title: mESC - Rb + E2F4 QKO (D1.9.1)

data_processing:
Reads were mapped to mouse reference genome mm10 with STAR2.5.1b using default settings. Genes that have at least ten reads in two out of four samples of either the control group or the E2F4KO group were further used for analysis. Differentially expressed genes were obtained using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: File including counts and FPM, log2 Foldchanges and p-values obtained with DEseq2

source_name: mESC - Rb + E2F4 QKO

extract_protocol:
Cells were grown at low density for four days. RNA extraction was performed using the RNeasy micro kit (Qiagen 74004).
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina RS-122-2101).
Four wild-type and four E2F4KO mESC lines were sequenced on a HiSeq4000, generating on average 42 million paired-end (2x76) reads per sample. Two of the wild-type lines (J3.3 and J3.14) were expanded from clones that had retained E2F4 protein expression following transfection with a gRNA against E2F4, and the other two wild-type lines (C1 and C2) were obtained following transfection of an empty pX330 vector. Similarly, four TKO and four QKO lines were sequenced on a separate run of a HiSeq4000, also generating on average 45 million paired-end (2x76) reads per sample.

value: ESC

value: Rb + E2F4 QKO


title: mESC - Rb + E2F4 QKO (D3.8)

status: Public on Apr 25 2019

type: SRA

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

growth_protocol: mESC lines were maintained feeder-free on 0.2% gelatin-coated (Sigma G9382) plates in Dulbecco’s modified Eagle’s medium (Gibco SH30243.01) containing 15% fetal bovine serum (Hyclone SH30071.03; VWR Seradigm 97068-085), MEM non-essential amino acids (Gibco 11140-050), penicillin-streptomycin-glutamine (Gibco 10378-016), and 0.1 mM beta-mercaptoethanol (Gibco 21985-023), and supplemented with LIF. Cells were passaged enzymatically using 0.05% Trypsin-EDTA (Gibco 15400-054). Single-cell suspensions of 1000 mESCs/mL were cultured in low density assays.

tag: cell type

tag: genotype


title: 3BSH

type: RNA

city: Baton Rouge

first: Thanh

last: Dang

state: LA

address: 6400 Perkins Rd

country: USA

institute: Pennington Biomedical Research Center

description:
SKG HF.AVG_signal
sample name:
3BSH
global knockout of Siah2

hyb_protocol: 750ng labeled RNA was hybridized to Illumina Mouse WG-6 v2 BeadChip arrays (Illumina) for females and Illumina MouseRef-8 v2.0 Expression BeadChip arrays for males according to manufacturer's protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6  Raw data were background-subtracted and normalized using the quantile normalization method using the preprocessCore package in R.
The "Matrix normalized" tab contains quantile normalized and background subtracted gene expression signals.  "Matrix non-normalized" contains background subtracted non-normalized data exported from GenomeStudio.

label: biotin

source_name: brown adipose tissue

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

extract_protocol: The brown adipose tissue was quickly removed, frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc. Cincinnati, Ohio) with modifications to remove DNA using Qiagen RNAeasy columns.

treatment_protocol: The mice were weaned at 4 weeks of age and randomized to either a low fat (10% fat) diet (Research Diets, New Brunswick, NJ, #D12450B) or high fat (45%) diet (Research Diets, D12451).  The mice remained on these diets until 20 weeks of age.

tag: tissue

value: brown adipose tissue

tag: gender

value: Male

tag: strain

tag: diet

value: high fat diet

tag: age

value: 20 weeks

value: Siah2 knockout


title: mESC - Rb + E2F4 QKO (D3.8.1)


title: PCGF1/3/5fl_UNT_K27me3_NatInput_rep3

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native cChIP-seq and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 (or hg19) reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6 (or hg19)/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
RING1B and SUZ12 peak sets were generated with MACS2 (--broad) using corresponding Input samples for background normalisation. For each factor, a set of peaks identified in all biological replicates (intersection) was manually curated to remove sequencing artefacts. Classical Polycomb chromatin domains were identified by k-means clustering of ±10 kb windows centred on RING1B peaks based on their RING1B and SUZ12 chromatin occupancy using deeptools (v.3.0.1). This generated three clusters, two of which displayed high enrichment of both RING1B and SUZ12 and were combined into one set of genomic intervals.
Allele-specific analysis of H2AK119ub1 cChIP-seq was performed as described previously (Pintacuda et al. 2017). Briefly, paired-end reads were aligned using STAR (with “--outFilterMultimapNmax 1”, “--outFilterMismatchNmax 2”, “--alignEndsType EndToEnd” parameters) against the concatenated mm10+dm6 genome, in which polymorphic SNPs for 129S1 and CAST mouse strains were N-masked. Reads that were mapped more than once were discarded and PCR duplicates were removed with Sambamba. Reads mapping to mm10 genome were randomly subsampled using downsampling factors calculated based on spike-in calibration as described previously. To separate reads specifically mapping to the 129S1 and CAST alleles, we used SNPsplit (Krueger et al. 2016) with the paired-end mode.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq and Input profiles
Supplementary_files_format_and_content: bed files with enrichment peaks for RING1B and SUZ12 generated with MACS2 (--broad) from at least three biological replicates (intersection)

molecule: genomic DNA

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Pcgf6fl/fl ESCs and Mus domesticus (129S1) x Mus castaneus F1 hybrid ESCs were grown on a monolayer of mitomycin-inactivated SNLP feeders (STO mouse fibroblasts expressing Neomycin, Puromycin resistance and Lif genes) in otherwise the same conditions as other mouse ESCs. Prior to harvesting these ES cells, the feeders were depleted by pre-plating trypsinised cells for 30 mins at 37°C on plates not coated with gelatin and discarding attached cells. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 Mm beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B, SUZ12, PCGF1, PCGF2, CBX7 and PHC1 cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C firstly with 2 mM DSG (Thermo Scientific) for 45 mins, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched by the addition of 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 min at 4˚C. The released nuclei were then washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 min at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to an average size of approximately 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST D22F2, 3 ul), anti-SUZ12 (CST D39F6, 3 ul), anti-PCGF1 (in-house, 3 ul), anti-PCGF2 (sc-10744, 3 ul), anti-Cbx7 (ab21873, 4 ul), anti-Phc1 (CST 1F3F3, 6 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 2 hours at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65°C with 200 mM NaCl and 2 µl of RNase A (Sigma). A matched input sample (corresponding to 10% of original ChIP reaction) was identically treated. The following day ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For H2AK119ub1 and H3K27me3 native cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4°C with 5 ul of anti-H2AK119ub1 (CST D27C4) or anti-H3K27me3 (in-house). Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicate unless otherwise specified. For allele-specific analysis in 129S1 x CAST hybrid ESC line with inducible fill-length Xist transgene, native cChIP-seq libraries were sequenced as 80 bp paired-end reads on Illumina NextSeq 500 platform to increase the number of reads overlapping allele-specific SNPs.

treatment_protocol: To induce conditional removal of distinct PRC1 complexes or their combinations in Pcgf4-/-; Pcgf2fl/fl, Pcgf1fl/fl, Pcgf3fl/fl, Pcgf5fl/fl, Pcgf6fl/fl, Pcgf3/5fl/fl, Pcgf1/3/5fl/fl, Pcgf1/3/5/2fl/fl, Pcgf1/3/5/6fl/fl and Ring1a-/-; Ring1bfl/fl ESC lines, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours. To induce expression of Xist transgene, 129S1 x CAST ESCs were treated with 1.5 μg/mL doxycycline for 72 hours.

tag: cell line

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: ChIP

tag: antibody


title: PCGF1/3/5fl_UNT_K27me3_NatInput_rep2


title: mESC - Rb + E2F4 QKO (D1.9)


title: 2BSH

description:
SKG HF.AVG_signal
sample name:
2BSH
global knockout of Siah2


title: B_272b

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
Sleuth for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: An Excel file including TPM of each gene for all 28 samples

organism: Homo sapiens

source_name: interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
TruSeq Stranded LT mRNA kit

value: iPSC-derived interneurons

tag: disease

value: healthy control


title: B_272c


title: 1BSH

description:
SKG HF.AVG_Signal
sample name:
1BSH
global knockout of Siah2


title: mESC - Rb TKO (D1.10.1)

source_name: mESC - Rb TKO

value: Rb TKO


title: WT Chol I vs M Chol II [Mtb]

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: polarity(+)

hyb_protocol: Commercial-custom M.smegmatis 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

organism: Mycobacterium tuberculosis H37Rv

source_name: WT Chol I

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: M. tuberculosis H37Rv (ATCC 27294) was propagated in Middlebrook 7H9 broth supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson, MD, USA) , 0.2% glycerol, and 0.05% Tyloxapol at 37°C with agitation (100 rpm) or on Middlebrook 7H11 agar containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson).

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions. Cell lysis was achieved through three cycles of bead beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 s.

treatment_protocol: Carbon utilization assays were performed using minimal medium and cholesterol (0.01%), ethanol (0.01%–1%) and glycerol.

tag: genotype/variation

value: wildtype

tag: treatment

value: Cholesterol

value: biol. replicate 1

source_name: M Chol II

value: KO mutant

value: biol. replicate 2


title: mESC - Rb TKO (D1.10)

tag: cell type

value: ESC

tag: genotype


title: PCGF1/3/5fl_UNT_K27me3_NatInput_rep1


title: PCGF1/3/5fl_TAM_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H3K27me3-seq

value: tamoxifen (OHT)

value: 72 hr

value: In house (Rose, 2016)


title: B_226c


title: B_226a


title: PCGF1/3/5fl_TAM_H3K27me3_rep2


title: B_292a


title: mESC - Rb TKO (D1.2.1)


title: mESC - Rb TKO (D1.2)


title: B_190b


title: PCGF1/3/5fl_TAM_H3K27me3_rep1


title: SO4_without Mg_14 days_rep2

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description: SO4 roots sampled after 14 days of growth without Mg. It is the second biological replicate of the SO4 -Mg 14 days used in this experiment.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing:
Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.
Text files include Nimblescan v2.5 software calculated RMA-normalized signal intensities.

organism: Vitis cinerea var. helleri x Vitis riparia

source_name: Two-week-old SO4 microcuttings, grown for 2 weeks in a dilute NS, treated for 14 days with a NS containing CaSO4

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Two-week-old grapevine in vitro propagated microcuttings of 1103P and SO4 rootstocks were hydroponically grown into 2-L plastic pots for two weeks using a dilute nutrient solution (NS) containing: 200 µM Ca(NO3)2, 50 µM MgSO4, 70 µM K2SO4, 10 µM KCl, 10 µM KH2PO4, 0.1 µM H3BO3, 0.05 µM MnSO4, 0.02 µM CuSO4, 0.05 µM ZnSO4, 0.001 µM (NH4)6Mo7O24 and 10 µM Fe-EDTA. The pH of solution was adjusted to 6.0 with KOH. The NS was changed every week and the microcuttings were grown in under control condition in a growth chamber (Photosynthetically Active Radiation, PAR, 200 µmol m-2 s-1, 16/8 h day/night regime, temperature 24°C).

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol: After the growth period in diluite NS, for the Mg starvation experiment was set-up a NS with the following composition: 1000 µM Ca(NO3)2, 350 µM K2SO4, 50 µM KCl, 50 µM KH2PO4, 0.5 µM H3BO3, 0.25 µM MnSO4, 0.1 µM CuSO4, 0.25 µM ZnSO4, 0.005 µM (NH4)6Mo7O24 and 50 µM Fe-EDTA. For both rootstocks, a half of microcuttings were grown in this new NS containing also 250 µM MgSO4 (+Mg) and the other half in a Mg-free NS in which was replaced with an equivalent mole of CaSO4 (-Mg). Three independent  experiments (biological replicates) were performed. In each experiment root tissues of six plants were collected and pooled for each sample (1103P +Mg, 1103P -Mg, SO4 +Mg and SO4 -Mg) both after 4 and 14 days of growth with or without Mg.

tag: tissue

value: root

tag: rootstock


title: PCGF1/3/5fl_UNT_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3-seq


title: SO4_without Mg_14 days_rep1

description: SO4 roots sampled after 14 days of growth without Mg. It is the first biological replicate of the SO4 -Mg 14 days used in this experiment.


title: SO4_with Mg_14 days_rep3

description: SO4 roots sampled after 14 days of growth with Mg. It is the third biological replicate of the SO4 +Mg 14 days used in this experiment.

source_name: Two-week-old SO4 microcuttings, grown for 2 weeks in a dilute NS, treated for 14 days with a NS containing MgSO4


title: mESC - E2F4KO (J3-26)

source_name: mESC - E2F4KO


title: B_139c


title: mESC - E2F4KO (J3-6)


title: PCGF1/3/5fl_UNT_H3K27me3_rep2


title: B_139a


title: mESC - E2F4KO (J1-23)


title: PCGF1/3/5fl_UNT_H3K27me3_rep1


title: PCGF1/3/5fl_TAM_uH2A_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), gDNA-seq


title: mESC - E2F4KO (J1-18)


title: B_107c


title: B_107b


title: SO4_without Mg_14 days_rep3

description: SO4 roots sampled after 14 days of growth without Mg. It is the third biological replicate of the SO4 -Mg 14 days used in this experiment.


title: 1103P_without Mg_14 days_rep3

description: 1103P roots sampled after 14 days of growth without Mg. It is the third biological replicate of the 1103P -Mg 14 days used in this experiment.

organism: Vitis cinerea var. helleri x Vitis rupestris

source_name: Two-week-old 1103P microcuttings, grown for 2 weeks in a dilute NS, treated for 14 days with a NS containing CaSO4


title: mESC - WT (J3-14)

source_name: mESC - WT

value: WT


title: PCGF1/3/5fl_TAM_uH2A_NatInput_rep2


title: B_190c


title: B_99c


title: 1103P_without Mg_14 days_rep2

description: 1103P roots sampled after 14 days of growth without Mg. It is the second biological replicate of the 1103P -Mg 14 days used in this experiment.


title: mESC - WT (J3-3)


title: PCGF1/3/5fl_TAM_uH2A_NatInput_rep1


title: 1103P_without Mg_14 days_rep1

description: 1103P roots sampled after 14 days of growth without Mg. It is the first biological replicate of the 1103P -Mg 14 days used in this experiment.


title: B_99b


title: 1103P_with Mg_14 days_rep3

description: 1103P roots sampled after 14 days of growth with Mg. It is the third biological replicate of the 1103P +Mg 14 days used in this experiment.

source_name: Two-week-old 1103P microcuttings, grown for 2 weeks in a dilute NS, treated for 14 days with a NS containing MgSO4


title: PCGF1/3/5fl_UNT_uH2A_NatInput_rep3


title: mESC - WT (C2)


title: A_L6ab

value: schizophrenia


title: PCGF1/3/5fl_UNT_uH2A_NatInput_rep2

value: 0 hr


title: SO4_with Mg_14 days_rep1

description: SO4 roots sampled after 14 days of growth with Mg. It is the first biological replicate of the SO4 +Mg 14 days used in this experiment.


title: A_1442e


title: 1103P_with Mg_14 days_rep2

description: 1103P roots sampled after 14 days of growth with Mg. It is the second biological replicate of the 1103P +Mg 14 days used in this experiment.


title: 1103P_with Mg_14 days_rep1

description: 1103P roots sampled after 14 days of growth with Mg. It is the first biological replicate of the 1103P +Mg 14 days used in this experiment.


title: PCGF1/3/5fl_UNT_uH2A_NatInput_rep1

value: Drosophila melanogaster


title: A_L6b

value: iPSC-derived interneurons


title: A_1442d


title: SO4_without Mg_4 days_rep3

description: SO4 roots sampled after 4 days of growth without Mg. It is the third biological replicate of the SO4 -Mg 4 days used in this experiment.

source_name: Two-week-old SO4 microcuttings, grown for 2 weeks in a dilute NS, treated for 4 days with a NS containing CaSO4


title: A_L10b


title: PCGF1/3/5fl_TAM_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H2AK119ub1 ChIP-seq

value: Cell Signaling Technology(#D27C4 )


title: Adult male hypoxia RRBS 4

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus St

institute: Loma Linda University

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptor sequences were removed from the reads using trim_galore v0.3.7 with option ‘--rrbs’ disabled due to special design of NuGEN Ovation RRBS system. After adaptor trimming, NuGEN’s diversity trimming was performed to remove diversity adaptors. The trimmed reads were aligned to rat genome NCBI Rnor6.0 by using Bismark v0.16.3 with all default parameter settings. The methylation call files including the location of each CpG sites and the methylation percentage (beta value) were generated by the bismark_methylation_extractor
Differential methylation sites (DMC) analysis was performed by methylKit. CpGs with coverage ≥ 10 were used for DMC analysis. DMCs were identified when the difference of methylation percentages between control and hypoxia were greater than 10% and q-value < 0.05.
Differential methylation region (DMR) analysis was performed by DMAP and methylKit. We first used DMAP to generate CpG region profiles. CpG regions with coverage ≥ 20 were used for DMR analysis. methylKit was used to perform DMR analysis. Same criteria of DMCs selection was applied for DMRs identification.
Genome_build: Rnor6.0

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
For genomic DNA (gDNA) extraction, heart tissues were minced and digested with 20 μL proteinase K (20 mg/mL) in digestion buffer (10mM Tris-Hcl, pH 8.0 containing 0.5 M EDTA, 1% SDS, 10 m NaCl, and 5mM CaCl2) for 3 h at 55°C. Next the tissue lysate was twice phenol/chloroform/isoamyl: (25/24/1) alcohol extracted and the aqueous layer was treated with RNAse AþT1 for 1 h at 37°C. The lysate was again phenol/chloroform/isoamyl alcohol extracted and the gDNA was precipitated with equal volume of isopropanol in presence of 0.3 M sodium acetate at -20°C overnight. The gDNA was finally centrifuged, washed with 70% ethanol, air dried and reconstituted in 10 mM Tris-HCl, pH 8.0. And then, gDNA was denatured with 2 N NaOH at 42°C for 15 min, treated with sodium bisulfite at 55°C for 16 h, and purified by EZ DNA Methylation-Gold KitTM.
RRBS libraries were constructed by standard protocols of the NuGEN Ovation® Ultralow Methyl-Seq Library Systems.

tag: strain

value: Sprague Dawley

value: heart

value: 5 months old

value: hypoxia


title: PCGF1/3/5fl_TAM_H2AK119ub1_rep2


title: Adult male hypoxia RRBS 5

tag: age


title: Adult male hypoxia RRBS 6


title: SO4_without Mg_4 days_rep2

description: SO4 roots sampled after 4 days of growth without Mg. It is the second biological replicate of the SO4 -Mg 4 days used in this experiment.


title: PCGF1/3/5fl_TAM_H2AK119ub1_rep1

tag: cell line


title: PCGF1/3/5fl_UNT_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

tag: replicate


title: A_L8c

source_name: interneurons


title: A_L10a


title: SO4_without Mg_4 days_rep1

description: SO4 roots sampled after 4 days of growth without Mg. It is the first biological replicate of the SO4 -Mg 4 days used in this experiment.


title: SO4_with Mg_4 days_rep3

description: SO4 roots sampled after 4 days of growth with Mg. It is the third biological replicate of the SO4 +Mg 4 days used in this experiment.

source_name: Two-week-old SO4 microcuttings, grown for 2 weeks in a dilute NS, treated for 4 days with a NS containing MgSO4


title: mESC - WT (C1)


title: Adult male hypoxia RRBS 3


title: Adult male hypoxia RRBS 2


title: A_L8a


title: PCGF1/3/5fl_UNT_H2AK119ub1_rep2

tag: treatment agent


title: PCGF1/3/5fl_UNT_H2AK119ub1_rep1

tag: treatment time point


title: A_755c


title: SO4_with Mg_4 days_rep1

description: SO4 roots sampled after 4 days of growth with Mg. It is the first biological replicate of the SO4 +Mg 4 days used in this experiment.


title: Adult male normoxia RRBS 6

value: control


title: PCGF3/5fl_TAM_NatInput_rep3

tag: spike-in reference organism


title: Adult male normoxia RRBS 5


title: A_755d


title: 1103P_without Mg_4 days_rep3

description: 1103P roots sampled after 4 days of growth without Mg. It is the third biological replicate of the 1103P -Mg 4 days used in this experiment.

source_name: Two-week-old 1103P microcuttings, grown for 2 weeks in a dilute NS, treated for 4 days with a NS containing CaSO4


title: 1103P_without Mg_4 days_rep2

description: 1103P roots sampled after 4 days of growth without Mg. It is the second biological replicate of the 1103P -Mg 4 days used in this experiment.


title: SO4_with Mg_14 days_rep2

description: SO4 roots sampled after 14 days of growth with Mg. It is the second biological replicate of the SO4 +Mg 14 days used in this experiment.


title: PCGF3/5fl_TAM_NatInput_rep1

tag: spike-in cell line


title: A_689b


title: Adult male normoxia RRBS 3


title: A_689a


title: 1103P_without Mg_4 days_rep1

description: 1103P roots sampled after 4 days of growth without Mg. It is the first biological replicate of the 1103P -Mg 4 days used in this experiment.


title: SO4_with Mg_4 days_rep2

description: SO4 roots sampled after 4 days of growth with Mg. It is the second biological replicate of the SO4 +Mg 4 days used in this experiment.


title: Adult male normoxia RRBS 2


title: Adult male hypoxia RRBS 1


title: A_483c


title: PCGF3/5fl_UNT_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq

tag: ChIP


title: 1103P_with Mg_4 days_rep3

description: 1103P roots sampled after 4 days of growth with Mg. It is the third biological replicate of the 1103P +Mg 4 days used in this experiment.

source_name: Two-week-old 1103P microcuttings, grown for 2 weeks in a dilute NS, treated for 4 days with a NS containing MgSO4


title: Adult male normoxia RRBS 1


title: 1103P_with Mg_4 days_rep2

description: 1103P roots sampled after 4 days of growth with Mg. It is the second biological replicate of the 1103P +Mg 4 days used in this experiment.


title: PCGF3/5fl_UNT_NatInput_rep2

tag: antibody


title: PCGF3/5fl_UNT_NatInput_rep1


title: Fetal hypoxia RRBS 3


title: A_483b

tag: disease


title: 1103P_with Mg_4 days_rep1

description: 1103P roots sampled after 4 days of growth with Mg. It is the first biological replicate of the 1103P +Mg 4 days used in this experiment.


title: A_285b


title: Adult male normoxia RRBS 4


title: PCGF3/5fl_TAM_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H3K27me3 ChIP-seq


title: Fetal hypoxia RRBS 1


title: PCGF3/5fl_TAM_H3K27me3_rep2


title: PCGF3/5fl_TAM_NatInput_rep2


title: A_285a


title: Fetal normoxia RRBS 3


title: A_282b


title: Fetal normoxia RRBS 2


title: PCGF3/5fl_TAM_H3K27me3_rep1


title: A_282d


title: PCGF3/5fl_UNT_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq


title: A_212b


title: A_212a


title: Fetal normoxia RRBS 1


title: PCGF3/5fl_UNT_H3K27me3_rep2


title: Fetal hypoxia RRBS 2


title: A_162b


title: A_162a


title: PCGF3/5fl_TAM_H2AK119ub1_rep2


title: PCGF3/5fl_UNT_H3K27me3_rep1


title: PCGF3/5fl_TAM_H2AK119ub1_rep1


title: A_128a


title: Adult male hypoxia RNAseq 5

description:
adult_gene_fpkm.csv
MH10

data_processing:
Illumina Casava1.8 software used for basecalling.
Hard trimming and adaptor trimming were performed by Trimmomatic v0.35. The trimmed reads were aligned to the rat reference genome NCBI Rnor6.0 with TopHat v2.1.1 with default parameter settings.
The aligned bam files were then processed using Cufflinks v2.2.1 for gene quantification.
The gene expression profiles (Fragments Per Kilo base per Million or FPKM) were used as the input for differential expression gene (DEG) analysis by using Cuffdiff. Differential expressed genes were based on FDR < 0.3 and fold change (FC) > 1.2.
Genome_build: Rnor6.0

extract_protocol:
Total RNA was isolated from heart tissue using TRIzol RNA Isolation reagent. Briefly, each solid tissue was homogenized in 1 mL TRIzol and the lysate was then extracted with chloroform and centrifuged at 14 000 rpm for 15 min at 4°C. Finally, total RNA was precipitated and washed thoroughly with 70% ethanol, airdried and reconstituted in nuclease free water. RNA quality was assessed using the 2200 TapeStation. Heart samples had an average RIN number of 9.5.
RNA-seq libraries were constructed using the Ovation Universal RNAseq System.


title: Adult male hypoxia RNAseq 2

description:
adult_gene_fpkm.csv
MH2


title: Adult male hypoxia RNAseq 1

description:
adult_gene_fpkm.csv
MH1


title: Adult male hypoxia RNAseq 3

description:
adult_gene_fpkm.csv
MH4


title: Donor_19

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Gene expression data of peripheral blood mononuclear cells

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: CHP files were generated using Affymetrix Expression Control.

source_name: peripheral blood mononuclear cells

label_protocol: 3' IVT Expression Kit (Affymetrix) was used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Venous blood was collected to K2EDTA contianing vacutainer tubes. Peripheral blood mononuclear cells were separated bx Ficoll gradient centrifugation. At the end of the separation cells lysated in Trizol reagent

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

treatment_protocol: Blood samples collected from patients before the anti-TNFα therapy.

tag: gender

value: female

tag: fmd

tag: imt

tag: pwv

tag: clinical response

value: cNR


title: PCGF3/5fl_UNT_H2AK119ub1_rep3


title: Donor_18


title: Donor_16

value: low

value: cR


title: A_117b

tag: cell type


title: PCGF3/5fl_UNT_H2AK119ub1_rep2


title: Adult male normoxia RNAseq 5

description:
adult_gene_fpkm.csv
MC9

tag: strain

tag: tissue

tag: treatment


title: Adult male hypoxia RNAseq 4

description:
adult_gene_fpkm.csv
MH9

tag: age


title: A_117a


title: Donor_15

value: high


title: Donor_17


title: Donor_13


title: AM25226 Rec8-3Ha ChIP-seq WT Input

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

description: Reads mapped to SK1 only

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 20, min. length 65)
To obtain reads mapping only to SK1;
ChIP-Seq reads were first mapped with MiniMap2 (-ax sr) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to SK1
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to SK1
Unmapped SK1 reads were filtered using samtools
Unmapped SK1 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Genome_build: SK1 (g833-1B) + s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to SK1 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (SK1)), calibrated SK1 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

organism: Saccharomyces cerevisiae

source_name: Meiotic yeast cells

growth_protocol: Yeast were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 5 hours in SPO media (0.3% Kac) to arrest in prophase. Cells were released from prophase arrest by addition of 1µM β-estradiol and grown for 75 minutes to arrest in metaphase I.

extract_protocol:
Cells were lysed by beating in MP biomedicals FastPrep-24 machine for 1 minute four times with 10 minute intervals on ice. Cell pellets were washed once in FA lysis buffer/0.1% SDS before sonicating for 30 cycles at 30sec on/off intervals. The supernatant was subject to IP with Sigma M2 anti-Flag antibody conjugated to Dynabeads over night. Dynabeads were washed and bound protein eluted using TES buffer. Samples were decrosslinked with Proteinase K and purified using Promega Wizard kit.
DNA was blunted using NEB Quick Blunting kit followed by Ampure purification of fragments over 100bp. dA tails were added using Klenow (exo-) and NextFlex adaptors ligated to each sample. This was followed by two Ampure purifications of fragments over 100bp and then fragments over 150-200bp. Libraries were amplified using NextFlex primers and Phusion DNA polymerase. Lastly, double-sided Ampure purification was carried out to obtain fragments between 100-300bp in size.

treatment_protocol: Cells were fixed in 1% formaldehyde for 30 minutes before washing twice in TBS and once in FA lysis buffer with 0.1% SDS.

tag: strain background

tag: chip antibody

value: none, input


title: Donor_14


title: Adult male normoxia RNAseq 4

description:
adult_gene_fpkm.csv
MC8


title: Donor_10


title: Donor_12


title: A_67b


title: Adult male normoxia RNAseq 3

description:
adult_gene_fpkm.csv
MC7


title: A_58b


title: A_67a


title: Adult male normoxia RNAseq 2

description:
adult_gene_fpkm.csv
MC4


title: AM24162 Spo13-3Flag ChIP-seq rec8Δ Input

description: Reads mapped to SK1 only

data_processing:
Basecalls performed using CASAVA
Reads were trimmed with cutadapt (MAPQ 10, min. length 30)
To obtain reads mapping only to SK1;
ChIP-Seq reads were first mapped with bwa (aln/sampe) to pombe
Unmapped pombe reads were filtered using samtools
Unmapped pombe reads were then mapped to SK1 (bwa mem)
Unmapped reads were filtered using samtools
rDNA regions were removed from chrXII (saturated with reads)
chrMito was excluded using bedtools
To obtain reads mapping only to Pombe;
Reads were also mapped to SK1
Unmapped SK1 reads were filtered using samtools
Unmapped SK1 reads were then mapped to pombe
Unmapped reads were filtered using samtools
chrMito was excluded using bedtools
Genome_build: SK1 (g833-1B) + s.pombe ASM294v2.22
Supplementary_files_format_and_content: bigwigs were created using bedtools genomeCoverageBed & wigToBigWig (RPM normalization), To obtain calibrated bigWigs;  samtools flagstat was used to count reads mapping to SK1 and pombe only for each sample  the occupancy ratio (OR) value was calculated as Wc*IPx/Wx*IPc (W=Input;IP=chIP;c=calibration genome (pombe);x=experimental genome (SK1)), calibrated SK1 chIP bigwigs were created using bedtools genomeCoverageBed & wigToBigWig

growth_protocol: Yeast were grown to saturation in YPDA media before transfer to pre-sporulation media (BYTA). Cells were grown to for approx. 16 hours to OD(600) of approx. 4. Cells were diluted to OD(600) = 1.8 and sporulated for 5 hours in SPO media (0.3% Kac).

tag: genotype/variation


title: Adult male normoxia RNAseq 1

description:
adult_gene_fpkm.csv
MC3


title: A_128b


title: A_58a


title: AM24162 Spo13-3Flag ChIP-seq rec8Δ IP

description: Reads mapped to SK1 only/calibrated to s.pombe

value: Mouse monoclonal M2 anti-FLAG (Sigma)


title: Adult female hypoxia RNAseq 5

description:
adult_gene_fpkm.csv
FH9


title: AM24161 Spo13-3Flag ChIP-seq WT Input

description: Reads mapped to SK1 only

value: wild type


title: iPSC-derived interneurons_healthy control (B_pyauma)

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
Sleuth for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: An tab-delimited file including TPM of each gene for all samples

tag: disease state

value: healthy control


title: Donor_11


title: PCGF3/5fl_TAM_H2AK119ub1_rep3

tag: cell line

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: spike-in reference organism

value: Drosophila melanogaster

tag: spike-in cell line

tag: ChIP


title: Adult female hypoxia RNAseq 4

description:
adult_gene_fpkm.csv
FH7

value: Sprague Dawley


title: AM24161 Spo13-3Flag ChIP-seq WT IP


title: iPSC-derived interneurons_healthy control (B_L9a)

value: iPSC-derived interneurons


title: Adult female hypoxia RNAseq 3

description:
adult_gene_fpkm.csv
FH6

value: heart

value: 5 months old


title: Donor_9

tag: gender

tag: fmd

tag: imt

tag: pwv

tag: clinical response


title: AM25226 Rec8-3Ha ChIP-seq WT IP

value: Mouse monoclonal 12CA5 anti-HA (Roche)


title: Donor_5

value: female

tag: age


title: iPSC-derived interneurons_healthy control (B_L7a)

tag: cell type


title: Donor_4


title: Donor_7

value: cNR


title: iPSC-derived interneurons_healthy control (B_365a)


title: AM23948 Sgo1-6Ha ChIP-seq spo13Δ Input

description: Reads mapped to SK1 only

tag: strain background

tag: chip antibody


title: AM22605 Sgo1-6Ha ChIP-seq WT Input

description: Reads mapped to SK1 only

tag: genotype/variation


title: Adult female hypoxia RNAseq 2

description:
adult_gene_fpkm.csv
FH4

tag: strain

tag: tissue

tag: treatment

value: hypoxia


title: Donor_3

value: male

value: low

value: cR


title: Adult female normoxia RNAseq 5

description:
adult_gene_fpkm.csv
FC7

value: control


title: Adult female hypoxia RNAseq 1

description:
adult_gene_fpkm.csv
FH3


title: AM22605 Sgo1-6Ha ChIP-seq WT IP

value: wild type


title: Adult female normoxia RNAseq 4

description:
adult_gene_fpkm.csv
FC6


title: iPSC-derived interneurons_healthy control (B_317b)

tag: disease state

value: healthy control


title: iPSC-derived interneurons_healthy control (B_292b)


title: Adult female normoxia RNAseq 3

description:
adult_gene_fpkm.csv
FC5


title: Donor_2


title: iPSC-derived interneurons_healthy control (B_139a)


title: Donor_1

value: high


title: Donor_8


title: AM23948 Sgo1-6Ha ChIP-seq spo13Δ IP


title: iPSC-derived interneurons_healthy control (B_107b)


title: Adult female normoxia RNAseq 2

description:
adult_gene_fpkm.csv
FC4


title: iPSC-derived interneurons_healthy control (B_99b)


title: Adult female normoxia RNAseq 1

description:
adult_gene_fpkm.csv
FC3


title: LC2

city: Anyang

first: Mingge

last: Han

address: 38 Huanghe Avenue

country: China

institute: Institute of cotton research of CAAS,China

data_processing:
A cDNA library constructed by technology from the pooled RNA from brain samples of cotton was sequenced run with Illumina sequence platform.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .
we aligned reads of all samples to the UCSC (http://genome.ucsc.edu/) cotton reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.After the ﬁnal transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://mascotton.njau.edu.cn/info/1054/1118.htm
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: leaf

growth_protocol: Initially experiment was carried out on 86 different cotton varieties to check their germination response against several concentrations of Cd stress. Han 242, cotton cultivars (Gossypium hirsutum L.), provided by Cotton Research Institute of CAAS, showed the highest germination rate among all varieties under Cd stress.

extract_protocol:
Samples were removed, flash frozen on dry ice, 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

treatment_protocol: Seeds were washed thoroughly and sown in pots containing well washed, clean, and sterilized sand (121 °C for 8 h). Four seedlings in each pot were cultivated in a 28 ℃/14 h light and 25 ℃/10 h dark cycle with a light intensity 150 μmol m-2 s-1 and 75% relative humidity. After 35 days, cotton plants with three true leaves and one heart-shaped leaf were washed out carefully, and transferred into conical flasks containing 0.5、1、2、4、6、8 and 10 mM CdCl2 solution to observe various phenotypic changes in time series of 1、3、6、9、12、24 h. Then 4 mM CdCl2 over 9 h was chosen as the most appropriate treatment for further study. Seedlings transplanted into ddH2O were used as the controls. After exposure for 9 h, leaf, stem and whole root samples were collected. Sample from whole root hair, young stalks and antepenultimate leaves were collected with three replications for each treatment and control to measure the Cd content and the transcriptome analysis.

tag: time

value: 35 days

value: antepenultimate leaves


title: LC1


title: LT3

value: 4 mM CdCl2 treat 9 h


title: Fetal hypoxia RNAseq 3

description:
fetal_gene_fpkm.csv
H5-3

value: Sprague Dawley


title: LT2


title: iPSC-derived interneurons_schizophrenia (A_L10a)

value: iPSC-derived interneurons

value: schizophrenia


title: iPSC-derived interneurons_schizophrenia (A_L8a)


title: M Chol I vs WT Chol II [Msmeg]

description: polarity(-)

organism: Mycolicibacterium smegmatis

source_name: M Chol I

growth_protocol: M. smegmatis mc2155 was propagated in Middlebrook 7H9 broth supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson, MD, USA) , 0.2% glycerol, and 0.05% Tyloxapol at 37°C with agitation (100 rpm) or on Middlebrook 7H11 agar containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson).

value: KO mutant

value: Cholesterol

tag: replicate

value: biol. replicate 1

source_name: WT Chol II

value: wildtype

value: biol. replicate 2


title: Donor_6

value: female

value: low


title: LC3

value: control


title: WT Chol I vs M Chol II [Msmeg]

description: polarity(+)

source_name: WT Chol I

source_name: M Chol II


title: M Eth I vs WT Eth II [Msmeg]

description: polarity(-)

source_name: M Eth I

value: Ethanol

source_name: WT Eth II


title: LT1


title: Fetal hypoxia RNAseq 1

description:
fetal_gene_fpkm.csv
H3-1

source_name: Heart

value: heart

value: hypoxia


title: Fetal normoxia RNAseq 3

description:
fetal_gene_fpkm.csv
C3-6


title: iPSC-derived interneurons_schizophrenia (A_483b)

source_name: interneurons


title: M Gly I vs WT Gly II [Msmeg]

description: polarity(-)

source_name: M Gly I

value: Glycerol

source_name: WT Gly II


title: WT Gly I vs M Gly II [Msmeg]

description: polarity(+)

source_name: WT Gly I

source_name: M Gly II


title: SC3

source_name: stem

value: 35 days

value: young stalks


title: SC2


title: M Chol I vs M Gly II [Msmeg]

description: polarity(-)


title: M Gly I vs M Chol II [Msmeg]

description: polarity(+)


title: WT Eth I vs M Eth II [Msmeg]

description: polarity(+)

source_name: WT Eth I

source_name: M Eth II


title: iPSC-derived interneurons_schizophrenia (A_689b)


title: Fetal hypoxia RNAseq 2

description:
fetal_gene_fpkm.csv
H3-2

value: Sprague Dawley


title: iPSC-derived interneurons_schizophrenia (A_755a)

value: iPSC-derived interneurons


title: ST3

value: 4 mM CdCl2 treat 9 h


title: iPSC-derived interneurons_schizophrenia (A_282a)

value: schizophrenia


title: iPSC-derived interneurons_schizophrenia (A_117b)


title: RC3

source_name: root

value: whole root hair


title: ST2


title: Fetal normoxia RNAseq 1

description:
fetal_gene_fpkm.csv
C1-6


title: M Gly I vs M Eth II [Msmeg]

description: polarity(+)

value: KO mutant

value: biol. replicate 1


title: ST1


title: iPSC-derived interneurons_schizophrenia (A_58a)


title: WT Gly I vs WT Chol II [Msmeg]

description: polarity(+)

value: wildtype

value: Cholesterol

value: biol. replicate 2


title: COF3

city: Rennes

first: Thomas

last: Enriquez

state: Bretagne

address: 263 av. du Général Leclerc

country: France

institute: Université de Rennes1

data_processing:
All bioinformatics analyses were performed using Galaxy (https://usegalaxy.genouest.org).
Raw data were trimmed using Trimmomatic (version 0.36)
Reads were then mapped to D. suzukii reference genome using Bowtie2 based Tophat (versions: 2.2.8 and 2.1.1, respectively) (reference genome: Chiu et al. 2013; doi: 10.1534/g3.113.008185)
Reads were assembled thanks to Cufflinks (version 2.2.1)
Differential expression of transcripts was computed using Cuffdiff (version 2.2.1)
Genome_build: Version 1.0
Supplementary_files_format_and_content: tab-delimited text files including P.values and fold changes

organism: Drosophila suzukii

source_name: whole body

extract_protocol:
RNA extractions were performed using a Nucleospin Kit (Macherey Nagel, Düren, Germany) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: Stage

value: adult

value: control (2 degrees C)


title: RC2

value: control


title: Fetal normoxia RNAseq 2

description:
fetal_gene_fpkm.csv
C2-11

value: heart


title: WT Eth I vs WT Gly II [Msmeg]

description: polarity(-)

value: Ethanol

value: Glycerol


title: ovary_NR rep2

city: Chengdu

first: jinshan

last: ran

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agriculture University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
HISAT2 was used to perform a comparative analysis of the reference genome for the filtered reads and transcription splicing
Quantitative analysis of mRNA transcripts using StringTie-eB software, FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA13342
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anser cygnoides

growth_protocol: All experiment animals were raised in Xingguo Grey Goose Research Base (annual average temperature is 18.9 °C, 115°35'E, 26°33’N) and were kept in a light-shelter room and exposed to an artificial short lighting program (11L: 13D) with ad libitum access to feed and water

extract_protocol:
Fresh ovary tissues were frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All geese were raised until 40 weeks old  and the broodiness group geese were treated with forced moulting method and short illumination

value: ovary

tag: developmental stage

value: broodiness


title: ovary_NR rep1


title: iPSC-derived interneurons_schizophrenia (A_285b)

value: iPSC-derived interneurons


title: ovary_NR rep3


title: SC1

value: 35 days

value: young stalks


title: WT Gly I vs WT Eth II [Msmeg]

description: polarity(+)


title: ovary_R rep3

value: reproduction


title: RT3

value: 4 mM CdCl2 treat 9 h

value: whole root hair


title: CAF3

value: cold acclimated (9 days at degrees C)


title: RTI


title: CAF2

value: cold acclimated (9 days at 10 degrees C)


title: COF1

value: whole body

value: control (25 degrees C)


title: ovary_R rep1


title: WT Chol I vs WT Gly II [Msmeg]

description: polarity(-)

value: wildtype

value: Cholesterol

value: biol. replicate 1

value: biol. replicate 2


title: CAF1

value: adult


title: COF2


title: RC1

value: control


title: RT2


title: BMDMs_WD control_replicate_1

status: Public on Apr 24 2019

city: Aachen

first: Oliver

last: Krenkel

address: Pauwels Str. 30

institute: University Hospital Aachen

data_processing:
Basecalling was performed with a pipeline, using HiSeq Control Software 2.2.58, RTA 1.18.64.0 and CASAVA-1.8.2
After quality assessment of the corresponding FASTQ files with FastQC v0.11.5 (1), adaptor sequences were trimmed from the reads.
Additionally, 10 bases were trimmed from the 5-prime end and 5 bases from the 3-prime end of each read.
Trimmed reads shorter than 50 nucleotides were discarded.
Low-quality sequences (Phred quality score < 30) were also removed.
These quality enhancement steps were performed using TrimGalore v0.4.1 (2).
The reads were subsequently aligned to the mm10 reference genome sequence using HISAT2 v2.0.5 (3) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

source_name: BMDMs_WD control

growth_protocol:
total bone marrow was isolated from donors that received standard chow or Western diet (high-fat, high-sugar, high-cholesterol) for 24 weeks.
isolated cells were seeded in RPMI-1640 + 10 % FCS + 1 % P/S + 30 % L929 cell culture supernatant

extract_protocol:
cells were lysed by adding 1 ml PeqGold (VWR, Germany) directly onto the dish, followed by Phenol-Chloroform extraction as detailed by the manufacturer
cDNA

treatment_protocol:
cells from standard chow diet fed mice were pretreated for the first 4 days with and without 10 mM fatty acid (palmitic and oleic acid 1:3) and with and without 200 nM TAK242,
followed by washing with PBS three times and culturing until day 7, were the cells were then stimulated with 100 ng/ml LPS from E.coli for 24h

tag: age of donors

value: 24 weeks

value: WD control

value: bone marrow derived macrophages


title: BMDMs_WD control_replicate_2


title: BMDMs_WD + LPS_replicate_3

source_name: BMDMs_WD + LPS

value: WD + LPS


title: BMDMs_ND - FA pretreatment /w TAK242 +  LPS_replicate_3

value: ND - FA pretreatment /w TAK242 +  LPS


title: BMDMs_WD + LPS_replicate_1


title: BMDMs_ND - FA pretreatment /w TAK242 +  LPS_replicate_1


title: BMDMs_WD control_replicate_3


title: BMDMs_ND + LPS_replicate_1

source_name: BMDMs_ND + LPS

value: ND + LPS


title: BMDMs_ND - FA pretreatment /wo TAK242 +  LPS_replicate_2

value: ND - FA pretreatment /wo TAK242 +  LPS


title: BMDMs_ND + LPS_replicate_2


title: BMDMs_ND + LPS_replicate_3


title: BMDMs_ND - FA pretreatment /wo TAK242 +  LPS_replicate_1


title: BMDMs_ND control_replicate_4

source_name: BMDMs_ND control

value: ND control


title: BMDMs_ND control_replicate_3


title: BMDMs_ND control_replicate_1


title: BMDMs_ND - FA pretreatment /w TAK242 +  LPS_replicate_2


title: BMDMs_WD + LPS_replicate_2


title: BMDMs_ND control_replicate_5


title: BMDMs_ND control_replicate_6


title: ChIP_seq_TOP2B_MEF_WAPL_FF_CRE

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Mouse embryonic fibroblasts

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen). MEFS were cultured and floxed alleles deleted as described (Busslinger et al., 2017). HCT116 cells were obtained from (Natsume et al., 2016), arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours.

extract_protocol:
Twenty million preB cells and HCT166, and four million MEFS were used for ChIP-seq.
Cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 2 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using the Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or using the Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. Ten microgram of respective antibody was incubated with 40 μl of Dynabeads Protein A for 15 min at room temperature. Antibody-bound beads were added to 1 ml of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo).The entire ChIP DNA was used to prepare Illumina sequencing libraries. End-repair was performed in 75 ul of T4 ligase reaction buffer, 0.4 mM of dNTPs, 4 U of T4 DNA polymerase (NEB), 13.5 U of T4 Polynucleotide Kinase (NEB) and 1.5 U of Klenow fragment (NEB) at 24ºC for 30 min in a ThermoMixer C at 400 rpm. End-repair reaction was cleaned using 2X Agencourt AMPure XP beads and eluted in 15 ul of EB that was used for A-tailing reaction in 30 ul of NEBNext dA-Tailing reaction buffer (NEB) with 7.5 U of Klenow fragment exo- (NEB) at 37ºC for 30 min. The 30 ul of the A-tailing reaction were mixed with Quick Ligase buffer 2X (NEB), 3,000 U of Quick ligase and 5 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 75 ul and incubated at 25C for 20 min. Adaptor was prepared by annealing the following HPLC oligos: 50-Phos/GATCGGAAGAGCACACGTCT-30and 50-ACACTCTTTCCCTACACGACGCT CTTCCGATC*T-30 (*phosphorothioate bond). Ligation was stopped by adding 50mM of EDTA and cleaned with 1.8X Agencourt AM- Pure XP beads and eluted in 15ul of EB that was used for PCR amplification in a 50 uL reaction with 10 uM primers TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T, TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98C followed by 15 cycles of 15 s at 98ºC, 30 s at 63ºC, 30 s at 72ºC and a final 5 min extension at 72ºC . PCR reactions were cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a smear of 200-500bp was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina Nextseq500 (75bp single end reads). Antibodies for ChiP-seq were: anti-Rad21 (ab992, Abcam), anti-CTCF (07-729, Millipore) and Topo IIb Antibody (H-286) (sc13059, SantaCruz).

treatment_protocol: Pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hr. MEFs, after 10 days in confluence and serum starvation (2% charcoaltreated FBS). HCT116 cells were arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours.

tag: genotype

value: Wapl f/f+cre

value: Mouse embryonic fibroblasts

value: Topo IIβ

value: rabbit polyclonal

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: ChIP_seq_CTCF_PB_LIG4

source_name: Abelson-transformed pre-B cell

value: Abelson-transformed pre-B cell

value: Anti-CTCF

value: Millipore


title: ChIP_seq_RAD21_PB_LIG4

value: Abcam


title: ChIP_seq_RAD21_HCT116

tag: cell line

value: WT


title: END_seq_aB_WT_0_5h_rep2

description: control: GSM2635561 END_seq_aB12h_NT.fastq.gz re-used

data_processing:
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -k1 -l 50
END-seq peaks were called using MACS 1.4.3  with the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
END-seq data from pre-B cells, where cells with ZFN break were spiked-in to the library at a 1:50 (2%) ratio, the RPKM value for each peak was divided by the signal around the spiked-in breaks and then multiplied by 2, to get values as cell-percentage. From this value, X, the #cells per lesion were calculated as 100/X.
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Activated primary B cells

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen). MEFS were cultured and floxed alleles deleted as described (Busslinger et al., 2017). Mature WT and  Top2b-/- B-cells were generated by bone marrow reconstitution of lethally irradiated recipient mice with fetal liver cells derived from WT and Top2b-/- embryos, respectively. Recipient mice were irradiated with 950 rads, 4 hours before injection of 3 million donor fetal liver cells. Between 6 to 12 weeks after reconstitution mature resting B cells were isolated from recipient mouse spleen with anti-CD43 MicroBeads (Miltenyi Biotech). B cells were activated with LPS (25 mg/ml; Sigma), IL-4 (5 ng/ml; Sigma) and RP105 (0.5 mg/ml; BD) for 12 hr as described (Callen et al., 2013) and treated for 30 minutes with 50uM of etoposide.HCT116 cells were obtained from (Natsume et al., 2016), arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours before 50uM etoposide treatment for 30 minutes.

extract_protocol:
Single cell suspensions of pre-B cells (40 million per agarose plug),  MEFS (4 million per agarose plug), and HCT116 (15 million per 2 agarose plugs) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016)
END-seq was performed as described in Canela et al., 2017. Agarose plugs were made using the Bio-Rad CHEF Mammalian Genomic DNA plug kit. Embedded cells were lysed and digested using Proteinase K (50º C, 1 hour then  37ºC for 7 hours). Plugs were rinsed in TE buffer and treated with RNase A at 37ºC, 1 hour. The next enzymatic reactions were performed with the DNA in agarose plugs to prevent shearing. DNA ends were blunted for 1 hour at 37C with Exonuclease VII followed by Exonuclease T (NEB) for 1 hour at 25ºC to detect all TOP2 lesions, or only with Exonuclease T (NEB) 1 hour at 25C to detect only DSBs, "ExoT END-seq". After blunting, A-tailing was performed, followed by ligation of “END-seq hairpin adaptor 1”, 5′-Phos-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase.  Agarose plugs were then melted and dialyzed and DNA was sonicated to a median shear length of 170bp using Covaris S220 sonicator. DNA was ethanol-precipitated and dissolved in 70 ul TE buffer. Biotinylated DNA was isolated using MyOne Streptavidin C1 Beads (ThermoFisher #650-01), followed by end repair and dA-tailing. The second end was ligated to “END-seq hairpin adaptor 2”, 5′-Phos-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase. Hairpins were digested using USER (NEB), and the resulting DNA fragments were PCR amplified using TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T and TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond).  PCR fragments were isolated by size selection from agarose gel, selecting 200-500 bp fragments followed by DNA purification using QIAquick Gel Extraction Kit. Libraries were quantified using KAPA Library Quantification Kit and sequenced using Illumina NextSeq 500 or 550.

treatment_protocol: Pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hr and then treated with etoposide for the times indicated. MEFs, after 10 days in confluence and serum starvation (2% charcoaltreated FBS) were treated with 50uM of etoposide during 30 minutes and 2 hours and 30 minutes. HCT116 cells were arrested in G1 by the treatment with 20uM of lovastatin for 24 hours and treated with auxin for 4 hours before 50uM etoposide treatment for 30 minutes. For transcription inhibition or stimulation, and proteasome inhibition drug pre-treatment was performed for 2 hours with 150 mM DRB (D-ribofuranosylbenzimidazole, Sigma) or 2uM of epoxomicin (Sigma) prior to etoposide treatment. Drugs were maintained during the treatment with etoposide.

tag: cell type

value: Reconsituted B-cells


title: nsRNA_seq_PB_IFNB

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -m1 -l 50
Peaks were called using the parameters: --nolambda,-- nomodel.
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen).

extract_protocol:
5 million preB cells were used for Nascent RNA sequencing
Nascent RNA sequencing was performed as previously described (Canela et al., 2017). Cells were washed 3 times in cold media and cultured back for new media, then 5 million cells were labeled with 0.5 mM 5-ethynyl uridine (EU) during 30 min keeping the transcriptional drugs in the media. Total RNA extraction was performed using TRIzol (Invitrogen) and 2 ug was rRNA depleted using the NEBNext rRNA Depletion kit (human/mouse/rat) (New England Biosciences). rRNA-depleted RNA was used for biotinylation via the Click-IT reaction (Click-iT Nascent RNA Capture Kit, ThermoFisher C10365) using manufacturer’s speciﬁcation. First-strand cDNA synthesis of the captured nascent RNA was done using SuperScript VILO cDNA synthesis kit (Invitrogen), followed by purification with 1.8X volume of AMPure XP beads (1.8X) and elution in 20 uL. Second-strand synthesis was performed using 0.6 mM dATP, 0.6 mM dCTP, 0.6 mM dGTP, and 1.2 mM dUTP in the presence of 2 Units of RNase H (Invitrogen) and 20 Units of E. coli DNA polymerase I (Invitrogen) in a total volume of 30 uL for 2.5 hours at 16º C. cDNA was purified using 1.8X volume AMPure XP beads and eluted in 20 uL of EB. Sequencing libraries were then prepared. End-repair was performed in 50 uL of T4 ligase reaction buffer (1X), dNTPs (0.4 nM), T4 DNA polymerase (NEB, 3 Units), T4 Polynucleotide Kinase (NEB, 9 Units) and Klenow fragment (NEB, 1 Unit) at 24ºC for 30 min in a ThermoMixer at 400 rpm. End-repair reaction was cleaned using 1.8X volume AMPure XP beads and eluted in 15 uL of EB. A-tailing was performed using NEBNext dA-Tailing reaction buffer (NEB, 1X) with Klenow fragment exo- (NEB, 7.5 U) at 37º C for 30 min. A-tailing reaction was mixed with Quick Ligase Buffer (NEB), Quick ligase (NEB, 3000 Units) and 5 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 75 uL and incubated at 25ºC for 20 min. The adaptor was prepared by annealing the following HPLC oligos: 5’-Phos/GATCGGAAGAGCACACGTCT-3’ and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’ (*phosphoro-thioate bond). Ligation reaction was stopped by adding 50 mM of EDTA, then DNA was purified with 1.8X volume AMPure XP beads and eluted in 15 ul of EB. 0.5 Units of Uracil-DNA glycosylase (Thermoﬁsher) was added for 15 min at 37º C. PCR ampliﬁcation was performed in 50 uL reaction with 10 mM primers TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T, TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). PCR program: 98º C, 45 s; 15 cycles [98º C, 15 s; 63º C, 30 s; 72 º C, 30 s]; 72º C, 5 min. PCR reactions were cleaned with AMPure XP beads, and 200-500 bp fragments were isolated after running on 2% agarose gel. Libraries were purified using QIA-quick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantiﬁcation Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed using Illumina Nextseq 500 (75bp single end reads).

treatment_protocol: pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hours and then pre-treated or not with drugs affecting transcription and treated with etoposide for 2.5 hours or untreated. For transcription inhibition or stimulation, drug pre-treatment was performed for 2 hours with 150 mM DRB (D-ribofuranosylbenzimidazole, Sigma) or 100 U/mL mouse interferon beta (PBL) prior to etoposide treatment or induction of AsiSI (24 hours pretreatment with doxocycline (1 μg/ml) and the last 4 hours with tamoxifen (1uM)). Drugs were maintained during the treatment with etoposide or induction of AsiSI.


title: ChIP_seq_RAD21_MEF_WAPL_FF_CRE

tag: strain background


title: nsRNA_seq_PB_DRB


title: END_seq_MEF_NT (re-used)

description: This is duplicated sample record of GSM2635571 for the convenient retrieval of the complete raw data from SRA


title: ChIP_seq_TOP2B_MEF_SMC3

value: Smc3 f/f

tag: chip antibody


title: END_seq_aB12h_NT (re-used)

description: This is duplicated sample record of GSM2635561 for the convenient retrieval of the complete raw data from SRA


title: ChIP_seq_RAD21_MEF_WAPL_FF

value: Wapl f/f


title: ChIP_seq_INPUT_HCT116


title: ChIP_seq_RAD21_MEF_WT


title: ChIP_seq_CTCF_HCT116


title: nsRNA_seq_PB_NT


title: END_seq_aB_WT_0_5h_rep1


title: BMDMs_ND - FA pretreatment /wo TAK242 +  LPS_replicate_3

value: 24 weeks

value: bone marrow derived macrophages


title: END_seq_MEF_Wapl_FF_0_5h (control)

description: control: GSM2635571 END_seq_MEF_NT.fastq.gz re-used

value: Waplf/f


title: END_seq_MEF_Wapl_FF_CRE_0_5h

description: control: END_seq_MEF_Wapl_FF_0_5h.fastq.gz

value: Waplf/f+CRE


title: ChIP_seq_RAD21_MEF_SMC3


title: END_seq_MEF_Smc3_FF_0_5h


title: END_seq_aB_TOP2Bko_0_5h_rep1


title: ovary_R rep2

value: ovary

value: reproduction


title: END_seq_MEF_Smc3_PP_0_5h

value: Mouse embryonic fibroblasts


title: END_seq_ExoT_PB_LIG4_WASH_0_5h_REVERSIBILITY

description: control: END_seq_ExoT_PB_LIG4_NT.fastq.gz


title: END_seq_aB_TOP2Bko_0_5h_rep2


title: END_seq_PB_LIG4_EPOX_WASH_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_WASH_0_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_ExoT_PB_LIG4_EPOX_WASH_2_5h_REVERSIBILITY


title: END_seq_PB_LIG4_TDP2_WASH_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_ExoT_PB_LIG4_TDP2_WASH_2_5h_REVERSIBILITY


title: END_seq_ExoT_PB_LIG4_EPOX_2_5h_REVERSIBILITY


title: END_seq_ExoT_PB_LIG4_2_5h_REVERSIBILITY


title: END_seq_ExoT_PB_LIG4_NT (control)

description: control: N/A


title: END_seq_PB_LIG4_EPOX_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_TDP2_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_ExoT_PB_LIG4_WASH_2_5h_REVERSIBILITY


title: END_seq_ExoT_PB_LIG4_TDP2_2_5h_REVERSIBILITY


title: END_seq_ExoT_PB_LIG4_2_5h_TIME_COURSE


title: END_seq_ExoT_PB_LIG4_7_5h_TIME_COURSE


title: END_seq_ExoT_PB_LIG4_12_5h_TIME_COURSE


title: END_seq_PB_LIG4_WASH_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_12_5h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_ExoT_PB_LIG4_0_5h_TIME_COURSE


title: ChIP_seq_TOP2B_MEF_WT

value: Topo IIβ

value: rabbit polyclonal


title: END_seq_PB_LIG4_7_5h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz

value: Abelson-transformed pre-B cell


title: END_seq_PB_LIG4_NT (control)

description: control: N/A


title: END_seq_PB_LIG4_2_5h_REVERSIBILITY

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_5h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_2_5h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_1h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_0_5h_TIME_COURSE

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_ExoT_PB_LIG4_1h_TIME_COURSE


title: END_seq_ExoT_PB_LIG4_5h_TIME_COURSE


title: END_seq_PB_LIG4_2_5h_IFNB_TRX


title: END_seq_PB_LIG4_AsiSI_DRB_TRX

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_2_5h_DRB_TRX

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_AsiSI_TRANSLOCATION

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: END_seq_PB_LIG4_2_5h_TRANSLOCATION

description: control: END_seq_PB_LIG4_NT.fastq.gz


title: BMDMs_ND control_replicate_2

value: ND control


title: 309-mut

city: Dallas

first: Emily

middle: Nicole

last: Arner

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

data_processing: The data were normalised using quantile normalisation by UT Southwestern Microarray Core.

label: Not provided

source_name: KIC pancreatic tumor

label_protocol: Not provided.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: KIC

tag: genotype/variation

value: TBK1 mutant

tag: age

value: 8 weeks

value: Pancreatic tumor


title: 329-mut

description: Replicate 1

scan_protocol: Standard Illumina hybridization protocol.

tag: strain

tag: tissue


title: 317-mut

description: Replicate 2


title: wt_6hAPF_RNAseq_Rep1

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

state: NY

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

data_processing:
RNASeq - sequenced reads were aligned to the genome using STAR (v2.5.2b) using parameters --alignIntronMax 50000 --alignMatesGapMax 50000.
RNASeq - The bam file was indexed and sorted using samtools (v1.3.1)
RNASeq - Subread (v1.24.2) was used to count reads mapping to genes (dm3 annotation)
RNASeq - Differentially expressed genes were identified using DESeq2 (v1.14.1), using the lfcShrink function to shrink log-fold changes
RNASeq - Normalized counts were generated using DESeq2 (v1.14.1)
processed data files format and content: comma delimited table that contains DESeq2 results for each comparison for each gene
processed data files format and content: comma delimited table that contains normalized counts for all genes in each sample
Genome_build: dm3

organism: Drosophila melanogaster

source_name: +6hAPF wings

growth_protocol: Animals were raised at 25C. For the -6hAPF time point, wandering (3LW) larvae were used. For the +6hAPF time point, animals were staged at the white, pre-pupae stage.

extract_protocol: Wings were individually dissected in 1XPBS  and then transferred to a 9-well dissecting dish on ice.

value: wing

value: wildtype

tag: cut&run antibody

tag: Sex

value: female

tag: library construction

value: Nugen Ovation RNA-seq System 1-16 for Model Organisms


title: wt_3LW_RNAseq_Rep2

source_name: -6hAPF wings


title: EcR-RNAi_6hAPF_RNAseq_Rep2

value: yw/yw; Vg-GAL4, UAS-Flp, Tub>>CD2>>GAL4; UAS-GFP / UAS-EcR-RNAi[104]

value: EcR-RNAi


title: wt_6hAPF_RNAseq_Rep2


title: 307-wt

description: Replicate 2

value: TBK1 WT


title: EcR-RNAi_6hAPF_RNAseq_Rep1


title: 290-wt

description: Replicate 1


title: EcR-RNAi_3LW_RNAseq_Rep1


title: 10-90_CAF-24

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

description: cntCAF.csv

data_processing:
The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode against the Homo_sapiens.GRCh38.79.gtf annotation table from http://www.ensembl.org.
Genome_build: hg38
Supplementary_files_format_and_content: The raw read counts described above are available in two tables, one for the PDAC samples (cntPdac.csv) and one for the CAF samples (cntCAF.csv).

molecule: polyA RNA

source_name: immortalized primary pancreatic cancer-associated fibroblast cell line

growth_protocol: PDAC cells and CAFs were seeded in 6-well plates in 5 different ratios: 100% PDAC, 50:50 PDAC:CAF, 30:70 PDAC:CAF, 10:90 PDAC:CAF, and 100% CAF. DMEM (high glucose, pyruvate) with 10% fetal bovine serum (FBS) and 100 U/mL Penicillin and 100 mg/mL Streptomycin was used for all cultures.

extract_protocol:
After 72 hours of culture, cells were trypsinized and resuspended in PBS solution, and micromanipulated. PDAC cells or CAFs were then individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK2 micromanipulator, transferred into PCR tubes containing RNA protective lysis buffer (Clontech Laboratories), and flash frozen in liquid nitrogen.
Amplified cDNA was synthesized from the entire cell lysate using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 kit (Clontech Laboratories). PCR amplification following second strand synthesis was run for 18 cycles. 1 ng of amplified cDNA was loaded into the Nextera XT kit. Normalization was done using the KAPA SYBR® FAST Universal qPCR Kit (Kapa Biosystems) rather than the bead-based normalization in the Nextera XT kit.

value: 100 CAF cells

tag: culture condition

value: 10:90 PDAC:CAF


title: 10-90_CAF-23

description: cntCAF.csv

value: single CAF cell


title: wt_3LW_RNAseq_Rep1

tag: developmental stage


title: 346-wt

description: Replicate 3


title: 10-90_CAF-22

description: cntCAF.csv


title: EcR-RNAi_3LW_RNAseq_Rep2


title: 10-90_CAF-18

description: cntCAF.csv


title: 10-90_CAF-17

description: cntCAF.csv


title: 10-90_CAF-19

description: cntCAF.csv


title: 10-90_CAF-21

description: cntCAF.csv


title: 10-90_CAF-14

description: cntCAF.csv


title: END_seq_ExoT_PB_LIG4_2_5h_DRB_TRX


title: 10-90_CAF-16

description: cntCAF.csv


title: 10-90_CAF-15

description: cntCAF.csv


title: 10-90_CAF-12

description: cntCAF.csv


title: 10-90_CAF-13

description: cntCAF.csv


title: 10-90_CAF-11

description: cntCAF.csv


title: 10-90_CAF-10

description: cntCAF.csv


title: 10-90_CAF-9

description: cntCAF.csv


title: 10-90_CAF-8

description: cntCAF.csv


title: 10-90_CAF-6

description: cntCAF.csv


title: 10-90_CAF-4

description: cntCAF.csv


title: 10-90_CAF-3

description: cntCAF.csv


title: 10-90_CAF-5

description: cntCAF.csv


title: 10-90_CAF-7

description: cntCAF.csv


title: 10-90_CAF-1

description: cntCAF.csv


title: 10-90_CAF-2

description: cntCAF.csv


title: 30-70_CAF-24

description: cntCAF.csv

value: 30:70 PDAC:CAF


title: 30-70_CAF-23

description: cntCAF.csv


title: 30-70_CAF-22

description: cntCAF.csv


title: M Eth I vs M Gly II [Msmeg]

description: polarity(-)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

source_name: M Eth I

value: KO mutant

tag: treatment

value: Ethanol

tag: replicate

value: biol. replicate 1

source_name: M Gly II

value: Glycerol

value: biol. replicate 2


title: 30-70_CAF-19

description: cntCAF.csv


title: 30-70_CAF-15

description: cntCAF.csv


title: 30-70_CAF-17

description: cntCAF.csv


title: 30-70_CAF-18

description: cntCAF.csv


title: 30-70_CAF-21

description: cntCAF.csv


title: 30-70_CAF-20

description: cntCAF.csv


title: END_seq_ExoT_PB_LIG4_2_5h_IFNB_TRX

tag: genotype

value: Abelson-transformed pre-B cell


title: 30-70_CAF-9

description: cntCAF.csv


title: 30-70_CAF-11

description: cntCAF.csv


title: 30-70_CAF-13

description: cntCAF.csv


title: 30-70_CAF-16

description: cntCAF.csv


title: 30-70_CAF-14

description: cntCAF.csv


title: 30-70_CAF-10

description: cntCAF.csv


title: 30-70_CAF-12

description: cntCAF.csv


title: 30-70_CAF-7

description: cntCAF.csv


title: 50-50_CAF-21

description: cntCAF.csv

value: 50:50 PDAC:CAF


title: 50-50_CAF-22

description: cntCAF.csv


title: 30-70_CAF-5

description: cntCAF.csv


title: 30-70_CAF-8

description: cntCAF.csv


title: 30-70_CAF-4

description: cntCAF.csv


title: 30-70_CAF-2

description: cntCAF.csv


title: 50-50_CAF-17

description: cntCAF.csv


title: 50-50_CAF-18

description: cntCAF.csv


title: 50-50_CAF-16

description: cntCAF.csv


title: 30-70_CAF-1

description: cntCAF.csv


title: 50-50_CAF-14

description: cntCAF.csv


title: 50-50_CAF-15

description: cntCAF.csv


title: 50-50_CAF-11

description: cntCAF.csv


title: 50-50_CAF-24

description: cntCAF.csv


title: 10-90_CAF-20

description: cntCAF.csv


title: 50-50_CAF-23

description: cntCAF.csv


title: 50-50_CAF-13

description: cntCAF.csv


title: 50-50_CAF-19

description: cntCAF.csv


title: 50-50_CAF-5

description: cntCAF.csv


title: 50-50_CAF-6

description: cntCAF.csv


title: 50-50_CAF-4

description: cntCAF.csv


title: 30-70_CAF-6

description: cntCAF.csv


title: 50-50_CAF-12

description: cntCAF.csv


title: 30-70_CAF-3

description: cntCAF.csv


title: 50-50_CAF-10

description: cntCAF.csv


title: 50-50_CAF-7

description: cntCAF.csv


title: 50-50_CAF-3

description: cntCAF.csv


title: 50-50_CAF-9

description: cntCAF.csv


title: 100_CAF-24

description: cntCAF.csv


title: 100_CAF-23

description: cntCAF.csv


title: 50-50_CAF-1

description: cntCAF.csv


title: 100_CAF-9

description: cntCAF.csv


title: 100_CAF-22

description: cntCAF.csv


title: 100_CAF-14

description: cntCAF.csv


title: 100_CAF-20

description: cntCAF.csv


title: 100_CAF-18

description: cntCAF.csv


title: 100_CAF-8

description: cntCAF.csv


title: 100_CAF-6

description: cntCAF.csv


title: 100_CAF-5

description: cntCAF.csv


title: 100_CAF-21

description: cntCAF.csv


title: 100_CAF-7

description: cntCAF.csv


title: 100_CAF-19

description: cntCAF.csv


title: 100_CAF-1

description: cntCAF.csv


title: 50-50_CAF-2

description: cntCAF.csv


title: 100_CAF-17

description: cntCAF.csv


title: 100_CAF-10

description: cntCAF.csv


title: 100_CAF-16

description: cntCAF.csv


title: 100_CAF-13

description: cntCAF.csv


title: 100_CAF-11

description: cntCAF.csv


title: 100_CAF-15

description: cntCAF.csv


title: 10-90_PDAC3-24

description: cntPdac.csv

source_name: primary pancreatic ductal adenocarcinoma cell line

value: 100 PDAC cells


title: 100_CAF-3

description: cntCAF.csv


title: 100_CAF-4

description: cntCAF.csv


title: 100_CAF-2

description: cntCAF.csv


title: 10-90_PDAC3-22

description: cntPdac.csv

value: single PDAC cell


title: 10-90_PDAC3-21

description: cntPdac.csv


title: 10-90_PDAC3-9

description: cntPdac.csv


title: 10-90_PDAC3-14

description: cntPdac.csv


title: 10-90_PDAC3-11

description: cntPdac.csv


title: 10-90_PDAC3-8

description: cntPdac.csv


title: 10-90_PDAC3-20

description: cntPdac.csv


title: 10-90_PDAC3-23

description: cntPdac.csv


title: 10-90_PDAC3-6

description: cntPdac.csv


title: 10-90_PDAC3-18

description: cntPdac.csv


title: 10-90_PDAC3-17

description: cntPdac.csv


title: 10-90_PDAC3-3

description: cntPdac.csv


title: 30-70_PDAC3-20

description: cntPdac.csv


title: 10-90_PDAC3-4

description: cntPdac.csv


title: 10-90_PDAC3-16

description: cntPdac.csv


title: 10-90_PDAC3-13

description: cntPdac.csv


title: 10-90_PDAC3-15

description: cntPdac.csv


title: 10-90_PDAC3-12

description: cntPdac.csv


title: 30-70_PDAC3-14

description: cntPdac.csv


title: 30-70_PDAC3-16

description: cntPdac.csv


title: 30-70_PDAC3-15

description: cntPdac.csv


title: 30-70_PDAC3-11

description: cntPdac.csv


title: 10-90_PDAC3-10

description: cntPdac.csv


title: 10-90_PDAC3-7

description: cntPdac.csv


title: 10-90_PDAC3-5

description: cntPdac.csv


title: 10-90_PDAC3-2

description: cntPdac.csv


title: 10-90_PDAC3-1

description: cntPdac.csv


title: 30-70_PDAC3-21

description: cntPdac.csv


title: 50-50_CAF-8

description: cntCAF.csv


title: 30-70_PDAC3-3

description: cntPdac.csv


title: 50-50_CAF-20

description: cntCAF.csv


title: 30-70_PDAC3-19

description: cntPdac.csv


title: 30-70_PDAC3-1

description: cntPdac.csv


title: 50-50_PDAC3-23

description: cntPdac.csv


title: 50-50_PDAC3-22

description: cntPdac.csv


title: 10-90_PDAC3-19

description: cntPdac.csv


title: 100_CAF-12

description: cntCAF.csv


title: 50-50_PDAC3-20

description: cntPdac.csv


title: 50-50_PDAC3-19

description: cntPdac.csv


title: 30-70_PDAC3-12

description: cntPdac.csv


title: 30-70_PDAC3-13

description: cntPdac.csv


title: 30-70_PDAC3-17

description: cntPdac.csv


title: 50-50_PDAC3-17

description: cntPdac.csv


title: 50-50_PDAC3-18

description: cntPdac.csv


title: 30-70_PDAC3-10

description: cntPdac.csv


title: 50-50_PDAC3-11

description: cntPdac.csv


title: 50-50_PDAC3-13

description: cntPdac.csv


title: 30-70_PDAC3-8

description: cntPdac.csv


title: 50-50_PDAC3-10

description: cntPdac.csv


title: 50-50_PDAC3-15

description: cntPdac.csv


title: 30-70_PDAC3-7

description: cntPdac.csv


title: 30-70_PDAC3-5

description: cntPdac.csv


title: 50-50_PDAC3-7

description: cntPdac.csv


title: 50-50_PDAC3-8

description: cntPdac.csv


title: 30-70_PDAC3-4

description: cntPdac.csv


title: 50-50_PDAC3-6

description: cntPdac.csv


title: 30-70_PDAC3-2

description: cntPdac.csv


title: 30-70_PDAC3-18

description: cntPdac.csv


title: 50-50_PDAC3-5

description: cntPdac.csv


title: 50-50_PDAC3-24

description: cntPdac.csv


title: 50-50_PDAC3-3

description: cntPdac.csv


title: 50-50_PDAC3-1

description: cntPdac.csv


title: 50-50_PDAC3-4

description: cntPdac.csv


title: 100_PDAC3-23

description: cntPdac.csv

value: 100% PDAC


title: 50-50_PDAC3-21

description: cntPdac.csv


title: 100_PDAC3-24

description: cntPdac.csv


title: 30-70_PDAC3-9

description: cntPdac.csv


title: 30-70_PDAC3-6

description: cntPdac.csv


title: 100_PDAC3-21

description: cntPdac.csv


title: 50-50_PDAC3-16

description: cntPdac.csv


title: 50-50_PDAC3-12

description: cntPdac.csv


title: 50-50_PDAC3-9

description: cntPdac.csv


title: 50-50_PDAC3-14

description: cntPdac.csv


title: 100_PDAC3-18

description: cntPdac.csv


title: 100_PDAC3-11

description: cntPdac.csv


title: 50-50_PDAC3-2

description: cntPdac.csv


title: 100_PDAC3-7

description: cntPdac.csv


title: 100_PDAC3-22

description: cntPdac.csv


title: 100_PDAC3-15

description: cntPdac.csv


title: 100_PDAC3-20

description: cntPdac.csv


title: 100_PDAC3-6

description: cntPdac.csv


title: 100_PDAC3-19

description: cntPdac.csv


title: HK-2 ATAC-seq shPBRM1 replicate 1

city: Bethesda

first: Benjamin

last: Carter

state: MD

address: 10 Center Drive

department: NHLBI

institute: National Institutes of Health

description:
ATAC_HK2_inc_HOMER.txt
ATAC_HK2_dec_HOMER.txt

data_processing:
RNA-seq reads were trimmed using Trimmomatic and aligned to the appropriate reference genome using STAR with the following parameters: readFilesCommand zcat outFilterType BySJout outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterIntronMotifs RemoveNoncanonical. ATAC-seq reads were trimmed using Trimmomatic and mapped to the appropriate reference genome using Bowtie2 in very sensitive end-to-end mode.
For RNA-seq, gene expression levels were computed using htseq-count using default parameters. For ATAC-seq, BAM files were converted to BED files using BEDtools.
For RNA-seq, differential expression analysis was performed with DESeq2 using default parameters. For ATAC-seq, peaks of differential enrichment were identified using SICER-df with a false discovery rate threshold of 0.05. The annotatePeaks utility of HOMER was used to annotate statistically significant peaks.
Genome_build: hg19 for Caki1, Caki2, and HK2. mm10 for NMuMG.
Supplementary_files_format_and_content: For RNA-seq, files are tab-delimted text with the differential expression output from DESeq2. For ATAC-seq, files are tab-delimited text containing the annotated peaks obtained from HOMER.

source_name: HK-2 cells

growth_protocol: Caki1 and Caki2 cells were cultured in McCoy’s 5A supplemented with 10% FBS, 1% nonessential amino acids, and 1% L-glutamine. HK-2 cells were cultured in RPMI supplemented with 10% FBS and 1% L -glutamine. NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10 µM/mL insulin, 1% L -glutamine, and 1% sodium pyruvate. All cell lines were grown at 37°C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
RNA was extracted using TRIzol reagent (Life Technologies Corporation, Grand Island, NY) according to the manufacturer’s instructions and cleaned up using RNeasy Mini Kit (Qiagen Inc., Valencia, CA). Genomic DNA for ATAC-seq was obtained according to the ENCODE ATAC-seq pipeline.
RNA and DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Lentiviral transfection of shPBRM1


title: 100_PDAC3-9

description: cntPdac.csv


title: 100_PDAC3-17

description: cntPdac.csv


title: 100_PDAC3-14

description: cntPdac.csv


title: 100_PDAC3-13

description: cntPdac.csv


title: 100_PDAC3-12

description: cntPdac.csv


title: smallRNA seq data from pancreatic cancer patient P34

city: Seoul

first: Kwondo

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: small RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence using Trimmomatic-0.32
Trimmed reads with the length not in range within 16~35bp were filtered out.
Reads were aligned against miRBase v21 and quantified using miRDeep2
Genome_build: miRBase v21
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: Serum

extract_protocol:
Serum samples were collected in 10-mL BD serum tubes and centrifuged at 4°C for 20 minutes at 3000 rpm. The supernatant serum was then aliquoted and total RNA containing miRNA was extracted from the samples using the Serum miRNA purification kit (Genolution, Seoul, Korea) according to the manufacturer’s instructions.
The libraries were prepared for 50bp single-end sequencing using the NEXTflex Small RNA-Seq Kit (Bioo Scientific Corp.). Namely, smallRNA molecules were isolated from 1μg of total RNA via the adapter ligation. The isolated smallRNAs were synthesized as single-stranded cDNAs through the RT (Reverse transcription) priming. By applying this as a template for second strand synthesis, double-stranded cDNA was prepared through PCR (Polymerase Chain Reaction). And, the fragments of ~150bp were extracted for sequencing through size selection by gel electrophoresis. Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA) followed by quantification with the KAPA library quantification kit (Kapa Biosystems, MA, USA) according to the manufacturer’s protocol. Following cluster amplification of denatured templates, sequencing was progressed as single-end (50bp) using Illumina HiSeq2500 (Illumina, CA, USA).

tag: group

value: pancreatic cancer


title: smallRNA seq data from pancreatic cancer patient P33

description: small RNA


title: 100_PDAC3-10

description: cntPdac.csv


title: 100_PDAC3-3

description: cntPdac.csv


title: 100_PDAC3-8

description: cntPdac.csv


title: 100_PDAC3-2

description: cntPdac.csv


title: 100_PDAC3-1

description: cntPdac.csv


title: smallRNA seq data from pancreatic cancer patient P30

description: small RNA


title: HK-2 ATAC-seq shPBRM1 replicate 2


title: 100_PDAC3-16

description: cntPdac.csv


title: HK-2 ATAC-seq shPBRM1 replicate 3


title: smallRNA seq data from pancreatic cancer patient P26

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P24

description: small RNA


title: smallRNA seq data from pancreatic cancer patient P23

description: small RNA


title: HK-2 ATAC-seq null replicate 3

value: Lentiviral transfection of empty vector