title: PC9R_RNA_rep

city: Shanghai

first: Dan

last: Li

address: Siping 1239

department: Life science and Technology department

country: China

institute: Tongji University

data_processing:
Basecalls performed using Off-Line Basecaller 1.9.4
Bowtie0.12.9 used for alignment
MACS2 used for peak-calling
TopHat used for RNA-seq reads mapping
HTseq and DEseq used for RNA-seq reads counting
Genome_build: hg19

source_name: lung cancer cell

growth_protocol: PC9 and PC9R cells were routinely generated by plating DMEM cultures

extract_protocol:
mRNA were extracted by Tiangen kits (#DP431 ) and whole DNA were extracted by Qiagen DNeasy 96 Blood & Tissue Kit kits, and ChIP antibody were from Abcam
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: PC9R were screened from PC9  treated by gefitinib for 1-2 weeks

value: lung cancer cell

tag: passages

tag: cell line


title: PC9R_RNA

status: Public on Nov 20 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: Drosophila simulans head small RNA [O002_dsim_head]

city: Stanford

first: Jaaved

last: Mohammed

state: CA

address: 265 Campus Drive

department: Chemical and Systems Biology

country: USA

institute: Stanford University

description: heads

data_processing:
3' adapter sequences were trimmmed using the fastx_clipper utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)

organism: Drosophila simulans

source_name: D. simulans head small RNA

extract_protocol:
Male and female bodies were isolated in bulk using sieves after sorting by sex. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol.
For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.

tag: tissue

value: head


title: Adult basal cell 5

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
RNA-seq reads were mapped to the mouse genome using the align function of Rsubread version 1.15.9
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

organism: Mus musculus

source_name: mammary gland

extract_protocol:
Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 using standard Illumina protocols.

tag: strain

value: FVB/NJ

tag: age

value: Adult

tag: cell source

value: Basal

tag: pcr plate

value: A


title: Adult basal cell 6


title: Drosophila simulans testis small RNA [O001_dsim_testis]

description: testes

source_name: D. simulans testis small RNA

value: testis


title: Adult basal cell 2


title: Drosophila persimilis head small RNA [V057_dper_head]

description: heads

organism: Drosophila persimilis

source_name: D. persimilis head small RNA


title: Adult basal cell 1


title: Adult basal cell 4


title: Adult basal cell 3


title: PC9R_H3K4me2

library_source: genomic

molecule: genomic DNA

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog


title: Erythroid cells fixed with 0.5% formaldehyde replicate 1

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
3C library preparation followed by double oligonucleotide capture
fixation_alpha.gfc
fixation_beta.gfc
fixation_slc25a37.gfc
05P1_S3_L001

data_processing:
Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Primary erythroid cells

growth_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde (this was varied for the reduced crosslinking experiments), quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNAse. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. Different strategies were used for the sequencing library preparation. For the low-input experiments, the LI Capture-C or Tag-Capture-C protocol was used, for which 50-200 ng of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra DNA Library Prep kit, or the Illumina Nextera DNA Library Prep kit, respectively. For the reduced cross-linking experiments, the NG Capture-C protocol was used, for which 5 ug of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng-2 ug of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina MiSeq (150bp paired end reads) platform.

value: Ter-119+ cells isolated from phenylhydrazine treated spleen

tag: genes analysed


title: Drosophila pseudoobscura male body small RNA [V112_dpse_male_body]

description: male bodies

organism: Drosophila pseudoobscura

source_name: D. pseudoobscura male body small RNA

value: abdomen and thorax


title: Drosophila persimilis embryo small RNA [V042_dper_embryo]

description: mixed embryos

source_name: D. persimilis embryo small RNA

value: whole embryo


title: PC9R_DHS


title: Drosophila persimilis head small RNA [V050_dper_head]

description: heads


title: PC9_RNA


title: PC9_RNA_rep


title: Drosophila persimilis male body small RNA [V111_dper_male_body]

description: male bodies

source_name: D. persimilis male body small RNA


title: NB490_shPDX1_48h_Dox_Bru

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description:
doxycycline treatment time: 48 hours
molecule: bru-labeled RNA

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) number of introns and exons; (9) length (sum of feature lengths, e.g. introns and exons); (10) read count (sense strand); (11) density (RPK) – count/length; (12) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: NB490, doxycycline treatment time: 48 hours

growth_protocol: The mouse pancreatic cancer cell line NB490 was maintained in DMEM supplemented with 10% FBS and 50 mg/mL gentamycin. Puromycin selection (5mg/mL) was used for stable expression of inducible PDX1 shRNA.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Cells were incubated in conditioned media containing 2 mM bromouridine (BrU) at 37C for a 30 min.

value: NB490 expressing inducible PDX1 shRNA


title: NB490_shPDX1_GrowOut_Dox_Bru

description:
doxycycline treatment time: > 3 weeks
molecule: bru-labeled RNA

source_name: NB490, doxycycline treatment time: > 3 weeks


title: Adult luminal cell 77

value: Luminal

value: C


title: NB490_shPDX1_uninduced_Bru

description:
doxycycline treatment time: 0 hours
molecule: bru-labeled RNA

source_name: NB490, doxycycline treatment time: 0 hours


title: NE01

city: Changchun

first: Jigang

last: Yin

address: 5333# Xi An Da Lu

institute: Jilin university

description: Biologic repetition

data_processing:
Raw reads were first discarded if containing more than 2-N bases
reads were processed by clipping adaptor, removing low quality bases, and discarding too short reads (less than 16nt)
FASTX-Toolkit (Version 0.0.13) was used to get the clean reads
clean reads were aligned to the Neospora caninium genome by bowtie (version 1.1.2) with one mismatch
Total mapped reads were used to calculate reads number and TPM value (TPM represents tags per million) for each sRNA gene according to reads and genes genome location.
Genome_build: Neospora caninum genome http://www.sanger.ac.uk/resources/downloads/protozoa/neospora-caninum.html
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Neospora caninum

source_name: Vero cells

growth_protocol: The N. caninum (NC1 isolate) strain was incubated with Vero cells. When Vero cells reached about 80% confluence, the medium was changed to maintenance medium (2% FBS) and N. caninum was added into cells. The parasites were grown in Vero monolayers and harvested after 3 or 4 days (~80% lysis of infected Vero cells).

extract_protocol:
Then the infected Vero cell monolayers were harvested, thereafter, the isolation of the parasites from host cells were performed by passaging through a 20 G needle one time and a 27 G needle three times. Cell debris was removed and parasites were purified by 40% percoll gradient centrifugation. Purified parasites were washed two times with fresh DMEM by centrifuging at 1000×g for 10 min. After washing, the pellet was resuspended in fresh medium and the number of tachyzoites was counted with a hemocytometer counting chamber.
Total RNAs of N. caninum were extracted using Trizol reagent (Invitrogen, SF, USA) performed as instructed in protocol provided by manufacturer. The quantification and quality of RNA purification were evaluated by Nanodrop 2000 spectrophotometer (Thermo Scientific CA, USA). Standard agarose gel electrophoresis was carried out to analyze the integrity of isolated total RNA. The purified total RNA was stored at -80ºC until cDNA library construction.

tag: time

value: 3.5 days

tag: isolate

value: NC1 isolate


title: NE02

description: Biologic repetition

treatment_protocol: Then the infected Vero cell monolayers were harvested, thereafter, the isolation of the parasites from host cells were performed by passaging through a 20 G needle one time and a 27 G needle three times. Cell debris was removed and parasites were purified by 40% percoll gradient centrifugation. Purified parasites were washed two times with fresh DMEM by centrifuging at 1000×g for 10 min. After washing, the pellet was resuspended in fresh medium and the number of tachyzoites was counted with a hemocytometer counting chamber.


title: PC9_DHS


title: Drosophila persimilis embryo small RNA [M021_dper_embryo]

description: mixed embryos


title: Drosophila grimshawi female body small RNA [M041_dgri_female_body]

description: female bodies

organism: Drosophila grimshawi

source_name: D. grimshawi female body small RNA


title: Drosophila persimilis female body small RNA [M042_dper_female_body]

description: female bodies

source_name: D. persimilis female body small RNA


title: Drosophila grimshawi male body small RNA [V109_dgri_male_body]

description: male bodies

source_name: D. grimshawi male body small RNA


title: DT1

status: Public on Nov 19 2017

city: Singapore

first: Russell

middle: Erick

last: Ericksen

address: 11 Biopolis Way, #02-02

department: Singapore Bioimaging Consortium (SBIC)

country: Singapore

institute: Agency for Science, Technology, and Research (A*Star Singapore)

description: DENTumor.txt

data_processing:
RPKM
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Liver

extract_protocol:
Livers were extracted and flash frozen in liquid nitrogen. RNA was extracted using Trizol (Life Technologies) and/or purified on RNAeasy columns (Qiagen), then analyzed for purity using RNA pico chips run on an Agilent 2100 bioanalyzer. Only samples with a RIN > 7 and 28s:18s ratio >1.0 were used in analysis
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: DEN- 8 months

tag: tumor/nontumor

value: tumor


title: DN3

description: DENTumor.txt

value: DEN- 5 months

value: nontumor


title: MT1

description: MorrisHepatoma.txt

organism: Rattus norvegicus

value: ACI

value: Morris Hepatoma Orthotopic


title: DT3

description: DENTumor.txt


title: MN3

description: MorrisHepatoma.txt & Regenerating.txt


title: RT1

description: Regenerating.txt

value: Partial Hepatectomy


title: DN1

description: DENTumor.txt


title: MT3

description: MorrisHepatoma.txt


title: RT4

description: Regenerating.txt


title: DT2

description: DENTumor.txt


title: RT2

description: Regenerating.txt


title: U2OS_Fucci_G2_2

status: Public on Nov 18 2017

city: Stockholm

first: Michael

last: Andäng

address: Nanna Svartz Väg 2

department: Department of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Modified with the Fucci System as described in  PMID: 18267078

data_processing:
Read quality filtering: Every read that was considered valid by the Illumina control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; c) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. Any reads with no alignments were re-aligned against an artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incomplete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation:  Reads that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned randomly to one of the exons, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads at all its possible mapping positions.
Genome_build: hg19
Supplementary_files_format_and_content: ReadCounts.csv contain total Read Counts for each sample.
Supplementary_files_format_and_content: RPKM.csv contains RPKM values derived by scaling to a total count of 1000000 in each cell, then dividing each value with the length in kilobases of the corresponding transcript model.

source_name: U2OS Fucci cancer cells

growth_protocol: Cells were grown until ~80% confluency, harvested through trypsination, and spun down, followed by suspension in PBS

extract_protocol:
RNeasy Micro Kit (Qiagen)
Illumina Low-Throughput TruSeq RNA Sample Preparation Kit protocol, barcoded samples, see raw file names for specific barcode per sample.

treatment_protocol: Cells were sorted using flow cytometry

tag: phase


title: MN1

description: MorrisHepatoma.txt & Regenerating.txt


title: U2OS_Fucci_G2_1


title: DN2

description: DENTumor.txt


title: MT2

description: MorrisHepatoma.txt


title: RT3

description: Regenerating.txt


title: MN2

description: MorrisHepatoma.txt & Regenerating.txt


title: PC9_H3K4me2

source_name: lung cancer cell

value: lung cancer cell

tag: passages


title: U2OS_Fucci_S_1

tag: cell line

value: S


title: U2OS_Fucci_S_2


title: U2OS_Fucci_G1_2


title: U2OS_Fucci_G1_1


title: MT4

description: MorrisHepatoma.txt


title: HeLa_Fucci_G2_2

source_name: HeLa Fucci cancer cells

value: HeLa


title: HeLa_Fucci_S_2


title: HeLa_Fucci_G2_1


title: HeLa_Fucci_G2_3


title: HeLa_Fucci_S_3


title: HeLa_Fucci_G1_2


title: HeLa_Fucci_G1_3


title: Gap_Malat_2

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

description: Gap_Malat vs Gap_con counts.xlsx

data_processing:
Illumina bcl2fastq version 2.18.0.12 software used for basecalling.
Sequenced reads were aligned using STAR version 2.5.2b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate
HTSeq-Count version 0.6.0 created the count for the genes in each sample with parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 performed the differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing count data from HTSeq

source_name: Bone marrow-derived macrophages

growth_protocol: Mouse bone marrow cells were cultured for 5 days in DMEM media containing 10% FBS and 50 ng/ml murine M-CSF. The established bone marrow-derived macrophages were then plated for experiments.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow-derived macrophages were transfected with 50nM Antisense LNA™ GapmeRs against Malat1 or Antisense LNA™ GapmeR Negative Controls (Exiqon). 48h after transfection, cells were collected.

tag: cell type

value: macrophages

tag: transfection


title: Gap_con_1

description: Gap_Malat vs Gap_con counts.xlsx

tag: strain

value: Negative Control


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep1)

city: Orlando

first: Laszlo

last: Nagy

state: Hungary

address: Sanger Road

institute: Sandford Burnham Prebys Institute

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep1)

data_processing:
Small RNA-seq samples were aligned by novoalign (with –r Random and –m options) to mm10 genome assembly (GRCm38.p1.)
SAM files were converted into BAM files using SAMtools 0.1.19.
The Rsubread package was used to quantify miRNAs using mature miRNA collection from MirBase (v21).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts file

source_name: bone marrow

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Small RNA-sequencing libraries were generated from 1 mg of total RNA using TruSeq Small RNA Sample Preparation Kit (Illumina) according to manufacturer’s protocol.

treatment_protocol: Cells were polarized on the 6th day of the differentiation with LPS (100 ng/ml) for the indicated period of time.

tag: age

value: 8-12 weeks

value: bone marrow-derived macrophages

tag: agent

value: LPS


title: IRF2_si_2

treatment_protocol: Bone marrow-derived macrophages were transfected with 50nM control siRNA or IRF2 siRNAs (Dharmacon). 48h after transfection, cells were collected.

value: IRF2 specific siRNAs


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep1)

value: control


title: con_si_1

value: control siRNA


title: 3C-seq_LPS-induced interactions within mir-155 coding region-associated sub-TAD in WT mouse BMDMs (LPS_3h)

description:
3C-seq
3C-seq-based analysis of LPS-induced interactions within mir-155 coding region-associated sub-TAD in WT mouse BMDMs (LPS_3h)

data_processing:
Library strategy: 3C-seq
Raw reads were aligned to mm10 genome assembly (GRCm38.p1.) by BWA 0.7.10.
The R package r3Cseq (qvalue<=0.1) was used to predict putative interactions and to generate bedgraphs with the filtered interactions.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Cells were treated with 100ng/ml LPS for 3 hours and crosslinked in 1% Formaldehyde for 10 minutes. Crosslinked cells were lysed in the following lysis buffer: 10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% (vol/vol) NP-40.
After the first digestion and ligation the 3C DNA pool was purified with phenol/chloroform/ isoamyl alcohol (25:24:1) (Sigma). Second restriction digestion was performed by using DpnII (NEB) for 16 hours per manufacturer’s instruction. Second ligation was performed at 16C for 6 hours with 200U of T4 DNA ligase. DNA was then purified again with phenol/chloroform/isoamyl alcohol (25:24:1) followed by QIAquick gel purification column (Qiagen) purification. Bait specific inverse PCRs were performed using primers coupled to Universal Illumina adapters and Barcode sequences. Reactions were purified by QIAquick gel purification columns. Amplicon libraries were quantified and qualified by Agilent using DNA 7500 chip cartridge. Amplicon libraries were sequenced on Illumina HiSeq2000 sequencer.


title: HeLa_Fucci_G1_1


title: 3C-seq_LPS-induced interactions within mir-155 coding region-associated sub-TAD in WT mouse BMDMs (ctrl)

description:
3C-seq
3C-seq-based analysis of LPS-induced interactions within mir-155 coding region-associated sub-TAD in WT mouse BMDMs (ctrl)


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep3)

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep3)


title: Gap_Malat_1

description: Gap_Malat vs Gap_con counts.xlsx

value: 50nM Antisense LNA™ GapmeRs against Malat1


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep3)

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep3)


title: IRF2_si_1


title: Gap_con_2

description: Gap_Malat vs Gap_con counts.xlsx


title: OB.Kdm2b(+BMP).d6 (ChIP-seq)

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm9 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peak calling was performed by Dfilter (version 1.6 ).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed and bedGraphToBigWig. Scores represent the number of fragments overlapping each genomic position.

source_name: reprogramming cells

growth_protocol: The cells infected with indicated factors were cultured in iCD1 reprogramming medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA library for NEXT Seq500 sequencing was constructed using VAHTS Turbo DNA Library Prep Kit for Illumina(Vazyme Biotech) according to the manufacturer's instruction. Briefly, 10ng ChIP DNA was end repaired and a dA was added. Then the DNA was ligated with adaptors. Adaptor-ligated DNA was purified using AMPure XP beads. The purified DNA was amplified by PCR for 15 cycles, followed by size selection using two round AMPure XP beads and eluted in 25 ul water. The library was quantified with VAHTS Library Quantification Kit for Illumina(Vazyme Biotech). The DNA was diluted to 10 nM before sequencing.

treatment_protocol: The cells treated with or without BMP4(10ng/ml) once we change the medium to iCD1 medium after two round infection.

value: reprogramming cells

tag: day of reprogramming

value: day 6

tag: chip antibody


title: OB.Kdm2b(-BMP).d6 (ChIP-seq)

value: Kdm2b-Flag:Sigma, F1804


title: OB.H2Aub.d14 (ChIP-seq)

value: day 14


title: OA.H2Aub.d14 (ChIP-seq)


title: ODR.H2Aub.d14 (ChIP-seq)


title: OB.H3K36me2.d14 (ChIP-seq)


title: OA.H3K36me2.d14 (ChIP-seq)


title: HeLa_Fucci_S_1


title: OB.H3K27me3 (ChIP-seq)

value: Millipore 17-622


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep2)

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (LPS_3h_rep2)


title: OA.H3K27me3 (ChIP-seq)


title: con_si_2


title: small RNA-Seq_Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)

description:
small RNA-seq
small RNA-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (ctrl_rep2)


title: ODR-D14 (MeDIP)

tag: reagent

value: BI-MEVY, EUROGENTEC

value: genomic DNA


title: ODR.H3K27me3 (ChIP-seq)


title: ODDR(-BMP)-D9 (RNA-seq)

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the ENSEMBL (mm10 v79) transcriptome using Bowtie2 (version 2.2.5) and RSEM 。
The gene expression level was calculated by using  EDASeq GC-normalize method
Genome_build: mm10

extract_protocol:
The cells were washed twice with PBS and Lysed with Trizol.
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.


title: ODB(+BMP)-D9 (RNA-seq)


title: ODB(-BMP)-D9 (RNA-seq)


title: OA-D14 (MeDIP)


title: ODDR(+BMP)-D9 (RNA-seq)


title: mESCs (RNA-seq)

source_name: ESC

value: ESC


title: ODR(+BMP)-D6.rep2 (RNA-seq)


title: OB(+BMP)-D6.rep1 (RNA-seq)


title: MEF (RNA-seq)

source_name: MEF

value: MEF


title: OB(-BMP)-D14.rep2 (RNA-seq)


title: OA(-BMP)-D14.rep3 (RNA-seq)


title: OB(-BMP)-D14.rep1 (RNA-seq)


title: OB(-BMP)-D14.rep3 (RNA-seq)


title: OA(-BMP)-D14.rep2 (RNA-seq)


title: OB(+BMP)-D6.rep2 (RNA-seq)


title: ODR(+BMP)-D6.rep1 (RNA-seq)


title: ODR(-BMP)-D14.rep3 (RNA-seq)


title: ODR(-BMP)-D14.rep1 (RNA-seq)


title: ODR(-BMP)-D14.rep2 (RNA-seq)


title: OB(-BMP)-D6.rep4 (RNA-seq)


title: OA(-BMP)-D14.rep1 (RNA-seq)


title: ODR.H3K36me2.d14 (ChIP-seq)


title: OB(-BMP)-D6.rep3 (RNA-seq)


title: OB(-BMP)-D6.rep2 (RNA-seq)


title: OA(-BMP)-D6.rep3 (RNA-seq)


title: OA(-BMP)-D6.rep2 (RNA-seq)


title: OA(-BMP)-D6.rep1 (RNA-seq)


title: ODR(-BMP)-D6.rep3 (RNA-seq)


title: ODR(-BMP)-D6.rep2 (RNA-seq)


title: ODR(-BMP)-D6.rep1 (RNA-seq)


title: OA(-BMP)-D1.rep2 (RNA-seq)


title: OB(-BMP)-D1.rep2 (RNA-seq)


title: OB(-BMP)-D1.rep1 (RNA-seq)


title: OA(-BMP)-D1.rep1 (RNA-seq)


title: ODR(-BMP)-D1.rep1 (RNA-seq)


title: ODR(-BMP)-D1.rep2 (RNA-seq)


title: OBD-D9-Kdm2b(+BMP).rep2 (ChIP-seq)

tag: antibody

value: day 9


title: OB(-BMP)-D6.rep1 (RNA-seq)


title: mRNA_Wzy42

city: Daejeon

first: Daeyoup

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
The quality of fastq files were checked by fastqc and trimmed by trim_galore
The qualified fastq files were aligned to SacCer3 genome fa file using Bowtie2 v2.2.3. Then, the aligned files were compressed and sorted by samtools v1.3.
The sorted BAM files of biological duplicates were compared by MACS2, bam2wig and deeptools.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated by MACS2, bam2wig and deeptools.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae cells

growth_protocol: Cell culture were inoculated twice. Cell cultures were inoculated with shaking for aeration at proper temperatures.

extract_protocol:
Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP  lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP  lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in  Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit.
Total RNA for mRNA-seq was prepared by the hot-phenol extraction.
For preparation of MNase-seq library, formaldehyde-fixed cell pellets were resuspended in 10 ml of pre-incubation buffer (20 mM EDTA, 0.7 M mercaptoethanol), washed, and resuspended in 2 ml of zymolyase buffer (1 M sorbitol, 50 mM Tris-Cl, pH 8.0, 5 mM mercaptoethanol) containing 2.5 mg ml-1 zymolyase (20T; US Biological). Lysed cells were spheroplasted at 30°C  for 20 min and chromatin was isolated. Pelleted nuclei were digested with 200 units of MNase (NEB) at 37°C for 20 min (confirmed as a typical digestion condition by comparison of fragment sizes, data not shown), and then reverse cross-linked in 10 mM EDTA and 1% SDS buffer with proteinase K for 6 hours at 37°C. The DNA was extracted with phenol/chloroform, purified by ethanol precipitation, and resolved by 2% agarose gel electrophoresis in TAE buffer.
Yeast cells (2.5 million) were harvested at O.D. 0.6~0.8/mL (mid-log phase), and spheroplasted in 200 μl of Sorbitol buffer (1.4 M Sorbitol, 40 mM Tris-HCl, pH 7.5, 0.5 mM MgCl2) with 10 μl of 50 mg ml-1 of zymolyase (20T; US Biological). After washing twice with 100 μl of ice-cold Sorbitol buffer, the spheroplasts were incubated in fresh TD buffer (20 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 20% dimethylformaldehyde) with transposase at 37°C for 4 hours. QIAquick PCR purification kit was used to purify DNA fragments, and transposition reactions and PCR amplifications were performed.
General Manual of Nextflex ChIP library preparation kit. mRNA isolation and mRNA-seq library preparation were performed using the NEXTflex Rapid Directional mRNA-Seq Bundle.

treatment_protocol: For ChIP and MNase: Final 1% formaldehyde fixation and 125mM glycine quencing were performed before cell harvest.

tag: genotype

value: mid-log phase

tag: medium

value: YPD


title: OBD-D9-Kdm2b(-BMP).rep2 (ChIP-seq)


title: OB-D14-MeDIP-seq (ChIP-seq)

tag: antibody:


title: OB-D14-Kdm2b(-BMP) (ChIP-seq)

tag: treatment


title: OB-D14-Kdm2b(+BMP) (ChIP-seq)


title: mRNA_set2DWzy42


title: mRNA_H3K79Rset2D


title: OBD-D9-Ring1b(-BMP) (ChIP-seq)


title: OBD-D9-Ring1b(+BMP) (ChIP-seq)


title: OBD-D9-H2Aub1(-BMP) (ChIP-seq)


title: OBD-D9-H2Aub1(+BMP) (ChIP-seq)


title: OBD-D9-Kdm2b(-BMP).rep1 (ChIP-seq)


title: OB-D14-H2Aub1(+BMP).rep2 (ChIP-seq)


title: OB-D14-H2Aub1(+BMP).rep1 (ChIP-seq)


title: OBD-D9-Kdm2b(+BMP).rep1 (ChIP-seq)


title: mRNA_Dot1G401Rset2D


title: OB-D14-H2Aub1(-BMP).rep2 (ChIP-seq)


title: mRNA_asf1Dset2D


title: ATAC_WT

value: WT


title: OB-D14-H2Aub1(-BMP).rep1 (ChIP-seq)


title: ATAC_set2D


title: "ESCAPED", experiment 3

city: Lodz

first: Konrad

last: Stawiski

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
automatic filtering, adapter trimming, error removing and quality control using AfterQC (v0.9.6)
mapping to miRbase (release 21) using Novocraft’s NovoAlign (v3.08.02)
Genome_build: miRbase release 21
Supplementary_files_format_and_content: counts.csv - count tables of known human mature miRNAs for all samples and duplicates

source_name: "ESCAPED" cells

extract_protocol:
RNA was extracted with the NucleoSpin miR, kit/50preps (Cat no: 740971.50; Macherey-Nagel), following the manufacturer’s instructions.
The library preparation for RNAseq and miRNAseq was carried out in the Greek Genome Center (GGC) of Biomedical Research Foundation of Academy of Athens (BRFAA). RNAseq libraries were prepared with the TruSeq RNA kit using 1 μg of total RNA. The libraries were constructed according to Illumina's protocols and then were mixed in equal amounts.

tag: status

value: ESCAPED


title: "ESCAPED", experiment 2


title: MNase_dot1D

tag: phase


title: 6th day "ON", experiment 3

source_name: "6d ON" cells

value: 6d ON


title: MNase_WT


title: mRNA_dot1Dset2D


title: 6th day "ON", experiment 2


title: 3rd day "ON", experiment 3

source_name: "3d ON" cells

value: 3d ON


title: 6th day "ON", experiment 1


title: mRNA_set2D


title: "OFF", experiment 3

source_name: "OFF" cells

value: OFF


title: MYC_WT

value: homemade; prepared by Lee Lab

value: YPR; Galactose induction


title: 3rd day "ON", experiment 1


title: MYC_dot1D


title: "OFF", experiment 2


title: FLAG_dot1D

value: F1804; SIGMA;


title: mRNA_WT


title: FLAG_WT


title: H3_WT


title: "OFF", experiment 1


title: H3_Dot1101-140D


title: H3_dot1Dset2D


title: ATAC_dot1D


title: H3_set2D


title: Z2015-13881

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

country: Germany

institute: Universitätsklinikum Bonn

description: Processed data files: annex 2_miRNA result tables.xlsx, annex 3_miRNA counts.xlsx, annex 3_piRNA counts.xlsx, annex 4_miRNA expression.xlsx, annex 4_piRNA expression.xlsx, annex 5_isomiR counts.xlsx, annex 5_piRNA result tables.xlsx, annex 6_counts other small RNAs.txt

data_processing:
Sequencing reads are processed using Cobra, Biogazelle’s proprietary small RNA sequencing pipeline for read QC, adapter trimming, read mapping and read annotation.
Mapped reads are annotated based on the latest miRBase release.  Read QC, read annotation and read length distribution are provided for each sample.
Raw and normalized expression data is reported for each mature miRNA in miRBase. In addition, expression levels for individual isomiRs is provided.
Genome_build: miRBase Release 21 (June 2014)
Supplementary_files_format_and_content: abundance measurements

source_name: serum

extract_protocol:
RNA was isolated using the miRNeasy serum/plasma Kit (Qiagen) following the manufacturer instructions. The RNA concentration was determined using the Nanodrop UV-Vis Spectrophotometer (Thermo Fisher Scientific).
NEBNext small RNA library prep kit (New England Biolabs) was used according to the manufacturers instructions, followed by Illumina single-end sequencing with read length of 75bp on the NextSeq 500 Sequencing System (Illumina). There were 20 M indexed reads per sample on average.

tag: gender

value: male

tag: disease state (dignity)

value: benign renal tumor

tag: t-stage

value: CTRL

tag: n-stage

tag: m-stage

tag: grade

tag: uicc


title: Z2015-13994

tag: age


title: ATAC_sas2D


title: Z2015-14301

value: female

value: renal cell carcinoma


title: "ESCAPED", experiment 1


title: H4ac_H3_dot1Dset2D

value: 06-866; Millipore


title: H4ac_H3_set2D


title: 3rd day "ON", experiment 2


title: Z2014-11261


title: Z2014-11137


title: H4ac_H3_WT


title: Z2014-11019


title: H4K16ac_WT


title: GFP-neg Control surrounding cells 2

city: Omaha

first: David

state: Nebraska

address: 2500 California Plaza

department: Department of Biomedical Sciences

institute: Creighton University

description: This biological replicate has paired-end sequencing and two associated raw reads files.

data_processing:
CLC Genomics Workbench software (CLC bio, Waltham, MA, USA) was used to map the reads to the GRCz10 zebrafish genome and generate gene expression values in the normalized form of reads per kilobase of transcript per million mapped reads (RPKM) values
Genome_build: GRCz10 zebrafish genome
Supplementary_files_format_and_content: Excel file of expression data of hair cells and surrounding control cells using RPKM values

organism: Danio rerio

source_name: 1,000 Inner ear surrounding cells

extract_protocol:
Qiagen miRNeasy mini plus kit
Clontech Smart-Seq

tag: cell type

value: GFP-neg cells isolated and pooled from  the lagena, utricle, and saccule

tag: passages

value: 11-13 month old adult female zebrafish

tag: strain


title: Z2014-11234


title: Z2014-10559


title: Z2014-10616


title: Z2013-8802


title: GFP+ Zebrafish Hair Cells Biological Replicate 3

source_name: 1,000 Inner ear hair cells

value: GFP+ Hair Cells isolated and pooled from the lagena, utricle, and saccule


title: H4K16ac_sas2D

tag: genotype

tag: antibody

value: mid-log phase

value: YPD


title: GFP+ Zebrafish Hair Cells Biological Replicate 2


title: Z2013-8278


title: H3_dot1D

tag: medium


title: H3K79me3_sas2D


title: Z2013-8083


title: GFP-neg Control surrounding cells 3


title: Z2014-9699


title: Z2015-11967


title: GFP+ Zebrafish Hair Cells Biological Replicate 1


title: H3K79me3_WT

value: WT


title: H3K79me1_WT


title: H3K79me1_sas2D


title: Z2012-5486


title: Z2013-6992


title: Z2013-7070


title: Z2012-6364


title: sd_d

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21 and to the long inverted repeat which is central to this study
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: snapdragon genome v 1.0
Supplementary_files_format_and_content: csv, raw abundances

organism: Antirrhinum majus

growth_protocol: Plants were grown together in a common environment under long days

extract_protocol:
Total RNA was extracted using TriReagent (Ambion) following manufacturer’s protocol.  Small RNAs (sRNAs) of each sample was further enriched using the mirVana miRNA isolation kitTM (Ambion) according to the manufacturer’s instructions.
standard IL sRNA library constructed using HD adapters [Sorefan et al 2012]
sequenced at Earlham Institute on HiSeq2500

tag: tissue

value: flower

tag: replicate

tag: line


title: sd_e


title: sd_b


title: Z2013-7282

tag: gender


title: input for ChIP

tag: phase


title: Z2013-7997

tag: disease state (dignity)

tag: t-stage


title: Z2013-8378

tag: n-stage

tag: m-stage


title: Z2013-8894

tag: grade

tag: uicc


title: Sigma Rep 2

status: Public on Nov 17 2017

city: Leuven

first: Juan

middle: Antonio Garcia

last: Leon

address: Oude Markt 13

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Low quality ends and adpator sequences were trimmed off from the Illumina reads.
Small reads (length <35 bp), ambiguous reads(containing N) and low quality reads ( more than 50% of the bases < Q25) were filtered).
Processed reads were aligned with Tophat v2.0.8b to the human reference genome (GRCh38), downloaded from the Genome Reference Consortium. Default Tophat parameter settings were used, except for 'min-intron-length=50', 'max-intron-length=500,000', 'nocoverage-search', and 'read-realign-edit-dist=3'.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Differentiated Stem Cells

extract_protocol:
Total RNA was collected from cells at the end of the differentiation protocol using the GenElute™ Mammalian Total RNA Miniprep Kit. RNA concentration and purity was measured using Nanodrop ND-1000 and RNA integrity was measured using a Bioanalyzer 2100. Per sample, an amount of 100 ng of total RNA was used as input. Using the Illumina TruSeq Stranded mRNA Sample Prep Kit, poly-A containing mRNA molecules were purified from total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequence-libraries of each sample were sequenced on an Illumina NextSeq 500 instrument (high output, 75bp, single reads, v2)

tag: cell type

value: ES-derived oligodendrocytes

tag: cell line

value: Sigma


title: Sigma Rep 1


title: sd_a


title: E2013-14097

tag: age


title: Z2012-5199


title: BJ1 Rep 3


title: BJ1 Rep 2


title: Z2012-6334


title: BJ1 Rep 1


title: E2015-6857


title: FGFR1(SP-/NLS+) NCC 3

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

data_processing:
Data was aligned to genome using tophat2 with hg38 genome
Expression and differential expression identifed using Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: FGFR1(SP-/NLS+) NCC

growth_protocol: NPC were maintained in DMEM/F12+glutamax with N2 and B27, and 1ug/ml laminin, 20ng/ml FGF2

extract_protocol:
Rneasy kit was used to extract RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce NCCs, NPCs were treated with 20ng/ml of BDNF, 20ng/ml GDNF, 1mM dibutyryl-cylic AMP, and 200 nM ascorbic Acid

value: NCC

tag: transfection


title: ChiPSC6b Rep 3


title: FGFR1(SP-/NLS+) NCC 2


title: FGFR1(SP-/NLS+)(TK-) NCC 2

source_name: FGFR1(SP-/NLS+)(TK-) NCC


title: FGFR1(SP-/NLS+)(TK-) NCC 1


title: ChiPSC6b Rep 2


title: H9 Rep 2


title: H9 Rep 3


title: Control NCC 1

source_name: Control NCC

value: Control


title: ChiPSC6b Rep 1


title: FGFR1(SP-/NLS+)(TK-) NCC 3


title: FGFR1(SP-/NLS+)(TK-) NPC 3

source_name: FGFR1(SP-/NLS+)(TK-) NPC

value: NPC


title: Sigma Rep 3


title: FGFR1(SP-/NLS+)(TK-) NPC 2


title: Control NPC 3

source_name: Control NPC


title: FGFR1(SP-/NLS+)(TK-) NPC 1


title: Control NPC 2


title: input DNA_D7_Brd4_KO

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
Sequencing reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
For ChIP-seq, peaks were called using SICER with following configuration: Windows (50), Gaps (50), FDR (1e-10 for Brd4 ChIP-Seq in MLL3 KO and MLL3/MLL4 KO cells, 1e-3 for all the other ChIP-Seq)
For RNA-seq, RPKM (Reads per kilobase per million) values were calculated to measure gene (RefSeq) expression levels using in-house script.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

source_name: Brown preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Brd4f/f mice and immortalized with SV40T-expressing retroviruses generated from the pBabepuro-large T plasmid

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.

treatment_protocol:
After immortalization, cells were infected with adenoviral Cre or GFP to generate WT or Brd4 KO cells
For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: immortalized Brd4-flox/flox brown preadipocytes

tag: stage of adipogenesis or myogenesis

value: Mature adipocytes (D7)

tag: strain


title: FGFR1(SP-/NLS+) NCC 1


title: input DNA_D2_Brd4_KO

value: Immature adipocytes (D2)


title: input DNA_D7_WT_replicate2

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: immortalized Pparg-flox/flox brown preadipocytes


title: input DNA_D0_Brd4_KO

value: Confluent preadipocytes (D0)


title: Control NPC 1


title: H9 Rep 1


title: Control NCC 3


title: Hi-C U266 MboI

city: Beijing

first: Cheng

last: Li

state: Beijing

address: 5 Yiheyuan Road, Haidian District

department: Center for Life Science, Academy for Advanced Interdisciplinary Studies

institute: Peking University

data_processing:
Library strategy: Hi-C
Basecalls performed using Illumina Casava 1.8.
WGS raw reads were filtered using NGS QC Toolkit v2.3.3.
WGS cleaned reads were aligned to the hg19 genome assembly using bwa version 0.7.12-r1039.
RNA cleaned reads were aligned to the hg19 genome assembly using tophat2 v2.0.14 with parameter " -G genes.gtf".
Transcripts assembly and gene expression quantification were using Cufflinks v2.2.1 and cuffdiff v2.2.1.
Hi-C raw reads were aligned to the hg19 genome assembly using Bowtie 2 version 2.2.4.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: WGS samples: Tab-delimited text files with estimated CNV.
Supplementary_files_format_and_content: WGS samples: Tab-delimited text files with estimated translocation.
Supplementary_files_format_and_content: RNA-seq samples: Tab-delimited text files with FPKM.
Supplementary_files_format_and_content: Hi-C samples: Raw count matrix for each sample replicate.

source_name: U266 multiple myeloma cells

growth_protocol: Cells were cultured in RPMI-1640 medium (ATCC-30-2001) with 10% fetal bovine serum and 5% CO2 at 37℃.

extract_protocol:
Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer.
Cross-linked DNA was digested with MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell).
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were isolated and cross-linked with 1% formaldehyde for 10 min at room temperature. After that, 2.5M glycine solution was added to a final concentration of 0.2M.

value: multiple myeloma cell line

tag: originating tissue

value: peripheral blood

tag: originating cell type

value: B lymphocyte

tag: age of donor

tag: gender of donor

value: male


title: input DNA_D0_WT_replicate2


title: Hi-C RPMI-8226 MboI

source_name: RPMI-8226 multiple myeloma cells


title: Hi-C U266 HindIII

extract_protocol:
Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer.
Cross-linked DNA was digested with HindIII, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. Other steps were following in-situ Hi-C protocol (Rao et al., 2014, Cell).
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: RNA-seq U266 Rep2

description: mRNA

data_processing:
Basecalls performed using Illumina Casava 1.8.
WGS raw reads were filtered using NGS QC Toolkit v2.3.3.
WGS cleaned reads were aligned to the hg19 genome assembly using bwa version 0.7.12-r1039.
RNA cleaned reads were aligned to the hg19 genome assembly using tophat2 v2.0.14 with parameter " -G genes.gtf".
Transcripts assembly and gene expression quantification were using Cufflinks v2.2.1 and cuffdiff v2.2.1.
Hi-C raw reads were aligned to the hg19 genome assembly using Bowtie 2 version 2.2.4.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: WGS samples: Tab-delimited text files with estimated CNV.
Supplementary_files_format_and_content: WGS samples: Tab-delimited text files with estimated translocation.
Supplementary_files_format_and_content: RNA-seq samples: Tab-delimited text files with FPKM.
Supplementary_files_format_and_content: Hi-C samples: Raw count matrix for each sample replicate.

extract_protocol:
Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: No treatment.


title: input DNA_D2_WT_replicate1


title: Control NCC 2


title: Hi-C RPMI-8226 HindIII


title: input DNA_D7_WT_replicate1


title: input DNA_D2_WT_replicate2


title: RNA-seq U266 Rep1

description: mRNA


title: input DNA_D0_WT_replicate1


title: input DNA_C2C12_D3

source_name: C2C12 myoblast cell

treatment_protocol:
Cells were infected with lentiviral shRNA to generate control or Brd4 knockdown cells
For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: C2C12 myoblast cell line

value: Differentiated myocytes


title: Brd4_ChIPSeq_D2_MLL3_MLL4_dKO

treatment_protocol:
After immortalization, cells were infected with adenoviral Cre or GFP to generate Mll3 KO or Mll3/Mll4 double KO cells
For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: immortalized Mll3-/-; Mll4f/f  brown preadipocytes

tag: chip antibody


title: Brd4_ChIPSeq_D2_MLL3_KO


title: RNA-seq RPMI-8226 Rep2

description: mRNA


title: RNA-seq RPMI-8226 Rep1

description: mRNA


title: RNA-seq RPMI-8226 Rep3

description: mRNA


title: Brd4_ChIPSeq_D0_MLL3_MLL4_dKO


title: WGS U266

description: WGS

extract_protocol:
Genome DNA was precipitated by adding 1.6X volume of pure ethanol and 0.1X volumes of 3M sodium acetate, pH5.2, and incubated at -80°C for 15 min. Then, DNA was collected by centrifuge at max speed for 5 minutes and dissolved in 1X Tris buffer.
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly, ends of sheared DNA were repaired using a combination of NEBNext End Prep Enzyme Mix and End Repair Reaction Buffer. "A" base was added to the blunt ends using NEBNext Blunt/TA Ligase Master Mix. After adapter ligation, DNA was PCR amplified with high-fidelity DNA polymerase, Illumina universal PCR primers and indexed primers for 8-12 cycles. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were degraded by proteinase K (NEB, P8102) at 55°C for 30 min.


title: Brd4_ChIPSeq_D0_MLL3_KO


title: RNA-seq U266 Rep3

description: mRNA


title: WGS RPMI-8226

description: WGS


title: RNA_D0_shCon_C2C12

extract_protocol: Total RNA was harvested using Trizol reagent. mRNA was further  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).

value: Undifferentiated myoblasts


title: RNA_D5_shBrd4_C2C12


title: RNA_D5_shCon_C2C12


title: RNA_D0_shBrd4_C2C12


title: Brd4_ChIPSeq_D3_C2C12


title: Brd4_ChIPSeq_D7_Brd4_KO


title: Brd4_ChIPSeq_D2_Brd4_KO


title: steckii_CM_rep1

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

description:
CM1
ste_c2_r1
processed data file: ste_counts.txt

data_processing:
Raw reads were mapped to the individual genomes using tophat2 (version 2.0.9)
read counts were quantified using HTSeq
Genome_build: P. coprophilum: MDDG00000000; P. nalgiovense: MOOB00000000; P. polonicum: MDYM00000000;  P. decumbens: MDYL00000000 , P. flavigenum: MLQL00000000;  P. steckii: MLKD00000000
Supplementary_files_format_and_content: Tab-delimited text files with raw counts

organism: Penicillium steckii

growth_protocol: Bioreactor fermentations in defined or complex medium

extract_protocol:
RNeasy Mini Kit (qiagen Cat No./ID: 74104)
Illumina TruSeq

tag: medium

value: complex medium (CM)

tag: sample type

value: biomass


title: steckii_CM_rep3

description:
CM3
ste_c2_r3
processed data file: ste_counts.txt


title: steckii_DM_rep2

description:
DM2
ste_c1_r2
processed data file: ste_counts.txt

value: defined medium (DM)


title: steckii_CM_rep2

description:
CM2
ste_c2_r2
processed data file: ste_counts.txt


title: steckii_DM_rep1

description:
DM1
ste_c1_r1
processed data file: ste_counts.txt


title: flavigenum_CM_rep3

description:
CM3
fla_c2_r3
processed data file: fla_counts.txt

organism: Penicillium flavigenum


title: RNA_D7_WT

treatment_protocol: After immortalization, cells were infected with adenoviral Cre or GFP to generate WT or Brd4 KO cells


title: Brd4_ChIPSeq_D2_WT_replicate2


title: Brd4_ChIPSeq_D7_WT_replicate1


title: RNA_D7 _Brd4 KO


title: Brd4_ChIPSeq_D2_WT_replicate1


title: Brd4_ChIPSeq_D0_Brd4_KO


title: Brd4_ChIPSeq_D0_WT_replicate1


title: decumbens_CM_rep3

description:
CM3
dec_c2_r3
processed data file: dec_counts.txt

organism: Penicillium decumbens


title: Brd4_ChIPSeq_D0_WT_replicate2


title: Brd4_ChIPSeq_D7_WT_replicate2


title: decumbens_CM_rep2

description:
CM2
dec_c2_r2
processed data file: dec_counts.txt


title: flavigenum_CM_rep1

description:
CM1
fla_c2_r1
processed data file: fla_counts.txt


title: RNA_D2_WT


title: RNA_D0 _Brd4 KO


title: steckii_DM_rep3

description:
DM3
ste_c1_r3
processed data file: ste_counts.txt


title: flavigenum_DM_rep2

description:
DM2
fla_c1_r2
processed data file: fla_counts.txt


title: flavigenum_DM_rep3

description:
DM3
fla_c1_r3
processed data file: fla_counts.txt


title: RNA_D2 _Brd4 KO


title: decumbens_DM_rep3

description:
DM3
dec_c1_r3
processed data file: dec_counts.txt


title: decumbens_DM_rep2

description:
DM2
dec_c1_r2
processed data file: dec_counts.txt


title: decumbens_CM_rep1

description:
CM1
dec_c2_r1
processed data file: dec_counts.txt


title: RNA_D0_WT


title: flavigenum_DM_rep1

description:
DM1
fla_c1_r1
processed data file: fla_counts.txt


title: polonicum_CM_rep3

description:
CM3
pol_c2_r3
processed data file: pol_counts.txt

organism: Penicillium polonicum


title: coprophilum_CM_rep3

description:
CM3
cop_c2_r3
processed data file: cop_counts.txt

organism: Penicillium coprophilum


title: nalgiovense_CM_rep3

description:
CM3
nal_c2_r3
processed data file: nal_counts.txt

organism: Penicillium nalgiovense


title: flavigenum_CM_rep2

description:
CM2
fla_c2_r2
processed data file: fla_counts.txt


title: decumbens_DM_rep1

description:
DM1
dec_c1_r1
processed data file: dec_counts.txt


title: coprophilum_CM_rep2

description:
CM2
cop_c2_r2
processed data file: cop_counts.txt


title: polonicum_CM_rep2

description:
CM2
pol_c2_r2
processed data file: pol_counts.txt


title: coprophilum_CM_rep1

description:
CM1
cop_c2_r1
processed data file: cop_counts.txt


title: polonicum_CM_rep1

description:
CM1
pol_c2_r1
processed data file: pol_counts.txt


title: nalgiovense_CM_rep2

description:
CM2
nal_c2_r2
processed data file: nal_counts.txt


title: coprophilum_DM_rep3

description:
DM3
cop_c1_r3
processed data file: cop_counts.txt


title: nalgiovense_CM_rep1

description:
CM1
nal_c2_r1
processed data file: nal_counts.txt


title: polonicum_DM_rep3

description:
DM3
pol_c1_r3
processed data file: pol_counts.txt


title: nalgiovense_DM_rep3

description:
DM3
nal_c1_r3
processed data file: nal_counts.txt


title: coprophilum_DM_rep2

description:
DM2
cop_c1_r2
processed data file: cop_counts.txt


title: polonicum_DM_rep2

description:
DM2
pol_c1_r2
processed data file: pol_counts.txt


title: nalgiovense_DM_rep2

description:
DM2
nal_c1_r2
processed data file: nal_counts.txt


title: polonicum_DM_rep1

description:
DM1
pol_c1_r1
processed data file: pol_counts.txt


title: nalgiovense_DM_rep1

description:
DM1
nal_c1_r1
processed data file: nal_counts.txt


title: coprophilum_DM_rep1

description:
DM1
cop_c1_r1
processed data file: cop_counts.txt


title: PU.1_LPS_rep1

status: Public on Nov 16 2017

city: New York

first: Lionel

middle: B.

last: Ivashkiv

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 (version 2.2.5, Langmead et al., 2012 Nat Methods) with default parameters.
HOMER (version 4.7.2, Heinz et al., 2010) was used to generate bigWig files.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.

treatment_protocol: Cells were were cultured with M-CSF (10 ng/ml) for 48 hrs and then stimulated with LPS (10 ng/ml) for 3 hours.

tag: tissue

value: monocytes

tag: antibody

value: anti-PU.1 (Santa Cruz sc-352)


title: C/EBPB_LPS_rep2

value: anti-C/EBPB (Santa Cruz sc-150)


title: C/EBPB_LPS_rep1


title: Parental-MYC T58A Rep 2

city: Durham

first: Kris

last: Wood

state: NC

address: Box 3813 DUMC Department of Pharmacology and Cancer Biology

institute: Duke University

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCm37r75 version of the human genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment. The false discovery rate was calculated to control for multiple hypothesis testing.
Genome_build: GRCm37r75
Supplementary_files_format_and_content: Tab delimited text file

source_name: melanocyte

growth_protocol: Cells were grown to ~80% confluency in normal culture conditions, see Materials and Methods

extract_protocol:
Cells were rinsed with PBS and RNA was harvested using Qiagen Rneasy Mini Kit. Kapa Stranded mRNA-Seq library prep kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source tumor

value: melanoma

value: melanocyte


title: Parental-MYC T58A Rep 1


title: Resistant-shMYC2 Rep 1


title: Resistant-shMYC1 Rep 3


title: Resistant-shMYC2 Rep 3


title: Parental-MYC T58A Rep 3


title: Resistant-shMYC1 Rep 2


title: Resistant Rep 3


title: Resistant Rep 2


title: Resistant-shMYC1 Rep 1


title: Parental Rep 3


title: Parental Rep 1


title: GFP-neg Control surrounding cells 1

description: This biological replicate has paired-end sequencing and two associated raw reads files.

value: GFP-neg cells isolated and pooled from  the lagena, utricle, and saccule

tag: passages

value: 11-13 month old adult female zebrafish


title: Parental Rep 2

tag: cell type


title: C661S_D6 – Late S fraction

city: Tallahassee

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

data_processing:
Library strategy: RepliSeq
Reads are mapped to hg19 using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio is calculated in 5kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 200kb windows
Genome_build: hg19
Supplementary_files_format_and_content: processed data are 200kb windows in hg19 genome.

growth_protocol: Human fibroblasts were maintained in DMEM containing 10% heat-inactivated FBS, 2 mM L-Glutamine, 1% penicillin and streptomycin (all from Invitrogen). Human ES cells and iPSCs were maintained on feeder-free culture on matrigel (BD Biosciences) with chemically defined mTeSR (Stemcell technologies) medium, as previously described (Ludwig et al., 2006).

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed either by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

value: Transformed fibroblasts

tag: disease

value: Healthy

value: Not speciied

tag: mutation

tag: transgene

value: doxycycline-inducible GFP-tagged C661S

tag: s phase fraction

value: Late S fraction


title: C661S_D4 – Early S fraction

tag: age

value: Early S fraction


title: C661S_D6 – Early S fraction


title: C661S_D4 – Late S fraction


title: C661S_D0 – Early S fraction


title: C661S_D0 – Late S fraction


title: LaminA_D6 – Late S fraction

value: doxycycline-inducible GFP-tagged lamin A


title: LaminA_D4 – Early S fraction


title: LaminA_D6 – Early S fraction


title: LaminA_D4 – Late S fraction


title: Resistant-shMYC2 Rep 2

tag: cell line


title: LaminA_D0 – Early S fraction


title: Progerin_D6 – Early S fraction


title: Progerin_D4 – Early S fraction


title: Progerin_D0 – Late S fraction


title: Progerin_D6 – Late S fraction


title: Resistant Rep 1


title: Progerin_D4 – Late S fraction


title: Redif_M_30yr – Late S fraction

value: Fibroblasts re-differentiated from iPSCs

value: 30 yr


title: Redif_HGPS_Blood – Late S fraction

value: Hutchinson-Gilford progeria syndrome

value: LMNA


title: Redif_M_30yr – Early S fraction


title: Redif_HGPS_Blood – Early S fraction


title: LaminA_D0 – Late S fraction


title: Redif_11yr – Late S fraction

value: 11 yr


title: Redif_HGPS_8yrs – Late S fraction

value: 8 yr


title: Redif_11yr – Early S fraction


title: Redif_HGPS_2yrs – Early S fraction

value: 2 yr


title: Redif_HGPS_2yrs – Late S fraction


title: iPSC_82yr – Early S fraction -2

value: iPSCs

value: 82 yr


title: iPSC_82yr – Late S fraction


title: Redif_RTS – Late S fraction

value: Rothmund-Thomson syndrome

value: 43 yr


title: Redif_HGPS_8yrs – Early S fraction


title: iPSC_82yr – Late S fraction -2

value: Healthy


title: Redif_RTS – Early S fraction


title: iPSC_82yr – Early S fraction


title: iPSC_M_30yr – Early S fraction


title: iPSC_M_30yr – Late S fraction


title: Progerin_D0 – Early S fraction

value: Transformed fibroblasts

value: Not speciied


title: iPSC_11yr – Late S fraction -2

value: Late S fraction


title: iPSC_0yr – Early S fraction

value: 0 yr

value: Early S fraction


title: iPSC_0yr – Late S fraction


title: iPSC_11yr – Early S fraction -2


title: iPSC_11yr – Late S fraction


title: iPSC_11yr – Early S fraction


title: iPSC_Fetal_R2 – Early S fraction


title: iPSC_RTS – Late S fraction


title: iPSC_HGPS_2yr – Late S fraction


title: iPSC_HGPS_8yr – Early S fraction


title: iPSC_RTS – Early S fraction


title: iPSC_HGPS_Blood – Early S fraction


title: iPSC_HGPS_2yr – Early S fraction


title: Ctrl_82yr – Late S fraction

value: Primary fibroblasts


title: Ctrl_82yr – Early S fraction


title: Ctrl_92yr – Early S fraction

value: 92 yr


title: Ctrl_81yr – Late S fraction

value: 81 yr


title: Ctrl_11yr – Late S fraction


title: Ctrl_81yr – Early S fraction


title: Ctrl_11yr – Early S fraction


title: Ctrl_10yr – Early S fraction

value: 10 yr


title: Ctrl_10yr – Late S fraction


title: PreS_0yr – Early S fraction


title: PreS_0yr – Late S fraction


title: iPSC_Fetal_R2 – Late S fraction


title: RTS – Late S fraction

source_name: RTS fibroblasts


title: HGPS_8yr_B – Late S fraction

source_name: Progeria fibroblasts

value: Hutchinson-Gilford progeria syndrome

value: LMNA


title: HGPS_8yr_B – Early S fraction

value: 8 yr


title: RTS – Early S fraction


title: Normal Human Melanocytes RNA-seq Rep 1 [NHM1]

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description:
RNA-seq Rep 1
RNA-gene_exp.diff

data_processing:
Native ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 40-65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10
XL ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters -k 1 -m 1 --best -S -n 2 -l 65 -q. BAM files were generated using SAMtools. duplicated reads were removed using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 --bw 200 —slocal 1000 -q 0.01.
ATAC-seq: Reads were trimmed from Illumina adapters using in-house script. Reads (40bp Paired-end) were aligned using Bowtie2 (version  2.1.0) with parameters -q -X 2000. BAM files were generated using SAMtools. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools.. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters –nomodel –nolambada –keepdup all –slocal 10000
RNA-seq: Reads (50bp, Paired-end) were aligned using TopHat (version 2.1.0). Transcriptome assemblies in FPKM, and differential expression ratios were computed with Cufflinks (version 2.1.1). In all samples, genes were called ‘expressed’ if normalized FPKM≥1.5. Genes were called downregulated upon JQ1 treatment if nFPKM≥1.5; log2FoldChange≤-0.625; and Padj<0.05. Genes were called overexpressed over NHM if nFPKM≥1.5 (in the melanoma sample); log2FoldChange≥2; and Padj<0.05. Genes were called downregulated upon AMIGO2 depletion if nFPKM≥1.5 (prior to depletion); log2FoldChange≤-1.2; and Padj<0.05. log2FoldChange≥1.2 for upregulated genes.
SEs calling: Enhancers (TEs) and super enhancers (SEs) were called based on ChIP-seq BRD4 enrichment in SKmel147 using the ROSE (Rank Ordering of Super-Enhancers) algorithm (stitching distance 12.5Kb and TSS exclusion zone size 2.5Kb. BRD4 levels were normalized to Input control; ChIP-Input)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup. diff - gene expression in normalized FPKM

source_name: Foreskin

growth_protocol: cultured in Melanocyte Growth Media 254 supplemented with Human Melanocyte Growth Supplement (Life Technologies), CaCl2 (0.2uM, Life Technologies: 50-9702) and PMA (10 ng/ml, Sigma: P8139).

extract_protocol:
RNA was extracted using QIAGEN miRNeasy minikit. RNA was then processed with Ribo-Zero rRNA Removal Kit (Illumina) to remove rRNA.
Totla RNA was processed into sequencing libraries using the Illumina ScriptSeq Complete Gold kit following manufacturer’s protocol.

treatment_protocol: untreated

value: foreskin, NHM1

tag: passage


title: HGPS_2yr – Early S fraction

value: 2 yr


title: iPSC_HGPS_8yr – Late S fraction

value: iPSCs


title: NRAS metastatic melanoma RNA-seq Rep 2 [SKmel2]

description:
RNA-seq Rep 2
RNA-gene_exp.diff

source_name: Cell culture

growth_protocol: grown in DMEM supplemented with 10% FBS, penicillin and streptomycin.


title: iPSC_HGPS_Blood – Late S fraction


title: Ctrl_92yr – Late S fraction


title: NRAS metastatic melanoma RNA-seq Rep1 [SKmel2]

description:
RNA-seq Rep1
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq Rep1 [SKmel239]

description:
RNA-seq Rep1
RNA-gene_exp.diff


title: HGPS_2yr – Late S fraction


title: BRAF metastatic melanoma RNA-seq Rep 2 [SKmel239]

description:
RNA-seq Rep 2
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq shA2 #2 Rep 2 [501MEL]

description:
RNA-seq shA2 #2 Rep 2
501MEL-RNA-AMIGO2KD-gene_exp.diff

treatment_protocol: cells stably transduced with shA2 #2 lentiviral constructs


title: BRAF metastatic melanoma RNA-seq shSCR Rep 2 [501MEL]

description:
RNA-seq shSCR Rep 2
501MEL-RNA-AMIGO2KD-gene_exp.diff

treatment_protocol: cells stably transduced with control (SCR) lentiviral constructs


title: BRAF metastatic melanoma RNA-seq shSCR Rep 1 [501MEL]

description:
RNA-seq shSCR Rep 1
501MEL-RNA-AMIGO2KD-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq shA2 #2 Rep 1 [501MEL]

description:
RNA-seq shA2 #2 Rep 1
501MEL-RNA-AMIGO2KD-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq shA2 #2 Rep 1 [SKmel147]

description:
RNA-seq shA2 #2 Rep 1
SKmel147-RNA-AMIGO2KD-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq shSCR Rep 2 [SKmel147]

description:
RNA-seq shSCR Rep 2
SKmel147-RNA-AMIGO2KD-gene_exp.diff


title: Normal Human Melanocytes RNA-seq JQ1 (-) 6 hours Rep 2 [NHM2]

description:
RNA-seq JQ1 (-) 6 hours Rep 2
RNA-gene_exp.diff

treatment_protocol: treated with enantiomer (JQ1(-)) for 6 hours

value: foreskin, NHM2


title: NRAS metastatic melanoma RNA-seq shSCR Rep 1 [SKmel147]

description:
RNA-seq shSCR Rep 1
SKmel147-RNA-AMIGO2KD-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq JQ1 (+) 24 hours Rep 2 [501MEL]

description:
RNA-seq JQ1 (+) 24 hours Rep 2
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff

treatment_protocol: treated with 10nM JQ1 (JQ1(+)) for 24 hours


title: Normal Human Melanocytes RNA-seq JQ1 (-) 6 hours Rep 1 [NHM2]

description:
RNA-seq JQ1 (-) 6 hours Rep 1
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq JQ1 (-) 24 hours Rep 1 [501MEL]

description:
RNA-seq JQ1 (-) 24 hours Rep 1
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff

treatment_protocol: treated with enantiomer (JQ1(-)) for 24 hours


title: BRAF metastatic melanoma RNA-seq JQ1 (-) 24 hours Rep 2 [501MEL]

description:
RNA-seq JQ1 (-) 24 hours Rep 2
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: Normal Human Melanocytes RNA-seq Rep 2 [NHM1]

description:
RNA-seq Rep 2
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq JQ1 (+) 24 hours Rep 1 [501MEL]

description:
RNA-seq JQ1 (+) 24 hours Rep 1
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq JQ1 (+) 6 hours Rep 1 [501MEL]

description:
RNA-seq JQ1 (+) 6 hours Rep 1
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff

treatment_protocol: treated with 10nM JQ1 (JQ1(+)) for 6 hours


title: BRAF metastatic melanoma RNA-seq JQ1 (-) 6 hours Rep 1 [501MEL]

description:
RNA-seq JQ1 (-) 6 hours Rep 1
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: BRAF metastatic melanoma RNA-seq JQ1 (+) 6 hours Rep 2 [501MEL]

description:
RNA-seq JQ1 (+) 6 hours Rep 2
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq JQ1 (+) 24 hours Rep 2 [SKmel147]

description:
RNA-seq JQ1 (+) 24 hours Rep 2
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq JQ1 (-) 24 hours Rep 2 [SKmel147]

description:
RNA-seq JQ1 (-) 24 hours Rep 2
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq JQ1 (+) 24 hours Rep 1 [SKmel147]

description:
RNA-seq JQ1 (+) 24 hours Rep 1
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq JQ1 (-) 24 hours Rep 1 [SKmel147]

description:
RNA-seq JQ1 (-) 24 hours Rep 1
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma Input-Native [SKmel147]

description: Input-Native

extract_protocol:
Native ChIP was done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).


title: NRAS metastatic melanoma RNA-seq JQ1 (+) 6 hours Rep 2 [SKmel147]

description:
RNA-seq JQ1 (+) 6 hours Rep 2
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: BRAF metastatic melanoma Input-Native [501MEL]

description: Input-Native


title: NRAS metastatic melanoma RNA-seq JQ1 (+) 6 hours Rep 1 [SKmel147]

description:
RNA-seq JQ1 (+) 6 hours Rep 1
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma RNA-seq JQ1 (-) 6 hours Rep 1 [SKmel147]

description:
RNA-seq JQ1 (-) 6 hours Rep 1
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma ChIP-H3K27me3 [SKmel147]

tag: antibodies


title: Normal Human Melanocytes Input-Native [NHM2]

description: Input-Native


title: NRAS metastatic melanoma RNA-seq JQ1 (-) 6 hours Rep 2 [SKmel147]

description:
RNA-seq JQ1 (-) 6 hours Rep 2
SKmel147-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: NRAS metastatic melanoma ChIP-MacroH2A2 [SKmel147]

value: macroH2A2 (Bernstein lab, in house)


title: NRAS metastatic melanoma ChIP-H3K4me3 [SKmel147]

value: H3K4me3 (Abcam, ab1012)


title: NRAS metastatic melanoma ChIP-MacroH2A1 [SKmel147]

value: macroH2A1 (Abcam, ab37264)


title: BRAF metastatic melanoma ChIP-H3K27ac [501MEL]


title: NRAS metastatic melanoma ChIP-H3K27ac [SKmel147]


title: Normal Human Melanocytes ChIP-H3K27ac [NHM2]


title: BRAF metastatic melanoma ChIP-H3K4me1 [501MEL]

value: H3K4me1 (Abcam, ab8895)


title: NRAS metastatic melanoma ChIP-H3K4me1 [SKmel147]


title: BRAF metastatic melanoma ATAC-seq [501MEL]

description: ATAC-seq

extract_protocol:
For all ATAC-seq libraries, 150k cells were harvested, tagmented with 5uL Nextera Tn5 Transposes from nextera kit (Illumina) for 30 min, amplified up to 10 cycles and purified essentially as previously described in ATAC protocols.. Purified libraries were then size selected on 2% agarose gel (150-700bp). Libraries were sequenced on Illumina Hi-Seq2500.
For all ATAC-seq libraries, 150k cells were harvested, tagmented with 5uL Nextera Tn5 Transposes from nextera kit (Illumina) for 30 min, amplified up to 10 cycles and purified essentially as previously described in ATAC protocols.. Purified libraries were then size selected on 2% agarose gel (150-700bp). Libraries were sequenced on Illumina Hi-Seq2500.


title: Normal Human Melanocytes ChIP-H3K4me1 [NHM2]


title: NRAS metastatic melanoma ATAC-seq [SKmel147]

description: ATAC-seq


title: BRAF metastatic melanoma RNA-seq JQ1 (-) 6 hours Rep 2 [501MEL]

description:
RNA-seq JQ1 (-) 6 hours Rep 2
501MEL-RNA-JQ1-gene_exp.diff
RNA-gene_exp.diff


title: Normal Human Melanocytes ATAC-seq [NHM1]

description: ATAC-seq


title: HQ1YP1

city: Wuhan

first: Qin

address: shizishan street

institute: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-28/plants/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.28.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text file includes expression variances between HQ1 and HQ including up-regulated and down-regulated genes

organism: Oryza sativa

source_name: young panicle

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

tag: strain

value: transgenic plants with Zhonghua11 as receptor

value: young panicle

value: during transition from vegetative to reproductive stage

tag: genotype

value: transgenic insertion caused OsAFB6 overexpression


title: HQ2YP1

value: correspondinng negative plants during the same transgenic event as control


title: HQ1YP2


title: HQ2YP2


title: NRAS metastatic melanoma RNA-seq shA2 #2 Rep 2 [SKmel147]

description:
RNA-seq shA2 #2 Rep 2
SKmel147-RNA-AMIGO2KD-gene_exp.diff


title: Input mES cell replicate 2

city: Boston

first: Behfar

last: Ardehali

state: Massachusetts

address: Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, CPZN7250

department: Molecular Biology

institute: MGH, Harvard Medical School

data_processing:
Paired-end sequencing reads were mapped to the mouse genome (mm9 build) using the aligner bwa.
Duplicate fragments were removed prior to generation of input-normalized coverage files (bigwig).
Genome_build: mm9
Supplementary_files_format_and_content: Input-normalized coverage files (bigwig) were generated over 50bp bins using Deeptools v. 2.4.0

organism: Mus musculus

source_name: Input mES cell

growth_protocol: Murine CJ7 or CCE28 cells were grown on 0.2% gelatin-coated 6-well plates seeded with irradiated or mitomycin C treated mouse embryonic fibroblast (MEF). ES cell medium contained: 1x DMEM knockOut medium, 15% hyclone FBS, 1x GlutaMAX, 1x NEAA, 1x pen/strep, 1-1.6x103 Units/ml of mLIF (Millipore), 55μM 2BME. Media was supplemented with 1µM and 3µM of PD0325901 and CHIR99021, respectively (2i). ES cells were depleted of MEF by plating the ES cell suspension at 37oC for 30min.

extract_protocol:
mESC were MEF depleted, crosslinked with 1% formaldehyde in PBS for 10min in conical tubes while gently rotating at RT and quenched by adding Glycine to a final concentration of 0.125M and left at RT for 5min on rotator. Crosslinked cells were spun down for 3min at 3500 rpm (2850 rcf) and lysed in cell lysis buffer  (50mM Tris PH 8.0, 50mM NaCl, 1mM EDTA, 5mM MgCl2, 0.25% NP-40, Roche complete EDTA-free protease inhibitor tablet(PI)* 0.2% PMSF* and 0.2% DTT*(*freshly-added)) at 2-2.5x107 cells/ml. Cells were left on ice for 10 min and dounced 10x using the tight pestle. Nuclei was spun down at 2850 rcf in 15ml conical tubes and the supernatnant was completely removed and nuclei was resuspended in sonication buffer (20mM Tris PH 8.0, 1% SDS, 2mM EDTA, 0.5mM EGTA, 0.5mM PMSF*, PI*(freshly added) at 5.0x107 nuclei/ml. Resuspended nuclei was left on ice for 10min and sonicated using the Bioruptor sonicator, at high setting 30’’ on 45’’ off twice for 15min. Water and ice was changed in between each sonication. IP was performed with using rabbit anti EZH2 (CST,D2C9), 1-2.5x106 nuclei were used per IP reaction, by adding 20-50 µl of sonicated chromatin to 1-1.25ml of IP buffer (20mM Tris PH 8.0, 0.5% Triton X-100, 150mM NaCl, 10% glycerol, 2mM EDTA) with the respective antibodies and after 4 hours of incubation protein A (40-50 µl) was added to the IP reaction and incubated for 4 more hours. Each wash was done on the rotator at RT for 5min as follows: x1 low salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl), x3 high salt wash (20mM Tris PH 7.8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl), x1 LiCl wash (20mM Tris PH 7.8, 1% NP-40, 1% NaDeoxycholate, 2mM EDTA, 250mM LiCl), x2 TE wash.Elution was done on the IPed samples in 2x250µl of elution buffer (1% SDS, 0.1M NaHCO3) on the rotator at RT. To the 500µl elution buffer, 20 µl of 5M NaCl was added and samples were incubated in a thrmomixer for 4hr-O/N at 65oC to reverse the crosslink (same was done for the Input material). Next, 15µl of 1M Tris PH 7.8, 1-2 µl glycoblue (Ambion) and 2 µl of proteinase K was added to the reaction mix and incubated at 65oC for 30-60min. DNA was extracted from the reversed crosslink material using phenol/chloroform extraction and EtOH precipitation.
Library constructing for sequencing was prepared as described elsewhere (Bowman et al., BMC Genomics 2013).

value: Embryonic stem cells (mESC)

tag: genotype/variation

value: wild type

tag: chip antibody


title: Input mES cell replicate 1


title: EZH2 ChIP mES cell replicate2

source_name: EZH2 ChIP mES cell

value: Ezh2(D2C9 XP Rabbit mAb, 5246S, Cell Signaling Technology)


title: Eed null  mESC Bru-seq rep2

description:
Bru-CJ7-EEDnull-2
processed data column: Bru-CJ7-EEDnull-average

data_processing:
Sequencing reads were mapped to the mouse genome (mm9 build) using the aligner BWA.
Sequencing reads were counted over an assembly of all putative introns for each gene and normalized by the length of the cumulative intron assembly and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: txt, bigwig: RPKM and genebrowser tracks

source_name: Eed null  mESC Bru-seq

growth_protocol: Murine CJ7 cells were grown on 0.2% gelatin-coated 6-well plates seeded with irradiated or mitomycin C treated mouse embryonic fibroblast (MEF). ES cell medium contained: 1x DMEM knockOut medium, 15% hyclone FBS, 1x GlutaMAX, 1x NEAA, 1x pen/strep, 1-1.6x103 Units/ml of mLIF (Millipore), 55μM 2BME. Media was supplemented with 1µM and 3µM of PD0325901 and CHIR99021, respectively (2i). ES cells were depleted of MEF by plating the ES cell suspension at 37oC for 30min.

extract_protocol:
Experiments were carried out on mouse ES cells gown on feeder-free, 1% gelatinized 100mm tissue culture dishes. 5-Bromouridine (BrU) was added to cells at a final concentration of 2mM (from a100mM BrU stock) and incubated in the incubator for 10 min. Media was aspirated off and cells were lysed in 4ml of Trizol. 800µl of chloroform was next added to the lysed cells in 5ml epp tubes, vortexed and spun down at 5200 g for 15min. Equal volume of isopropanol was added to the aqueous phase, mixed, left at RT for 5-10 min and spun down at 4oC for 20min at max speed (14000 g) in a tabletop centrifuge to precipitate the RNA.  Resulting RNA pellet was washed twice with 70% EtOH, air dried and resuspended in 200-400 µl Nuclease-free water. The amount of RNA was quantified using Nanodrop, and a small fraction of the total RNA was run on agarose gel to determine the quality of purified total RNA.
Bru-RNA enrichment: Mouse aBrdU antibody (SCBT, sc-32323) was coupled to Dynabeads M-280 Sheep Anti-Mouse IgG (11201D). 1ml of magnetic beads was washed 4 x with PBS-DEPC/0.1%BSA and 500ul of Ab  was incubated with 1ml of beads and yeast RNA (500ng/µl final concentration) for 2-3 hours at 4oC, washed 3x with PBS-DEPC/0.1%BSA/Tween 0.05%.The final volume was raised to 1ml. For enrichment of Bru-RNA, 25-50µg of total RNA (after preheating at 95oC and immediate cooling) was added to 50µl of Antibody-bound beads in 1 ml of PBS-DEPC/0.1%BSA/Tween 0.05% and incubated for 90 min at RT with a foil wrapped around the tube. Beads were washed 4x with PBS-DEPC/0.1%BSA/Tween 0.05%, 5-10min (last wash was done with Tween-free buffer). Enriched RNA was either eluted by addition of 25µl of DEPC-water and incubation at 95oC for 10min with occasional flicking/shaking, or Trizol extraction. The enriched RNA was depleted of ribosomal RNA and used for generation of RNA-seq library.

treatment_protocol: 5-BromoUridine (BrU) was added to CJ7 mES cells growing in plates at a final concentration of 2mM for 10min in 10mm plates. Media was aspirated off and RNA was extracted by addition of 4ml of Trizol.

tag: cell line background

value: EloA null

tag: molecule subtype

value: BrU-labelled nascent RNA


title: Eed null mESC Bru-seq rep1

description:
Bru-CJ7-EEDnull-1
processed data column: Bru-CJ7-EEDnull-average

source_name: Eed null mESC Bru-seq


title: Wild Type CJ7 mESC Bru-seq rep2

description:
Bru-CJ7-2
processed data column: Bru-CJ7-WT-average

source_name: Wild Type CJ7 mESC Bru-seq

value: Wild Type


title: H4ac_H3_dot1D

data_processing:
The quality of fastq files were checked by fastqc and trimmed by trim_galore
The qualified fastq files were aligned to SacCer3 genome fa file using Bowtie2 v2.2.3. Then, the aligned files were compressed and sorted by samtools v1.3.
The sorted BAM files of biological duplicates were compared by MACS2, bam2wig and deeptools.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated by MACS2, bam2wig and deeptools.

source_name: S.cerevisiae cells

extract_protocol:
Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP  lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP  lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in  Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit.
Total RNA for mRNA-seq was prepared by the hot-phenol extraction.
For preparation of MNase-seq library, formaldehyde-fixed cell pellets were resuspended in 10 ml of pre-incubation buffer (20 mM EDTA, 0.7 M mercaptoethanol), washed, and resuspended in 2 ml of zymolyase buffer (1 M sorbitol, 50 mM Tris-Cl, pH 8.0, 5 mM mercaptoethanol) containing 2.5 mg ml-1 zymolyase (20T; US Biological). Lysed cells were spheroplasted at 30°C  for 20 min and chromatin was isolated. Pelleted nuclei were digested with 200 units of MNase (NEB) at 37°C for 20 min (confirmed as a typical digestion condition by comparison of fragment sizes, data not shown), and then reverse cross-linked in 10 mM EDTA and 1% SDS buffer with proteinase K for 6 hours at 37°C. The DNA was extracted with phenol/chloroform, purified by ethanol precipitation, and resolved by 2% agarose gel electrophoresis in TAE buffer.
Yeast cells (2.5 million) were harvested at O.D. 0.6~0.8/mL (mid-log phase), and spheroplasted in 200 μl of Sorbitol buffer (1.4 M Sorbitol, 40 mM Tris-HCl, pH 7.5, 0.5 mM MgCl2) with 10 μl of 50 mg ml-1 of zymolyase (20T; US Biological). After washing twice with 100 μl of ice-cold Sorbitol buffer, the spheroplasts were incubated in fresh TD buffer (20 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 20% dimethylformaldehyde) with transposase at 37°C for 4 hours. QIAquick PCR purification kit was used to purify DNA fragments, and transposition reactions and PCR amplifications were performed.
General Manual of Nextflex ChIP library preparation kit. mRNA isolation and mRNA-seq library preparation were performed using the NEXTflex Rapid Directional mRNA-Seq Bundle.

treatment_protocol: For ChIP and MNase: Final 1% formaldehyde fixation and 125mM glycine quencing were performed before cell harvest.

tag: antibody

value: 06-866; Millipore

tag: phase

value: mid-log phase

tag: medium

value: YPD