vs Knockdown control rep1

city: nanjing

first: chen

last: wanghao

state: jiangsu

address: Ding Jiaqiao 87th

department: School of Medicine

institute: southeast university

description:
Biological replicate 1 of 3
SAMPLE 2

hyb_protocol: According to the Agilent lncRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images. The signal ratio of Cy5 intensity and Cy3 intensity on the same array was subjected to quantile normalization. The microarray data were quantile normalized using the R limma package. Series supplementary file shows log2 ratio (treated/untreated) data.

label_protocol: Labeled RNAs were heat denatured and hybridized to Agilent lncRNA microarray, according to manufacturer's protocol.

growth_protocol: The GBM cell lines U87 was obtained from the American Type Culture Collection. The cells were cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum. All cells were maintained in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 1000

treatment_protocol: siRNAs targeting the Lnc_RVT1 sequence or control were transfected into U87 using Lipofectamine 2000.Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: Human Glioblastoma cell

tag: transfected with

source_name: Control siRNA_2

value: Control siRNA_2


title: Knockdown RVT1(siRNA-RVT1)#a vs Knockdown control rep3

description:
Biological replicate 3 of 3
SAMPLE 5

source_name: Control siRNA_1

value: Control siRNA_1


title: Knockdown RVT1(siRNA-RVT1)#b vs Knockdown control rep3

description:
Biological replicate 3 of 3
SAMPLE 6


title: Knockdown RVT1(siRNA-RVT1)#b vs Knockdown control rep2

description:
Biological replicate 2 of 3
SAMPLE 4


title: History-dependence BAR-Seq [8]

description:
sample name:
8
DNA barcode of deleted cassette


title: Knockdown RVT1(siRNA-RVT1)#a vs Knockdown control rep2

description:
Biological replicate 2 of 3
SAMPLE 3


title: PR8 infected 293T, AgoIP

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Ago-bound RNA

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences (Kozomara and Griffiths-Jones, 2014), Ensembl noncoding RNA database release 70 (Flicek et al., 2014), human functional RNA database version 3.4 (Mituyama et al., 2009), the IAV PR8 sequence (concatenated segment accessions nos. EF190971-EF190978), and finally human genome hg19.  No mismatches were allowed for alignments to the different references except the human genome for which two mismatches were allowed.
Genome_build: IAV PR8 sequence (segment accessions nos. EF190971-EF190978), 8 segments concatenated in order of: PB2-PB1-PA-HA-NP-NA-M-NS
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the PB2 genome segment beginning at 1, ending position of the aligned read, aligned reads per million of total assignable reads (total count of reads that could be aligned to miRbase, Ensembl ncRNA, fRNAdb, PR8 virus, and HG19), and the strand (+ or -) that the read aligns to.

source_name: IAV PR8

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 9% fetal bovine serum and Gentamicin

extract_protocol:
Small RNA were extracted with the miRvana microRNA isolation kit (Thermo Fisher) or RNA co-immunoprecipitated with an Ago2 antibody for the AgoIP samples
Small RNA processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

treatment_protocol: Cells infected with influenza virus for 1 hour, virus replaced with DMEM with 0.01% FBS and 0.35% BSA. Harvested 24 hours post infection.

tag: virus infection

value: Delta-NS1 PR8 mutant

tag: transfected plasmid

tag: illumina small rna sequencing index


title: PR8 infected 293T, input control for AgoIP

description: Total small RNA (<200nt)


title: PR8 infected A549

description: Total small RNA (<200nt)


title: NB4_JMJD3_rep1

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

description:
JMJD3_NB4_1_fpkm
CHG005765-0115lane17-0115lane17-JMJD3-NB4-1_S8_L001

data_processing:
Basecalls performed using CASAVA version 1.8
Adapter sequences were removed by using SeqPrep, and then poor quality reads filtered by sickle(version 1.200) for quality control
Quality filtered reads were then mapped to GRCh38 using TopHat (v2.0.4)
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
GO functional enrichment and KEGG pathway analysis were carried out by Goatools  and KOBAS
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file of expression analysis result of  EdgeR and annotation

growth_protocol: NB4 were grown in DMEM supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduced with

value: JMJD3-expression vector


title: NB4_Vector_rep2

description:
Control_NB4_2_fpkm
CHG005765-0115lane17-0115lane17-Control-NB4-2_S3_L001

value: control vector


title: NB4_JMJD3_rep2

description:
JMJD3_NB4_2_fpkm
CHG005765-0115lane17-0115lane17-JMJD3-NB4-2_S9_L001


title: C6: bronchial tissue, OA-challenged

city: Tokyo

first: Yoshihiko

last: Chiba

address: 2-4-41 Ebara, Shinagawa-ku

department: Department of Physiology and Molecular Sciences

country: Japan

institute: Hoshi University School of Pharmacy

hyb_protocol: Each labeled cRNA (600 ng) was fragmented by adding 5 μL 10 x blocking agent and 1 μL of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μL 2 x GE hybridization buffer was added to dilute the labeled cRNA. The hybridization solution (40 µL) was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, v2 Microarrays (Agilent Technologies). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven, and then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (v6.5, Agilent Technologies).

scan_protocol: The hybridized array was immediately scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: The captured array images were analyzed using Agilent Feature Extraction Software (v11.0.1.1, Agilent Technologies). The raw data for same gene was then summarized automatically in Agilent Feature Extraction Protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

organism: Mus musculus

source_name: bronchial tissue, OA-challenged

label_protocol: Total RNA (100 ng) of each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified using RNAeasy Mini Kit (Qiagen, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (Thermo Fisher Scientific Inc.).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol.

value: bronchus

value: male

tag: strain

value: BALB/c

tag: age

value: 11 weeks


title: N6: bronchial tissue, Control

source_name: bronchial tissue, Control

tag: tissue


title: N4: bronchial tissue, Control


title: C3: bronchial tissue, OA-challenged


title: C5: bronchial tissue, OA-challenged


title: N2: bronchial tissue, Control


title: N5: bronchial tissue, Control


title: KDM5-C70 treated MCF7 cells replicate 1

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

country: USA

institute: Yale University

description:
Sample_CA3-17
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv

data_processing:
Raw 100-bp R1 single-end reads were mapped to human genome with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons independent of the transcriptome annotation.
The uniquely mapped reads (cutoff by MAPQ>10) were counted to ENCODE gene annotation (v24) using featureCounts.
Differential gene expression were performed with DESeq2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Comma-delimited text files include count of reads mapped to each annotated gene, or normalized gene expression measurements.
Supplementary_files_format_and_content: geneCount.csv: Raw counts of sequencing reads to each gene.
Supplementary_files_format_and_content: geneExpr.VST_blind.csv: Gene abundance measure on log2 scale normalized with DESeq2 VarianceStabilzationTransformation function.

source_name: MCF7 cells

growth_protocol: MCF7 cells were routinely generated by re-plating every four days (typically 2-4x10e6 cells into a 100 mm dish) with refeeding once between two splits in RPMI-1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated by using RNeasy mini kit (Qiagen) and following the handbook provided.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: At Day 0, 2x10e6 MCF7 cells were seeded into a 100 mm dish. At Day 1, Day 3, and Day 5, cells were refed with fresh medium plus indicated chemicals. At Day 7, cells were harvested from dishes for total RNA isolation.

value: Breast cancer cell line

tag: treatment 1

value: DMSO

tag: concentration 1

tag: treatment 2

tag: concentration 2

value: 3 uM

tag: time

value: 6 days


title: NB4_Vector_rep1

description:
Control_NB4_1_fpkm
CHG005768-0115lane20-0115lane20-Control-NB4-1_S8_L004


title: CPI-48 treated MCF7 cells replicate 2

description:
Sample_CA3-16
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv

tag: cell type


title: KDM5-C70 treated MCF7 cells replicate 2

description:
Sample_CA3-18
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv


title: PAR-CLIP_seb1_rep2

city: San Francisco

first: Hiten

last: Madhani

state: CA

department: Department of Biochemistry and Biophysics

institute: University of California, San Francisco

description:
Seb1-associated RNA
Replicate2

data_processing:
adapter sequences were removed and reads were mapped to the S. pombe genomeusing Bowtie1 allowing for 3 mismatches
Seb1 binding site read clusters were identified with PARalyzer (Corcoran et al. 2011).  Reads of < 20nt were omitted, and read clusters required at least 10 reads and at least two T→C conversions per cluster to be called as a Seb1 binding site called the "OUTPUTCLUSTERS" file.
The PARalyzer OUTPUTCLUSTERSFILE file was converted to a genome browser readable file (.bam) for visualization.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.20.dna.AB325691.fa from Pombase.org
Supplementary_files_format_and_content: .csv files are the "OUTPUTCLUSTERS" files (derived from PARalyzer) listing genome coordinates of RNA transcripts bound by Seb1. Bedgraph files are of the Seb1 binding clusters that are output by PARalyzer.

organism: Schizosaccharomyces pombe

source_name: Yeast Cell

growth_protocol: Cells were grown in 2L of SC medium to an OD600 of 0.75.

extract_protocol:
RNA-protein complexes were  isolated by ball mill (15hz, 3 minutes, 5 cycles) and purification on IgG-sepharose (GE Healthcare).
Illumina RNA 3' Adapter (from the TruSeq Small RNA Sample Prep) was ligated to the Rna followed by 5' labeling with P32.  Illumina RNA 5' Adapter (from the TruSeq Small RNA Sample Prep) was then ligated. RNA-protein complexes were run on an SDS-PAGE gel, extracted, and electroeluted to isolate the complexes. RNA was isolated by proteinase K digestion, reverse transcribed and PCR amplified to produce our final libraries.
PAR-CLIP and CRAC

treatment_protocol: 4-thiouracil (Sigma, #440736-1G) was added to a final concentration of 1.3mM for 15 minutes in the dark at 30°C. Samples were immediately crosslinked using the UV Power-Shot Handheld UV Curing System (SPDI UV) at a 365 nm wavelength for 15 minutes while continuously stirring.  Samples were collected by filtration, resuspended in 6mL of buffer TMN150 (50mM Tris-HCl pH 7.8, 150mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 5mM beta-mercaptoethanol) and frozen as “yeast popcorn” by dropwise addition to liquid nitrogen.

value: clr4delta seb1-cHTP


title: CPI-48 treated MCF7 cells replicate 1

description:
Sample_CA3-15
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv


title: DMSO treated MCF7 cells replicate 2

description:
Sample_CA3-14
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv


title: PAR-CLIP_seb1_rep1

description:
Seb1-associated RNA
Replicate1


title: dNS1 infected A549

description: Total small RNA (<200nt)


title: C1: bronchial tissue, OA-challenged

tag: gender


title: Sample97_B6_2

city: New York

first: Patricia

middle: K

last: Martin

state: NY

institute: NYU School of Medicine

data_processing:
Reads were imported into QIIME2-2018.2 for demultiplexing and quality filtering with default parameters.
Amplicon sequence variants were extracted from amplicon data using DADA2 with default parameters.
Taxonomic clustering was performed using the naive bayes classifier implemented in Qiime2 using SILVA release 132 rRNA database.
PCoA plots were generated using QIIME 2 Emperor plugin.
Genome_build: SILVA release 132 rRNA database
Supplementary_files_format_and_content: biom

extract_protocol:
DNA was extracted using Macherey Nagel NucleoSpin Soil kit following manufacturer's instructions
Amplicon library preparation was performed using an automated platform (Biomek SPRIworks HT) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using EMP primer set 515F/806R. Each unique barcoded amplicon was generated in pairs of 25μl reactions with the following reaction conditions: 13μl PCR-grade H2O, 10μl HotStart MasterMix, 0.5μl of forward and reversed barcoded primer (10μM) and 1μl template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94°C for 3 min followed by 35 cycles of denaturation at 94°C for 45 seconds, annealing at 50°C for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72°C. Amplicons were quantified using Agilent 2200 TapeStation system and pooled.
EMP 16s Illumina Amplicon Protocol

tag: genotype

value: F

tag: infection status

value: Yes

tag: infection days

value: Stool

tag: barcode

value: GGCACACCCTTA


title: Sample99_B6_4

value: TCGCGCAACTGT


title: Sample96_B6_1

value: TCAATCGCTTTC


title: Sample94_Jackson_4

value: Jackson

value: No

value: AACGTTAGTGTG


title: Sample98_B6_3

value: GTCCAGCTATGA


title: Sample91_Jackson_1

value: GAAGTAGCGAGC


title: Sample95_Jackson_5

value: TGCATGACAGTC


title: Sample92_Jackson_2

value: TTGCGGACCCTA


title: Sample89_Taconic_4

value: Taconic

value: CCGAAGATTCTG


title: Sample9_HM_4

value: HM

value: CTGTAAAGGTTG


title: Sample88_Taconic_3

value: F

value: CTTTCGTTCAAC


title: Sample87_Taconic_2

value: Stool

value: TGTGGTGATGTA


title: Knockdown RVT1(siRNA-RVT1)#a vs Knockdown control rep1

description:
Biological replicate 1 of 3
SAMPLE 1

tag: cell line

value: Human Glioblastoma cell

tag: transfected with

value: Control siRNA_1


title: Sample90_Taconic_5

value: GTTGGCGTTACA


title: DMSO treated MCF7 cells replicate 1

description:
Sample_CA3-13
processed data file: geneCount.csv
processed data file: geneExpr.VST_blind.csv

value: Breast cancer cell line

value: DMSO

value: 6 days


title: Sample86_Taconic_1

value: No

value: GTGTCCGGATTC


title: Sample81_Charles_River_1

value: TCTGGAACGGTT


title: Sample84_Charles_River_4

value: CTATCCAAGTGG


title: Sample79_HM_Caspases_1.11_4

value: TGCGAGTATATG


title: Sample85_Charles_River_5

value: CAGTCTAGTACG


title: Sample83_Charles_River_3

value: TTCCTGTTAACC


title: Sample80_HM_Caspases_1.11_5

value: F

value: TACCACAACGAA


title: Sample82_Charles_River_2

value: Stool

value: GTACTACCTCGG


title: Sample78_HM_Caspases_1.11_3

value: M

value: TTGCGACAAAGT


title: Sample75_Caspases_1.11_5

value: ACACCTGCGATC


title: Sample76_HM_Caspases_1.11_1

value: GGCGTTGCATTC


title: Sample93_Jackson_3

value: Jackson

value: GCGGAAACATGG


title: Sample8_HM_3

value: HM

value: No

value: GAGGTTCTTGAC


title: Sample77_HM_Caspases_1.11_2

value: ACTAGCGTTCAG


title: Sample71_Caspases_1.11_1

value: GCCTTACGATAG


title: Sample73_Caspases_1.11_3

value: AACGAGGCAACG


title: Sample72_Caspases_1.11_2

value: TACCTGTGTCTT


title: HOXA9

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

institute: KULeuven / VIB

description:
ChIP-seq ChIPmentation DNA
xenograft sample from patient XE89 - HOXA9 ChIP

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 (ChIP)
call peaks with MACS2
normalize sample with deeptools
Genome_build: Homo Sapiens (hg19)
Supplementary_files_format_and_content: bedgraph file with normalized mapped signal (ChIP)

extract_protocol: DNA libraries were prepared for sequencing using standard Illumina protocols

value: xenograft

tag: chip antibody

value: HOXA9 Sigma Atlas Antibodies Cat#HPA061982 Lot#86503

tag: sample type

value: xenograft sample from patient XE89


title: Sample70_HM_NLRP3_5

value: F

value: Stool

value: TGGCGATACGTT


title: Sample7_HM_2

value: CCTAGAGAAACT


title: Rao-2017-CHIP038-input-treated

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
Reads were aligned using BWA against the b37 human build
Reads were deduplicated using PicardTools
Reads were analyzed with MACS 2.0 (Liu, 2014). All data was normalized against the corresponding input control using the ‘-c’ option of MACS 2.0.
Genome_build: b37 (human)

source_name: Colorectal carcinoma

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
ChIP-Seq for H3K27Ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3, H3K9me3, H4K16Ac, H4K20me3, H3K79me2, and H2.AZ was performed using a native ChIP-Seq protocol. Chromatin from untreated HCT-116 RAD21-mAC cells or cells treated for 6 hours with 500uM IAA was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five microgram of respective antibody was incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. Libraries were prepped for Illumina sequencing and 50bp single-end reads were sequenced on a HiSeq2000 or 2500 (Illumina). We also performed ChIP-Seq for RAD21 and CTCF following the same protocol as above, except that cells were fixed with 1% formaldehyde for 10 minutes at 37°C and fixation was quenched by the addition of glycine to a final concentration of 125mM for 10 minutes. The fixed cells were sonicated using a Branson sonifier at amplitude 35%, 12 cycles of 20 seconds of sonication and 30 seconds of pause. Antibody was added to the sonicated chromatin as above and the samples were further processed as above.    We also performed ChIP-Seq for SMC1 and an additional replicate for CTCF following the protocol outlined by the ENCODE consortium (2012).
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

treatment_protocol: Cells were treated with 500uM auxin as described in the characteristics above

tag: protocol

value: ChIP-Seq

tag: treatment

value: 500uM auxin (360 min)


title: Rao-2017-CHIP039-input-treated


title: Sample68_HM_NLRP3_3

tag: tissue

value: AATCAGAGCTTG


title: History-dependence BAR-Seq [26]

description:
sample name:
26
DNA barcode of deleted cassette

tag: background strain

value: BY4730, NatR:MAL63::MAL13, MAL12:yEcitrine:LEU2, MAL11:mCherry:URA3

tag: condition

value: End of maltose growth after 10h glucose


title: Rao-2017-CHIP036-input-treated


title: Sample67_HM_NLRP3_2

value: M

value: No

value: ACTGGCAAACCT


title: Sample74_Caspases_1.11_4

value: GAAGACAGCGAC


title: Sample66_HM_NLRP3_1

value: CAATTCTGCTTC


title: Rao-2017-CHIP037-input-untreated


title: Rao-2017-CHIP035-input-untreated


title: Rao-2017-CHIP032-input-treated


title: Sample65_NLRP3_5

value: TTGCCTGGGTCA


title: Sample64_NLRP3_4

value: CTCCTTAAGGCG


title: Sample63_NLRP3_3

value: TAGGCTCGTGCT


title: Sample62_NLRP3_2

value: TGACAACCGAAT


title: Rao-2017-CHIP031-input-untreated


title: Sample60_Atg4b_5

value: F

value: Stool

value: TGCAAGCTAAGT


title: MAC310_S2_H3K27ac [ChIP-seq]

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling.
ChIP-seq reads were trimmed for adapter sequences and low-quality score bases using Trim Galore. The resulting reads were mapped to the human reference genome using Bowtie 2 with the following option: -N 1.
Only reads that had a unique alignment were retained, and PCR duplicates were further removed using Picard tools (http://broadinstitute.github.io/picard/).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *_H3K27ac.bw: bigWig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region.

source_name: Monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained by centrifugation on Ficoll-Paque, and monocytes were isolated by positive selection with CD14 magnetic beads (Miltenyi Biotec). Monocytes were differentiated into macrophages by adding rhM-CSF (20ng/mL; R&D Systems Inc.) in the cell culture medium.

extract_protocol:
DNA from macrophages was extracted using the DNeasy Blood and Tissue Kit (Qiagen).
Samples were crosslinked with 1% w/v formaldehyde for 20 minutes at RT and immediately quenched for 5 minutes with 1.25M Glycine at RT. The formaldehyde fixed samples were then sonicated to 150-500 bp using an S2 sonicator (Covaris), and subsequently ChIP-DNA was prepared using a manual chromatin immunoprecipitation method with Antibodies-Antigen incubation for 18 hours, followed by bead incubation for 135 minutes, and 6 5-minute washing steps. Approximately 1 × 106 cells were used for each ChIP and 500,000 cells for the input. The following antibody for H3K27ac was used: Abcam, Ab4729, Lot No.: GR200563-1. ChIP and Input libraries were prepared using the MicroPlex Library Preparation Kit (C05010010, Diagenode), with alterations including: PCR enrichment (13 to 14 cycles) prior to size selection and use of Ampure beads for size selection (250-350 bp). Libraries were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Macrophages were infected with Salmonella typhimurium as previously described (Nédélec et al. 2016). Briefly, macrophages were infected at MOI of 10:1 for 2 hours, washed, and cultured for 1 hour with 50μg/ml gentamycin, then washed again and cultured in complete medium with 3μg/ml gentamycin for an additional 2, 4, 8, 12, 24 or 48 h, the time points we refer to in the main text.

tag: donor id

value: Monocyte-derived macrophages

value: S

tag: time (h)


title: MAC310_NI2_H3K27ac [ChIP-seq]

tag: cell type

value: NI


title: Sample6_HM_1

value: HM

tag: gender

value: GCACCTGTTGAA


title: Sample61_NLRP3_1

tag: genotype

value: M

value: GTGTGTGCCATA


title: DC1_NI18 [ATAC-seq]

data_processing:
Illumina bcl2fastq software used for basecalling.
ATAC-Seq reads were mapped to the human reference genome using BWA-MEM in paired-end mode at default parameters.
Reads that had a unique alignment and mapping quality of ≥10 were retained.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include number of reads that mapped within a genomic region for each sample.

source_name: Monocyte-derived dendritic cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained by centrifugation on Ficoll-Paque, and monocytes were isolated by positive selection with CD14 magnetic beads (Miltenyi Biotec). Monocytes were differentiated into DCs by adding rhIL-4 (20 ng/mL; Shenandoah Biotechnology, Inc) and rhGM-CSF (20 ng/mL; R&D Systems Inc.) in the cell culture medium.

extract_protocol:
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
ATAC-seq libraries were generated from 50,000 cells, as previously described (Buenrostro et al., 2013).

treatment_protocol: DCs were infected with MTB for 2, 18, 24, 48, and 72 h at a multiplicity of infection (MOI) of 1:1 or with heat-killed MTB at MOI of 5:1, as this MOI induces virtually the same transcriptional response at all four time points compared to that observed with live MTB.

value: Monocyte-derived dendritic cells


title: DC1_NI24 [ATAC-seq]


title: DC1_NI48 [ATAC-seq]


title: DC1_NI2 [ATAC-seq]


title: DC1_HI72 [ATAC-seq]

value: HI MTB


title: DC1_NI72 [ATAC-seq]


title: Sample59_Atg4b_4

tag: infection status

value: No

value: CATGTAAGGCTC


title: Sample58_Atg4b_3

value: CCGACATTGTAG


title: DC1_HI24 [ATAC-seq]


title: DC1_HI18 [ATAC-seq]


title: Sample54_T316AE_4

value: ACGGATGTTATG


title: Sample56_Atg4b_1

value: GTAGGAACCGGA


title: Sample57_Atg4b_2

value: F

value: ACATCTAGCAGA


title: DC558_TB72 [RNA-seq]

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Read count estimates per gene were obtained using the alignment-free method Kallisto.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include count values for each sample.

extract_protocol:
Total RNA was extracted from the same samples using the miRNeasy kit (Qiagen). RNA quantity was evaluated spectrophotometrically, and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies). Only samples with no evidence for RNA degradation (RNA integrity number > 8) were kept for further experiments.
RNA-seq libraries were generated via polyA+ selection of mRNA from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: DCs were infected with MTB for 2, 18, 48, and 72 h at a multiplicity of infection (MOI) of 1:1 or with heat-killed MTB at MOI of 5:1, as this MOI induces virtually the same transcriptional response at all four time points compared to that observed with live MTB.

value: Live MTB


title: Sample69_HM_NLRP3_4

value: Stool

value: CAATGTAGACAC


title: DC1_HI48 [ATAC-seq]


title: DC558_TB48 [RNA-seq]


title: DC558_TB18 [RNA-seq]


title: Sample50_HM_Sting_5

value: CTACCACGGTAC


title: Sample55_T316AE_5

value: TTGAGGCTACAA


title: DC1_HI2 [ATAC-seq]


title: Sample53_T316AE_3

value: TTCTAGAGTGCG


title: Sample52_T316AE_2

value: GTACATGTCGCC


title: Sample51_T316AE_1

value: CGGTCTGTCTGA


title: DC558_NI72 [RNA-seq]

value: Monocyte-derived dendritic cells

value: NI


title: Sample48_HM_Sting_3

value: No

value: TTGTATGACAGG


title: DC558_HI48 [RNA-seq]

value: HI MTB


title: DC555_TB72 [RNA-seq]


title: Sample5_B6_5

value: AGATGTCCGTCA


title: DC558_NI48 [RNA-seq]


title: Sample49_HM_Sting_4

value: GGTAAGTTTGAC


title: DC555_TB48 [RNA-seq]


title: Sample42_Sting_2

value: Sting

value: F

value: CATAGCTCGGTC


title: DC558_NI18 [RNA-seq]


title: DC558_HI72 [RNA-seq]


title: Sample46_HM_Sting_1

value: M

value: Stool

value: GATGATAACCCA


title: Sample47_HM_Sting_2

value: GGCCCAATATAA


title: Sample45_Sting_5

value: ACTACCTCTTCA


title: DC555_TB2 [RNA-seq]

value: Live MTB


title: DC558_HI18 [RNA-seq]


title: DC555_NI48 [RNA-seq]


title: DC555_TB18 [RNA-seq]


title: Sample43_Sting_3

value: AACCATGCCAAC


title: Sample4_B6_4

value: ATACGCATCAAG


title: Sample44_Sting_4

value: TATGGAGCTAGT


title: DC555_NI18 [RNA-seq]

value: Monocyte-derived dendritic cells

value: NI


title: Sample41_Sting_1

value: No

value: GTAACCACCACC


title: Sample37_HM_MAVSE_2

value: TGGAATTCGGCT


title: Sample39_HM_MAVSE_4

value: TGCCGAGTAATC


title: DC555_NI72 [RNA-seq]


title: Sample36_HM_MAVSE_1

value: TCTTCAACTACC


title: DC555_NI2 [RNA-seq]


title: DC555_HI2 [RNA-seq]

value: HI MTB


title: DC555_HI18 [RNA-seq]


title: DC555_HI48 [RNA-seq]


title: DC552_TB72 [RNA-seq]


title: Sample33_MAVSE_3

value: MAVSE

value: F

value: GCAAATCAGCCT


title: Sample38_HM_MAVSE_3

value: Stool

value: TAAGATGCAGTC


title: Sample40_HM_MAVSE_5

value: M

value: ACCTTGACAAGA


title: DC552_TB48 [RNA-seq]

value: Live MTB


title: DC552_NI72 [RNA-seq]


title: DC552_TB18 [RNA-seq]


title: Sample30_HM_CCR2_5

value: AGTCATCGAATG


title: Sample29_HM_CCR2_4

value: CGGGATCAAATT


title: DC555_HI72 [RNA-seq]

value: Monocyte-derived dendritic cells


title: DC552_NI48 [RNA-seq]

value: NI


title: Sample28_HM_CCR2_3

value: No

value: ATAGCTTCGTGG


title: DC552_NI2 [RNA-seq]


title: Sample35_MAVSE_5

value: AGCGGCCTATTA


title: Sample34_MAVSE_4

value: GCAAGCTGTCTC


title: Sample27_HM_CCR2_2

value: TAAGCGTCTCGA


title: DC552_HI72 [RNA-seq]

value: HI MTB


title: Sample26_HM_CCR2_1

value: AAGCTTGAAACC


title: Sample32_MAVSE_2

value: MAVSE

value: F

value: AGCACCGGTCTT


title: Sample22_CCR2_2

value: Stool

value: GTCAACGCTGTC


title: DC5_TB18 [RNA-seq]

value: Live MTB


title: DC552_TB2 [RNA-seq]


title: Sample21_CCR2_1

value: M

value: TAGACCGACTCC


title: Sample3_B6_3

value: AGCTTCGACAGT


title: Sample20_HM_IFNAR_5

value: TCAGCGCCGTTA


title: Sample31_MAVSE_1

value: No

value: ATCTTGGAGTCG


title: DC552_HI48 [RNA-seq]

value: Monocyte-derived dendritic cells


title: DC5_NI48 [RNA-seq]

value: NI


title: Sample25_CCR2_5

value: ATAGAGGCCATT


title: Sample24_CCR2_4

value: GCTGTCGTCAAC


title: DC552_HI18 [RNA-seq]

value: HI MTB


title: Sample18_HM_IFNAR_3

value: AAGCAGATTGTC


title: DC552_HI2 [RNA-seq]


title: DC552_NI18 [RNA-seq]


title: DC5_NI2 [RNA-seq]


title: Sample23_CCR2_3

value: F

value: ACAGGAGGGTGT


title: DC5_TB2 [RNA-seq]


title: DC5_NI18 [RNA-seq]


title: DC5_TB48 [RNA-seq]


title: DC4_TB18 [RNA-seq]


title: DC5_HI48 [RNA-seq]


title: Sample19_HM_IFNAR_4

value: Stool

value: TAGAGGCGTAGG


title: Sample17_HM_IFNAR_2

value: CGAGTTCATCGA


title: Sample153_HM_3

value: HM

value: Yes

tag: infection days

value: GATTTAGAGGCT


title: Sample2_B6_2

tag: barcode

value: CTCGATGTAAGC


title: Sample150_B6_5

value: TCTCGCACTGGA


title: DC5_HI2 [RNA-seq]


title: DC4_HI48 [RNA-seq]


title: Sample154_HM_4

value: GTCAGCCGTTAA


title: Sample155_HM_5

value: ACGGTTTCTGGA


title: Sample148_B6_3

value: GTTACAGTTGGC


title: DC4_HI2 [RNA-seq]

value: Monocyte-derived dendritic cells


title: Sample152_HM_2

value: GTCCACTTGGAC


title: Sample151_HM_1

value: TTCTGGTCTTGT


title: DC4_NI48 [RNA-seq]

value: NI


title: DC4_TB2 [RNA-seq]

value: Live MTB


title: Sample16_HM_IFNAR_1

value: M

value: No

value: TGATAGGTACAC


title: DC4_NI18 [RNA-seq]


title: MAC302_S24 [SeqCap Epi]

data_processing:
Library strategy: SeqCap Epi
Illumina bcl2fastq software used for basecalling. Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) lambda phage genome using Bismark. Only reads that had a unique alignment were retained.
Methylation levels for each CpG site were estimated by counting the number of sequenced C (‘methylated’ reads) divided by the total number of reported C and T (‘unmethylated’ reads) at the same position of the reference genome using Bismark’s methylation extractor tool. We performed a strand-independent analysis of CpG methylation where counts from the two Cs in a CpG and its reverse complement (position i on the plus strand and position i+1 on the minus strand) were combined and assigned to the position of the C in the plus strand. To assess MethylC-seq bisulfite conversion rate, the frequency of unconverted cytosines (C basecalls) at lambda phage CpG reference positions was calculated from reads uniquely mapped to the lambda phage reference genome.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *_methcov.txt: Tab-delimited text files include methylation levels for each targeted CpG site for each sample.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained by centrifugation on Ficoll-Paque, and monocytes were isolated by positive selection with CD14 magnetic beads (Miltenyi Biotec). Monocytes were differentiated into either DCs by adding rhIL-4 (20 ng/mL; Shenandoah Biotechnology, Inc) and rhGM-CSF (20 ng/mL; R&D Systems Inc.) or macrophages by adding rhM-CSF (20ng/mL; R&D Systems Inc.) in the cell culture medium.

extract_protocol:
DNA from DCs was extracted using the PureGene DNA extraction kit (Gentra Systems). DNA from macrophages was extracted using the DNeasy Blood and Tissue Kit (Qiagen).
Libraries were generated with KAPA Library Preparation Kit for Illumina Platforms (KAPA Biosystems), as per the manufacturer’s instructions. Briefly, genomic DNA was fragmented to 100-300 bp with an S2 sonicator (Covaris). Fragments were then end-repaired, A-tailed, and ligated with methylated sequencing adapters. Between every enzymatic step, libraries were purified using AMPure beads (Agencourt). After ligation, in addition to the AMPure bead purification, a DUAL-SPRI size selection was performed to further select for fragments with adapters in the window of 200-400 bp. Sodium bisulfite conversion was performed with EZ DNA Methylation Lightning Kit (Zymo Research), and libraries were amplified using KAPA Hifi HotStart Uracil Tolerant Enzyme (KAPA Biosystems). Library quality was assessed by 2100 Bioanalyzer (Agilent Technologies). Samples showing the desired profile were pooled together in equal mass according to Qubit quantification. We then performed a hybridization using the SeqCap Epi kit (Roche NimbleGen). The sample pool, indexes corresponding to the sequences of the adapters used for library preparation, and repetitive DNA (C0t) were desiccated and then incubated in hybridization buffer with a set of customized probes for 72 hours to select and sequence target regions only. Specifically, DNA methylation data was collected for 33,059 target regions spanning >130,000 CpG sites (mean length = 300 bp; mean number of CpG sites = 5), which is less than 1% of the ~28 million CpGs contained in the human genome. These regions were primarily comprised of MTB-induced differentially methylated regions identified at 18 hours post-infection using whole-genome bisulfite sequencing, as well as other distal regulatory elements in DCs where changes in DNA methylation have been shown to be most likely to occur. Moreover, these candidate regions were nearby differentially expressed genes in response to MTB at 18 hours. Probes targeting a two kilobase region between coordinates 4500 and 6500 bp of the lambda genome (NC_001416.1) are included by default in the SeqCap Epi design, as a control for bisulfite conversion efficiency. Sequencing was performed using the Illumina HiSeq 2500, as per the manufacturer’s instructions.

treatment_protocol: DCs were infected with MTB for 2, 18, 48, and 72 h at a multiplicity of infection (MOI) of 1:1 or with heat-killed MTB at MOI of 5:1, as this MOI induces virtually the same transcriptional response at all four time points compared to that observed with live MTB. Macrophages were infected with Salmonella typhimurium as previously described (Nédélec et al. 2016). Briefly, macrophages were infected at MOI of 10:1 for 2 hours, washed, and cultured for 1 hour with 50μg/ml gentamycin, then washed again and cultured in complete medium with 3μg/ml gentamycin for an additional 2, 4, 8, 12, 24 or 48 h, the time points we refer to in the main text.

value: Monocyte-derived macrophages

value: S


title: MAC302_S12 [SeqCap Epi]


title: Sample145_HM_5

value: HM

value: F

value: Yes

value: Stool

value: TTGGTGCCTGTG


title: Sample15_IFNAR_5

value: IFNAR

value: TGCTCCGTAGAA


title: DC4_TB48 [RNA-seq]

value: Monocyte-derived dendritic cells


title: DC4_NI2 [RNA-seq]


title: MAC302_S48 [SeqCap Epi]


title: Sample141_HM_1

value: TGCTTCCAATTC


title: Sample146_B6_1

value: CATCGGATCTGA


title: MAC302_S8 [SeqCap Epi]


title: Sample143_HM_3

value: ACTTACGCCACG


title: Sample149_B6_4

value: CGGACTCGTTAC


title: Sample142_HM_2

value: GAATGACGTTTG


title: MAC302_S4 [SeqCap Epi]


title: MAC302_S2 [SeqCap Epi]


title: Sample140_B6_5

value: GGACCGCTTTCA


title: DC4_HI18 [RNA-seq]

value: HI MTB


title: Sample14_IFNAR_4

value: M

value: No

value: CATGCGGATCCT


title: Sample147_B6_2

value: F

value: CATGTCTTCCAT


title: MAC302_NI12 [SeqCap Epi]

value: Monocyte-derived macrophages

value: NI


title: MAC302_NI24 [SeqCap Epi]


title: MAC302_NI48 [SeqCap Epi]


title: MAC302_NI8 [SeqCap Epi]


title: MAC302_NI4 [SeqCap Epi]


title: DC5_HI18 [RNA-seq]


title: Sample138_B6_3

value: Yes

value: Stool

value: GAAGATCTATCG


title: Sample137_B6_2

value: CACCGTGACACT


title: MAC302_NI2 [SeqCap Epi]


title: Sample144_HM_4

value: HM

value: ACGCCTTTCTTA


title: Sample136_B6_1

value: CACAAAGCGATT


title: Sample139_B6_4

value: GACGGAACAGAC


title: DC558_TB72 [SeqCap Epi]

value: Monocyte-derived dendritic cells

value: Live MTB


title: Sample132_HM_3

value: CCGCGATTTCGA


title: DC558_TB18 [SeqCap Epi]


title: Sample134_HM_4

value: ACACACCCTGAC


title: Sample131_HM_1

value: AGTCCGAGTTGT


title: DC558_TB2 [SeqCap Epi]


title: DC558_NI48 [SeqCap Epi]


title: Sample130_B6_5

value: F

value: TGGAAACCATTG


title: Sample13_IFNAR_3

value: IFNAR

value: No

value: TGCACAGTCGCT


title: DC558_HI72 [SeqCap Epi]

value: HI MTB


title: DC558_NI2 [SeqCap Epi]

value: NI


title: Sample129_B6_4

value: Yes

value: Stool

value: AGTAGACTTACG


title: Sample128_B6_3

value: GAAGAGGGTTGA


title: DC558_NI18 [SeqCap Epi]


title: Sample127_B6_2

value: ACCTCCCGGATA


title: DC558_HI48 [SeqCap Epi]

value: Monocyte-derived dendritic cells


title: DC558_HI18 [SeqCap Epi]


title: Sample125_HM_5

value: HM

value: TGCTGTGACCAC


title: Sample124_HM_4

value: AGGTCATCTTGG


title: DC558_HI2 [SeqCap Epi]


title: Sample126_B6_1

value: ACACTTCGGCAA


title: DC555_TB18 [SeqCap Epi]

value: Live MTB


title: Sample123_HM_3

value: F

value: TAGTAGCACCTG


title: DC555_NI72 [SeqCap Epi]


title: Sample122_HM_2

value: ACGTCTCAGTGC


title: DC555_TB72 [SeqCap Epi]


title: DC558_NI72 [SeqCap Epi]


title: Sample119_B6_4

value: CGTCCGTATGAA


title: Sample12_IFNAR_2

value: IFNAR

value: No

value: CTCTAGAAGAGT


title: DC555_TB2 [SeqCap Epi]


title: Sample121_HM_1

value: Yes

value: Stool

value: CGATTAGGAATC


title: Sample118_B6_3

value: ACCCGGATTTCG


title: DC555_HI72 [SeqCap Epi]

value: Monocyte-derived dendritic cells

value: HI MTB


title: DC555_NI18 [SeqCap Epi]

value: NI


title: DC555_NI2 [SeqCap Epi]


title: Sample135_HM_5

value: HM

value: TCACGAGTCACA


title: DC555_HI18 [SeqCap Epi]


title: Sample115_HM_5

value: CTTGGTAGTGCC


title: DC555_HI48 [SeqCap Epi]


title: Sample117_B6_2

value: F

value: AGTAGGAGGCAC


title: DC552_TB72 [SeqCap Epi]

value: Live MTB


title: Sample116_B6_1

value: GTGCTGCGCTTA


title: DC555_HI2 [SeqCap Epi]


title: Sample114_HM_4

value: GGCTCAGATTCC


title: Sample113_HM_3

value: CTAAGACGTCGT


title: DC552_TB48 [SeqCap Epi]


title: DC552_TB18 [SeqCap Epi]


title: DC555_NI48 [SeqCap Epi]


title: Sample110_B6_5

value: CACGTACACGTA


title: DC552_TB2 [SeqCap Epi]


title: Sample111_HM_1

value: Yes

value: CAGAGCTAATTG


title: Sample108_B6_3

value: Stool

value: ATGAATGCGTCC


title: DC552_NI48 [SeqCap Epi]

value: Monocyte-derived dendritic cells


title: DC552_NI72 [SeqCap Epi]


title: Sample11_IFNAR_1

value: IFNAR

value: No

value: TACGGCAGTTCA


title: DC552_HI48 [SeqCap Epi]

value: HI MTB


title: DC552_NI2 [SeqCap Epi]

value: NI


title: Sample107_B6_2

value: F

value: CGCTTGTGTAGC


title: DC552_NI18 [SeqCap Epi]


title: DC552_HI2 [SeqCap Epi]


title: Sample112_HM_2

value: HM

value: TTATCCAGTCCT


title: Sample104_HM_4

value: ACTAGTTGGACC


title: Sample103_HM_3

value: CCACGGTACTTG


title: Sample101_HM_1

value: TGGTTCATCCTT


title: DC5_TB2 [SeqCap Epi]

value: Live MTB


title: DC5_NI48 [SeqCap Epi]


title: Sample100_B6_5

value: Yes

value: ATTCCTCTCCAC


title: Sample102_HM_2

value: Stool

value: AGCACTTTGAGA


title: DC5_NI2 [SeqCap Epi]

value: Monocyte-derived dendritic cells


title: DC5_NI18 [SeqCap Epi]


title: Sample1_B6_1

value: M

value: No

value: TGGAGCCTTGTC


title: Sample10_HM_5

value: TGAGTCATTGAG


title: DC5_HI18 [SeqCap Epi]

value: HI MTB


title: Sample109_B6_4

value: F

value: ATGTAGGCTTAG


title: DC5_HI2 [SeqCap Epi]


title: DC5_TB48 [SeqCap Epi]


title: Sample106_B6_1

value: ATGCGAGACTTC


title: Sample105_HM_5

value: HM

value: GATCAACCCACA


title: DC5_TB18 [SeqCap Epi]


title: 3C_GL_IGCR1del/del_DHQ51-JH1bait_set13

city: BOSTON

first: Suvi

last: Jain

state: MA

address: 300 LONGWOOD AVE

department: Molecular Medicine

institute: Boston Children's Hospital

data_processing:
Library strategy: 3C-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 AJ851868/mm9 hybrid reference genome (Lin et al., 2016) in which Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, 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 and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016). Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, if using DHFL16.1JH4 line or its derivatives.
Supplementary_files_format_and_content: Bedgraph file type that allows display of continuous-valued data in track format from bed file. Contains header line with track type, file name, visibility level, and RGB color levels. Also, the following tab delimited information succeeding the header line: chromosome, start coordinate, end coordinate, number of junctions at the start and end coordinates.

source_name: v-Abl kinase transformed pro-B cell

extract_protocol:
10 million cells were crosslinked with 2% (v/v) formaldehyde for 10’ at room temperature, followed by quenching with glycine at a final concentration of 125 mM. Cells were lysed in 50 mM Tris-HCl, pH 7.5, containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TritonX-100 and protease inhibitors (Roche, #11836153001). Nuclei were digested with 700 units of NlaIII (NEB, #R0125) or MseI (NEB, #R0525) restriction enzyme at 37℃ overnight, followed by ligation under dilute conditions at 16℃ overnight. Crosslinks were reversed and samples were treated with Proteinase K (Roche, #03115852001) and RNase A (Invitrogen, #8003089) prior to DNA precipitation. The 3C DNA thus obtained was use dto prepare HTGTS libraries.
Libraries were prepared using 3C samples by HTGTS.

value: v-Abl kinase transformed pro-B cell

value: Germline Rag2-/- IGCR1del/del

tag: bait region

tag: restriction enzyme

value: NlaIII

tag: alignment genome

value: AJ851868/mm9 hybrid genome

tag: growth conditions


title: 3C_GL_IGCR1del/del_VH81X-CBEscr/scr_Emubait_set12

value: Germline Rag2-/- IGCR1de/dell VH81X-CBEscr/scr

value: iEm


title: 3C_GL_IGCR1del/del_Emubait_set13


title: DC5_HI48 [SeqCap Epi]

value: Monocyte-derived dendritic cells


title: 3C_WT_Emubait_set11

value: DHFL16.1JH4 AJ851868/mm9 hybrid genome


title: 3C_GL_WT_Emubait_set12

value: Germline Rag2-/-


title: 3C_IGCR1del_Emubait_set11

value: Rag2-/- IGCR1del


title: DJ_IGCR1del_VH5-1-CBEins_rep1

data_processing:
Library strategy: 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 AJ851868/mm9 hybrid reference genome (Lin et al., 2016) 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 and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016)
Supplementary_files_format_and_content: tab delimited text files contain all filtered junctions including duplicates 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 extracted overnight at 55 degree Celcius in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using HTGTS.

treatment_protocol: 10 million v-Abl transformed pro-B cells were cultured in R-15 medium containing 3 mM STI-571 for 4 days.

value: IGCR1del VH5-1-CBEins

tag: treatment protocol

value: 4 mM STI-571 to induce G1 arrest

value: JH4 coding end


title: 3C_IGCR1del_VH5-1-CBEins_1_Emubait_set11

value: Rag2-/- IGCR1del VH5-1-CBEins


title: 3C_GL_IGCR1del/del_Emubait_set12


title: DJ_IGCR1del_VH5-1-CBEins_rep2

value: 5 mM STI-571 to induce G1 arrest


title: DJ_IGCR1del_VH5-1-CBEins_rep3

value: 6 mM STI-571 to induce G1 arrest


title: DJ_VH81X-CBEinv_rep4

value: 3 mM STI-571 to induce G1 arrest


title: DJ_VH81X-CBEinv_rep3

value: v-Abl kinase transformed pro-B cell


title: DJ_VH81X-CBEinv_rep2


title: 3C_IGCR1del_VH5-1-CBEins_2_Emubait_set11


title: DJ_VH81X-CBEinv_rep1


title: 3C_IGCR1del_VH81X-CBEdel_Emubait_set10

data_processing:
library strategy: 3C-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 AJ851868/mm9 hybrid reference genome (Lin et al., 2016) in which Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, 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 and bait sequences shorter than 50nt.
Genome_build: AJ851868/mm9 hybrid genome (Lin et al., 2016). Chr12 coordinates from 114671120 to 114734564 were replaced with CCCCT to incorporate the DHFL16.1 to JH4 rearrangement, if using DHFL16.1JH4 line or its derivatives.
Supplementary_files_format_and_content: Bedgraph file type that allows display of continuous-valued data in track format from bed file. Contains header line with track type, file name, visibility level, and RGB color levels. Also, the following tab delimited information succeeding the header line: chromosome, start coordinate, end coordinate, number of junctions at the start and end coordinates.

tag: genotype/variation

value: Rag2-/- IGCR1del VH81X-CBEdel


title: 3C_WT_Emubait_set10

tag: tissue

value: NlaIII


title: LoVo

city: Heidelberg

first: Tianzuo

last: Zhan

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

description: replicate 1

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing: Data were normalized using the 'affy' R/Bioconductor package. Normalization steps include background correction using the 'rma' method and quantile normalization.

label: biotin

source_name: cancer cell line

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA, Label: Biotin

growth_protocol: HCT116 was cultured in McCoy’s 5A medium + 10% FCS. RKO, CaCo2 and HT55 were cultured in DMEM with 4 mM glutamine + 10% FCS. LoVo and SNU-C2A were cultured in RPMI + 10% FCS. GP2d and HCA-24 were cultured in DMEM with 2 mM glutamine + 10% FCS. WiDr was cultured in EMEM +10% FCS with 1% NEAA. CL-14 was cultured in DMEM / Ham's F12 (1:1 mixture) + 20% FCS and LIM2405 was cultured in RPMI + 10% FCS with 25 mM HEPES, 10 µM thioglycerol and 0,6 µg/ml insulin (all supplements from Sigma Aldrich, Waltham, USA).

extract_protocol: Qiagen RNeasy Extraction Kit

treatment_protocol: cells were harvested without treatment

value: colorectal cancer


title: WiDr

description: replicate 1


title: GP2d

description: replicate 1


title: 3C_IGCR1del_Emubait_set10


title: HCA-24

description: replicate 1


title: SNU-C2A

description: replicate 1


title: SW403

description: replicate 1


title: 3C_IGCR1del_Emubait_set9


title: 3C_WT_Emubait_set9


title: RKO

description: replicate 1


title: LIM2405

description: replicate 1


title: 3C_IGCR1del_VH81X-CBEdel_Emubait_set9


title: CL-14 2

description: replicate 1


title: HCT116

description: replicate 1


title: HT55

description: replicate 1


title: CaCo2

description: replicate 1