title: Axenic replicate 1, 13:11 day:night cycle, Time 24

description:
A24L_1
Processed data file: extended_darkness_counts.txt


title: 240min D310N 1

status: Public on May 01 2018

type: SRA

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

country: United Kingdom

institute: University College London

library_source: transcriptomic

data_processing:
The RSEM package (version 1.2.31) in conjunction with the STAR alignment algorithm (version 2.5.2a)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 Refseq genes downloaded from the UCSC Table Browser on 19th Feb 2016
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3)
Genome_build: mm10 Refseq
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data from DESEQ2 output. Rows represent Refseq mouse genes and columns represent individual samples.

molecule: total RNA

organism: Mus musculus

growth_protocol: Bone marrow cells were cultured for 7 days on non-adherent plates in RPMI containing 10% FCS and 10% L929 supernantant

extract_protocol:
RNA was extracted using the Rneasy kit (Qiagen) following the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were treated with 100ng/ml LPS for the times indicated

tag: cell line

value: BMDM

tag: treatment

value: LPS (100ng/ml)


title: 240min D310N 2


title: 120min D310N 2


title: Axenic replicate 2, 13:11 day:night cycle, Time 20

city: Cambridge

first: Steven

last: Biller

state: MA

address: 15 Vassar St, MIT 48-424

department: Civil and Environmental Engineering

country: USA

institute: MIT

description:
A20L_2
Processed data file: extended_darkness_counts.txt

data_processing:
Low-quality sequence removed using quality_trim (CLCbio) using default parameters.
Alignment of paired-end reads to references using the Burrows-Wheeler Aligner V0.7.12.
Number of aligned read pairs mapping in the sense orientation to each ORF determined using HTSeq (Anders, S., Pyl, P. T., & Huber, W. (2014). HTSeq–A Python framework to work with high-throughput sequencing data. Bioinformatics (Oxford, England)).
Genome_build: NCBI accessions CP000095.2 (Prochlorococcus marinus) and JXRW01000000.1 (Alteromonas macleodii).
Supplementary_files_format_and_content: extended_darkness_counts.txt: Tab-delimited text file with the number of reads mapping to each ORF for all timepoints and replicates, as well as associated annotation data.

organism: Prochlorococcus marinus str. NATL2A

source_name: Bacterial culture, normal light regime, 20hr

growth_protocol: Cultures were grown in natural seawater-based PRO99 media under a 13:11 day:night light cycle.

extract_protocol:
Culture samples added to cold RNAlater at each timepoint, cells collected onto a 0.2µm filter, and total RNA extracted with the mirVana kit (Ambion).
Strand-specific RNA-seq library construction starting with 100ng of total RNA using the dUTP second-strand approach; duplex-specific normalization was performed to reduce ribosomal RNA content in each sample.

treatment_protocol: Cultures were split after 24 hours of sampling under the day:night light cycle; at 'sundown', half experienced the normal light regime, the other half stayed in the dark.

tag: p. marinus strain/background

tag: condition

value: 13:11 light:dark light cycle

tag: timepoint

value: 20 hours


title: 60min D310N 1


title: 120min D310N 3


title: 120min D310N 1


title: Axenic replicate 3, 13:11 day:night cycle, Time 20

description:
A20L_3
Processed data file: extended_darkness_counts.txt


title: 30min D310N 3


title: Axenic replicate 2, 13:11 day:night cycle, Time 16

description:
A16L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 16hr

value: 16 hours


title: 0min D310N 3

value: unstimulated


title: Axenic replicate 3, 13:11 day:night cycle, Time 16

description:
A16L_3
Processed data file: extended_darkness_counts.txt


title: 30min D310N 1


title: Axenic replicate 1, 13:11 day:night cycle, Time 16

description:
A16L_1
Processed data file: extended_darkness_counts.txt


title: 0min D310N 1


title: 0min D310N 2


title: 360min WT 3


title: Axenic replicate 3, 13:11 day:night cycle, Time 12

description:
A12L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 12hr

value: 12 hours


title: 360min D310N 3


title: 30min D310N 2


title: 360min WT 2


title: 360min WT 1


title: Axenic replicate 2, 13:11 day:night cycle, Time 12

description:
A12L_2
Processed data file: extended_darkness_counts.txt


title: 240min WT 2


title: 60min D310N 3


title: 60min D310N 2


title: 240min WT 1


title: Axenic replicate 3, 13:11 day:night cycle, Time 8

description:
A8L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 8hr

value: 8 hours


title: 120min WT 3


title: Axenic replicate 1, 13:11 day:night cycle, Time 20

description:
A20L_1
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 2, 13:11 day:night cycle, Time 8

description:
A8L_2
Processed data file: extended_darkness_counts.txt


title: Axenic replicate 1, 13:11 day:night cycle, Time 8

description:
A8L_1
Processed data file: extended_darkness_counts.txt


title: 60min WT 2


title: 60min WT 3


title: 60min WT 1


title: 30min WT 3


title: 0min WT 3


title: 0min WT 2


title: Axenic replicate 1, 13:11 day:night cycle, Time 0

description:
A0L_1
Processed data file: extended_darkness_counts.txt

source_name: Bacterial culture, normal light regime, 0hr

value: 0 hours


title: 30min WT 1


title: Axenic replicate 2, 13:11 day:night cycle, Time 0

description:
A0L_2
Processed data file: extended_darkness_counts.txt


title: 30min WT 2


title: Axenic replicate 1, 13:11 day:night cycle, Time 12

description:
A12L_1
Processed data file: extended_darkness_counts.txt


title: 240min WT 3


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 144

description:
H144D_2
Processed data file: extended_darkness_counts.txt

organism:
Alteromonas macleodii
Prochlorococcus marinus str. NATL2A

source_name: Bacterial co-culture, extended darkness, 144hr

tag: a. macleodii strain/background

value: 13:11 light:dark light cycle -> extended darkness

value: 144 hours


title: 0min WT 1


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 144

description:
H144D_3
Processed data file: extended_darkness_counts.txt


title: T7134_wt_localhic

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

description: local HiC

library_source: genomic

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: generate contact matrix: juicer runnning with default parameter
4C-Seq: filtering: each read pair was tested for the presence of a perfect match to the respective bait primer as well as the bait spacer  between the  end of the primer and the restriction sites  used  in  the  corresponding  experiment.
4C-Seq: mapping: bowtie-1.1.1/bowite -X 500 -p 3 -v2 -k2 -m1 --phred64-quals -sam
4C-Seq: frequency: assign to DPNII/CSP6i fragment to calculate fraction of restriction fragments for which 4C reads were found
ChIAPET: followed the process described in Li et al.,2010
ChIAPET: interaction call by chiapettool v2 program with default parameter
ChIA-PET: Chia-PET processing pipeline is described in greater detail in Li et al., 2010 (PMCID: PMC2872882)
local HiC: preprocess & normalization: juicer.sh using default parameter
local HiC: 5kb resolution matrices extraction: juicebox dump obsevered NONE .hic BP 5000
local HiC: R & custom script: generate genome wide contact matrix as in Sanborn et al. PNAS 2015
local HiC: estimation of number of in silico spike-ins: median of the genome-wide per-bin coverage of the local HiC matrix at the targeted region
local HiC: reconstruct HiC matrix: combine the targeted region local HiC with the global CH12 wt matrix which matched to spike-ins
local HiC: re-normalization: Knight-Ruiz balancing algorithm with the juicebox pre -r 5000
ChromRNA_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChromRNA_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
ChromRNA_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content:
ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Gro-Seq: .wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
HiC-Seq: .hic format including contact matrix, normalization information generated by juicer.sh
ChIAPET: bed12 format by editting the result of chiapettool by restricting to show only interactions having more than or equal to 3 PETs
4C-Seq: bed file showing read frequency in 100K window normalized by the number of fragments in each window
mRNA-Seq:.wig files tag density divided by library size in millions to obtain normalized read density (rpkm)
ChromRNA: strand-specific density tracks are generated by using bedtools genomecov program divided by library size in millions to obtain normalized read density (rpm)

molecule: genomic DNA

source_name: Tumor 7134 cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at 37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing. Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).
HiC-Seq: we used the same protocol for in situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)
Gro-seq: Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation. Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis was performed the next day as described in (Wang et al., 2011). However, for reverse transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
4C-seq: The 4C assay was performed as previously described van de Werken et al. (2012) with minor modifications. Ten million of CH12 B cell line were crosslinked in 2% formaldehyde at 37°C for 10 min. The reaction was quenched by the addition of glycine (final concentration of 0.125 M). Cells were then washed with cold PBS and lysed (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40, 1× complete protease inhibitors [Roche]) at 4°C for 1 hr. Nuclei were incubated at 65°C for 30 min, 37°C for 30 min in 500 μl of restriction buffer (New England BioLabs DpnII buffer) containing 0.3% SDS. To sequester SDS, Triton X-100 was then added to a final concentration of 1.8%. DNA digestion was performed with 400 U of DpnII (New England Biolabs) at 37°C overnight. After heat inactivation (65°C for 30 min), the reaction was diluted to a final volume of 7 ml with ligation buffer containing 100 U T4 DNA Ligase (Roche) and incubated at 16°C overnight. Samples were then treated with 500 μg Proteinase K (Ambion) and incubated overnight at 65°C to reverse formaldehyde crosslinking. DNA was then purified by phenol extraction and ethanol precipitation. For circularization, the ligation junctions were digested with Csp6I (Fermentas) at 37°C overnight. After enzyme inactivation and phenol extraction, the DNA  was  religated  in  a  7 ml  volume  (1,000 U  T4  DNA  Ligase,  Roche).  Three micrograms of 4C library DNA was amplified with Expand Long template PCR System (Roche). Thermal cycle conditions were DNA denaturing for 2 min at 94°C, followed by 30 cycles of 15 s at 94°C, 1 min at 58°C, 3 min at 68°C, and a final step of 7 min at 68°C.  Bait was amplified with inverse PCR primers as follows: 3RR with DpnII:_4C 5'-GCTTATCTGTAAAGAATGGGTC-3', 3RR_Csp6i 5'-GGCCTTAGAAGGCTCTGTAC-3'. 4C-amplified DNA was microsequenced with the Illumina platform.
mRNA-seq: Total RNA from 106 of WT or ZF9-11 CH12 cells was isolated by Trizol extraction. mRNA was then isolated .
local Hi-C: 500ng of Hi-C library (8 cycles of amplification) was mixed with 2.5 µg of mouse Cot-1 DNA and 10µg of salomon sperm DNA in a total volume of 25µl. The sample was heated to 95℃ for 5 minutes. Next the temperature was diminished to 65℃ and the samples incubated for at least 5 minutes at 65℃. In the meantime 6µl of a RNA probe mixture (500ng of RNA probes, 20U of supreRNAseIn) and 33µl of hybridization buffer (10xSSPE, 10xDenhardt buffer, 10mM EDTA, 0.2% SDS) were incubated at 65℃. Next, the hybridization buffer and the RNA probe mixture were added to the sample. The final mix was incubated at 65℃ for 24 hours. Following the hybridization, 50 µl of MyOne Streptavidin T1 beads were washed 3 times with Bind-and-Wash buffer (1M NaCl, 10 mM Tris-HCl, pH=7.5, 1mM EDTA) and then resuspended in 134 µl of Bind-and-Wash buffer and added to the sample. The mixture was incubated for 30 minutes at room temperature with occasional swirling. Next, beads were separated using a magnet and the supernatant discarded. Beads were then washed once with 200µl of low-stringency buffer (1xSSC, 0.1%SDS) and incubated for 15 minutes at RT. Beads were separated and washed 3 times with high stringency.
ChromRNA-seq: chromatin RNA fraction was prepared from 3*10^6 cells following the method previously described (Pandya-Jones & Black, RNA, 2009) with some modifications. The pellet was lysed in a cytoplasm lysis buffer (20mM Hepes-KOH pH 7.6, 2mM MgCl2, 10% glycerol, 0.1% NP40, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). The lysate was then layered on top of a sucrose buffer in order to isolate the nuclei fraction from the cytoplasmic one (10mM Hepes-KOH pH7.6, 10mM NaCl, 1.5mM MgCl2, 10% glycerol, 0.5mM EDTA, 0.5mM DTT, 34% sucrose w/v with protease inhibitor, phosphatase inhibitor and RNase inhibitor).
ChromRNA-seq: The nuclei fraction was resuspended and lysed in a nuclear lysis buffer (10mM Hepes-KOH pH 7.6, 100mM NaCl, 0.5mM EDTA, 50% glycerol, 0.5mM DTT with protease inhibitor, phosphatase inhibitor and RNase inhibitor). Chromatin was precipitated by adding a Urea c

treatment_protocol: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

tag: genotype

value: WT

value: lymphoma cell line


title: 120min WT 2


title: T7134_SAd_localhic

description: local HiC

value: SA deletion


title: ch12_wt_localhic

description: local HiC

source_name: CH12 B cell line


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 96

description:
H96D_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 96hr

value: 96 hours


title: 120min WT 1


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 72

description:
H72D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 72hr

value: 72 hours


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 72

description:
H72D_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 96

description:
H96D_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 96

description:
H96D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 72

description:
H72D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 48

description:
H48D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 48hr

value: 48 hours


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 48

description:
H48D_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 40

description:
H40D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 40hr

value: 40 hours


title: Axenic replicate 3, 13:11 day:night cycle, Time 0

description:
A0L_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 48

description:
H48D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 40

description:
H40D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 36

description:
H36D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 36hr

value: 36 hours


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 144

description:
H144D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 32

description:
H32D_1
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 32hr

value: 32 hours


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 28

description:
H28D_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, extended darkness, 28hr

value: 28 hours


title: Co-culture replicate 3, 13:11 day:night cycle -> extended darkness, Time 32

description:
H32D_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 48

description:
H48L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 48hr

value: 13:11 light:dark light cycle


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 32

description:
H32D_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 36

description:
H36D_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle -> extended darkness, Time 28

description:
H28D_1
Processed data file: extended_darkness_counts.txt


title: B16 IFNg 2

city: New york

first: Ariella

last: Glasner

state: NY

address: 504 E 89th Street, Apt 3A

department: Immunology

institute: MSKCC

data_processing:
Quality-trimming of both ends with a threshold of 33.
Filtering of short reads, less than 15 nt.
Alignment with TopHat2, version 2.0.11, allowing 5 mismatches.
Counting, normalization and differential expression with Cufflinks, version 2.2.1, using parameters -b, -u and -c 4.
Genome_build: GRCm38
Supplementary_files_format_and_content: Standard cuffdiff output, combined with gene details from BioMart (Ensembl release 76), as an Excel sheet.

growth_protocol: 1*10^6 B16 cells were seeded in triplicates in supplemented DMEDM.

extract_protocol:
mRNA was isolated using R1055 Quick-RNA MiniPrep Kit
The libraries were constructed using TrueSeq RNA V2 kit by Illumina.

treatment_protocol: Recombinant mouse IFNγ (carrier free) (BioLegend) (50 µg /ml) was added to the medium for 24 hours

tag: strain

tag: agent

value: IFN-gamma

tag: cell type

value: B16F10.9 melanoma cells


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 28

description:
H28D_2
Processed data file: extended_darkness_counts.txt


title: B16 IFNg 1


title: Co-culture replicate 1, 13:11 day:night cycle, Time 48

description:
H48L_1
Processed data file: extended_darkness_counts.txt


title: B16 IFNg 3


title: B16 3


title: B16 1


title: AdrGland WT M 2105 ACTH TREAT

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Illumina’s Basespace was used to convert bcl files to FASTQ files and de-multiplex the samples
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using TopHat2 v2.0.13 and Bowtie2 v2.2.5.0 with --b2-sensitive option and default parameters
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model (2016-02-02)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count and RPKM values for each sample

source_name: adrenal gland tissue

growth_protocol: adrenal glands were harvested from mice not treated or  injected IP with 100ug/kg of ACTH for 1 hour

extract_protocol:
Total RNA was extracted from adrenal glands using TRIzol (Ambion) and digested with DNase I. cDNA was synthesized using oligo-dT and random hexamer primers
barcoded libraries were made using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Libraries were pooled and single-end sequenced (1X75) on an Illumina NextSeq 500 using the High Output V2 kit (Illumina).

treatment_protocol: mice were  injected IP with 100ug/kg of ACTH for 1 hour

tag: gender

value: Male

value: wild type

tag: tissue

value: adrenal gland

value: ACTH


title: B16 2


title: Co-culture replicate 2, 13:11 day:night cycle, Time 40

description:
H40L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 40hr


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 36

description:
H36D_2
Processed data file: extended_darkness_counts.txt

value: 13:11 light:dark light cycle -> extended darkness


title: AdrGland WT F 2103 ACTH TREAT

value: Female


title: AdrGland KO F P2 ACTH TREAT

value: Siah1a -/-


title: Co-culture replicate 2, 13:11 day:night cycle -> extended darkness, Time 40

description:
H40D_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 40

description:
H40L_1
Processed data file: extended_darkness_counts.txt


title: AdrGland KO M 2013 ACTH TREAT


title: AdrGland KO F 2062


title: AdrGland KO M 1923


title: Co-culture replicate 2, 13:11 day:night cycle, Time 48

description:
H48L_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 2, 13:11 day:night cycle, Time 36

description:
H36L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 36hr


title: AdrGland WT F 2055


title: Co-culture replicate 2, 13:11 day:night cycle, Time 32

description:
H32L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 32hr


title: Co-culture replicate 1, 13:11 day:night cycle, Time 36

description:
H36L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 32

description:
H32L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 2, 13:11 day:night cycle, Time 28

description:
H28L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 28hr


title: Co-culture replicate 2, 13:11 day:night cycle, Time 24

description:
H24L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 24hr

value: 24 hours


title: Co-culture replicate 3, 13:11 day:night cycle, Time 32

description:
H32L_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 24

description:
H24L_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 28

description:
H28L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 2, 13:11 day:night cycle, Time 20

description:
H20L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 20hr

value: 20 hours


title: Co-culture replicate 1, 13:11 day:night cycle, Time 20

description:
H20L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 24

description:
H24L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 2, 13:11 day:night cycle, Time 16

description:
H16L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 16hr

value: 16 hours


title: Co-culture replicate 3, 13:11 day:night cycle, Time 16

description:
H16L_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 12

description:
H12L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 12hr

value: 12 hours


title: Co-culture replicate 3, 13:11 day:night cycle, Time 20

description:
H20L_3
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 2, 13:11 day:night cycle, Time 12

description:
H12L_2
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 16

description:
H16L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 36

description:
H36L_3
Processed data file: extended_darkness_counts.txt

value: 36 hours


title: Co-culture replicate 3, 13:11 day:night cycle, Time 8

description:
H8L_3
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 8hr

value: 8 hours


title: Co-culture replicate 1, 13:11 day:night cycle, Time 12

description:
H12L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 1, 13:11 day:night cycle, Time 8

description:
H8L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 40

description:
H40L_3
Processed data file: extended_darkness_counts.txt

value: 40 hours


title: Co-culture replicate 2, 13:11 day:night cycle, Time 0

description:
H0L_2
Processed data file: extended_darkness_counts.txt

source_name: Bacterial co-culture, normal light regime, 0hr

value: 13:11 light:dark light cycle

value: 0 hours


title: Co-culture replicate 1, 13:11 day:night cycle, Time 0

description:
H0L_1
Processed data file: extended_darkness_counts.txt


title: Co-culture replicate 3, 13:11 day:night cycle, Time 0

description:
H0L_3
Processed data file: extended_darkness_counts.txt


title: AdrGland WT M 1919


title: Co-culture replicate 3, 13:11 day:night cycle, Time 28

description:
H28L_3
Processed data file: extended_darkness_counts.txt

value: 28 hours


title: KO_2 5hmC

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Anti-5hmC Biotinylated
Counts of reads within each peak investigated

data_processing:
Library strategy: hMeSeal-Seq
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the GRCm38 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
hMeSeal reads were aligned to the GRCm38 genome assembly using BWA
Peak calling was performed with MACS2
Peaks were filtered using the IDR pipeline from the Encode Project with an IDR cutoff of 0.02.
Number of reads in peaks were counted using HTSeq-count.
Genome_build: GRCm38
Supplementary_files_format_and_content: Count files were generated using either STAR or HTSeq-count.

source_name: KO_2 5hmC

extract_protocol:
Qiagen RNEasy or Qiagen DNA Mini
hMeSeql or TruSeq RNA Prep kit v2

treatment_protocol: M-CSF

value: Macrophages

tag: passage

value: Passage 0

value: Tet2 Knockout


title: KO_2 RNA

description:
Ribodepleted RNA
Counts of reads in each gene

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the GRCm38 transcriptome using STAR
RNA-seq counts were generated during alignment using STAR
hMeSeal reads were aligned to the GRCm38 genome assembly using BWA
Peak calling was performed with MACS2
Peaks were filtered using the IDR pipeline from the Encode Project with an IDR cutoff of 0.02.
Number of reads in peaks were counted using HTSeq-count.
Genome_build: GRCm38
Supplementary_files_format_and_content: Count files were generated using either STAR or HTSeq-count.

source_name: KO_2 RNA


title: WT_1 5hmC

source_name: WT_1 5hmC

value: Wild-Type


title: WT_2 5hmC

source_name: WT_2 5hmC


title: KO_1 5hmC

source_name: KO_1 5hmC


title: KO_1 RNA

source_name: KO_1 RNA


title: WT_1 RNA

source_name: WT_1 RNA


title: S21_btPAR_EH

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

institute: University of Illinois at Urbana-Champaign

data_processing:
Single-end reads were first filtered using Trimmomatic 0.33 using a minimum quality score of 28 leading and trailing with a minimum length of 30 bp long and subsequently checked using FastQC 0.11.4. Reads were then mapped to the Bos taurus UMD 3.1.1 reference genome (1/29/16 NCBI release) using default settings of STAR 2.5.1b with the quantMode option for gene counts.
Genome_build: Bos taurus UMD 3.1.1 reference genome (1/29/16 NCBI release)
Supplementary_files_format_and_content: Tab files include data matrix containing read counts for each feature in each library. The data frame includes 4 columns:column 1: (1) gene ID, (2) counts for unstranded RNA-seq, (3) counts for the 1st read strand aligned with RNA, (4) counts for the 2nd read strand aligned with RNA

organism: Bos taurus

source_name: Mammary Parenchyma

growth_protocol: Holstein Heifers or 1 wk old (6.0 ± 2 d) and weighed 39.0 ± 4.4 kg at the time of purchase were randomly assigned to treatments, individually housed in outdoor hutches on crushed rock without bedding, and quarantined from the Virginia Tech Dairy herd. Heifers were given ad libitum access to water.

extract_protocol:
Tissue was weighted (PAR, ~0.10 g; MFP, ~0.20 g), immediately placed in QIAzol Lysis Reagent (cat#79306, Qiagen) (1.20 mL) and homogenized using a Mini-Beadbeater-24 (cat#112011, Biospec Products Inc.) with two 30 s cycles, and 1 min incubation on ice in between the cycles. Samples were then centrifuged for 10 min at 12,000 ´ g and 4 °C, and the supernatant was transferred to a separate tube and mixed with Chloroform (cat#C298, Fisher Chemical) (0.24 mL). After centrifugation for 15 min at 12,000 ´ g and 4 °C, the aqueous phase was transferred to a new tube, mixed with 100% Ethanol (cat#2701, Decon Labs; 0.90 mL), and total RNA was cleaned using miRNeasy mini kit columns (cat# 217004, Qiagen) following manufacturer’s protocols. During purification, genomic DNA was removed using the RNase-Free DNase Set (cat#79254, Qiagen). Quantity and purity were determined using a NanoDrop ND-1000 (NanoDrop Technologies Inc.), while integrity was assessed via a Fragment Analyzer™ (Advance Analytical). All samples had an RQN score greater than 8.0. RNA samples were stored at -80 °C until analysis.
RNA-Seq cDNA libraries were constructed using total RNA isolated from both MFP and PAR sampled at weaning (wk 8) slaughter. The Illumina TruSeq v2 RNA Sample Prep kit was used for single-end read library construction following the manufacturer’s instructions with mRNA enrichment. Libraries were multiplexed across flow cell lanes of the Illumina HiSeq2500 (Illumina Inc., San Diego, CA) platform.

treatment_protocol: Calves were assigned to 1 of 2 experimental milk replacer (MR): (1) a restricted MR diet (R; 20.9% CP, 19.8% fat, DM basis; Southern States Cooperative Inc., Richmond, VA) fed at 0.44 kg of MR powder/animal per d, DM basis, or (2) an enhanced MR (EH; 28.9% CP, 26.2% fat, DM basis; Land O’Lakes Animal Milk Products Co., Shoreview, MN) fed at 1.08 kg of MR powder/animal per d, DM basis. Milk replacers had similar fatty acid profiles due to edible lard being the main fat source, and were fed at 15% solids. Milk replacer was fed in 2 equal portions twice daily at 0600 and 1700 h for the first 7 wk of trial. At wk 8, heifers were fed half the usual amount 1× daily at 1700 h to prepare for weaning. Weaning occurred at the end of wk 8. Starter (25.6% CP, 4.0% fat, 19.8% NDF, DM basis; Southern States Cooperative Inc., Richmond, VA) was offered at the end of wk 4 of the trial. In an effort to keep starter intakes similar between treatments, starter was pair fed between R and EH calves. Simply put, R-fed calves were offered starter in the amount of what was consumed by EH-fed calves on the previous day. For example, on d 1, all EH-fed calves were offered starter ad libitum. Their starter intake was then averaged, and that average intake amount was offered to R-fed calves the following day. This was done daily as it was assumed R-fed calves would consume more starter than EH-fed calves if offered ad libitum.

tag: pre-weaning diet

value: EH

tag: time

value: 8 wk


title: S22_btPAR_EH


title: S17_btPAR_R

value: R


title: S18_btPAR_EH


title: S16_btPAR_R


title: WT_3 RNA

source_name: WT_3 RNA


title: S14_btPAR_EH


title: S15_btPAR_R


title: S11_btMFP_EH

source_name: Mammary Fat Pad


title: S19_btPAR_R


title: Co-culture replicate 2, 13:11 day:night cycle, Time 8

description:
H8L_2
Processed data file: extended_darkness_counts.txt


title: S13_btPAR_R


title: S12_btPAR_EH


title: S10_btMFP_R


title: S5_btMFP_R


title: S6_btMFP_R


title: S8_btMFP_EH


title: S4_btMFP_EH


title: S9_btMFP_R


title: S7_btMFP_R


title: S3_btMFP_R


title: S20_btPAR_R


title: WT_2 RNA

source_name: WT_2 RNA


title: CLIP_RNMT_3

city: Dundee

first: Dhaval

last: Varshney

address: Dow Street

department: Centre for Gene Regulation and Expression

institute: University of Dundee

description: CLIP-counts.csv

data_processing:
Base calling performed using the BCL2Fastq2
CLIP data was preprocessed by CIMS pipeline as in Moore et at, Nat. Protocols, 2014. Briefly, 3' adapter (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) was trimmed and PCR duplicates collapsed. 5nt barcode at the 5' end was stripped and appended to the tag name
CLIP data was aligned using novoaligm with 85 as the maximum alignment score acceptable for the best alignment, step size of 1 and read length of 20. RNASeq and ChIPSeq reads were aligned using STAR 2.5.1b.
Number of CLIP aligned per transcript were counted using htseq-count with Gencode v24 annotation. RNASeq reads were quantified using -quantmode GeneCounts for genome indexed with Gencode v24 annotation. Number of ChIP aligned per gene locus were counted using htseq-count with Gencode v24 annotation.
Differential expression analysis performed using edgeR Bioconductor package. ChIPSeq pileups were obtained from pooled alignment files using macs2 pileup utility.
Genome_build: hg38
Supplementary_files_format_and_content: CLIP processed data contains raw counts from htseq-count. RNASeq processed data contains raw counts output from STAR 2.5.1b -quantmode GeneCounts per ensembl gene id. ChIP processed data contains macs2 pileup output from pooled alignment files.

organism: Homo sapiens

source_name: HeLa Cells

growth_protocol: HeLa cells grown in DMEM 10% FCS at 37 degree celsius and 5% CO2

extract_protocol:
RNA extracted using Trizol. ChIP-Seq performed as in Varshney et al, Nat. Comms, 2015
CLIP libraries prepared as in Huppertz et al, Methods, 2014 with a modified 3' RNA linker (3'-UGGAAUUCUCGGGUGCCAAGG-5'). RNASeq libraries were prepared according to Illumina's TruSeq Stranded Total RNA with Ribo-Zero Gold for Human/Mouse/Rat (RS-122-2303). ChIP-Seq libraries prepared as in Wiechens et al, PLoS genetics, 2016.

treatment_protocol: siRNA transfections performed using Lipofectamine RNAimax (Thermo Fisher).

value: HeLa

tag: replicate

value: Replicate 3

value: Untreated


title: CLIP_RNMT_1

description: CLIP-counts.csv

value: Replicate 1


title: S1_btMFP_EH


title: S2_btMFP_EH


title: Myc_control

city: Fujisawa

first: Kenichi

last: Iwai

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

country: Japan

institute: TAKEDA pharaceutical comapny

data_processing:
Illumina mRNA-Seq reads were imported into TopHat v2.0.14 for alignment into BAM files.
Cufflinks was used to quantify gene expression FPKM values.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: Melanoma cell line

growth_protocol: SK-MEL-28 cells were cultured in recommended medium containing G418

extract_protocol:
RNA was harvested using RNAeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Doxycycline was added into cultured medium, and incubated  for 54 hours

tag: vector

value: myc

tag: doxycycline


title: CLIP_RNMT_2

description: CLIP-counts.csv

tag: cell line

value: Replicate 2

tag: treatment


title: vector_Dox

value: empty


title: Myc_Dox


title: vector_control


title: 172_73

city: Palo Alto

first: Brian

middle: D

last: Piening

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford

data_processing:
Reads were trimmed of adapter sequences using trim_galore
Trimmed reads were mapped to the mm9 mouse reference genome using the STAR aligner.
Read counting was performed at the gene level using the featureCounts function in HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files listing raw read counts for each sample

source_name: Brain

extract_protocol:
To obtain RNA, mice were sacrificed 3 days after stroke. Strokes are visible by eye at this time-point, and cortical tissue was dissected at 4°C that contained the stroke core and 1-2 mm of surrounding penumbral tissue, and then snap-frozen on liquid nitrogen and stored at -80°C. RNA was extracted from frozen tissue with Trizol.
RNA library preparation was performed using an Agilent Bravo automated liquid handling platform using Illumina TruSeq Stranded Total RNA HT reagents. Final libraries were assessed for quantity and quality on a Fragment Analyzer instrument (Advanced Analytical). Multiplexed paired-end libraries were sequenced on an Illumina HiSeq 4000 instrument at 300 cycles, generating on average 20-30 million reads per library sample.

value: Sham

tag: high fat diet

value: HFD

tag: weeks


title: 169_68

value: Stroke


title: 168_66


title: 170_70

value: Control


title: 171_72


title: 175_80


title: 174_79


title: 173_77


title: 165_61


title: 176_81


title: 166_64


title: 167_65


title: 161_56


title: 162_57


title: 164_59


title: 163_58


title: 160_55


title: HeLa_EWS-CLIP2

city: San Francisco

first: Marcus

last: Breese

address: 1550 Fourth St, 382

institute: UCSF

description:
processed data file:
EWS-CLIP.filtered.bins.bed

data_processing:
library strategy: CLIP-seq
Preprocessed using NGSUtils (quality trimming)
Aligned to hg19 using STAR
CLIP reads filtered for duplicates using NGSUtils and enriched sites calculated using custom software (Poisson based probabilities)
Differential splicing predicted using custom software
Gene-level read counts calculated using NGSUtils, (Ensembl v74 GTF)
Genome_build: hg19
Supplementary_files_format_and_content: BED, CLIP enriched regions; BED, predicted differentally spliced events
Both of the BED files are in BED6 format and can be viewed by the UCSC Genome Browser.

extract_protocol:
RNA Isolated and Solexa linkers ligated onto isolated RNA, reverse transcribed and PCR amplified
RIP w/ EWSR1 antibody

tag: genotype/variation

value: wild-type

tag: molecule subtype

value: nuclear RNA


title: HeLa_EWS-CLIP1


title: U87_cell_line_dTW_rep4

city: Houston

first: LEI

last: HUANG

state: TX

department: Systems medicine and Bioengineering

institute: Houston Methodist Research Institute

data_processing:
Illumina CASAVA v1.8.2 software was used for basescalling.
Fragment reads were mapped to the UCSC mouse genome (hg38) using Tophat2.
Raw counts for each gene were obtained by HTSeq2, and we also obatined the FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) of raw counts using Cufflinks and scaled via the median of the genomic means for each gene across all libraries as described (Anders and Huber, 2010 [PMID 20979621]).
Adjusted p values for each gene were obtained by Deseq 2.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text file includes rawcounts for each Sample.

growth_protocol: U87MG glioma cells  with WT TWIST1 and CRISPR mediated TWIST1 deletion were maintaned in DMEM supplemented with 10% Fetal bovine Essence (VWR).  Cells plated at 1.2 x10^6 in 60 mm plate were harvested 48h later. Same cells were injected in the brain of nude mice. Animals were sucrificed after when clinical manifestation is detected. Animals were perfuced with PBS and tumors were collected under fluorescent dissecting microscope.

extract_protocol:
Harvested cells were lysed  in Trizol reagent. Tumor fragments ground in liquid nitrogen were lysed in Trizol reagent. RNAesy kit was used to extract RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: genotype


title: U87_cell_line_dTW_rep3


title: U87_cell_line_dTW_rep2


title: U87_cell_line_dTW_rep1


title: 156_49

tag: strain


title: 155_47


title: U87_cell_line_TW_rep3

value: TWIST1 Wild


title: U87_cell_line_TW_rep4


title: U87_cell_line_TW_rep2


title: U87_tumor_dTW_687_rep2


title: 153_43


title: 151_41


title: 152_42


title: U87_cell_line_TW_rep1


title: Fundc1-MKO biological rep2

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

description: Gastrocnemius muscle total RNA from Fundc1 muscle specific knock-out mouse

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Gastrocnemius muscle from Fundc1-MKO mouse

extract_protocol:
Gastrocnemius muscle  were harvested and flash frozen on liquid nitrogen, and RNA was harvested using RNAiso reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Gastrocnemius muscle

tag: age

value: 8 weeks of age

value: Muscle specific Fundc1 knock-out mouse


title: U87_tumor_dTW_686_rep1


title: Fundc1-MKO biological rep1


title: WT biological rep2

description: Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific Fundc1 knock-out

source_name: Gastrocnemius muscle from wild-type mouse

value: Wild-type mouse - control mouse for muscle specific Fundc1 knock-out


title: 159_53


title: U87_tumor_dTW_683_rep2


title: 158_52


title: U87_tumor_dTW_682_rep2


title: U87_tumor_dTW_686_rep2


title: U87_tumor_dTW_683_rep1


title: WT biological rep1


title: 157_50


title: U87_tumor_TW_681_rep1


title: U87_tumor_TW_679_rep2


title: U87_tumor_TW_679_rep1


title: U87_tumor_TW_677_rep2


title: U87_tumor_dTW_682_rep1


title: U87_tumor_TW_681_rep2


title: U87_tumor_TW_677_rep1


title: U87_tumor_TW_676_rep1


title: 154_44


title: U87_tumor_dTW_687_rep1


title: V13930/8181-A_L6

city: Foster City

first: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Clipping adapters and low-quality bases.
STAR
RSEM
edgeR
limma
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene level counts from RSEM output

source_name: PHH

extract_protocol:
On-column DNase I treatment was performed during RNA isolation with the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).

tag: cell type

value: Primary human hepatocytes

tag: donor

tag: infection

value: NO

value: MOCK-CM


title: V13930/8181-J_L4


title: V13930/8181-X_L3

value: HBV+


title: H40170/8181-U_L8.D709


title: V13930/8181-K_L5


title: V13930/4239-I_L7


title: H40170/8181-T_L8.D708


title: H40170/8181-S_L8.D707


title: V13930/8181-W_L2


title: H40170/8181-V_L8.D710


title: H40170/8181-R_L8.D706


title: H40170/8181-Q_L8.D705


title: H40170/8181-I_L7.D709


title: H40170/8181-M_L7.D701


title: H40170/8181-P_L8.D704


title: H40170/8181-N_L7.D702


title: H40170/8181-O_L7.D703


title: H40170/8181-H_L6.D708


title: H40170/8181-G_L6.D707


title: H40170/8181-F_L6.D706


title: H40170/8181-D_L6.D704


title: H40170/8181-C_L6.D703


title: H40170/8181-E_L6.D705


title: C. elegans flp-6 mutants

city: Taipei

first: Chun-Liang

last: Pan

address: No.7.Chung San South Road

department: Institute of Molecular Medicine

country: Taiwan

institute: National Taiwan University

data_processing:
ConDeTri (Ref. PLOS One 2011, 6: e26314) was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks(Ref. Nature Protocol 2012; 7: 562-578) for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
For differential expression analysis, the software CummeRbund (through Open Source Initiative, Artistic License 2.0) was employed to perform statistical analyses of gene expression profiles. The reference genome (WBcel235(GCA_000002985.3)) and gene annotations were retrieved from Ensembl database.
Initially, differentially expressed genes were defined as FKPM  0.3 with a fold change  2 or  0.5 (Ramskold D and Sandberg R, PLOS Comput Biol 2009; 5: e1000598). This resulted in 717 transcripts as differentially expressed in the flp-6 mutant. We therefore set a stringent criterion of FKPM  5, which reduced the number of differentially expressed transcripts to 239.
Genome_build: WBcel235(GCA_000002985.3)/Ensembl database
Supplementary_files_format_and_content: Microsoft excel file includes: 1. FPKM for each sample and the ratio of flp-6 FPKM/ N2 FPKM as well as p and q value, 2. sorted data with FKPM no less than 0.3 and a fold change  2 or  0.5, 3. GO term, 4. KEGG PATHWAY

organism: Caenorhabditis elegans

source_name: whole-animal

growth_protocol: Strains were maintained at 25C as described (Brenner, 1974).

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
All procedures were carried out according to the manufacture’s protocol from Illumina. Library construction of all samples were used by TruSeq RNA Sample Prep Kits v2 for 50SE bp (Single-End or Paired-End) sequencing on Solexa platform. The sequence was directly determined using sequencing-by-synthesis technology via the TruSeq SBS Kit. Raw sequences were obtained from the Illumina GA Pipeline software CASAVA v1.8 and expected to generate 30M (million reads or Gb) per sample.

value: flp-6 mutant

tag: developmental stage

value: L4 lavae

tag: growth temperature

value: 25 degree celsius


title: H40170/8181-B_L6.D702

tag: time


title: H40170/4239-W_L5.D711


title: H40170/4239-V_L5.D710


title: H40170/4239-X_L5.D712


title: H40170/4239-O_L4.D703


title: H40170/4239-U_L5.D709


title: H40170/4239-R_L4.D706


title: H40170/4239-N_L4.D702


title: H40170/4239-Q_L4.D705


title: H40170/4239-T_L5.D708


title: H40170/4239-P_L4.D704


title: H40170/4239-S_L5.D707


title: H40170/4239-M_L4.D701


title: H40170/8181-L_L7.D712


title: H40170/4239-L_L4.D712


title: H40170/4239-G_L3.D707


title: H40170/4239-F_L3.D706


title: H40170/4239-J_L3.D710


title: C. elegnas control animals

value: wild type


title: H40170/4239-H_L3.D708


title: AXL KO3 (tumor graft)

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the GRCm38 genome with TopHat v2.0.10
Raw alignment counts were calculated with Htseq-count v0.5.3.
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCm38
Supplementary_files_format_and_content: Diff files with differential expression

source_name: MMTV-Neu Tumor Graft

extract_protocol:
Total RNA was extracted using Trizol reagent and RNA samples were further purified using RNeasy columns (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

tag: tissue

value: Tumor graft

value: AXL KO


title: A_WT2_empty

last: Huntly

address: Hills Road

department: Department of Haematology

institute: University of Cambridge

data_processing:
ATAC pipeline: All the adapter sequenced of ATAC paired end reads were trimmed and mapped against mm10 reference genome using Bowtie. Uniquely mapped reads were retained and peaks were called with MACS2 with – nomodel and –nolambda parameters
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and bed files

source_name: Lin- BM progenitors (HSPCs)

growth_protocol: For ATACseq using CRISPR/Cas9 mediated editing of Brg1/empty HSPCs was extracted from bone marrow using the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858). Cells were cultured for 7 days in M3434 semi-solid media and expanded for further 5 days in liquid culture. CRISPR/Cas9 genome editing of Brg1 was performed in both Utx+/+ and Utx-/- cells with expression of empty gRNA construct used as a control. At 6 days post gene editing (transduction) we analyzed chromatin accessibility by ATAC-Seq

extract_protocol:
HSPCs was extracted from bone marrow using the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858). The ATAC-seq method was used based on the protocol from Buenrostro et al, 2013 with modifications as described in Kumasaka et al, 2016. Samples were processed with Nextera® Index Kit (Illumina, #FC-121-1011) and Nextera® DNA Sample Preparation Kit (Illumina, # FC-121-1030)
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols

value: Lin- BM progenitors (HSPCs)

value: UTX_WT, Cas9


title: A_WT2_gRNA_Chd4_1


title: A_WT1_empty


title: AXL KO1 (tumor graft)


title: H40170/4239-C_L2.D703


title: WT2 (tumor graft)

value: WT


title: WT3 (tumor graft)


title: A_WT1_gRNA_Chd4_1


title: H40170/4239-E_L3.D705


title: H40170/4239-B_L2.D702


title: H40170/4239-K_L3.D711


title: H40170/4239-A_L2.D701


title: WT1 (tumor graft)


title: AXL KO2 (tumor)

source_name: MMTV-Neu Tumor

value: Tumor


title: WT2 (tumor)


title: AXL KO2 (tumor graft)


title: WT1 (tumor)


title: Sample 24: BJ P6

city: Stockholm

first: Cheng

last: Zhang

address: Tomtebodavägen 23A, Solna

department: Division of Proteomics and Nanobiotechnology

country: Sweden

institute: Royal Institute of Technology, KTH

data_processing:
Illumina Casava 1.8 software used for basecalling.
Transcripts per million (TPM) were calculated using Kallisto version 0.43.1 from Nicolas et al., Nature Biotechnology, 2016.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files including gene length, counts and TPM values for each Sample

source_name: Cell line

growth_protocol: SK-Mel 24, SK-Mel 28, U2OS, A549, U251, BJ, RT4, HepG2 and Caco2, were cultivated at 37 °C in a humidified atmosphere containing 5 % CO2. A549 and BJ cells were grown in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, Carlsbad, CA) supplemented with 10 % FBS and 1 % streptomycin. SK-Mel 24 cells were grown in EMEM supplemented with 15 % FBS and 1 % streptomycin. Caco2, Hep2G, SK-Mel 28 and U251 were grown in EMEM supplemented with 10 % FBS and 1 % streptomycin. RT4 and U2-OS were grown in McCoy supplemented with 10 % FBS and 1 % streptomycin.

extract_protocol:
RNA was extracted from the cells using the RNEasy® kit (Qiagen), generating high‐quality total RNA (i.e., RIN > 8) that was used as input material for library construction with Illumina TruSeq Stranded mRNA reagents.
Illumina TruSeq Stranded mRNA, Poly-A selection, default

value: Epithelial

value: BJ


title: Sample 23: BJ P5


title: Sample 12: A549 P3

value: Lung


title: D4_Unreated

first: Cory

middle: Haley

last: White

address: 320 Bent St

department: DAGS

institute: Merck

description:
HERV_Raw_Count_Table.csv
processed data file header: 2738_DMSO

data_processing:
CASAVA
Sequenced reads were trimmed for adaptor sequence and filtered for low quality sequences.
Reads were mapped to the HERVd reference dataset, included as HERVd.fa, using Bowtie v0.12.8 with settings -v 0 and -m 1.  Each read pair was mapped separately.
After mapping, Samtools view was used with filter settings - F 4 to remove unmapped reads.  Then bam files from each read pair were merged with samtools merge.
Read counts were calculated with HTSeq (htseq-count) using the following parameters:  --stranded=reverse.  Mapped files were counted against the HERVd database with a custom created gtf file which treated each HERV as a single long exon.
Data filtering was performed for HERVs before differential expression analysis with EdgeR.  Any HERV which did not achieve 1 count per million in at least 4 samples removed from future analysis.  Data was normalized with TMM normalization.  Significance was determined at an FDR corrected p-value < 0.05.
Genome_build: HERVd sequence reference file (included)
Supplementary_files_format_and_content: Comma separated file with all rows for HERV designation and columns for sample label.

source_name: CD4 T-cell RNA extract

extract_protocol:
Total RNA was extracted from cell samples using the Rneasy Plus Mini Kit (QIAGEN, Cat. No. 74134) with the addition of an on-column DNase treatment (Rnase-free Dnase Set, QIAGEN, Cat. No. 79254)
Paired end RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primaray CD4+T cells (2.5 million cells per ml) were platd into 6-well tissue plates and either treated with a high dose of vorinostat (10uM) disolved in dimethyl sulfoxide (DMSO) or left untreated (DMSO only) for a period of 24 hours.

value: CD4 T cell

tag: treatment state

value: Untreated (DMSO)


title: D2_Vorinostat

description:
HERV_Raw_Count_Table.csv
processed data file header: 2616_SAHA

value: Vorinostat (SAHA)


title: D1_Vorinostat

description:
HERV_Raw_Count_Table.csv
processed data file header: 2596_SAHA


title: D3_Vorinostat

description:
HERV_Raw_Count_Table.csv
processed data file header: 2623_SAHA


title: D3_Unreated

description:
HERV_Raw_Count_Table.csv
processed data file header: 2623_DMSO


title: D4_Vorinostat

description:
HERV_Raw_Count_Table.csv
processed data file header: 2738_SAHA


title: Sample 22: BJ P8

tag: cell line


title: Sample 9: U2-OS P5

value: Bone


title: Sample 10: A549 P6


title: Sample 20: Hep2G P5

value: Liver


title: D2_Unreated

description:
HERV_Raw_Count_Table.csv
processed data file header: 2616_DMSO


title: D1_Unreated

description:
HERV_Raw_Count_Table.csv
processed data file header: 2596_DMSO


title: 786O_300nM

source_name: Kidney cancer cell line

growth_protocol: Cancer cell lines were cultured in recommended medium

treatment_protocol: T-025 was added into cultured medium, and incubated  for 6 hours

tag: treatment


title: B_KO1_empty

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all paired end reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped reads were retained and peaks were called using SICER with W200 and G600 for broad peaks and W200 and G200 for narrow peaks.
ATAC pipeline: All the adapter sequenced of ATAC paired end reads were trimmed and mapped against mm10 reference genome using Bowtie. Uniquely mapped reads were retained and peaks were called with MACS2 with –nomodel and –nolambda parameters
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and bed files

value: UTX_KO, Cas9


title: B_KO1_gRNA_Smarca4_2


title: B_KO2_gRNA_Smarca4_2


title: B_KO2_empty


title: AXL KO1 (tumor)


title: Sample 8: U2-OS P6


title: B_WT2_gRNA_Smarca4_2


title: 786O_100nM


title: B_WT2_empty


title: Sample 11: A549 P4


title: Sample 19: Hep2G P7


title: B_WT1_empty


title: Sample 7: U2-OS P7


title: B_WT1_gRNA_Smarca4_2


title: 786O_0nM

value: Control


title: 786O_30nM


title: Input_10RT_KO1

extract_protocol:
HSPCs was extracted from bone marrow using the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: UTX KO

tag: chip antibody

value: INPUT


title: H1048_100nM

source_name: Lung cancer cell line


title: H1048_300nM


title: Sample 17: Caco2 P8

value: Colon


title: Sample 18: Caco2 P9


title: Input_10RT_WT1

value: Lin- BM progenitors (HSPCs)

value: UTX WT


title: H40170/4239-D_L2.D704

value: Primary human hepatocytes

value: NO

value: MOCK-CM


title: PU.1_KO3_F

value: PU.1 (Santa Cruz Biotechnology, #sc-352)


title: Sample 28: Hep2G P4


title: Sample 16: Caco2 P7


title: PU.1_KO2_F


title: MB468_300nM

source_name: Breast cancer cell line


title: H1048_0nM


title: MB468_100nM


title: Sample 6: SK-Mel 28 P8

value: Skin

value: SK-Mel 28


title: H1048_30nM


title: PU.1_WT3_F


title: Sample 27: RT4 P4

value: Kidney


title: MB468_0nM


title: MB468_30nM


title: PU.1_WT2_F


title: PU.1_WT1_F


title: KAMX52_1I_H3K4me1

value: H3K4Me1 (Diagenode, #pAb-194-050)


title: Sample 15: U251 P4

value: Brain


title: Sample 3: SK-Mel 24 P8

value: SK-Mel 24


title: KAMX52_1F_H3K4me1


title: COLO320_100nM

source_name: Colon cancer cell line


title: Sample 5: SK-Mel 28 P9


title: COLO320_30nM


title: Sample 26: RT4 P6


title: Sample 14: U251 P5


title: Sample 2: SK-Mel 24 P9


title: COLO320_0nM


title: PU.1_KO1_F


title: KAMX52_1H_H3K4me1


title: KAMX52_1G_H3K4me1


title: Sample 4: SK-Mel 28 P10


title: Sample 13: U251 P6


title: Sample 25: RT4 P7


title: Sample 1: SK-Mel 24 P10


title: H6

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
For all generated raw reads, adaptor sequences, low-quality reads, contaminant reads, and reads that were shorter than 18 nt or larger than 30 nt were eliminated and trimmed with the Fastx-Toolkit software.
The resulting set of trimmed reads were then mapped against the Homo sapiens or Mus musculus genome of Ensembl (Release 80, http://www.ensembl.org/) using the program SOAP . Subsequently, by the same approach, the perfectly matched reads were screened against miRBase (Release 21, http://www.mirbase.org/)  and human or mouse non-coding RNA sequence of Ensembl (Release 80, http://www.ensembl.org/) to obtain the annotation of known mature miRNAs and other small non-coding RNAs (allowing two mismatches)
To correct for the difference in tag counts between samples, the tag counts were scaled to the copy number of transcripts per million (TPM) based on the total number of tags aligned to known human or mouse mature miRNAs in miRBase 21.
Genome_build: hg38 and mm8
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Hippocampus (CA1)

extract_protocol:
Total RNA from the frozen hippocampus was purified using Trizol (Invitrogen, USA) protocol with no modifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: race/strain

value: Asian

value: Hippocampus

value: 51 year

tag: gender

value: male


title: H4

value: 52 year


title: H5

value: 50 year


title: Idx77 BiliaryTract SNU1079

city: Daejeon

first: Kyuheum

last: Jeon

address: 125 Gwahak-ro

country: South Korea

institute: KRIBB

data_processing:
basecalling was performed Macrogen Inc. (KOREA)
Alignemnt of reads were conducted using 'BISMARK; A bisulfite read mapper and methylation caller'.
Percent DNA methylation levels were determined by 'bismark_methylation_extractor'.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing amplicon counts and methylation level (%) in each cancer cell line

source_name: Biliary tract cancer cell line

extract_protocol:
Each genomic DNAs are obtained from other groups and extracted using Quiagen genomic DNA extraction Kit (69504)
Entire amplicons obtained from eight rounds of multiplex PCR were pooled together in equal volumes. For sequencing library construction, we performed a series of enzymatic reactions such as 5’-end phosphorylation, adaptor ligation, and two additional cycles of PCR to attach barcode and other modules, as described elsewhere (Min et al., 2016). Every intermittent purification was conducted using ExpinTM PCR (GeneAll). The sequencing libraries were pooled with equal amount and applied to a multiple parallel sequencing in the same flow cell using Illumina Hi-seq 2500.

tag: histopathology

value: biliary tract cancer


title: Idx02 Stomach SNU620

source_name: Stomach cancer cell line

value: adenocarcinoma


title: Idx93 Stomach SNU5


title: Idx85 Stomach SNU638


title: Idx73 BiliaryTract SNU1196


title: Idx84 Stomach SNU668

value: carcinoma


title: Idx97 Control C2

value: embryonic kidney


title: Idx4 Stomach SNU16


title: Idx74 Stomach NUGC-2


title: Idx3 Stomach MKN74


title: shSORD #3

city: Erlangen

first: Arif

middle: B

last: Ekici

address: Schwabachanlage 10

country: Germany

institute: Institute of Human Genetics

data_processing:
Quality filtering of raw reads was performed using cutadapt 1.9.1 (max-n=0.1, 50 bp minimum length, Q-value cutoff of 20).
Reads were aligned to the human reference genome (GRCh37 release 87) using STAR 2.5.2b with default settings.
Read counts were obtained using subread featureCounts 1.5.1 and the GRCh37 87 .gtf annotation file.
Differential expression calls were generated using DESeq2 1.12.3.
Genome_build: GRCh37 release 87
Supplementary_files_format_and_content: tab delimited text file containing raw counts for each sample.

source_name: human cancer cell line from lung adenocarcinoma (A549)

growth_protocol: All cell lines were cultured in media supplemented with 5% FBS, 1% Pen/Strep and 1% L-Glutamine (Sigma) at 37 °C and 5% CO2 in a humidified incubator

extract_protocol:
RNA was extracted using Qiazol and the miRNeasy Mini Kit (Qiagen).
Libraries were constructed using the TruSeq stranded mRNA kit (Illumina).

treatment_protocol: shRNA-mediated specific gene inhibition

value: cell line A549

value: SORD inhibited by shRNA


title: shAKR1B1 #3

value: AKR1B1 inhibited by shRNA


title: Idx21 Stomach MKN45


title: Idx62 Stomach SNU719


title: Idx86 Stomach MKN28


title: Idx76 Stomach Fu97


title: shAKR1B1 #1


title: H2

value: 53 year


title: plko #1

value: scrambled controls


title: shAKR1B1 #2


title: Idx72 Stomach SNU1


title: Idx10 Lung WI38

source_name: Lung fibroblast

value: normal


title: H1

value: 55 year


title: Idx26 Lung A549


title: plko #3


title: shSORD #2


title: COLO320_300nM


title: Idx25 Stomach SNU216


title: Idx27 Lung H460


title: H3

value: Asian

value: 54 year


title: shSORD #1


title: H7

value: Hippocampus

value: 57 year


title: spt6_0h_Rep_1

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description:
SPT6 siRNA transfection_no IFN treatment.
mRNA

data_processing:
Paired-end sequencing reads were aligned to the mouse genome (mm10 assembly) using tophat2 (version 2.1.0) with the default parameters.
Tables with counts of mRNA that were mapped to all mouse genes were generated by htseq-count package (version 0.6.1p1), using the following parameters: htseq-count --format=bam --stranded=no -m intersection-strict
Differentially expressed genes were obtained using the DESeq2 package in R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files with the tables with mRNA counts for all mouse genes, generated by htseq-count package.

source_name: NIH3T3 cells, SPT6 siRNA, untreated

growth_protocol: NIH3T3 cells were grown in Dulbecco's minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.

extract_protocol:
RNA from NIH3T3 cells was extracted using TRIzol regent (Invitrogen) according to manufacturer's protocol.
Library preparation including ligating barcode was conducted using a Mondrian SP (NuGEN Technologies Inc.) and the Ovation SP Ultralow Library system (NuGEN). Fragments were selected ranging from 250 to 450 bp and subjected to paired-end sequencing on a HiSeq2000 (Illumina).

treatment_protocol: Negative control (NC) siRNA (Ambion #4390843) and siRNA for SPT6 (Ambion s74583) were transfected into NIH3T3 cells with Lipofectamine 2000 (Invitrogen). After 48h siRNA transfection, cells were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 4h.

tag: sirna


title: Idx82 Liver Huh7

source_name: Liver cancer cell line

value: hepatocellular carcinoma


title: Idx28 Lung H1299


title: Idx88 Liver SNU886


title: spt6_4h_Rep_1

description:
SPT6 siRNA transfection_IFN 4h treatment_Rep_1.
mRNA

source_name: NIH3T3 cells, SPT6 siRNA, IFNbeta

value: IFNbeta

tag: treatment duration


title: Idx29 Lung H1650


title: WT_0h_Rep_1

description:
NC siRNA transfection_no IFN treatment.
mRNA

source_name: NIH3T3 cells, NC siRNA, untreated

value: Negative control (NC)


title: WT_4h_Rep_1

description:
NC siRNA transfection_IFN 4h treatment_Rep_1.
mRNA

source_name: NIH3T3 cells, NC siRNA, IFNbeta


title: spt6_4h_Rep_2

description:
SPT6 siRNA transfection_IFN 4h treatment_Rep_2.
mRNA


title: Idx83 Liver SNU878


title: Idx31 Liver SNU761


title: Idx90 Liver SNU739


title: Idx32 Liver Hep3B

value: hepatoma


title: Idx34 Liver SNU398


title: Idx80 Liver SNU475


title: KAMX-KO3

city: Cambridge

data_processing:
Peaks were called using MACS2 and P Value 10e-11 was used as cutoff
Genome_build: mm10
Supplementary_files_format_and_content: Raw files, processed files, peak files are in BAM, bigwig and bed formats respectively

source_name: Lin- BM progenitors (HSPCs)

extract_protocol:
HSPCs was extracted from bone marrowusing the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858), cells were lysed and tagmentation was performed using Nextera tagmentation master mix(Illumina FC-121-1030)
ATAC-Seq libraries were prepared for sequencing using FC-121-1030 Nextera® DNA Sample Preparation Kit and FC-121-1011 Nextera® Index Kit

tag: genotype

tag: strain


title: KAMX-WT3

tag: cell type


title: KAMX-KO2


title: Idx89 Liver SKHep1

value: adenocarcinoma


title: KAMX-WT2


title: UTX-IP-IgG-D-Control

data_processing:
peaks are called using SICER at 10e-08 cut off
Genome_build: mm10
Supplementary_files_format_and_content: Raw files, processed files, peak files are in BAM, bigwig and bed formats respectively

extract_protocol:
HSPCs was extracted from bone marrowusing the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858), Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols

value: UTX WT

value: IgG (Diagenode, C15410206)


title: KAMX-WT1


title: Idx81 Liver HLE

value: carcinoma

value: HLE


title: Idx79 Liver PLCPRF5


title: UTX_INPUT_A


title: Idx36 Colon LoVo

value: LoVo


title: BCOR-IP-IgG-Control


title: Idx37 Colon SNU61


title: Idx38 Colon SNU-C1


title: Idx40 Colon SNU283


title: plko #2

value: cell line A549

value: scrambled controls


title: KAMX-KO1


title: KDM6A-H3K27Ac-KO2

value: H3K27Ac (Diagenode, #pAb-196-050)


title: UTX-IP-BETHYL-C-WT

value: UTX (Bethyl, A302-374A)


title: Idx39 Colon SW480


title: KDM6A-H3K27Ac-KO1


title: KAMX34-4C-UTX-BETHYL-WT


title: Idx66 Colon HT-29


title: Idx35 Liver SNU387


title: Idx33 Liver HepG2

value: hepatocellular carcinoma


title: KDM6A-H3K27Ac-WT2


title: Idx67 Colon SNU1033


title: KDM6A-H3K27Ac-WT1


title: KAMX52-KO2-H3K27Me3

value: UTX KO


title: Idx70 Colon SW620

value: colorectal carcinoma


title: KAMX52-KO1-H3K27Me3


title: KAMX52-WT2-H3K27Me3


title: Idx71 Colon WiDr

value: WiDr


title: Idx69 Colon SNU-C4


title: KDM6A-H3K27Ac-INPUT


title: Idx96 Control C3

value: embryonic kidney


title: Idx78 Colon HCT116


title: KAMX52-WT1-H3K27Me3


title: Idx95 Control C2


title: Idx94 Contol C1


title: Idx50 BiliaryTract SNU308

value: biliary tract cancer


title: Idx91 BiliaryTract SNU245


title: Idx87 Stomach SNU719


title: Idx68 Colon SNU407


title: Idx59 Stomach SNU668


title: Idx24 Stomach SNU16


title: Idx5 Stomach SNU216


title: Idx52 BiliaryTract SNU1079


title: Idx60 Stomach SNU638


title: Idx92 Stomach SNU5


title: Idx47 Stomach SNU1


title: Idx49 Stomach NUGC-2


title: Idx1 Stomach MKN45


title: Idx61 Stomach MKN28


title: Idx7 Lung H460


title: Idx8 Lung H1299


title: Idx30 Lung WI38

value: normal


title: Idx9 Lung H1650

value: adenocarcinoma


title: Idx63 Liver SNU886

value: hepatocellular carcinoma


title: Idx23 Stomach MKN74


title: Idx58 Liver SNU878


title: Idx6 Lung A549


title: Idx51 Stomach Fu97


title: Idx14 Liver SNU398


title: Idx57 Liver Huh7


title: Idx48 BiliaryTract SNU1196


title: Idx22 Stomach SNU620


title: Idx11 Liver SNU761


title: Idx65 Liver SNU739


title: Idx55 Liver SNU475


title: Idx15 Liver SNU387


title: Idx54 Liver PLCPRF5

value: hepatoma


title: Idx13 Liver HepG2


title: CD34_25

city: Nijmegen

first: Arjen

last: Brinkman

address: NCMLS #274, Geert Grooteplein Zuid 30

department: Molecular Biology

country: Netherlands

institute: Radboud University, Nijmegen Center for Molecular Life Sciences

description: MeCP2 protein methyl-CpG binding domain

data_processing:
Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) platform according to standard protocols of the manufacturer (Illumina). The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequence reads (35 bases, 1st base was discarded) were aligned to the human (hg18) reference genome using the Illumina Analysis Pipeline, allowing one mismatch. Only the 36 bp sequence reads uniquely aligning to the genome were considered for further analysis. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All sequence analyses were conducted based on the Homo sapiens hg18 genome assembly.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files were generated by counting the number of sequence reads (directionally extended to 234 bp) per 10-bp genomic window; BED files contain genomic coordinates of directionally extended (to 234 bp) sequence reads; AML_MethylCap_peaks_tagcounts.gz (readcounts table) contains genomic coordinates of merged MethylCap peaks from all samples along with a per-sample readcount in each peak; AML_MethylCap_peaks_hyper_DMRs.gz (differential methylation scoring table) and AML_MethylCap_peaks_hypo_DMRs.gz (differential methylation scoring table) contains genomic coordinates of merged MethylCap peaks from all samples along with a per-sample score (0 or 1) for the presence of a hyper-DMR or hypo-DMR for each peak, respectively.

source_name: CD34+ healthy progenitor cells

extract_protocol:
MethylCap (Capturing of methylated DNA) was done using in automated procedure using a SX-8G/IP-StarTM robot (Diagenode). 2 µg of His6–GST–MBD (Diagenode) was incubated with 1 µg of fragmented DNA in binding buffer (BB, 20 mM Tris–HCl pH 8.5, 0.1% Triton X-100) with 200 mM NaCl in a final volume of 200 µl. This solution is mixed at 4°C for 2 h. Magnetic GST-beads were prepared by washing 35 µl of a well-mixed beads suspension (Promega) with 200 µl of binding buffer + 200 mM NaCl at 4 °C. The suspension was mixed and a magnet was used to collect the beads. After removal of the supernatant the procedure is repeated once. After the second wash the supernatant is removed, but the beads are not allowed to get dry. The GST–MBD solution is added to the washed beads and this suspension is mixed for another hour at 4°C. After removal of the supernatant (the ‘flow-through’) the beads–GST–MBD–DNA complexes are washed/eluted. 200 µl of binding buffer with increasing concentrations of NaCl is added and the suspension is rotated for 10 min at 4°C. Beads are captured on the magnet, and the supernatant is collected. Three different eluates were collected (LOW, MEDIUM, HIGH), corresponding 500 mM, 600 mM and 800 mM NaCl. For MethylCap-seq the MEDIUM and HIGH eluates were sequenced separately.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E.coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel (E-gel). DNA was purified and PCR-amplified with Illumina primers for 16 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: CD34+ healthy progenitor cells

tag: binding protein

value: His6-GST-MBD (Diagenode)


title: Idx12 Liver Hep3B


title: AML_257

description: MeCP2 protein methyl-CpG binding domain

source_name: acute myeloid blasts

value: acute myeloid blasts


title: AML_254

description: MeCP2 protein methyl-CpG binding domain


title: Idx64 Liver SKHep1


title: AML_253

description: MeCP2 protein methyl-CpG binding domain


title: AML_251

description: MeCP2 protein methyl-CpG binding domain


title: CD34_23

description: MeCP2 protein methyl-CpG binding domain


title: AML_252

description: MeCP2 protein methyl-CpG binding domain


title: CD34_28

description: MeCP2 protein methyl-CpG binding domain


title: Idx18 Colon SNU-C1


title: Idx16 Colon LoVo

value: LoVo


title: Idx17 Colon SNU61

value: carcinoma


title: Idx56 Liver HLE

value: HLE


title: AML_235

description: MeCP2 protein methyl-CpG binding domain


title: AML_233

description: MeCP2 protein methyl-CpG binding domain


title: AML_237

description: MeCP2 protein methyl-CpG binding domain


title: AML_228

description: MeCP2 protein methyl-CpG binding domain


title: Idx20 Colon SNU283


title: Idx19 Colon SW480


title: Idx41 Colon HT-29


title: Idx42 Colon SNU1033


title: WT_4h_Rep_2

description:
NC siRNA transfection_IFN 4h treatment_Rep_2.
mRNA

value: Negative control (NC)

value: IFNbeta


title: AML_226

description: MeCP2 protein methyl-CpG binding domain


title: AML_224

description: MeCP2 protein methyl-CpG binding domain


title: AML_187

description: MeCP2 protein methyl-CpG binding domain


title: Idx43 Colon SNU407


title: Idx44 Colon SNU-C4


title: AML_120

description: MeCP2 protein methyl-CpG binding domain


title: Idx45 Colon SW620


title: AML_112b

description: MeCP2 protein methyl-CpG binding domain


title: AML_109

description: MeCP2 protein methyl-CpG binding domain


title: AML_231

description: MeCP2 protein methyl-CpG binding domain


title: HeLa_EWS3

description:
processed data file:
merged.ensembl.74.hg19.counts.txt
EWSR1-star-combined.events.txt.junctions.bed

data_processing:
Preprocessed using NGSUtils (quality trimming)
Aligned to hg19 using STAR
CLIP reads filtered for duplicates using NGSUtils and enriched sites calculated using custom software (Poisson based probabilities)
Differential splicing predicted using custom software
Gene-level read counts calculated using NGSUtils, (Ensembl v74 GTF)
Genome_build: hg19
Supplementary_files_format_and_content: BED, CLIP enriched regions; BED, predicted differentally spliced events
Both of the BED files are in BED6 format and can be viewed by the UCSC Genome Browser.

extract_protocol:
Illumina Tru-Seq prep
Trizol extraction

value: HeLa

tag: genotype/variation


title: HeLa_Control2

value: GFP-siRNA


title: HeLa_Control1


title: HeLa_Control3


title: HeLa_EWS4


title: H3-LOG

city: Amsterdam

first: Tessy

last: Korthout

state: Noord-Holland

address: Plesmanlaan 121

department: Gene Regulation

institute: The Netherlands Cancer Institute

data_processing:
reads were aligned with BWA version 0.6.1
coverage was calculated around TSS
nucleosomes were called using Template Filtering
data was normalized to the sequencing depth
Genome_build: S288C genome build R64-2-1
Supplementary_files_format_and_content: txt files with ~2000 data columns representing the coverage of the normalized reads in a window of -1000 to 1000 bp around the +1 nucleosome, for each verified yeast gene. So column 1000 represents the +1 nucleosome.occupancy around +1 nucleosome for each sample.

organism: Saccharomyces cerevisiae

source_name: yeast cells in log phase

growth_protocol: Yeast cells were grown in YEPD at 30C

extract_protocol:
Lysates were sonicated, MNase treated and histone-DNA complexes were purified using antibodies.
Libraries were prepared according to Illumina DNA Sample Kit instructions

treatment_protocol: Yeast cells were grown in YEPD at 30C with alpha factor for 4 hours.

value: V5 (R960-25, Invitrogen)


title: H2A.Z-V5

source_name: G1-arrested yeast cells


title: HeLa_EWS2


title: H3_HA

value: HA (12CA5, Sigma)


title: H2A.Z-HA


title: HeLa_EWS1


title: AML_108

description: MeCP2 protein methyl-CpG binding domain


title: H3-V5


title: SiNC

city: Shanghai

first: Linlin

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institutes for Biological Sciences

description: Control RKO cells

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in MappingStatistic_SiASF.xls and MappingStatistic_SiNC.xls
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19

source_name: RKO cells treated by control siRNA

extract_protocol:
RKO cells 48 hours after tranfected with siRNA were collected , and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RKO

value: colon carcinoma


title: SiASF

description: siSRSF1 treated RKO cells

source_name: RKO cells treated by siSRSF1


title: SDIMO gene sequencing of Consortium B Before Enrichment

first: Ya

last: He

state: Texas

department: Department of Civil and Environmental Engineering

institute: Rice University

description: PCR product produced using genomic DNA as the template

data_processing:
Remove the barcodes, primers and short sequences<150bp
Remove ambigous base calls
Denoise sequences
Define Operational Taxonomic Units(OUT):97% similarity
Classify OTUs Using BLASTn against NCBI, GreenGenes, RDPII databases
Supplementary_files_format_and_content: Excel file, the genus level percentage of the bacteria contained in each consortium; the predominance of SDIMOs in each consortium

source_name: Bacterial consortium

growth_protocol: AMS medium amended with 1,4-dioxane as the sole carbon source

extract_protocol:
Ultra clean Microbial DNA extraction kit (MO BIO)
Illumina DNA library for Miseq

tag: function

value: degrade 1,4-dioxane

value: Bacterial Consortium B

tag: molecule subtype

value: SDIMO gene PCR product

tag: carbon source


title: SDIMO gene sequencing of Consortium A Before Enrichment

value: Bacterial Consortium A


title: 16S rRNA gene sequencing of Consortium B Before Enrichment

data_processing:
Remove the barcodes, primers and short sequences<150bp
Remove ambiguous base calls
Denoise sequences
Define Operational Taxonomic Units(OUT):97% similarity
Classify OTUs Using BLASTn against NCBI, GreenGenes, RDPII databases
Supplementary_files_format_and_content: Excel file, the genus level percentage of the bacteria contained in each consortium; the predominance of SDIMOs in each consortium

source_name: a 1,4-dioxane degrading consortium

value: 16S rRNA gene PCR product


title: 16S rRNA gene sequencing of Consortium A Before Enrichment


title: Idx46 Colon WiDr

source_name: Colon cancer cell line

value: adenocarcinoma

value: WiDr


title: H2A.Z-LOG


title: Idx53 Colon HCT116

value: colorectal carcinoma


title: 8hr_wild type

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

description: Gene expression, 8 hours after P. syringae pv. tomato J4 infection

data_processing:
Illumina Casava1.7 software used for basecalling.
Several quality measures were performed using the software program  FastQC  to check the data quality of the reads and detect any potential errors introduced during sequencing or library preparation. The Cutadapt software program was used to remove low quality reads from the final dataset. Reads with a Phred-like score of <20 and read length <40 bases were excluded. The transcripts of the garden tomato Solanum lycopersicum from the NCBI were used as reference sequences for RNA-seq analysis using the Bowtie2 mapper.
The mapping results were processed with the samtools and scripts developed in house at ICBR to remove potential PCR duplicates and select uniquely mapping reads for gene expression estimation. The number of mapped reads for each individual gene were counted and some genes from different treatments were selected for downstream analysis against the genes from tomato and arabidopsis
Genome_build: GCF_000188115.3_SL2.50_rna
Supplementary_files_format_and_content: tab-delimited text files include the mapped read counts for each Sample

organism: Solanum lycopersicum

source_name: wild type, 8hr

growth_protocol: Tomato seeds were germinated in potting soil.  After germination, the seedlings were transplanted into 5 cm pots with potting soil and kept in the greenhouse at 28°C.

extract_protocol: About 100 mg leaf tissues were ground into a fine powder in liquid nitrogen and total RNA was extracted using the Quick-Start RNeasy Plant mini kit (Qiagen) following the manufacture's instructions and resuspended in DEPC-treated water.

treatment_protocol: Four-week-old tomato plants were spray inoculated with a P. syringae pv. tomato J4 suspension (10^8 cfu/mL).  The plants were then immediately covered with plastic bags and rubber band to increase humidity for 40hr. Inoculated plants were incubated in the growth chamber and maintained at 22°C under a 12hr-dark/12hr-light regiment.

tag: cultivar

value: Moneymaker'

tag: time

tag: tissue

value: leaf

value: wildtype


title: 24hr_wild type

description: Gene expression, 24 hours after P. syringae pv. tomato J4 infection

source_name: wild type, 24hr


title: 0hr_transgenic plant

description: Gene expression, 0 hours after P. syringae pv. tomato J4 infection

source_name: transgenic plant, 0hr

value: transgenic overexpression of A.thaliana ELP4


title: 8hr_transgenic plant

source_name: transgenic plant, 8hr


title: 16S rRNA gene sequencing of Consortium B

data_processing:
Remove the barcodes, primers and short sequences<150bp
Remove ambigous base calls
Denoise sequences
Define Operational Taxonomic Units(OUT):97% similarity
Classify OTUs Using BLASTn against NCBI, GreenGenes, RDPII databases
Supplementary_files_format_and_content: Excel file, the genus level percentage of the bacteria contained in each consortium


title: 16S rRNA gene sequencing of Consortium A


title: 24hr_transgenic plant

source_name: transgenic plant, 24hr


title: SDIMO gene sequencing of Consortium B

data_processing:
Remove the barcodes, primers and short sequences<150bp
Remove ambigous base calls
Denoise sequences
Define Operational Taxonomic Units(OUT):97% similarity
Classify OTUs Using BLASTn against databases containing all of the SDIMOs from NCBI
Supplementary_files_format_and_content: Excel file, the predominance of SDIMOs in each consortium


title: 0hr_wild type

source_name: wild type, 0hr


title: M408 DMSO

status: Public on Apr 30 2018

city: Los Angeles

first: Jennifer

last: Tsoi

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

data_processing:
Paired end 50 bp reads generated from the melanoma cell line RNA sequencing were mapped using HISAT2 to the Homo sapiens hg38 genome build and raw counts per quantified using HTSeq.
Raw counts were normalized to FPKM values using conditional quantile normalization (CQN) to adjust for gene length and GC content.
genome build: hg38
processed data files format and content: Matrix of gene expression measurements in FPKM

source_name: Melanoma cell line

extract_protocol:
AllPrep DNA/RNA Mini kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells have been treated with DMSO for 48 hours.

tag: cell line

tag: disease state

value: Melanoma


title: M403 DMSO


title: M311 DMSO


title: M416 DMSO


title: M368 DMSO


title: M412b DMSO


title: M262 DMSO_2


title: M249AR DMSO


title: M421 DMSO


title: M285 DMSO


title: M417 DMSO


title: M412a DMSO


title: M230 DMSO


title: SDIMO gene sequencing of Consortium A


title: M249 DMSO


title: M202 DMSO


title: M397 DMSO


title: M395AR DMSO


title: M397AR DMSO


title: PB DMSO

value: PB


title: M375 DMSO


title: M376 DMSO


title: M399 DMSO


title: M398_DMOS


title: M308 DMSO


title: M263 DMSO


title: M229 DMSO


title: M395 DMSO


title: M420 DMSO


title: M255 DMSO


title: M238AR DMSO


title: M402 DMSO


title: M411 DMSO


title: M423 DMSO


title: M370 DMSO


title: M409AR DMSO


title: M243 DMSO


title: M229AR DMSO


title: M238 DMSO


title: M418 DMSO


title: M233 DMSO


title: M245 DMSO


title: M207 DMSO


title: M406 DMSO


title: M381 DMSO


title: M318 DMSO


title: M297 DMSO


title: M257 DMSO


title: M410 DMSO


title: M409 DMSO


title: Sbcl2 DMSO


title: murine hepatocytes (MMH-D3) H3K27me3

city: Wuppertal

first: Jan

last: Postberg

state: NRW

address: Heusnerstr. 40

institute: HELIOS University Hospital Wuppertal, Witten/Herdecke University

data_processing:
bcl2fastq2 v2.15.0 was used for demultiplexing
Fastqc 0.10.1 was used for read quality assessment
Cutadapt-1.2.1 was used for adaptor trimming.
Fastq files were uploaded onto the Galaxy server and converted using FASTQ Groomer
Read mapping was done using Bowtie2 with the ‘very sensitive end-to-end’ option.
The resulting BAM file was used for direct visualization of mapped reads in Geneious R9 software or further processed for comparative analyses using a DeepTools pipeline in Galaxy (1. bamCoverage [variable bin sizes, 50kbp among others] to generate coverage bigWig files for visualization in the UCSC genome browser (genome.ucsc.edu); 2. bigwigCompare with default options to normalize and compare two bigwig files and visualize the results in the UCSC genome browser.
Alternative color grading look-up tables (LUT) contained in WCIF ImageJ software were assigned to the UCSC genome browser greyscale dense coverage tracks for improved visualization.
Genome_build: Mus musculus genome mm9 or Homo sapiens hg38, respectively
Supplementary_files_format_and_content: bigwig format, files contain mapped reads on chromosomes Y, 15, 3, 1 for visualization of each investigated marker

source_name: murine hepatocytes (MMH-D3)

extract_protocol:
Briefly, lysates from cells crosslinked for 10 min in 1% formaldehyde were layered onto a 1.6 M sucrose cushion (1.6 M sucrose in 60 mM, KCl 15 mM NaCl, 5 mM MgCl2, 0.1 mM ethylene glycol tetraacetic acid (EGTA), 15 mM Tris-HCl (pH 7.5), 0.5 mM DTT, 0.1 mM phenylmethanesulfonylfluoride (PMSF), 3.6 ng/mL aprotinin) and centrifuged. Nuclei were collected and portions corresponding to 50μg chromatin were sheared by ultrasonic treatment using a Bioruptor UCD-200 (Diagenode) and 30× [30 s ON/30 s OFF] at position ‘high’. Chromatin fragment size was controlled on agarose gels, and one of the chromatin aliquots was saved as input. For ChIP analyses, sheared chromatin samples were incubated with the respective antibody-of-interest in a rotator for 16 h at 4°C. Subsequently 20 μl protein G magnetic beads (Diagenode) were added and incubated for 4 hrs at 4°C rotating. Immunocomplexes attached to protein G magnetic beads were separated using a magnetic rack and washed repeatedly. To elute DNA fragments enriched by immunoprecipitation, immunocomplexes were incubated with elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris–HCl, (pH 8.1)) for 30 min at 65°C on a shaker. Eluted immunocomplexes were treated with proteinase K overnight at 55°C. Antibodies used for IP were directed against HBxAg (mouse monoclonal antibody, clone 3F6-G10; Bio-Rad Laboratories Inc.), Pol2 (Active Motif, Carlsbad, CA, USA), H3K4me3 (Diagenode, Liège, Belgium), H3K4me1 (Diagenode, Liège, Belgium), H3K9me3 (Diagenode, Liège, Belgium), H3K9ac (Diagenode, Liège, Belgium), H3K27me3 (Diagenode, Liège, Belgium), H3K27ac (Diagenode, Liège, Belgium), H3K36me3 (Diagenode, Liège, Belgium) or H3K36ac (Diagenode, Liège, Belgium). DNA associated with enriched immunocomplexes was purified by phenol:chloroform:isoamylic alcohol extraction and precipitated with isopropylic alcohol.
Illumina-compatible libraries were prepared using the MicroPlex Library Preparation kit v2 (Diagenode, Liège, Belgium). Massive parallel sequencing was performed as described below.
ChIP-seq was performed with the paired-end or, alternatively, with the single read option (42nt paired-end in mmu experiments/50nt single-end in hsa experiments) and the Illumina NextSeq 500 High Output Kit

tag: tumour stage

value: non-transformed

tag: source

value: liver

tag: antibody


title: murine hepatocytes (MMH-D3) H3K36me3


title: murine hepatocytes (MMH-D3) H3K9me3


title: murine hepatocytes (MMH-D3) Pol2


title: murine hepatocytes (MMH-D3) H3K9ac


title: murine hepatocytes (MMH-D3) H3K36ac


title: murine hepatocytes (MMH-D3) NLS-HBx-RFP

value: NLS-HBx-RFP


title: murine hepatocytes (MMH-D3) H3K4me1


title: M296 DMSO