title: RPMI_d1_rep2_H3K4me1

source_name: RPMI d1 rep2 H3K4me1


title: Mo_d0_H3K9me3

status: Public on Nov 18 2016

type: SRA

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the three studied histone marks at p-value of 10-10. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac and H3K4me3 were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: bam files sequence and quality, and BigWig files for tracks. All data have been normalized ("Normalized") to a depth per mark except few which have been marked as "NotNormalized"

molecule: genomic DNA

organism: Homo sapiens

source_name: Mo d0 H3K9me3

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Tolerization was induced by treatment of monocytes with 10-100ng/mL LPS for 24 hours, followed by washout and five days culture in RPMI + 10% human serum, while trained innate immunity was induced by treatment with 5 ng/mL BG for 24 hours, followed by washout and 5 days in culture. Establishment of tolerance or training in the resulting macrophages at day 6 was determined by TNF and IL6 release at 24 hours following LPS stimulation using ELISA. For ChIP-seq, 10x106 monocytes were seeded in 10cm dishes, for RNAseq and ATAC-seq 1.5 x 106 monocytes were seeded in 6 well plates.

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 67µl of chromatin (1 million cells) was incubated with 229µl dilution buffer, 3µl protease inhibitor cocktail and 0.5-1µg of H3K27ac, H3K4me3, H3K4me1, H3K27me3, H3K9me3 or H3K36me3 antibodies (Diagenode) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.

tag: background strain

value: Adult Human Peripheral Blood

tag: cell type

value: Monocyte

tag: treatment

value: Monocyte (negative selected)

tag: chip antibody

value: Rabbit polyclonal anti-H3K9me3 (Diagenode, cat. # pAb-193-050)


title: LPS_1h_rep2_H3K27ac

source_name: LPS 1h rep2 H3K27ac

value: Mono_1h_LPS (LPS exposed, collected at 1 hour of exposure)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: RPMI_4h_rep2_H3K4me1

source_name: RPMI 4h rep2 H3K4me1

value: Mono_4h_Naive (culture only, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: RPMI_d1_rep1_H3K4me3

source_name: RPMI d1 rep1 H3K4me3

value: Mono_day1_Naive (RPMI media exposed 24 hours, collected at 24 hours)

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: BG_4h_H3K27me3

source_name: BG 4h H3K27me3

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K27me3 (Diagenode, cat. # pAb-195-050)


title: RPMI_4h_rep1_H3K27ac

source_name: RPMI 4h rep1 H3K27ac


title: LPS_d1_rep2_H3K4me1

source_name: LPS d1 rep2 H3K4me1

value: Mono_day1_LPS (LPS exposed for 24 hours, collected at 24 hour of exposure)


title: LPS_1h_rep2_H3K4me1

source_name: LPS 1h rep2 H3K4me1


title: LPS_4h_H3K27me3

source_name: LPS 4h H3K27me3

value: Mono_4h_LPS (LPS exposed, collected at 4 hour of exposure)


title: BG_4h_rep2_H3K4me1

source_name: BG 4h rep2 H3K4me1

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)Mono_4h_LPS (LPS exposed, collected at 4 hour of exposure)


title: BG_1h_rep1_H3K27ac

source_name: BG 1h rep1 H3K27ac

value: Mono_1h_BG (BG exposed, collected at 1 hour of exposure)


title: LPS_4h_rep1_H3K27ac

source_name: LPS 4h rep1 H3K27ac


title: RPMI_d6_rep2_H3K4me3

source_name: RPMI d6 rep2 H3K4me3

value: Naïve-Mf (culture for 6 days to macrophage)


title: BG_d7_rep1_H3K27ac

source_name: BG d7 rep1 H3K27ac

value: Adult Human Peripheral Blood

value: BG-Mf LPS exposed (BG exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)


title: RPMI_4h_H3K9me3

source_name: RPMI 4h H3K9me3

value: Monocyte


title: d0_rep1_H3K4me1

source_name: d0 rep1 H3K4me1

value: Monocyte (negative selected)


title: LPS_d6_rep1_H3K27me3

source_name: LPS d6 rep1 H3K27me3

value: LPS-Mf (LPS exposed 24 hours, culture for 5 days to macrophage)


title: BG_d7_rep1_H3K4me1

source_name: BG d7 rep1 H3K4me1


title: RPMI_R_rep2_H3K27me3

source_name: RPMI R rep2 H3K27me3

value: Naïve-Mf LPS exposed (culture for 6 days to macrophage, LPS exposed for 4 hours)


title: d0_rep2_H3K4me1

source_name: d0 rep2 H3K4me1


title: RPMI_d1_rep1_H3K4me1

source_name: RPMI d1 rep1 H3K4me1


title: BG_d6_rep2_H3K27me3

source_name: BG d6 rep2 H3K27me3

value: BG-Mf (BG exposed 24 hours, culture for 5 days to macrophage)


title: d0_rep2_H3K27ac

source_name: d0 rep2 H3K27ac

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: LPS_d7_rep1_H3K4me3

source_name: LPS d7 rep1 H3K4me3

value: LPS-Mf LPS re-exposed (LPS exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)


title: RPMI_4h_rep2_H3K4me3

source_name: RPMI 4h rep2 H3K4me3

value: Mono_4h_Naive (culture only, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: BG_d1_rep2_H3K4me1

source_name: BG d1 rep2 H3K4me1

value: Mono_day1_BG (BG exposed for 24 hours, collected at 24 hour of exposure)

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: BG_R_rep2_H3K27me3

source_name: BG R rep2 H3K27me3

value: Rabbit polyclonal anti-H3K27me3 (Diagenode, cat. # pAb-195-050)


title: LPS_d6_rep1_H3K4me1

source_name: LPS d6 rep1 H3K4me1


title: RPMI_d1_rep2_H3K27ac

source_name: RPMI d1 rep2 H3K27ac

value: Mono_day1_Naive (RPMI media exposed 24 hours, collected at 24 hours)


title: BG_d1_rep1_H3K4me1

source_name: BG d1 rep1 H3K4me1


title: RPMI_d7_rep1_H3K27ac

source_name: RPMI d7 rep1 H3K27ac


title: d0_H3K27me3

source_name: d0 H3K27me3


title: RPMI_4h_H3K27me3

source_name: RPMI 4h H3K27me3


title: RPMI_d6_rep2_H3K4me1

source_name: RPMI d6 rep2 H3K4me1


title: don74_LPS_d6_H3K27ac

source_name: don74 LPS d6 H3K27ac


title: LPS_R_H3K9me3

source_name: LPS R H3K9me3

value: Rabbit polyclonal anti-H3K9me3 (Diagenode, cat. # pAb-193-050)


title: LPS_1h_rep1_H3K4me3

source_name: LPS 1h rep1 H3K4me3

value: Mono_1h_LPS (LPS exposed, collected at 1 hour of exposure)


title: BG_d1_rep1_H3K27ac

source_name: BG d1 rep1 H3K27ac

value: Adult Human Peripheral Blood


title: don74_LPS_d6_24hr_BG_H3K4me1

source_name: don74 LPS d6 24hr BG H3K4me1

value: Rescue-Mf (LPS exposed 24 hours, then BG exposed 24 hours, culture for 4 days to macrophage)


title: LPS_d7_rep1_H3K4me1

source_name: LPS d7 rep1 H3K4me1

value: Monocyte


title: BG_d6_rep1_H3K4me3

source_name: BG d6 rep1 H3K4me3


title: RPMI_d7_rep1_H3K4me1

source_name: RPMI d7 rep1 H3K4me1

value: Naïve-Mf LPS exposed (culture for 6 days to macrophage, LPS exposed for 4 hours))


title: LPS_4h_rep2_H3K27ac

source_name: LPS 4h rep2 H3K27ac

value: Mono_4h_LPS (LPS exposed, collected at 4 hour of exposure)


title: RPMI_d1_H3K27me3

source_name: RPMI d1 H3K27me3


title: LPS_d1_H3K9me3

source_name: LPS d1 H3K9me3

value: Mono_day1_LPS (LPS exposed for 24 hours, collected at 24 hour of exposure)


title: RPMI_4h_rep2_H3K27ac

source_name: RPMI 4h rep2 H3K27ac

value: Mono_4h_Naive (exposed to RPMI media only, collected at 4 hour of exposure)


title: BG_d1_H3K27me3

source_name: BG d1 H3K27me3


title: RPMI_4h_rep1_H3K4me3

source_name: RPMI 4h rep1 H3K4me3


title: RPMI_d1_rep2_H3K4me3

source_name: RPMI d1 rep2 H3K4me3


title: BG_4h_rep2_H3K4me3

source_name: BG 4h rep2 H3K4me3

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)


title: RPMI_1h_rep2_H3K27ac

source_name: RPMI 1h rep2 H3K27ac

value: Mono_1h_Naive (culture only, collected at 1 hour of exposure)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: don74_LPS_d6_24hr_BG_H3K27ac

source_name: don74 LPS d6 24hr BG H3K27ac

value: LPS-Mf (LPS exposed 24 hours, culture for 5 days to macrophage)


title: RPMI_d1_rep1_H3K27ac

source_name: RPMI d1 rep1 H3K27ac


title: BG_1h_rep2_H3K27ac

source_name: BG 1h rep2 H3K27ac

value: Mono_1h_BG (BG exposed, collected at 1 hour of exposure)


title: d0_rep1_H3K4me3

source_name: d0 rep1 H3K4me3

value: Monocyte (negative selected)

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: LPS_4h_H3K9me3

source_name: LPS 4h H3K9me3


title: RPMI_d6_rep2_H3K27me3

source_name: RPMI d6 rep2 H3K27me3

value: Naïve-Mf (culture for 6 days to macrophage)

value: Rabbit polyclonal anti-H3K27me3 (Diagenode, cat. # pAb-195-050)


title: don73_LPS_d6_H3K27ac

source_name: don73 LPS d6 H3K27ac


title: LPS_d6_rep2_H3K27me3

source_name: LPS d6 rep2 H3K27me3


title: LPS_4h_rep2_H3K4me3

source_name: LPS 4h rep2 H3K4me3


title: RPMI_1h_rep2_H3K4me1

source_name: RPMI 1h rep2 H3K4me1

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: RPMI_d6_rep2_H3K27ac

source_name: RPMI d6 rep2 H3K27ac

value: Adult Human Peripheral Blood


title: BG_d6_rep2_H3K4me1

source_name: BG d6 rep2 H3K4me1

value: BG-Mf (BG exposed 24 hours, culture for 5 days to macrophage)


title: RPMI_d6_rep1_H3K27me3

source_name: RPMI d6 rep1 H3K27me3

value: Monocyte


title: LPS_R_rep2_H3K27me3

source_name: LPS R rep2 H3K27me3

value: LPS-Mf LPS re-exposed (LPS exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)


title: don74_RPMI_d6_H3K4me1

source_name: don74 RPMI d6 H3K4me1


title: BG_d6_H3K9me3

source_name: BG d6 H3K9me3

value: Rabbit polyclonal anti-H3K9me3 (Diagenode, cat. # pAb-193-050)


title: BG_1h_rep1_H3K4me3

source_name: BG 1h rep1 H3K4me3


title: LPS_d6_rep2_H3K4me1

source_name: LPS d6 rep2 H3K4me1


title: BG_1h_rep2_H3K4me3

source_name: BG 1h rep2 H3K4me3


title: don74_LPS_d6_H3K4me1

source_name: don74 LPS d6 H3K4me1


title: RPMI_1h_rep2_H3K4me3

source_name: RPMI 1h rep2 H3K4me3

value: Mono_1h_Naive (exposed to RPMI media only, collected at 1 hour of exposure)


title: don73_RPMI_d6_H3K4me1

source_name: don73 RPMI d6 H3K4me1


title: LPS_d1_rep1_H3K4me1

source_name: LPS d1 rep1 H3K4me1

value: Mono_day1_LPS (LPS exposed 24 hours, collected at 24 hours)


title: don74_LPS_d6_co_iBET_H3K4me1

source_name: don74 LPS d6 co iBET H3K4me1


title: RPMI_4h_rep1_H3K4me1

source_name: RPMI 4h rep1 H3K4me1

value: Mono_4h_Naive (exposed to RPMI media only, collected at 4 hour of exposure)


title: don73_RPMI_d6_H3K27ac

source_name: don73 RPMI d6 H3K27ac


title: LPS_d7_rep1_H3K27ac

source_name: LPS d7 rep1 H3K27ac


title: BG_4h_rep2_H3K27ac

source_name: BG 4h rep2 H3K27ac

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)


title: RPMI_R_H3K9me3

source_name: RPMI R H3K9me3

value: Naïve-Mf LPS exposed (culture for 6 days to macrophage, LPS exposed for 4 hours)


title: RPMI_1h_rep1_H3K4me1

source_name: RPMI 1h rep1 H3K4me1


title: LPS_1h_rep1_H3K4me1

source_name: LPS 1h rep1 H3K4me1

value: Mono_1h_LPS (LPS exposed, collected at 1 hour of exposure)


title: RPMI_d6_rep1_H3K4me3

source_name: RPMI d6 rep1 H3K4me3


title: BG_d1_rep2_H3K27ac

source_name: BG d1 rep2 H3K27ac

value: Mono_day1_BG (BG exposed 24 hours, collected at 24 hours)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: LPS_d6_rep1_H3K27ac

source_name: LPS d6 rep1 H3K27ac

value: LPS-Mf (LPS exposed 24 hours, culture for 5 days to macrophage)


title: LPS_d1_rep2_H3K27ac

source_name: LPS d1 rep2 H3K27ac


title: BG_R_rep1_H3K27me3

source_name: BG R rep1 H3K27me3

value: BG-Mf LPS re-exposed (BG exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)


title: LPS_d1_rep1_H3K4me3

source_name: LPS d1 rep1 H3K4me3

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: BG_d6_rep1_H3K27ac

source_name: BG d6 rep1 H3K27ac


title: LPS_d1_rep1_H3K27ac

source_name: LPS d1 rep1 H3K27ac


title: d0_rep2_H3K4me3

source_name: d0 rep2 H3K4me3

value: Monocyte (negative selected)


title: LPS_d1_H3K27me3

source_name: LPS d1 H3K27me3

value: Adult Human Peripheral Blood

value: Rabbit polyclonal anti-H3K27me3 (Diagenode, cat. # pAb-195-050)


title: don73_LPS_d6_H3K4me1

source_name: don73 LPS d6 H3K4me1

value: Monocyte

value: Rabbit polyclonal anti-H3K4me1 (Diagenode, cat. # pAb-003-050)


title: don74_LPS_d6_co_iBET_H3K27ac

source_name: don74 LPS d6 co iBET H3K27ac

value: LPS-IBET-Mf (Exposed to LPS and IBET151 together for 24 hours, culture for 5 days to macrophage)


title: BG_4h_rep1_H3K4me3

source_name: BG 4h rep1 H3K4me3


title: RPMI_d7_rep1_H3K4me3

source_name: RPMI d7 rep1 H3K4me3


title: Rescue_LPS_BGd2_d6_10653

library_source: transcriptomic

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation (Ensemble release 68).
Genome_build: hg19

molecule: total RNA

source_name: Adult Human Peripheral Blood

extract_protocol: Libraries were prepared according to Illumina's instructions.

tag: treatment protocol

value: LPS exposed 24 hours, BG exposed for 24 hours, culture for 4 days to macrophage.

tag: library strategy

value: RNA-Seq


title: Rescue_LPS_BGd2_d6_10645


title: BG_1h_rep1_H3K4me1

source_name: BG 1h rep1 H3K4me1

value: Mono_1h_BG (BG exposed, collected at 1 hour of exposure)


title: BG_d7_rep1_H3K4me3

source_name: BG d7 rep1 H3K4me3


title: LPS_1h_rep1_H3K27ac

source_name: LPS 1h rep1 H3K27ac


title: RPMI_d6_Restim_don70_10648

value: Culture only for 6 days to macrophage, LPS exposed for 4 hours.


title: Rescue_LPS_BGd2_Restim_10646

value: LPS exposed 24 hours, BG exposed for 24 hours, culture for 4 days to macrophage, LPS exposed for 4 hours.


title: Rescue_LPS_BGd2_Restim_10654


title: RPMI_d6_don70_10647

value: Culture only, collected at 6 days post culture.


title: LPS_R_rep1_H3K27me3

source_name: LPS R rep1 H3K27me3

value: LPS-Mf LPS re-exposed (LPS exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours)


title: BG_4h_rep1_H3K27ac

source_name: BG 4h rep1 H3K27ac

value: Mono_4h_BG (BG exposed, collected at 4 hour of exposure)

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: RPMI_d6_Restim_9246


title: RPMI_d6_Restim_8749


title: RPMI_d6_Restim_8754


title: RPMI_d6_9243


title: RPMI_d6_8752


title: RPMI_d6_8746


title: RPMI_d6_6718


title: RPMI_d6_6095


title: RPMI_d1_6092

value: Culture only, collected at 24 hours post culture.


title: RPMI_4h_don73_10834

value: Culture only, collected at 4 hours post culture.


title: RPMI_1h_rep1_H3K4me3

source_name: RPMI 1h rep1 H3K4me3

value: Mono_1h_Naive (culture only, collected at 1 hour of exposure)

value: Rabbit polyclonal anti-H3K4me3 (Diagenode, cat. # pAb-003-050)


title: RPMI_4h_6089


title: RPMI_d1_6715


title: RPMI_1h_6709

value: Culture only, collected at 1 hour post culture.


title: RPMI_1h_6086

value: Monocyte


title: Monocyte_d0_don73_10833

value: Negatively selected monocyte. No culture


title: Monocyte_d0_6085


title: Monocyte_d0_6708


title: LPSthenIBET_d6_Restim_don70_10832

value: LPS exposed 24 hours, 5 uM IBET151 exposed for 24 hours, culture for 4 days to macrophage, LPS exposed for 4 hours.


title: LPSthenIBET_d6_don70_10831

value: LPS exposed 24 hours, 5 uM IBET151 exposed for 24 hours, culture for 4 days to macrophage.


title: LPS_d6_Restim_don70_10650

value: LPS exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours.

value: RNA-Seq


title: LPS_d6_don70_10649

value: LPS exposed 24 hours, culture for 5 days to macrophage.


title: LPS_d6_9244


title: LPS_d6_Restim_9247


title: LPS_d6_6719


title: LPS_d6_8747


title: LPS_d6_6097


title: LPS_d1_6716

value: LPS exposed, collected at 24 hours post exposure.


title: LPS_4h_don73_10835

value: LPS exposed, collected at 4 hours post exposure.


title: LPS_d1_6094


title: LPS_4h_6713


title: LPS_1h_6710

value: LPS exposed, collected at 1 hour post exposure.


title: RPMI_4h_6712


title: LPS_4h_6091


title: LPS_1h_6088


title: Monocyte_d0_IBET_9885


title: IBET_d6_RPMI_5uM_Restim_10528

value: 5 uM IBET151 exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours.


title: IBET_d6_RPMI_5uM_9878

value: 5 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_RPMI_0uM_Restim_10527

value: Culture only, collected at 6 days post culture.


title: IBET_d6_RPMI_5uM_10526


title: IBET_d6_RPMI_0uM_9876


title: IBET_d6_RPMI_1uM_9877

value: 1 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_RPMI_0uM_10525


title: IBET_d6_LPS_5uM_Restim_10652

value: LPS and 5 uM IBET151 exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours.


title: IBET_d6_LPS_5uM_9881

value: LPS and 5 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_LPS_5uM_Restim_10644


title: LPS_d6_Restim_8750


title: IBET_d6_LPS_5uM_10530


title: IBET_d6_LPS_5uM_Restim_10532


title: IBET_d6_LPS_0uM_Restim_10531


title: IBET_d6_LPS_0uM_9879


title: IBET_d6_LPS_5uM_10651


title: IBET_d6_BG_5uM_9884

value: BG and 5 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_LPS_1uM_9880

value: Monocyte

value: LPS and 1 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_BG_1uM_9883

value: BG and 1 uM IBET151 exposed 24 hours, culture for 5 days to macrophage.


title: IBET_d6_LPS_0uM_10529


title: IBET_d6_LPS_5uM_10643


title: IBET_d6_BG_0uM_9882

value: BG exposed 24 hours, culture for 5 days to macrophage.


title: BG_d6_Restim_8755

value: BG exposed 24 hours, culture for 5 days to macrophage, LPS exposed for 4 hours.


title: BG_d6_Restim_9248

value: RNA-Seq


title: IBET_4h_RPMI_don73_10837

value: IBET151 exposed, collected at 1 hour post culture.


title: BG_d6_Restim_8751


title: BG_d6_8753


title: BG_d1_6717

value: BG exposed, collected at 24 hours post exposure.


title: BG_4h_don73_10836

value: BG exposed, collected at 4 hours post exposure.


title: BG_4h_6090


title: BG_d6_8748


title: BG_1h_6711

value: BG exposed, collected at 1 hour post exposure.


title: BG_d6_6720


title: Adjacent liver tissue_p1 [0FU_nt]

city: New Orleans

first: Jinqiang

last: Zhang

address: 1430 Tulane Ave

department: Pathology

country: USA

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat-2.0.6 with parameters --bowtie1 --solexa-quals -r -31 --mate-std-dev56 --fusion-search -p 7
Cufflink 2.0.1 was used for FPKM files
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking.txt file including FPKM values for each Sample

molecule: polyA RNA

source_name: Adjacent liver tissue

extract_protocol:
Total RNAs were isolated from these frozen tissues with Qiagen RNeasy Mini kit
Poly A RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: adjacent non-tumor tissue

tag: tumor stage

value: stage II


title: HCC tissue_p2 [0MB_t]

source_name: HCC tissue

value: hepatocellular carcinoma (HCC)


title: Adjacent liver tissue_p2 [0MB_nt]


title: HCC tissue_p3 [00Q_t]

value: stage I


title: Adjacent liver tissue_p3 [00Q_nt]


title: HCC tissue_p1  [0FU_t]


title: T24 H3K27ac

city: Lebanon

first: Michael

middle: D

last: Cole

state: NH

address: One Medical Center Dr

institute: Geisel School of Medicine at Dartmouth

description:
ChIP
barcode: CTTGTA

data_processing:
ChIP-seq reads were aligned against the hg19 genome assembly using BOWTIE version 0.12.7 to yield .sam output files
Samtools was used to convert .sam files to .bam files
Peaks were called using MACS version 1.4.0beta with the following specifications: inputs were considered "control" files and ChIPs were considered "treatment" files; band width was set to 300; all parameters were used in "default" mode (i.e. p-value cutoff was set to 1.00e-5)
Wiggle files were generated using MACS with the same specifications and were visualized using IGV
Genome_build: hg19
Supplementary_files_format_and_content: Bed files represent peaks called using MACS and the files list for each peak: chr, chr start, chr end, MACS peak #,  and score - where scores represent −10*log10(p-value) such that a higher score indicates a lower p-value. Txt files were generated from the wiggle files and listed in the file for each peak are: chr, chr start, chr end, length of peak, summit location from chr start, number of reads in peak region, −10*log10(p-value) for peak, fold enrichment for this region, FDR %

source_name: T24 bladder cancer cell line

growth_protocol: Cell lines were cultured in DMEM with 10% FBS and 1% pen/strep

extract_protocol:
Chromatin lysates were isolated from sonicated nuclei (from a 10-cm plate containing 1-2 x 106 cells) and histone-DNA interactions were extracted using an antibody against H3K27ac
Libraries were prepared at Global Biologics (Missouri) using the Illumina ChIP-seq kit, beginning with 20-30ng of pooled DNA sample (from replicates). Barcodes were used to multiplex the sequencing run and the barcodes used were the following: CGATGT, TGACCA, ACAGTG, GCCAAT, CAGATC, CTTGTA. Libraries were sequenced on the HiSeq2000 according to the manufacturer's protocols at the University of Delaware

value: bladder cancer cell line T24

value: H3K27ac (Abcam, catalog# ab4729, lot# GR132150-1)


title: T24 Input

description:
Input DNA
barcode: CAGATC


title: 7.5h in SPO medium_IME1_IME4_RNA-seq

city: Stony Brook

first: Bruce

last: Futcher

state: NY

address: STONY BROOK UNIVERSITY

department: Molecular Genetics & Microbiology

institute: Stony Brook University

data_processing:
self-written script for Basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  whole genome UCSC R64-1-1 (SacCer3) using bowtie 2v2.2.62
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks 2.2.1
Genome_build: UCSC R64-1-1 (SacCer3)
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: yeast cells_7.5h in SPO medium (IME1 IME4 induction)

growth_protocol: cells were grow in YPD plates and then YPD liquid medium to saturation. Diluted in BYTA medium overnight. Shifted into SPO medium

extract_protocol:
total RNA prepared by Ambion Ribopure Yeast Extraction kit (Am1926)
NuGen ovation universal RNA-seq system 1-96 (PN 0402-A01) primed with random hexamer

treatment_protocol: cultured in SPO medium for 2 hours and 25mM CuSO4 is added to the culture to induce IME1 and IME4 expression to generate synchronized meiotic culture

tag: strain

value: strain A 33606

tag: timepoint


title: 8h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_8h in SPO medium (IME1 IME4 induction)


title: 7h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_7h in SPO medium (IME1 IME4 induction)


title: 5637 H3K27ac

description:
ChIP
barcode: GCCAAT

source_name: 5637 bladder cancer cell line

value: bladder cancer cell line 5637


title: 6.5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_6.5h in SPO medium (IME1 IME4 induction)


title: BG_d6_9245

value: Monocyte


title: 6h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_6h in SPO medium (IME1 IME4 induction)


title: BG_d1_6093


title: BG_d6_6096


title: 5637 Input

description:
Input DNA
barcode: ACAGTG


title: BG_4h_6714


title: 5.75h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_5.75h in SPO medium (IME1 IME4 induction)


title: BG_1h_6087

source_name: Adult Human Peripheral Blood


title: 5.5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_5.5h in SPO medium (IME1 IME4 induction)


title: Whole testis small RNA from Miwi2 KO/WT at 16.5 dpc

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

description: total 18-30nt RNA

data_processing:
The 3' adapter sequences were searched in the reads (3' adapter sequence “TGGAATTCTCGGGTGCCAAG”)
The trimmed sequencing reads of each sRNA-seq library were analyzed with ncPRO-seq (v1.5.1, Chen CJ., et al 2012).
Genome_build: mm10
Supplementary_files_format_and_content: Text files with the trimmed sequencing reads and the number of times sequenced.

organism: Mus musculus

source_name: 16.5 dpc testis

extract_protocol:
Whole testis RNA was extracted using Trizol, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Agilent RNA 6000 Assay on a Bioanalyzer.
Small RNA 18-30 nt size selection in polyacrylamide gels, purification, and library construction done by FASTERIS (https://www.fasteris.com/dna/) using stantard protocol.

tag: gender

value: male

tag: genotype

value: Miwi2 KO Heterozygous control

tag: tissue

value: testis

tag: developmental stage


title: Whole testis small RNA from Miwi2 KO/KO at 16.5 dpc

description: total 18-30nt RNA

value: Miwi2 KO Homozygous mutant


title: 5.25h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_5.25h in SPO medium (IME1 IME4 induction)


title: J82 Input

description:
Input DNA
barcode: CGATGT

source_name: J82 bladder cancer cell line

value: bladder cancer cell line J82


title: DN2_TSLPHKM_24H

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street Hansen Life Sciences Bldg, HANS, 225

department: Biochemistry and Computer Science

institute: Purdue University

description: RNA-seq (donor2-HKM+TSLP treated-24hr)

data_processing:
Basecalls performed using CASAVA 1.8
The expression values obtained by RSEM v1.2.21 using the following parameters (rsem-calculate-expression --forward-prob 0 --no-bam-output --bowtie-n 1 --bowtie-m 100 --seed-length 28). Rsem index was created based on hg19.
Differentially expressed genes between any two conditions were obtained using edgeR. The raw read counts were obtained from the "expected counts" column in rsem results. The criteria for selecting differentially expressed genes are Fold Change >2, FDR<0.1, and RPKM>4 in at least one of the two compared conditions.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements(text file)

source_name: donor2-HKM+TSLP treated-24hr

growth_protocol: neutrophils isolated from healthy human blood donors

extract_protocol:
extraction using Qiagen kit
KAPA Stranded mRNA-Seq kit, PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: treated with PBS or TSLP +/- HKSA for 4 or 24 hours

tag: donor number

value: neutrophil

value: Blood


title: 10h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_10h in SPO medium (IME1 IME4 induction)


title: Whole testis small RNA from Dnmt3C IAP/WT at 16.5 dpc

description: total 18-30nt RNA

value: C3H/HeJ - C57BL/6J hybrid background

value: Dnmt3C IAP Heterozygous control


title: Whole testis small RNA from Dnmt3C IAP/IAP at 16.5 dpc

description: total 18-30nt RNA

value: Dnmt3C IAP Homozygous mutant


title: 4.75h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_4.75h in SPO medium (IME1 IME4 induction)


title: 4.5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_4.5h in SPO medium (IME1 IME4 induction)


title: DN2_HKM_24H

description: RNA-seq (donor2-HKM treated-24hr)

source_name: donor2-HKM treated-24hr


title: 4.25h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_4.25h in SPO medium (IME1 IME4 induction)


title: gDNA from 10 dpp FACS-isolated germ cells Dnmt3L Control

description: bisulfite-treated DNA

data_processing:
Raw reads were cleaned by removal of reads following the criteria: containing more than 5 bp of adapter sequence on their 5' extremity; reads with 50% of bases with quality lower than 20 or reads with at least 10% of N nucleotides.
Cleaned reads were aligned onto the mouse reference genome assembly (GRCm38/mm10) using Bismark v0.12.5 with Bowtie2-2.1.0 using default parameters.
Only reads mapping uniquely to the genome were kept, and methylation calls were extracted after duplicate removal by considering only CpG dinucleotides covered by a minimum of 5 reads.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig format containing percentage of CG methylation

source_name: 10 dpp total germ cells

extract_protocol: Germ cells ere isolated from single-cell dissociated 10 dpp testis by FACS  (BD FACSAria II; SSC low/DAPI negative/beta-2 microglobulin negative/EpCAM positive), DNA was extracted using QIAmp DNA Micro Kit, quantified on Qubit, and spiked in with unmethylated Lambda DNA to a 0,1% of the total DNA mass of the sample, followed by bisulfite treatment using the Imprint DNA Modification Kit (SIGMA).

value: C57BL/6J background

value: Heterozygous control


title: gDNA from 10 dpp FACS-isolated germ cells Dnmt3L Mutant

description: bisulfite-treated DNA

value: Homozygous mutant


title: DN2_CTL_24H

description: RNA-seq (donor2-untreated-24hr)


title: DN2_TSLPHKM_4H

description: RNA-seq (donor2-HKM+TSLP treated-4hr)

source_name: donor2-HKM+TSLP treated-4hr


title: 4h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_4h in SPO medium (IME1 IME4 induction)


title: J82 H3K27ac

description:
ChIP
barcode: TGACCA

value: H3K27ac (Abcam, catalog# ab4729, lot# GR132150-1)


title: DN2_HKM_4H

description: RNA-seq (donor2-HKM treated-4hr)

source_name: donor2-HKM treated-4hr


title: gDNA from 10 dpp FACS-isolated germ cells Dnmt3C Control

description: bisulfite-treated DNA


title: gDNA from 10 dpp FACS-isolated germ cells Dnmt3C Mutant

description: bisulfite-treated DNA


title: 3.75h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_3.75h in SPO medium (IME1 IME4 induction)

value: strain A 33606


title: DN2_TSLP_4H

description: RNA-seq (donor2-TSLP treated-4hr)

source_name: donor2-TSLP treated-4hr


title: 3.5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_3.5h in SPO medium (IME1 IME4 induction)


title: 3.25h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_3.25h in SPO medium (IME1 IME4 induction)


title: 5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_5h in SPO medium (IME1 IME4 induction)


title: DN2_CTL_4H

description: RNA-seq (donor2-untreated-4hr)


title: Whole testis RNA from Dnmt3C IAP/WT at 20 dpp 1

data_processing:
Paired-end 2x100bp reads were mapped to the Mouse reference genome (mm10) Using Tophat v2.0.6 and the Refseq gene annotation allowing 5 mismatches.
Gene-scaled quantification was performed with HTSeq v0.6.1
Reads mapping to ribosomal RNA (rRNA) Sequences were first removed with Bowtie v1.0.0 allowing 3 mismatches.
The rRNA depleted libraries were then mapped on the Mouse reference genome (mm10) Using Bowtie v1.0.0 allowing zero mismatch and 10 000 best alignments per read. Exonic reads were removed.
In order to count reads mapping to transposable elements, Read were weighted by the number of mapping sites and each library was intersected with the reconstructed RepeatMasker annotation, Conserving only reads overlapping at least at 80% With a given transposon.
Genome_build: mm10
Supplementary_files_format_and_content: Text files represent gene or transposon-scaled expression value in log

source_name: 20 dpp testis

extract_protocol: Whole testis RNA was extracted using Trizol, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Agilent RNA 6000 Assay on a Bioanalyzer.


title: Whole testis RNA from Dnmt3C IAP/IAP at 20 dpp 2


title: 3h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_3h in SPO medium (IME1 IME4 induction)


title: Whole testis RNA from Dnmt3C IAP/WT at 20 dpp 2


title: DN1_TSLPHKM_24H

description: RNA-seq (donor1-HKM+TSLP treated-24hr)

source_name: donor1-HKM+TSLP treated-24hr


title: 2.75h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_2.75h in SPO medium (IME1 IME4 induction)


title: DN1_HKM_24H

description: RNA-seq (donor1-HKM treated-24hr)

source_name: donor1-HKM treated-24hr


title: 2.5h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_2.5h in SPO medium (IME1 IME4 induction)


title: DN2_TSLP_24H

description: RNA-seq (donor2-TSLP treated-24hr)

source_name: donor2-TSLP treated-24hr


title: Whole testis RNA from Dnmt3C IAP/WT at 10 dpp

source_name: 10 dpp testis


title: 2.25h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_2.25h in SPO medium (IME1 IME4 induction)


title: DN1_CTL_24H

description: RNA-seq (donor1-untreated-24hr)


title: Whole testis RNA from Dnmt3C IAP/IAP at 20 dpp 1


title: Whole testis RNA from Dnmt3C IAP/IAP at 10 dpp


title: 2h in SPO medium_IME1_IME4_RNA-seq

source_name: yeast cells_2h in SPO medium (IME1 IME4 induction)


title: 0h in SPO medium_RNA-seq

source_name: yeast cells_0h in SPO medium


title: Whole testis RNA from Dnmt3C IAP/WT at 16.5 dpc

source_name: 16.5 dpc testis


title: DN1_TSLP_4H

description: RNA-seq (donor1-TSLP treated-4hr)

source_name: donor1-TSLP treated-4hr


title: DN1_HKM_4H

description: RNA-seq (donor1-HKM treated-4hr)

source_name: donor1-HKM treated-4hr


title: DN1_CTL_4H

description: RNA-seq (donor1-untreated-4hr)


title: Mcl1_38B_Set-3

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

description: Δ(129): chr3:95644053-95655885

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/)
Reads were aligned to in silico constructed versions of the 129S1 and CastEiJ genomes using Tophat.
Mapped reads were split into 129, Cast or unknown using custom scripts and variant data, only variant bases sequenced with Phred score > 20 (on standard 33 offset) were considered for allele calling
BedGraphs were generated using bedtools v2.17.0 genomecov script with standard settings.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: embryonic stem cells

growth_protocol: All cells were maintained on gelatin-coated plates in ES media supplemented with LIF and two inhibitors (2i, CHIR99021 and PD0325901).

extract_protocol:
RNA was isolated using Trizol (Life Technologies) and DNase treated prior to library construction.
NEBNext mRNA Library Prep Reagent Set for Illumina

treatment_protocol: Enhancer cluster deleted clones contain heterozygous or homozygous deletions of clusters within the study.  Deletions were generated in F1 ES cells using Cas9 endonuclease and guide RNA as specified in publication.

value: Deletion Present


title: F1_Set-3

value: wild type


title: Mcl1_31B_Set-3

description: Δ(129): chr3:95644053-95655885


title: Etl4_15B_Set-3

description: Δ(129): chr2:20642059-20658958


title: Whole testis RNA from Dnmt3C IAP/IAP at 16.5 dpc

value: male


title: Dppa5a_USC_17_Set-3

description: Δ(129): chr9:78368337-78376479


title: Med13l_B_MTD_28_Set-2

description: Δ(129): chr5:118432886-118452483, Δ(Cast): chr9:78358933-78365818


title: Dppa5a_DSC_5_Set-3

description: Δ(129): chr9:78358933-78365818


title: Esrrb_B_MTD_65_Set-2

description: Δ(129): chr12:86496798-86505014, Δ(Cast): chr9:78358933-78365818


title: Dppa5a_USC_43_Set-3

description: Δ(129): chr9:78368337-78376479, Δ(Cast): chr9:78358933-78365818


title: Macf1_B_Med13l_C_MTD_3_Set-2

description: Δ(129): chr4:123618309-123637993, Δ(Cast): chr5:118432886-118452483, Δ(129): chr9:78358933-78365818


title: Esrrb_B_Med13l_B_MTD_34_Set-2

description: Δ(129): chr12:86496798-86505014, Δ(129): chr5:118432886-118452483


title: Dppa5a_DSC_2_Set-3

description: Δ(129): chr9:78358933-78365818


title: DN1_TSLP_24H

description: RNA-seq (donor1-TSLP treated-24hr)

source_name: donor1-TSLP treated-24hr


title: Macf1_B_MTD_13_Set-2

description: Δ(129): chr4:123618309-123637993, Δ(129): chr9:78358933-78365818


title: Ranbp17_18B_Set-2

description: Δ(129): chr11:33524486-33543505


title: Cbfa2t2_9B_Set-2

description: Δ(129): chr2:154419404-154431952


title: Tet1_30B_Set-1

description: Δ(129): chr10:62891757-62906804


title: F1_Set-2


title: Tet1_59B_Set-1

description: Δ(129): chr10:62891757-62906804


title: DN1_TSLPHKM_4H

description: RNA-seq (donor1-HKM+TSLP treated-4hr)

source_name: donor1-HKM+TSLP treated-4hr


title: Sall1_25D_Set-1

description: Δ(129/Cast): chr8:88986501-89018827


title: Stage B of Limonium bicolor Leaf Development

city: Jinan

first: Baoshan

last: Wang

state: Shandong

address: No.88 East Wenhua Road, Jinan 250014, Shandong, China

department: College of Life Sciences

country: China

institute: Shandong Normal University

data_processing:
Clean reads of five developmental stages were aligned to the coding sequences of the Arabidopsis thaliana transcriptome using the BLAST-like alignment tool BLAT program in protein level.
Supplementary_files_format_and_content: Processed data files.xls: RPKM

organism: Limonium bicolor

source_name: leaf

growth_protocol: Tissue culture

extract_protocol:
Around 5000 leaves from stage A, 4000 from stage B, 2000 from stage C, 1000 from stage D, and 1000 from stage E in total were dissected and sequenced in two separate lanes for biological replicates. Total RNA from different samples was extracted using Total Plant RNA Extraction Kit (Karroten, Beijing, China) and purified by the RNAeasy Mini RNA kit’ (Qiagen, Shanghai, China) including on-column DNase digestion. The Poly(A) RNA was isolated from purified total RNA (at least 4 μg) using two rounds of purification with oligo d(T) beads (Dynabeads).
First-strand cDNA was generated using random hexamer-primed reverse transcription. After second strand cDNA synthesis and adaptor ligation, cDNA fragments of approximately 200 bp were isolated by gel electrophoresis.

treatment_protocol: Different developmetal stages of the first true leaves

tag: developmetal stage

value: Salt Gland Differentiated Leaf of Stage B


title: Stage E of Limonium bicolor Leaf Development

value: Mature Leaf of Stage E


title: Stage D of Limonium bicolor Leaf Development

value: Epidermis Differentiated Leaf of Stage D


title: Mir290_67B_Set-1

description: Δ(129): chr7:3199611-3215602


title: Stage C of Limonium bicolor Leaf Development

value: Stomata Differentiated Leaf of Stage C


title: 20-days hypocotyl, biological replicate 2

city: Esch/Alzette

first: Marc

last: BEHR

address: 5, avenue des Hauts-Fourneaux

department: ERIN

country: Luxembourg

institute: LIST

data_processing:
Sequences were filtered and trimmed as follows: sequence length>55bp, sequence quality score <0.01, no ambiguity in the sequence, trimming for Illumina adaptors and trim of a 13bp region at the 5’ extremity, resulting in final sequence average length of 60 bp.
Duplicates were removed from each library using the duplicate read removal plugin.
The de novo assembly of sequences into contigs was performed with a wording size ranging from 20 to 54. The optimal parameters were an auto-wording of 24, bubble sizing in automatic mode.
The reads were mapped back to the assembly with a mismatch, insertion and deletion cost of 3, a coverage>0.8 and similarity>0.95.
For each library, the mapping was performed with the following criteria: a maximum hit per reads of 3, similarity fraction>0.95, a length fraction>0.7, a mismatch, insertion and deletion cost of 3. The expression values were then calculated using the RPKM method.
Genome_build: Mapping using "in house" de novo assembly of hemp (cv. Santhica 27) transcriptome
Supplementary_files_format_and_content: tab-delimited text file includes: contig number, FDR p-value, TAIR ID,  contig size, gene annotation; unique gene reads, RPKM values for each sample, average of the three biological replicates.

organism: Cannabis sativa

source_name: 20-days hypocotyl

growth_protocol: Hemp (cv. Santhica 27) hypocotyl of 6, 9, 15 and 20 days were grown in controlled conditions in incubators following a cycle of 16h light 25°C / 8h dark 20°C. Each of the 3 biological replicates consisted of 20 hypocotyls randomly selected among all incubators. Sampling was performed on a single experimental batch to minimize technical variability. Samples were immediately frozen in liquid nitrogen and conserved at -80°C until RNA extraction.

extract_protocol:
Libraries were prepared from 3µg of total RNA using the SMARTer Stranded RNA-Seq kit (Clontech). The isolation of mRNAs was performed using the Illumina beads and the TruSeq protocol (Illumina).The final elution of the mRNAs was performed using the Illumina elution buffer (19.5 µl).  The isolated mRNAs were quantified using a Qubit fluorometer, as described above.
10 ng mRNA were used for the cDNA synthesis and shearing. Indexing was performed using the Illumina indices 1-12. The enrichment step was carried out using 12 cycles of PCR. Subsequently, libraries were checked using 2100 Bioanalyzer (DNA-1000) to evaluate the mean fragment size. Quantification was done using the KAPA library quantification kit (KAPA Biosystems) using a ViiA7 Real-Time PCR System (Applied Biosystems). The pooled libraries were sequenced on an Illumina MiSeq in 6 consecutive runs (2x150 paired end: MiSeq reagent kit V3, 300cycles).

treatment_protocol: Hypocotyls were crushed to a fine powder using a mortar, a pestle and liquid nitrogen. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen), treated with DNase I on column, quantified by Qubit 2.0 Fluorometer (Invitrogen) using Qubit RNA Assay Kit (Molecular Probes) and quality-checked with a NanoDrop 1000 Spectrophotometer (Thermo Scientific) and a 2100 Bioanalyzer (Agilent Life Sciences).

tag: cultivar

value: cv. Santhica 27

tag: time point

value: 20 days after sowing

value: hypocotyl


title: 20-days hypocotyl, biological replicate 3


title: 20-days hypocotyl, biological replicate 1


title: 15-days hypocotyl, biological replicate 3

source_name: 15-days hypocotyl

value: 15 days after sowing


title: 15-days hypocotyl, biological replicate 1


title: 15-days hypocotyl, biological replicate 2


title: PCDH7-3

city: Dallas

first: Kathryn

last: O'Donnell

state: TX

address: 6000 Harry Hines Blvd, NA6.300

institute: UT Southwestern Medical Center

description:
Replicate 3
Processed data files: cds_exp.diff_A_B_cds.txt, gene_exp.diff_A_B_Gene.txt, isoform_exp.diff_A_B_Isoform.txt, tss_group_exp.diff_A_B_tss.txt

data_processing:
Illumina HiSeq 2500 used for basecalling.
Reads were trimmed to remove low-quality regions in the ends.
Trimmed reads were mapped to the human genome (hg19) using TopHat v2.0.1227 guided by iGenomes GTF file. Alignments with mapping quality less than 10 were discarded.
Expression abundance estimation and differential expression analysis were carried out using Cufflinks/Cuffdiff (v2.1.1) software.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-separated text files include RPKM values and statistic results of sample A (Control) vs. sample B (PCDH7) generated with Cuffdiff.

source_name: HBEC-shp53, PCDH7

growth_protocol: Immortalised HBEC-shp53 cells were cultured in keratinocyte serum-free medium containing 50 μg/mL of bovine pituitary extract and 5 ng/mL of EGF.

extract_protocol:
Total RNA was purified from HBEC-shp53-PCDH7 or control HBEC-shp53-GFP cells using RNeasy Mini Kit (Qiagen).
Four micrograms of total DNase-treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA were A-tailed and indexed adapters were ligated. Samples were PCR amplified and purified with AmpureXP beads and validated on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit (Invitrogen). Sequencing was performed on an Illumina HiSeq 2500 to generate 51-bp single-end reads.

treatment_protocol: Cells with enforced expression of PCDH7 or control cells were generated by infecting cells with a PCDH7 or GFP lentivirus, respectively. Seven days after drug selection, cells were maintained in the medium without the drug for 3 more days until it reached 70-80% confluency. Then, the cells were harvested and total RNA was isolated for sequencing.

tag: cell type

value: Immortalised Human Bronchial Epithelial Cells (HBEC-shp53)

tag: stable expression


title: PCDH7-1

description:
Replicate 1
Processed data files: cds_exp.diff_A_B_cds.txt, gene_exp.diff_A_B_Gene.txt, isoform_exp.diff_A_B_Isoform.txt, tss_group_exp.diff_A_B_tss.txt


title: PCDH7-2

description:
Replicate 2
Processed data files: cds_exp.diff_A_B_cds.txt, gene_exp.diff_A_B_Gene.txt, isoform_exp.diff_A_B_Isoform.txt, tss_group_exp.diff_A_B_tss.txt


title: 9-days hypocotyl, biological replicate 1

source_name: 9-days hypocotyl

value: 9 days after sowing


title: Ranbp17_16B_Set-2

description: Δ(129): chr11:33524486-33543505


title: 9-days hypocotyl, biological replicate 2


title: 6-days hypocotyl, biological replicate 3

source_name: 6-days hypocotyl

value: 6 days after sowing


title: Sall1_54B_Set-1

description: Δ(129): chr8:88986501-89018827


title: Control-3

source_name: HBEC-shp53, control

value: GPF


title: 6-days hypocotyl, biological replicate 2


title: Sall1_1B_Set-1

description: Δ(129): chr8:88986501-89018827


title: 6-days hypocotyl, biological replicate 1


title: ATAC_RPMI_d6_8454

data_processing:
Library strategy: ATAC-seq
Illumina Casava software 1.8.2  used for basecalling of NextSeq 500 data.
Library strategy: ATAC-seq. Paired-end reads were mapped to human reference genome hg19 using bwa mem. Reads with mapQ>=30 were kept for downstream analysis. Peak calling was done for individual samples using macs (version 2.0.10.20130306) with “-g hs --nomodel -p 1e-10”.
Genome_build: hg19

source_name: Adult Human Peripheral Blood

extract_protocol:
Monocytes or macrophages (100,000 cells) were scrapped in a well of a 6-well plate with cold PBS and then spun down at 800 x g for 5 min at 4 ˚C. Cells were washed with 50 µL of cold 1x PBS buffer, incubated in 50 µl of cold lysis buffer (10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2 0,1 % IGEPAL) and spun down at 800 x g for 10 min at 4˚C. The nuclei were immediately resuspended in the transposition reaction mix (22.5 µL TD buffer, 2.5 µL Tn5 Transposase, 25 µL NF H2O) and incubated for 30 min at 37˚C. Following transposition, 100 µL AMPure beads were added to the reaction (sample-to-bead ratio of 1:2), mixed thoroughly by pipetting, and incubated for 15 min at RT. Samples and beads were washed on the magnetic rack with 80% ethanol, dried for 5 min, and resuspended in 15 µl EB buffer. DNA was amplified with 10 - 15 PCR cycles using the mix (15 µL transposed DNA, 0.3 µL 100x SYBR Green I, 25 µL NEBNext High-Fidelity master mix, 2.5 µL Nextera Primer index N7.. (25 µM), 2.5 µL Nextera Primer index S5.. (25 µM), 4.7 µL NF H2O).  In order to reduce GC and size bias in PCR, the PCR reaction is monitored using qPCR to stop amplification prior to saturation. Following amplification, samples were incubated purified twice using SPRI beads, first using negative selection with a sample-to-bead ratio of 1-0.65  and then positive selection with a sample-to-bead ratio of 1-1.8. After 80% Ethanol wash and drying, the sample was eluted in 20 µl EB buffer, and quality checked before sequencing. Detailed protocol can be found on the Blueprint website (http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/ATAC_Seq_Protocol.pdf).
Library was constructed using the Nextera kit.

value: Monocyte

tag: treatment

value: Culture only, collected at 6 days post culture.

value: Peripheral blood


title: Stage A of Limonium bicolor Leaf Development

value: Undifferentiated Leaf of Stage A


title: Control-2


title: ATAC_RPMI_d1_8451

value: Culture only, collected at 24 hours post culture.


title: ATAC_RPMI_4h_8448

value: Culture only, collected at 4 hours post culture.


title: Control-1


title: ATAC_Mono_8444

value: None.


title: Mir290_47D_Set-1

description: Δ(129/Cast): chr7:3199611-3215602

value: Deletion Present


title: ATAC_LPS_d6_8455

value: LPS exposed 24 hours, culture for 5 days to macrophage.


title: 9-days hypocotyl, biological replicate 3

value: cv. Santhica 27


title: ATAC_LPS_d1_8452

value: LPS exposed, collected at 24 hours post exposure.


title: ATAC_LPS_4h_8449

value: LPS exposed, collected at 4 hours post exposure.


title: ATAC_BG_d1_8453

value: BG exposed, collected at 24 hours post exposure.


title: ATAC_BG_1h_8447

value: BG exposed, collected at 1 hour post exposure.


title: ATAC_LPS_1h_8446

value: LPS exposed, collected at 1 hour post exposure.


title: ATAC_BG_4h_8450

value: BG exposed, collected at 4 hours post exposure.


title: ATAC_BG_d6_8456

value: BG exposed 24 hours, culture for 5 days to macrophage.


title: 0.5h KCl treatment replicate 2

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
Full genomic sequence for mouse (mm9) was downloaded from the UCSC Genome Browser database. Full transcriptomic sequences were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
We assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

source_name: DIV10 hippocampal neurons

extract_protocol:
TriReagent
TruSeq RNA library prep kit V2

value: Primary neurons

value: 0.5h 55mM KCl


title: 3h KCl treatment replicate 1

value: 3h 55mM KCl


title: Untreated neurons replicate 1

value: No KCl


title: 0.5h KCl treatment replicate 1


title: Untreated neurons replicate 2


title: 3h KCl treatment replicate 2


title: ATAC_RPMI_1h_8445

value: Monocyte

value: Culture only, collected at 1 hour post culture.

value: Peripheral blood


title: Cohort2.P.2 (ATAC-seq)

status: Public on Nov 17 2016

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: chromatin DNA

data_processing:
Library strategy: ATAC-seq
Reads were aligned to mm9 assembly using tophat2 (for RNA-seq), BSMap 2.7 (for WGBS), and bowtie2 (for ATAC-seq), using paired-end alignments.
RNA-seq read counts were obtained using Htseq. Smoothed ATAC-seq density profiles were calculated using spp 1.3 package.
For WGBS, CpG methylation calls were made, excluding duplicate reads as well as the first four bases of each read, only taking into account CpGs with quality scores ≥ 20 as well as requiring that surrounding bases exhibit quality scores ≥ 10. Here, CpG methylation calling is defined as the computation of the number of reads overlapping a particular CpG harboring a C or a T at the cytosine coordinate of the CpG. In the processed BED files, each line corresponds to the analyzed CpG site, with the columns specifiying 1) chromsome 2) start position 3) end position 4) number of methylated reads/total reads 5) methylation fraction*1000 6) strand (should be ignored as both alignment orientation are considered in the alignment).
scRNA-seq heterogeniety was analyzed using PAGODA (scde 1.99.2)
Genome_build: UCSC mm9
Supplementary_files_format_and_content: .txt (RNA-seq), .tdf (ATAC-seq), .txt (scRNA-seq), .bed (Bisulfite-Seq)

growth_protocol: Development of the HUe transgenic construct utilized a fluorescent cassette that was originally adapted for the neural system (Livet et al., 2007), with some modifications.  In brief, a STOP sequence flanked by a pair of LoxP variants was inserted in front of a fluorescent cassette containing GFP, EYFP, tDimer2, and Cerulean cDNA sequence interspersed by multiple LoxP sites such that no background fluorescence was expressed in the absence of Cre recombinase (Figure S1).  The whole construct was placed under a ubiquitous chicken beta actin promoter and the linearized construct was microinjected into C57BL6/J embryos to generate transgenic mouse lines.  Six founder lines were established and fluorescence was observed in multiple founders.  Experiments performed in this study used founder six, which has approximately 20 copies of transgene insertion. PIpC induced Mx1-Cre;HUe mice at 6-8 weeks old were used as donors. Bone marrow cells from 8-12 donors were pulled, lineage-depleted and flow sorted for LineageLoSca+cKit+ cells before transplantation. One hundred thousand flow sorted fluorescent LineageLoSca+cKit+ cells mixed with 500,000 Sca- C57BL/6J support cells were transplanted into each of 20 lethally irradiated C57BL/6J recipients. Sixteen weeks were allowed for hematopoietic reconstitution.  Experiment was repeated 6-8 times.

extract_protocol:
For each mouse, tibiae, femurs, iliac crests, and spines were collected for bone marrow cells.  Isolation and enumeration of different hematopoietic cell types was performed by flow cytometry.  Bone marrow cells harvested from each animal were ACK lysed before antibody staining.  We routinely stain 5x10e7 cells per sample for the stem population, and 1x10e7 cells per sample for each progenitor and mature population.  Lineage cocktail consists of biotinylated B220, CD3e, CD4, CD8a, CD19, CD11b, Gr1, Ter119, CD11c, and NK1.1 antibodies.  Fluorescence conjugated to streptavidin was used to recognize lineage cocktail.  Using the following antibody combinations, we were able to identify hematopoietic subpopulations at the stem-cell level: hematopoietic stem cells (HSCs) (Lineage-Pacific Orange, cKit-APC-Cy7, Sca-PE-Cy7, CD48-APC, CD150-PE-Cy5)
For WGBS, purified genomic DNA was fragmented to a size range of 100-400bp, 20-50ng of DNA fragments from each sample were end-repaired and ligated with indexed adapters using the NuGen’s Ovation® Ultralow Methyl-Seq Library Systems.  Adapter-equipped DNA fragments were subjected to bisulfite treatments using the QIAGEN Epitect Bisulfite kit followed manufacture’s recommendation with modifications. Bisulfite converted library DNA was PCR-amplified and sequenced at the Broad Institute Genomics Platform. For RNA-Seq, RNA was extracted from sample, reverse transcribed to cDNA, and was subjected to whole genome sequencing at Partners Healthcare Center for Personalized Genetic Medicine. For single-cell RNA-seq, Single-cells were sorted using a BD FACSAria II (BD Biosciences) into PCR 384 well plates (ThermoFisher Scientific) containing standard lysis buffer. Whole transcriptome amplification was performed using the Smart-seq2 protocol (Picelli et al., 2013), and libraries prepared by Nextera XT (Illumina). Samples were pooled and sequenced on an Illumina Nexseq 500 instrument using a 50 bp paired-end-reads. For ATAC-seq, 10,000 cells of each clone were lysed in 50μl of cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately subjected to a transposition reaction at 37oC for 30 min with 2.5μl transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using Qiagen MinElute PCR purification Kit and subjected to library amplification using NEBNext High-Fidelity 2X PCR Master Mix, Invitrogen SYBR Green I Dye, and primers (Table S2). Prior to sequencing, the ATAC-Seq library was assayed for quality using TapeStation and BioAnalyzer instruments, and qPCR.

tag: fluorescent color

value: purple

value: LKS SLAM cells


title: Cohort3 (single-cell RNA-seq)

description: cDNA

data_processing:
Reads were aligned to mm9 assembly using tophat2 (for RNA-seq), BSMap 2.7 (for WGBS), and bowtie2 (for ATAC-seq), using paired-end alignments.
RNA-seq read counts were obtained using Htseq. Smoothed ATAC-seq density profiles were calculated using spp 1.3 package.
For WGBS, CpG methylation calls were made, excluding duplicate reads as well as the first four bases of each read, only taking into account CpGs with quality scores ≥ 20 as well as requiring that surrounding bases exhibit quality scores ≥ 10. Here, CpG methylation calling is defined as the computation of the number of reads overlapping a particular CpG harboring a C or a T at the cytosine coordinate of the CpG. In the processed BED files, each line corresponds to the analyzed CpG site, with the columns specifiying 1) chromsome 2) start position 3) end position 4) number of methylated reads/total reads 5) methylation fraction*1000 6) strand (should be ignored as both alignment orientation are considered in the alignment).
scRNA-seq heterogeniety was analyzed using PAGODA (scde 1.99.2)
Genome_build: UCSC mm9
Supplementary_files_format_and_content: .txt (RNA-seq), .tdf (ATAC-seq), .txt (scRNA-seq), .bed (Bisulfite-Seq)

value: mixed


title: Cohort2.G.1 (ATAC-seq)

description: chromatin DNA

value: green


title: Cohort2.P.1 (ATAC-seq)

description: chromatin DNA


title: Cohort2.G.2 (ATAC-seq)

description: chromatin DNA


title: Cohort2.G.2 (RNA-seq)

description: cDNA


title: Cohort2.P.2 (RNA-seq)

description: cDNA


title: Cohort2.G.2 (WGBS)

description: BS-converted DNA


title: Cohort2.P.1 (WGBS)

description: BS-converted DNA


title: Cohort2.P.2 (WGBS)

description: BS-converted DNA


title: Cohort2.P.1 (RNA-seq)

description: cDNA


title: Cohort2.G.1 (WGBS)

description: BS-converted DNA


title: Cohort2.G.1 (RNA-seq)

description: cDNA


title: Cohort1.R (WGBS)

description: BS-converted DNA

value: red


title: Cohort1.Y.2 (RNA-seq)

description: cDNA

value: yellow


title: RNA_embryo_BAT

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
RNA-seq was aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Aligned reads on exonic regions from RNA-Seq were used to calculate RPKM to measure the gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: For RNA-seq data, tab-delimited text files were generated to include RPKM values for each gene.

source_name: Brown adipose tissue

growth_protocol: Primary preadipocytes were isolated from interscapular BAT of new born Ppargf/f pups and immortalized by SV40T

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1x105 cells per well in 6-well plate 4 days before induction of adipogenesis. The confluent cells (0h) were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 1uM dexamethasone, and 0.125mM indomethacin.

value: Brown adipose tissue

tag: stage of adipogenesis

value: Embryo


title: Cohort1.R.2 (RNA-seq)

description: cDNA


title: Cohort1.R.1 (RNA-seq)

description: cDNA


title: RNA_Pparg_1h

source_name: Brown preadipocyte cell

value: Brown preadipocyte cell

value: imortalized PPARg-flox/flox brown preadipocytes


title: Cohort1.Y (WGBS)

description: BS-converted DNA


title: RNA_Pparg_D2

description: duplicate sample GSM1912998

value: day 2


title: Cohort1.Y.3 (RNA-seq)

description: cDNA


title: RNA_adult_BAT

value: Adult


title: RNA_Pparg_4h


title: RNA_Pparg_D7

description: duplicate sample GSM1912999

value: day 7


title: Cohort1.R.3 (RNA-seq)

description: cDNA


title: F1_Set-1

value: wild type


title: RNA_Pparg_2h


title: RNA_Pparg_0h

value: day 0 (0h)


title: RNA_3T3-L1_D2

source_name: 3T3-L1 cell

value: 3T3-L1 cell

value: imortalized white preadipocytes


title: RNA_3T3-L1_2h


title: RNA_3T3-L1_4h


title: ATAC-seq Mitosis rep1

city: Berkeley

first: Sheila

middle: S

last: Teves

state: California

address: 475D Li Ka Shing Center

department: Molecular Cell Biology

institute: UC Berkeley

data_processing:
Library strategy: ATAC-seq
Illumina Casava1.7 software used for basecalling.
Sequenced paired mates were mapped on mm10 genome build using Bowtie2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 –I 10 –X 2000.
From the length distribution of sequenced reads, two size classes were used: short reads (under 100 bp) and mono-nucleosome sized reads (180 – 247 bp). Fragment sizes corresponding to these size classes were mapped separately using the same parameters as above.
Peak calling was performed using the Homer suite package for asynchronous and mitotic samples, and using either total reads, or each size class.
Genome_build: mm10
Supplementary_files_format_and_content: HOMER Peaks

source_name: Embryonic stem cells

extract_protocol: Libraries were prapared according to the Nextera DNA library preparation kit

treatment_protocol: Mitosis samples were synchronized by addition of 100ng/uL of Nocodazole for 6 hours

tag: cell line


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c_4

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

data_processing:
Alignment to human reference genome with TopHat 2.0.14 with default parameters
Quantification of reads mapping to Ensembl GRCh38.80 gene models using Rsamtools, GenomicFeatures and GenomicAlignments R packages with the "Union" overlap mode.
Transformation of raw read counts to Reads Per Kilobase of gene model per Millions of mapped reads (RPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text containing RPKM expression values

source_name: THP-1 cell line

growth_protocol: The THP-1 cell line was cultured in RPMI 1640 medium, supplemented with FBS 10% and 2mM final concentration of Ultraglutamine (Lonza), at 37°C in 5% CO2 in a humidified incubator as described (Olioso et al., submitted). Briefly, in a typical experiment, on day one the cells were seeded at a density of 2.5x105 cells/mL in 24-well plates in 1 ml medium with 2mM Ultraglutamine and 2% FBS. On day 2 all the cell cultures were supplemented with 20 ng/mL of PMA and on day 3 the cultures were treated with IL-4 at a concentration of 50 ng/mL for 24h. On day 4 the plates were washed twice with culture medium and the cultures were again supplemented with 50 ng/mL IL-4 and incubated for 24h.

extract_protocol:
Total RNA was isolated using the RNeasy mini Kit (Qiagen).
RNA aliquots (2.5μg) were used to isolate poly(A) mRNA for the preparation of a directional Illumina RNA-Seq library using the TruSeq RNA Sample Prep Kit v2 (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Macrophages were exposed for 24 h to Arnica m. centesimal dilutions (2c) or control solvent (1 ml cell culture + 110 μl test solutions).


title: ATAC-seq Mitosis rep2


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c_3


title: RNA_3T3-L1_0h


title: RNA_3T3-L1_1h


title: ATAC-seq Asynchronous rep1


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c_5


title: ATAC-seq Asynchronous rep2


title: Cohort1.Y.1 (RNA-seq)

description: cDNA


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c_2


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c_1


title: THP-1 cells untreated control_4

value: untreated


title: THP-1 cells untreated control_5


title: THP-1 cells untreated control_3


title: THP-1 cells untreated control_1


title: THP-1 cells untreated control_2


title: RNA_3T3-L1_D7


title: THP-1 cells exposed at Arnica m. centesimal dilution 15c

treatment_protocol: Macrophages were exposed for 24 h to Arnica m. centesimal dilutions (2c, 3c, 5c, 9c, 15c) or control solvent (1 ml cell culture + 110 μl test solutions).


title: THP-1 cells untreated control

description: Control

value: untreated control


title: THP-1 cells exposed at Arnica m. centesimal dilution 3c


title: THP-1 cells exposed at Arnica m. centesimal dilution 9c


title: THP-1 cells exposed at Arnica m. centesimal dilution 5c


title: Mock group

city: Xi’an

first: Hong-Wei

last: Ma

state: Shaanxi

address: 169 Changle West Road

department: Department of Microbiology

institute: Fourth Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The experimental process includes sample preparation and sequencing. The main reagents and supplies are Illumina Gene Expression Sample Prep Kit and Solexa Sequencing Chip (flowcell), and the main instruments are Illumina Cluster Station and Illumina HiSeq™ 2000 System. Specified Experimental Process : Extract 6 µg total RNA, use Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize the first and second-strand cDNA. The 5' ends of tags can be generated by two types of Endonuclease: NlaIII or DpnII (see table 1 for recognition sites). Usually, the bead-bound cDNA is subsequently digested with restriction enzyme NlaIII, which recognizes and cuts off the CATG sites. The fragments apart from the 3' cDNA fragments connected to Oligo(dT) beads are washed away and the Illumina adaptor 1 is ligated to the sticky 5' end of the  digested bead-bound cDNA fragments. The junction of Illumina adaptor 1 and CATG site is the recognition site of MmeI, which is a type of Endonuclease with separated recognition sites and digestion sites. It cuts at 17bp downstream of the CATG site, producing tags with adaptor 1. After removing 3' fragments with magnetic beads precipitation, Illumina adaptor 2 is ligated to the 3' ends of tags, acquiring tags with different adaptors of both ends to form a tag library. After 15 cycles of linear PCR amplification, 105bp fragments are purified by 6% TBE PAGE Gel electrophoresis. After denaturation, the single-chain molecules are fixed onto the  Illumina Sequencing Chip (flowcell). Each molecule grows into a single-molecule cluster sequencing template through Situ amplification. Then add in four types of nucleotides which are labeled by four colors, and perform sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 49bp.
Principle and procedure of Tag preparation. Beads of Oligo(dT) are used to enrich mRNA from the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. 4 base recognition enzyme NlaIII is used to digest this cDNA, and Illumina adaptor 1 is ligated. Mmel is used to digest at 17bp downstream of CATG site; Illumina adaptor 2 is ligated at 3' end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 95bp fragments through 6% TBE PAGE. The DNA was purified and followed by Illumina sequencing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human NCBI genome build 36 using bowtie v0.12.2.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: all genes with different expression between different groups

source_name: HUVECs

growth_protocol: HUVECs purchased from ScienCell (San Diego, CA, Catalog#8000) were cultured in Endothelial Cell Medium (ECM) (ScienCell, Catalog1001)

extract_protocol:
Total cellular RNAs were extracted with RNAiso (TaKaRa, Dalian, China), and the concentration of which was measured using NanoDrop 1000 Spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HTNV strain 76-118 was propagated in Vero E6 cells (a green monkey kidney epithelial cell line; ATCC no.CRL-1586), titers of which were measured by ELISA as we previously described (Xu Z et al,BBRC, 2002;298:552-558). For infection, cells with a confluence of 70-80% in the 35 mm dishes were rinsed twice by Dulbecco’s phosphate-buffered saline (DPBS, HyClone, Logan City, UT), and then the HTNV diluted to the desired MOI were added. After incubating for 90 min at 37 °C, the supernatant was discarded. Thereafter, the celled were washed twice with DPBS and added with the complete medium. As a control, cells were incubated with culture supernatant from uninfected Vero E6 cells or Co60-inactivated HTNV.

tag: multiplicity of infection (moi)

value: 24 hours post treatment


title: Co60-inactivated HTNV infection group

value: Co60-inactivated HTNV which was propagated in the E6 cells

value: 24 hours post infection


title: HUVEC RNY5 Treatment 6 hr replicate 2

city: Woodbury

first: Ashwin

last: Prakash

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description: HUVEC RNY5 Treatment 6 hr

data_processing:
Read Mapping done by STAR
Read counted by HTSeq
Differential expression analysis DESeq
Genome_build: hg18
Supplementary_files_format_and_content: read count data, .txt files

source_name: Endotheloal Cell

growth_protocol: K562 cells were grown in complete RPMI1640 medium (10% FBS + 1% penicillin-streptomycin), and all other cells were grown in DMEM (10% FBS and 1% penicillin-streptomycin). When the cells reached approximately 70%–80% confluence, the media were replaced with serum-free conditioned medium and incubated for another 24 h.

extract_protocol:
RNA isolation was performed using Ambion's Mirvana miRNA Isolation kit (cat. no. AM1560) following the manufacturer's protocol. Prior to RNA isolation, EVs were treated with Ambion RNase cocktail (cat. no. AM2286) at 37° for 15 min. One milliliter of lysis/binding buffer was immediately added to the RNase treated EVs to deactivate the RNase.
Small RNA was isolated with Mirvana miRNA Isolation kit (Life Tech) and DNase treated with Ambion Turbo-DNase (Life Tech). Ribosomal RNA depletion was performed on whole cell RNA using the Eukaryote Ribominus kit (Life Tech) following the manufacturer's protocol. Both EV and whole cell RNA were treated with tobacco acid pyro-phosphatase (Epicenter) to make 5′ capped and triphosphate RNAs amenable to adapter ligation. Libraries were constructed using Illumina TruSeq Small RNA kit according to the manufacturer’s protocol, except reverse transcription was performed using Superscript III. Amplified libraries were run on 2% agarose gel and the 20–200 nucleotide (nt) region was cut and gel-purified with Qiagen Gel Extraction kit. Libraries were quantified on Agilent Bio-analyzer HS-DNA chip and sequenced on Illumina HiSeq2000.
Long RNA was isolated with Mirvana miRNA Isolation kit and DNase treated (Ambion, cat. no. AM2238) following the manufacturer’s protocols. Construction of complementary-DNA libraries was performed using Illumina TruSeq Stranded Total RNA kit (cat. no. RS-122-2201). Libraries were quantified using Agilent Bioanalyzer HS-DNA chip and run on Illumina Hi-Seq 2000 platform.

treatment_protocol: The conditioned medium was then centrifuged at 300g for 10 min. The cell pellet was discarded and the supernatant was further centrifuged at 2000g for 10 min. The pellet comprised of mostly cell debris and apoptotic bodies was discarded and the supernatant was again centrifuged at 10000g for 30 min. The pellet comprised of microvesicles was discarded and the supernatant was filtered at 3500g for 15 min using Centricon Plus70 100KD NMWL cut-off (Millipore). The filtrate was discarded and the residue, enriched with EVs and other proteins, was collected. The collected residues were precipitated overnight using ExoQuick-TC (System Biosciences) at 1:5 ratio (by volume) of Exo-quick to filtration residue. The next morning, the sample was centrifuged at 1500g for 30 min. The supernatant was discarded and the pellet was centrifuged again at 1500g for 5 min. Leftover supernatant, if any, was discarded and the pellet was resuspended in 500 μL PBS.

value: HUVEC

value: RNY5 6 hr

tag: replicate

tag: rna type

value: long RNA


title: HUVEC RNY5 Treatment 2 hr replicate 2

description: HUVEC RNY5 Treatment 2 hr

value: RNY5 2 hr


title: HUVEC RNY5 Untreated replicate 2a

description: HUVEC RNY5 Untreated

value: RNY5 untreated


title: HUVEC RNY5 Untreated replicate 2b

description: HUVEC RNY5 Untreated


title: HUVEC RNY5 Treatment 24 hr replicate 1

description: HUVEC RNY5 Treatment 24 hr

value: RNY5 24 hr


title: HUVEC RNY5 Untreated replicate 1b

description: HUVEC RNY5 Untreated


title: HUVEC RNY5 Untreated replicate 1a

description: HUVEC RNY5 Untreated


title: HUVEC exosome treatment 2 hr replicate 2

description: HUVEC exosome treatment 2 hr

tag: cell

value: exosome

value: Treatment 2 hr


title: HUVEC exosome treatment 2 hr replicate 3

description: HUVEC exosome treatment 2 hr


title: HUVEC RNY5 Treatment 2 hr replicate 1

description: HUVEC RNY5 Treatment 2 hr


title: HUVEC exosome treatment 24 hr replicate 2

description: HUVEC exosome treatment 24 hr

value: Treatment 24 hr


title: HUVEC RNY5 Treatment 6 hr replicate 1

description: HUVEC RNY5 Treatment 6 hr


title: HUVEC exosome treatment 2 hr replicate 4

description: HUVEC exosome treatment 2 hr


title: HUVEC exosome treatment 2 hr replicate 1

description: HUVEC exosome treatment 2 hr


title: HUVEC exosome treatment 24 hr replicate 1

description: HUVEC exosome treatment 24 hr


title: HUVEC exosome untreated replicate 2

description: HUVEC exosome untreated


title: HUVEC exosome untreated replicate 1

description: HUVEC exosome untreated


title: THP-1 cells exposed at Arnica m. centesimal dilution 2c


title: HTNV infection group

value: HTNV propagated  in the E6 cells


title: BJ RNY5 Treatment 6 hr replicate 2

description: BJ RNY5 Treatment 6 hr

source_name: Foreskin Fibroblast

value: BJ


title: BJ RNY5 Treatment 2 hr replicate 2

description: BJ RNY5 Treatment 2 hr


title: BJ RNY5 Treatment 2 hr replicate 1

description: BJ RNY5 Treatment 2 hr


title: BJ RNY5 Treatment 24 hr replicate 2

description: BJ RNY5 Treatment 24 hr


title: BJ exosome treatment 24 hr replicate 2

description: BJ exosome treatment 24 hr


title: BJ exosome treatment 2 hr replicate 1

description: BJ exosome treatment 2 hr


title: BJ exosome treatment 2 hr replicate 2

description: BJ exosome treatment 2 hr


title: BJ RNY5 Treatment 24 hr replicate 1

description: BJ RNY5 Treatment 24 hr


title: BJ exosome treatment 24 hr replicate 1

description: BJ exosome treatment 24 hr


title: HUVEC RNY5 Treatment 24 hr replicate 2

description: HUVEC RNY5 Treatment 24 hr


title: BJ exosome untreated replicate 2

description: BJ exosome untreated


title: U2OS TAP treatment replicate 2

description: U2OS TAP treatment

source_name: Uterine Carcinoma

value: TAP

value: short RNA


title: U2OS TAP treatment replicate 1

description: U2OS TAP treatment


title: BJ exosome untreated replicate 1

description: BJ exosome untreated

value: untreated


title: K562 CIP treatment replicate 2

description: K562 CIP treatment

source_name: Chromic myeloid Leukemia

value: CIP


title: HUVEC Untreated replicate 1

description: HUVEC Untreated

source_name: Endothelial Cell


title: HUVEC TAP treatment replicate 2

description: HUVEC TAP treatment


title: K562 Untreated replicate 2

description: K562 Untreated


title: U2OS replicate 1

tag: molecule

value: exosomal short


title: MCF7 replicate 2

source_name: Adenocarcinoma Breast


title: BJ TAP treatment replicate 2

description: BJ TAP treatment


title: K562 TAP treatment replicate 1

description: K562 TAP treatment


title: BJ TAP treatment replicate 1

description: BJ TAP treatment


title: MCF7 replicate 1


title: BJ RNY5 Treatment 6 hr replicate 1

description: BJ RNY5 Treatment 6 hr


title: K562 replicate 1

source_name: Chromnicmyeloud Leukemia


title: IMR90 replicate 2

source_name: Embryonic Fibroblast


title: K562 replicate 2


title: HUVEC replicate 2

description: HUVEC

source_name: Endothelial cell


title: HUVEC replicate 1

description: HUVEC


title: A549 replicate 2

source_name: Adenocarcinoma Lung


title: HELA replicate 1

description: HELA

source_name: Cervical Carcinoma

value: HELA


title: BJ replicate 2

description: BJ


title: BJ replicate 1

description: BJ


title: HELA replicate 2

description: HELA


title: HMEC replicate 1

description: HMEC

value: HMEC


title: A549 replicate 1


title: U2OS replicate 2


title: HUVEC CIP treatment replicate 1

description: HUVEC CIP treatment

value: HUVEC


title: C4 Control

city: Varanasi

first: Geeta

last: Rai

state: Uttar Pradesh

address: Institute of Science

department: Molecular and Human Genetics

country: India

institute: Banaras Hindu University

data_processing:
Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 72 gene model of human with default parameter settings
Differentially expressed transcripts/ genes were idenified using Cufflinks program
Genome_build: hg19 - Ensembl Release 72 database

source_name: Blood

extract_protocol:
Total RNA was isolated from blood using TRI reagent, Sigma-Aldrich. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA samples, free of DNA and protein contamination was resuspended in nuclease free water. 1ug of RNA for each sample was used for Next Generation Sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: control


title: C3 Control


title: S19 Anti-ENA+ SLE patient

value: Systemic lupus erythematosus

tag: group

value: anti-ENA


title: NA19257

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
The reads were mapped to hg19 using STAR with option --outSAMstrandField intronMotif
The alignment were filtered to remove mapped reads with quality less than 10 using samtools -q 10
We used the WASP alignment strategy to filter read that may be mismapped owing to the human genome reference allele bias (pmid26366987)
We also used WASP to remove cofounding effect from sample-specific GC biases and read count differences to allow comparison between samples.
We standardize the values by genes (row) and qqnorm by individuals (column) to get our final quantitative measurements
Genome_build: hg19
Supplementary_files_format_and_content: Each column represnets and individual and each row represnets a gene. Counts are processed and normalized as described above.

source_name: Induced pluripotent stem cell

growth_protocol: iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media.

extract_protocol:
RNA was extracted from from frozen cell pellets using the Zymo ZR-Duet DNA/RNA MiniPrep kit, per manufacture specifications.
Libraries were prepared using Illumina TruSeq library preperation per manufacutre specifications.

value: Induced pluripotent stem cell


title: C2 Control


title: NA19239


title: IMR90 replicate 1

value: exosome


title: C1 Control


title: S21 Anti-ENA+ SLE patient


title: S18 Anti-ENA+ SLE patient


title: S25 Anti-ENA+ SLE patient


title: NA19225


title: NA19238


title: NA19210


title: HMEC replicate 2

description: HMEC


title: S15 Anti-dsDNA+ENA+ SLE patient

value: anti-dsDNA and anti-ENA


title: S14 Anti-dsDNA+ENA+ SLE patient


title: NA19209


title: S16 Anti-dsDNA+ENA+ SLE patient


title: NA19207


title: NA19206


title: S06 Anti-dsDNA+ SLE patient

value: anti-dsDNA


title: NA19204


title: S09 Anti-dsDNA+ SLE patient


title: NA19193


title: S03 Anti-dsDNA+ SLE patient


title: NA19192


title: NA19190


title: S02 Anti-dsDNA+ SLE patient


title: NA19159


title: MDA_S_1

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: processed data: MDA primary s mature Small RNA sample MDA Primary S size grouped on mature.xlsx

data_processing:
CLC genomic workbench 7.0
Illumina adapter sequences and sequences tags of length less than 17 and more than 27 were removed
miRNA sequences were aligned to human genome (homo sapiens GRCh 37.57) and known miRNA database (miRBase-19)
Statistical analysis: Bonferroni and FDR corrected
Filtering: Significant, above 2; Kalz test: FDR pvalue <0.05; Kalz test: FC abs value>2
Genome_build: miRBase 19
Supplementary_files_format_and_content: Excel files xlsx containing expression values  of miRNAs of monolayer and spheroid MDA

growth_protocol: The monolayer and spheroid MDA cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.

extract_protocol:
Total RNA with retention of small RNAs from the cells were extracted using miRNA easy
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina Tru-seq small RNA

tag: cell line source

tag: cell type origin

value: estrogen-independent human breast adenocarcinoma cell line

tag: culture condition (cell subtype)

value: Spheroid

tag: culture dimension

tag: molecule subtype

value: microRNA


title: NA19160

tag: cell type


title: NA19153


title: MDA_P_3

description: processed data: MDA parental mature   Small RNA sample sub-size grouped on mature.xlsx

value: Monolayer


title: MDA_P_1


title: NA19140


title: NA19138


title: MDA_P_2


title: S12 Anti-dsDNA+ENA+ SLE patient


title: NA19144


title: NA19152


title: NA19130


title: NA19128


title: MDA_S_2


title: MDA_S_3


title: NA19116


title: NA19127


title: NA19114


title: NA19119


title: NA19102


title: NA19108


title: NA19098


title: NA19099


title: NA19101


title: NA19093


title: NA18913


title: NA18912


title: NA18907


title: NA19143


title: NA18861


title: NA18858


title: NA18870


title: NA18862


title: NA18859


title: NA18856


title: NA18853


title: NA18519


title: NA18520


title: NA18511


title: NA18510


title: NA18517


title: NA18852


title: NA18522


title: NA18502


title: NA18501


title: NA18489


title: NA18486


title: NA18498


title: SOX5 OverExp 5

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

description: Lentiviral overexpression of full-length SOX5  protein for 14 days. Total RNA isolated using miRNeasy kit, Qiagen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37.73 whole genome using Tophat2 v2.07 with parameters -g 10 -p 8 -r 99 --no-novel-juncs -G GRCh37.73.gtf
Counts were estimated using union exon model using HTSeq-Counts v0.6.1
RPKM values were estimated using CQN package (Hansen et al 2012) in R using default options, but setting cqn=FALSE which turns of quantile normalization
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: primary human neuronal progenitors

extract_protocol:
Primary neurons were dissociated and RNA was harvested using Trizol reagent. SMARter Stranded Total RNA sample prep kit (Clontech) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARter Stranded Total RNA sample prep kit, Clontech
50-bp paired end RNA-Seq using HiSeq2500

tag: tissue

value: fetal cortex

tag: construct

tag: treatment

value: SOX5 Overexpression


title: SOX5 OverExp 6


title: SOX5 OverExp 4


title: SOX5 OverExp 3


title: SOX5 OverExp 1


title: SOX5 OverExp 2


title: Control 6

description: Lentiviral overexpression of GFP for 14 days. Total RNA isolated using miRNeasy kit, Qiagen

value: pLVU-GFP

value: GFP Overexpression


title: NA18855


title: Control 3


title: Control 5


title: Control 2


title: Control 1


title: NA18505


title: NA18507


title: NA18508


title: NCD 1

city: Shanghai

first: Sun

middle: hong

last: ling

address: No.639  Zhizaoju Raod , Shanghai

department: Institute and Department of Endocrinology and Metabolism

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using the methylation-aware mapper bismark (version 0.13.0).
Samtools (version 0.1.19) was used to sort SAM files produced by bismark and de-duplicate reads.
SAM files were analyzed using the Bismark_methylation_extractor which was a subroutine of the methylation-aware mapper bismark (version 0.13.0)
Differential methylation was defined as a Fisher test correct p-value which was less than 0.01 for the type of CG and less than 0.05 for the type CHG and CHH(H was dedined as A,T or C) .
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: bigwig files include Methlation levels for each Sample

organism: Rattus norvegicus

growth_protocol: 8-week-old Wistar rats were purchased from SLAC Laboratories, SIBS, Shanghai, China. Animals were housed at an ambient temperature of 22 ± 2∘C and maintained under a normal 12 hours light/dark cycle and allowed access to normal chow diet food ad libitum.

extract_protocol:
Livers were sampled, flash frozen in liquid nitrogen, and Genomic DNA was isolated and purified from 25 mg of frozen liver tissue with  the DNeasy Tissue Kit (Qiagen, Germany, cat. no. 51306) .
Libraries were prepared according to Illumina's instructions. Breifly,Genomic DNA was isolated and purified from 25 mg of frozen liver tissue with the DNeasy Tissue Kit (Qiagen, Germany, cat. no. 51306).3ug of genomic DNA were broken into fragments by Covaris S2 system (Covaris, MA) for 52 seconds with 20% duty cycle, level 5 intensity and 200 cycles per burst. Fragmented DNA were purified by Ampure XP Beads (Beckman Coulter, CA) and the fragments were end-repaired, and a single A nucleotide was added to the 3' ends of the fragments in preparation for ligation to a methylated adapter (Illumina, CA) with a single-base T overhang. The ligation products were purified and size-selected (300-400bp) using agarose gel electrophoresis (Qiagen Minelute Gel Extraction Kit). DNA was modified with sodium bisulfite to convert unmethylated cytosine to uracil using the Zymo Gold methylation kit (Zymo Research, CA) according to the manufacturer's protocol and then purified. The purified converted DNA was amplified with PfuTurbo Cx Hotstart DNA Polymerase (Agilent Technologies, CA) and was purified again using AMPure XP beads. Library quality was monitored using the Agilent 2100 Bio-Analyzer (Agilent) and KAPA Library Quantification Kit (Kapa Biosystem). Paired-end sequencing (2×100 bp) was then carried out using the Illumina Hi-Seq 2000.

treatment_protocol: Rats of the NCD group were treated normal drinking water for 21 weeks, rats of NCD+0.05%Pb group were exposed to 0.05% dosages of lead acetate through drinking water for 21 weeks

tag: strain

value: Wistar

value: liver


title: NCD 2


title: ChIP-Seq-mES-H2Bub USP7-KO

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 using bowtie 1.0 with n = 1 and m = 3
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Embryonic stem cells

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates.

extract_protocol:
Genomic DNA were extracted using antibodies for EPOP, H3K4me3, Elongin B, RNA Polymerase II S5, USP7 or H2Bub.
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol

treatment_protocol: For ChIP cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps.

value: USP7 Knockout

tag: chip antibody

value: H2Bub; Cell Signaling, 5546S


title: ChIP-Seq-mES-USP7 EPOP-KO

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 or human genome hg19 using bowtie 1.0 with n = 1 and m = 3
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v0.9 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1 using a gffread filtered gencode.vM6.basic.annotation.gtf file as template
Genome_build: mm9, mm10, hg19
Supplementary_files_format_and_content: bigwig, txt

source_name: Embryonic stem cell

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates, SH-SY5Y cells were cultured in DMEM, 10% FCS, 1 x Penicillin/Streptomycin

extract_protocol:
Genomic DNA were extracted using antibodies for EPOP, H3K4me3, Elongin B, RNA Polymerase II S5, USP7 or H2Bub. RNA-Seq samples were prepared by isolating total RNA using Trizol, mRNA Isolation, heat fractionation, reverse transcription and second strand synthesis
Libraries were constructed of 10-50 ng of DNA following Illumina’s® protocol

value: EPOP Knockout

value: USP7, Bethyl, A300-033A


title: ChIP-Seq-mES-USP7 Control

value: Control


title: ChIP-Seq-mES-H3K4me3 USP7-KO

value: H3K4me3; Millipore, #04-745


title: NCD+0.05%Pb 1


title: NCD+0.05%Pb 2


title: ChIP-Seq-mES-ElonginB EPOP-KO Repl2

value: Elongin B; abcam, ab168836


title: ChIP-Seq-SH-SY5Y Input


title: ChIP-Seq-mES-ElonginB Control Repl2


title: ChIP-Seq-SH-SY5Y-H3K4me3 EPOP-OE

data_processing:
ChIP-Seq data were aligned to mouse genome mm9 or human genome hg19 using bowtie 1.0 with n = 1 and m = 3
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
RNA-Seq data were aligned by Tophat v0.9 to mm10, using the Galaxy Platform. Normalized Values were derived using Cuffdiff v2.2.1 using a gffread filtered gencode.vM6.basic.annotation.gtf file as template
Supplementary_files_format_and_content: bigwig, txt

value: EPOP Overexpression


title: ChIP-Seq-mES-EPOP Ab3 EPOP-KO

value: EPOP (Ab3), Active Motif #61753


title: ChIP-Seq-mES-PolIIS5 EPOP-KO Repl2

value: PolII S5; BioLegend, 904001


title: ChIP-Seq-SH-SY5Y-H3K4me3 EPOP-KD

value: EPOP Knockdown


title: ChIP-Seq-mES-EPOP Ab3 Control

value: EPOP (Ab3) , Active Motif #61753


title: ChIP-Seq-mES-EPOP Ab2 Control

value: EPOP (Ab2)


title: ChIP-Seq-mES-H2Bub EloB-KO

value: Elongin B Knockout


title: ChIP-Seq-mES-H3K4me3 Control (For EloB KO)


title: ChIP-Seq-mES-H2Bub Control (For EloB KO)


title: ChIP-Seq-mES-H3K4me3 Control (For USP7 KO)


title: ChIP-Seq-mES-EPOP Ab2 EPOP-KO


title: ChIP-Seq-mES-EloB EloB-KO


title: ChIP-Seq-mES-H2Bub Control (For USP7 KO)


title: RNA-Seq-mES-RescueL40A

value: EPOP knockout re-expressing L40A-mutated EPOP


title: ChIP-Seq-mES-EloB Control


title: ChIP-Seq-mES-H3K4me3 EloB-KO


title: RNA-Seq-mES-RescueWT

value: EPOP Knockout re-expressing WT EPOP


title: ChIP-Seq-mES-PolIIS5 Control Repl2

value: PolII S5, BioLegend, 904001


title: ChIP-Seq-mES-Input EPOP-KO

value: none (input)


title: C2-121213

city: Madison

first: Ning

last: Leng

state: WI

address: 330 N Orchard St

institute: Morgridge Institute for Research

data_processing:
alignment: bowtie
quantification: RSEM
normalization: median-by-ratio
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq values for all genes AdGFP AdNfatc1 and AdNfatc2 with posterior probabilities for DE

extract_protocol: Total RNA was isolated from mouse islets using RNeasy spin columns according to the manufacturer’s directions (Qiagen). RNA quantity was determined using a Nanodrop (Thermo Scientific) and the quality assessed by a Bioanalyzer (Agilent). Total mouse RNA was used for RNA-sequencing on an Illumina HiSeq 2000.

value: whole pancreatic islets

tag: transduction


title: C2-121813


title: ChIP-Seq-SH-SY5Y-H3K4me3 Control


title: C2-121913


title: ChIP-Seq-mES-Input Control


title: C1-121913


title: ChIP-Seq-mES-H2Bub EPOP-KO

value: EPOP Knockout

value: H2Bub; Cell Signaling, 5546S


title: C2-121113


title: C1-121813


title: C2-120613


title: ChIP-Seq-mES-ElonginB EPOP-KO Repl1

value: EPOP knockout


title: C1-121213


title: ChIP-Seq-mES-H2Bub Control

value: Control


title: ChIP-Seq-mES-PolIIS5 EPOP-KO Repl1

value: PolII S5; Covance, MMS-128P


title: GFP-121813

source_name: GFP

value: GFP


title: C1-121113


title: GFP121213


title: GFP121913


title: C1-120613


title: Control 4

value: fetal cortex

value: pLVU-GFP

value: GFP Overexpression


title: ChIP-Seq-mES-H3K4me3 Control

value: H3K4me3; Millipore, #04-745


title: ChIP-Seq-mES-H3K4me3 EPOP-KO


title: ChIP-Seq-mES-PolIIS5 Control Repl1

value: PolII S5, Covance, MMS-128P


title: ChIP-Seq-mES-EPOP Ab1 EPOP-KO

growth_protocol: E14 mouse ES cells (ES-E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine (Invitrogen), 1 x Non-essential amino acids (Invitrogen), 1 x Penicillin/Streptomycin (Invitrogen) and LIF (Millipore) on gelatin-coated plates, SH-SY5Y cells were cultured in DMEM, 10% FCS, 1 x Penicillin/Streptmycin

value: EPOP (Ab1)


title: GFP121113


title: EIP1_OX_7-2-2

first: He

last: zuhua

state: Shanghai

address: 300 Fenglin Road

department: SIBS

institute: Institute of Plant Physiology and Ecology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice reference genome Nipponbare genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

organism: Oryza sativa Japonica Group

source_name: leaf

growth_protocol: The RNA samples were isolated from the leafs of the variety ZH11, ebr1 and EIP1_OX plants  grown in the isolated paddy field in our research station (Shanghai) during natural growing seasons.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: booting stage

value: leaf

tag: genotype

tag: age

value: two month old plants