title: WT7dCeru_P19

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

data_processing:
ATACseq, H3K27ac ChIPseq, H3K4me3 ChIPseq were used to generate genome wide maps of histone landscape in CTR and EZH2KO UN-KC6141 cells. ATACseq peaks were called using the HOMER command with the following parameters: -style factor -L 0 -C 0 -fdr 0.9 -minDist 200 -size 200). IDR was used to test for reproducibility of peaks; only peaks with an IDR < 0.05 were used for subsequent analysis. For differential peak analysis ATACseq tags were annotated using the HOMER command “annotatePeaks.pl” with the following parameters: -size 200 -raw. Differential H3K27ac ChIPseq or H3K4me3 analysis was performed by annotating merged peaks with ChIPseq tag directories using the HOMER command “annotatePeaks.pl” parameters -size 1000 -raw. Differential ATAC and H3K27ac sites were called using the HOMER command “getDiffExpression.pl” using default parameters.
Supplementary files format and content: Peaks.idr
Supplementary files format and content: differential_peaks.txt
Supplementary files format and content: normalized_matrix_count.txt
Supplementary files format and content: Matrix with RNAseq normalized counts

source_name: Mouse total pancreas

extract_protocol:
ChIP-Seq libraries preparation
ChIP-Seq experiments for H3K27ac, H3K4me3, H3K27me3were performed as described elsewhere (PMID: 28546318 and PMID: 32362324). Briefly, cells were fixed with 1% formaldehyde (ThermoFisher, #28906) at room temperature for 10 min. Cells were washed once again with 0.01%Triton-X-100 in PBS, pelleted, snap frozen and stored at -80ºC. Cells were thawed and lysed in a buffer containing 10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% deoxcycholate, 0.5% sarkosyl, 1 3 protease inhibitor cocktail (SIGMA). Lysate was soni- cated using a Covaris for 12 cycles with the following setting: time, 60 s; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. One percent of sonicated lysate was kept as ChIP input for analysis. Immunoprecipitation mix consisting of Protein G Dynabeads (Invitrogen, #10003D) and 1 μg of H3K27ac (Active Motif, AB_2561016) or H3K4me3 (Millipore, 04-745). Beads were washed four times each with wash buffer I (20 mM tris-HCl, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, and 2 mM EDTA), wash buffer II (10 mM tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, and 1 mM EDTA), tris-EDTA (TE) 0.2% Triton X-100, and TE 50 mM NaCl and then resuspended 25 μl of TT buffer (10 mM tris-HCl (pH 8.0) and 0.05% Tween 20, and sequencing libraries were prepared as following. ChIP libraries were prepared while bound to Dynabeads using a NEBNext Ultra II Library preparation kit (NEB) using half reactions. DNA was polished, poly(A)–tailed and ligated using dual UDI (IDT) or single (Bioo Scientific). Then crosslinks were revered by adding 33.5 μl of mix containing 18.4 μl nuclease free water, 4 μl 10% SDS, 3 μl  0.5 M EDTA, 1.6 μl 0.2M EGTA, 1 μl 10mg/ml Proteinase K (Biolabs, #P8107S), 1 μl 10mg/ml RNase A, 4.5 μl 5M NaCl by incubating at 55ºC for 1h followed by 75ºC for 30 min. Dynabeads were removed and libraries were cleaned by adding 3 μl of SpeadBeads in 125 μl of 20% PEG 8000/1.5M NaCl, washed by adding 120 μl 80% etOH, air dry and eluted in 12.5 μl of buffer containing 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was PCR-amplified for 15 cycles using NEBNext Ultra II PCR master mix using Solexa 1GA and Solexa 1GB primers. Libraries were size selected 200-500 bp by running in 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX) and sequenced using a HiSeq 4000 or a NextSeq 500.

ATAC-seq library preparation
Transposase reactions and sequencing libraries were generated as described previously (PMID: 24097267) 100,000 cells. Tagmented DNA was purified using Zymo ChIP Clean & Concentrate columns and PCR amplified for 10-12 cycles using barcoding primers. Libraries were size selected by gel excision to 175-225 bp using 10% TBE acrylamide gels (ThermoFisher, #EC62752BOX).
RNA-Seq library preparation
It was performed as described somewhere else (PMID: 28546318 and PMID: 32362324). Briefly, cells were lysed in Trizol. RNA and DNase treatment was carried out using Direct-zol RNA MicroPrep kit (Zymoresearch, #11-33MB). 1 μg total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94ºC in 2X Superscript III first-strand buffer containing 10mM DTT (Invitrogen, #P2325). Reverse-transcription (RT) reaction was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987). Libraries were ligated with dual UDI (IDT) or single (Bioo Scientific), PCR-amplified for 11-13 cycles, size-selected using one-sided 0.8× AMPure cleanup beads, quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and sequenced on a HiSeq 4000 or NextSeq 500 (Illumina).

value: Mouse total pancreas

value: Cerul 7 days after injection


title: KRas7dCeru_P17

status: Public on Feb 20 2025

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: strain

tag: genotype

value: Pdx1-Cre;LSL-KrasG12D (termed KrasG12D/PEC )

tag: treatment


title: SHY5Y cell line, Untreated, replicate 3

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

description: Library name: Negative_3

data_processing:
Initial quality assessment of sequencing reads was performed using FastQC. Single-end reads were mapped in strand-specific mode, enabling alignment in both directions.
Adapter trimming was implemented with parameters optimized to remove four nucleotides from the 5’ end of each read while enforcing an average quality threshold of 20. A minimum read length of 30 bases was required for retention in downstream analyses.
Sequence alignment and preprocessing were performed using STAR aligner against the Homo sapiens reference genome (GENCODE GRCh38.p13, Release 42, Annotation date: 2023-01-30) with the accompanying gene annotation file (genes.gtf).
Quantification of gene expression was carried out using the FeatureCounts tool, processing all nine samples
Assembly: GENCODE GRCh38.p13, Release 42, Annotation date: 2023-01-30
Supplementary files format and content: raw counts column for each sample are merged with ENSMBL id within csv files

organism: Homo sapiens

source_name: SHY5Y cell line

extract_protocol:
RNeasy Plus Micro Kit, Qiagen
RNA libraries for RNA-seq were prepared using Smartseq II Library Prep following manufactorer's protocol

treatment_protocol: SH-SY5Y cells were transfected with a 1:1 ratio of TDP-REG (TDP-REGv2) and hyperactive piggyBac transposase (pCMV-hyPBase) plasmids using Lipofectamine 3000 (ThermoFisher), following the manufacturer’s protocol. Negative control samples were transfected without the transposase vector to confirm complete cell death after selection. All the condition, but Negative samples, were treated with Atto 488-fluorescently labeled TDP-43 aggregates.

tag: cell line

value: SHY5Y cell line

value: Neuroblastoma

value: Untreated

tag: batch


title: IL1R_KO1_brain_candida_8h

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

institute: ETH Zürich

description: Library name: IL1R_KO1_brain_candida_8h

data_processing:
Sequenced libraries were aligned with STAR to the mouse reference genome GRCm38.p6 (release M23) and FeatureCounts was used to count mapped reads per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including gene name and raw counts per sample

source_name: Brain

extract_protocol:
Total RNA was isolated from whole mouse brain (Il1r-/- and Il1r+/- mice, 8h after infection with 105 CFU C. albicans) using RNeasy plus micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared using SMART-Seq RNA Stranded sample kit (Takara Bio) and sequenced by NovaSeq X Plus (Illumina). Sequencing was done using paired-end 150bp reads with a final sequencing depth of 25M paired-end reads per sample on average.

treatment_protocol: Il1r-/- and Il1r+/- mice were infected intraveneusly with 10^5CFU Candida albicans, 8 hours prior to harvesting of the brains.

tag: tissue

value: Brain

value: Candida albicans


title: KRas7dCeru_P18


title: IL1R_KO2_brain_candida_8h

description: Library name: IL1R_KO2_brain_candida_8h


title: SHY5Y cell line, Untreated, replicate 2

description: Library name: Negative_2


title: 17097_STZDFO_M3B1_rat_92_S15

city: Saint Paul

first: Jared

last: Fine

state: MN

address: 295 Phalen Blvd

institute: HealthPartners

data_processing:
Sequencing reads were mapped to the rat reference genome (rattus_norvegicus/Rnor_6.0) using Hisat2.
Differentially expressed genes were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: rattus_norvegicus
Supplementary files format and content: 9FineRawcounts.txt

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
RNA was harvested using the RNeasy mini plus kit (Qiagen).
Illumina TruSeq libraryprep kit

treatment_protocol: Rats were treated with intranasal insulin or deferoxamine

value: hippocampus

value: neural

value: ICV STZ (surgical)

value: IN DFO


title: WT7dCeru_P10


title: IL1R_WT2_brain_candida_8h

description: Library name: IL1R_WT2_brain_candida_8h


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, mScarlet activation, replicate 3

description: Library name: mScarlet_3

value: TDP-43 aggregates + mScarlet plasmid transduction


title: WT7dCeru_P9


title: WT7dCeru_P8


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, replicate 3

description: Library name: Atto_3

value: TDP-43 aggregates


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, mScarlet activation, replicate 1

description: Library name: mScarlet_1


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, mScarlet activation, replicate 2

description: Library name: mScarlet_2


title: brain, WT rep 1, PBS

city: Naples

first: Gabriella

last: Lania

address: Via Pietro Castellino

country: Italy

institute: IGB-CNR

data_processing:
Sequence reads were trimmed using bbduk softwareto remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR] on the reference provided by UCSC Genome Browser
The expression levels of genes were determined with htseq-count using the Gencode/Ensembl gene model
Differential expression analysis was performed using edgeR [5], a statistical package based on generalized linear models, suitable for multifactorial experiments.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw count for each sample

molecule: polyA RNA

source_name: brain hemisphere

growth_protocol: Adult Tbx1+/- and wt mice  4 weeks old

extract_protocol:
Qiagen RNeasy micro/mini plus Kit for RNA isolation and provide 10 μl of RNA at the exact concentration of 50 ng/μL
Quantseq 3′-biased protocol

treatment_protocol: intraperitoneal injection of vB12 dissolved in PBS 20 mg/kg (stored away from light) or with PBS, twice a week for 4 weeks

value: brain hemisphere

value: WT

value: PBS


title: 17097_Sham_M3B2_rat_112_S14

value: wild type

value: IN saline


title: IL1R_WT1_brain_candida_8h

description: Library name: IL1R_WT1_brain_candida_8h


title: KRas3dCeru_P12

value: Mouse total pancreas

value: Pdx1-Cre;LSL-KrasG12D (termed KrasG12D/PEC )

value: Cerul 3 days after injection


title: WT3dCeru_P3


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, replicate 2

description: Library name: Atto_2

value: SHY5Y cell line

value: Neuroblastoma


title: IL1R_WT3_brain_candida_8h

description: Library name: IL1R_WT3_brain_candida_8h

value: Brain

value: Candida albicans


title: K-ras/on

type: RNA

city: Guangzhou

first: Liu

last: Rui

state: Guangdong

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

description: Test

data_processing: For the normalization it uses the average of two housekeeping genes: GAPDH, ACTB. The normalization and all the data analysis were performed according to the manufacturers instructions using double delta Ct analysis method. 2^-deltaCt, deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: Human embryonic kidney cell line

label_protocol: RNA was extracted from the cells using Trizol (T9424, Sigma), and cDNA was synthesized with the PrimeScript™ RT-PCR Kit (RR014B, Takara). Equal amount of total RNA extracted from cells with different pre-treatment was quantified prior to RT-PCR assay. Gene expression was analyzed by qPCR using TB Green® Fast qPCR Mix (RR430S, Takara) on a CFX384 Real-Time System (Biorad). Microarray analyses were performed according to the protocol for human tumor metastasis RT² Profiler PCR Arrays (PAHS-028Z, QIAGEN). Changes in gene expression were further validated by quantitative RT-PCR.

growth_protocol: HEK293 T-Rex/K-ras cells were cultured in DMEM medium (C11885500BT, GIBCO) supplemented with 10% tet-free fetal bovine serum (FBS, 10099141C, GIBCO).

extract_protocol: Total RNA was extracted from the cells using Trizol (T9424, Sigma) follow manufacturer' instruction.

treatment_protocol: HEK293 T-Rex/K-ras cells were induced by doxycycline (20 ng/mL) for 6 h, K-ras/Off cells were treated with 15 mU GOx for 6 h, whereas K-ras/On cells were treated with 2 mM NAC for 6 h.

value: 20 ng/mL doxycycline

tag: time

value: 24 hours


title: K-ras/off +GOX

description: Test

value: 15 mU glucose oxidase

value: 6 hours


title: K-ras/on + NAC

description: Test

value: 20 ng/mL doxycycline, 2mM N-acetylcysteine

value: 24 hours + 6 hours


title: SHY5Y cell line, Untreated, replicate 1

description: Library name: Negative_1

value: Untreated


title: WT3dCeru_P1


title: mixed sample [SCABDJUR1309_S1]

city: Moscow

first: Natalia

last: Moiseeva

state: Moscow

address: Kashirskoe Shosse 24

country: Russia

institute: N.N. Blokhin National Medical Research Center of Oncology

description:
Library name: SCABDJUR1309_S1
Immune Response Targeted Panel (Human)

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed via the standard Rhapsody analysis pipeline (BD Biosciences) on Seven Bridges (https://www.sevenbridges.com) and BD Rhapsody Targeted Analysis Pipeline Version 1.11 per the manufacturer’s instructions. Initial processing included quality control, read alignment, cell identification, UMI deduplication, and count gene-barcode matrix. Resulting gene-barcode matrices with distribution-based error correction (DBEC) UMI counts were imported to Seurat in the R environment for further analysis.
Assembly: hg38
Supplementary files format and content: Zip archive containing gene-barcode matrices and quality metrics produced in the BD Rhapsody Targeted Analysis Pipeline Version 1.11

source_name: Peripheral blood mononuclear cells or tumor

extract_protocol:
PBMCs were separated using Ficoll density gradient centrifugation within 1 hour of blood collection and preserved in a freezing medium consisting of 90% fetal bovine serum (FBS) and 10% DMSO for future use. For non-responder patient were available biopsy samples of tumor tissue on days 3 and 21 after the first course of NAC. Each sample was collected using two 16-gauge needles. Samples were placed in the RPMI-1640 medium (Gibco, USA) and enzymatically digested no more than 20 minutes after collection. Tissues were washed extensively with 1× PBS with 200 U/mL penicillin. For collagenase/hyaluronidase treatment, tissue specimens were mechanically dissociated using a scalpel to remove vascular material, transferred to a solution of 300 U/ml collagenase and 100 U/ml hyaluronidase (STEMCELL Technologies, USA) in DMEM media, and then incubated at 37°C and 600×g for 30 min in a shaking incubator (BioSan TS-100, Poland). Once mucin clots formed, 5 U/ml of DNA hydrolyzing enzyme DNAase I (Sigma Aldrich, USA) was added to the suspension, followed by incubation under the same conditions for 10 min. To remove cell aggregates and debris, the cell suspension was filtered using a sterile cell strainer with a 70 μm pore diameter (Becton Dickinson, USA). Immediately after dissociation, the cell suspension was incubated with ROCK inhibitor (10 μM/ml) for 1 h, followed by cryopreservation in a solution of 95% FBS with 5% DMSO on ice. After isolation, cryovials with PBMCs or tumor cell suspensions were transferred in Mr.  Frosty Freezing Containers (Thermo Fisher Scientific, USA) containing isopropyl alcohol for gradient cooling and placed in a freezer, where they were stored for 24 hours at -80°C. Then the tubes were transferred to liquid nitrogen for long-term storage for up to 6 months at -196°C. For scRNA-seq, cells were removed from storage and rapidly thawed by immersion in a 37°C water bath with gentle agitation. Each cryovial was thawed individually until only a small amount of ice crystals remained. Samples were immediately transferred to round-bottom tissue culture tubes. Then, 10 ml of RPMI 1640 containing 10% FBS was added over 4 min with agitation, and the tubes were centrifuged immediately at 300×g for 5 min. The cells were then suspended in PBS containing 2% bovine serum albumin, followed by cell counting and viability assessment.
The cellular viability of all PBMCs and tissue samples exceeded 75%, as evaluated by Calcein (BD Bioscience, USA) vs DRAQ7 (Thermo Fisher Scientific, USA) via flow cytometry. According to the manufacturer’s protocol, 8 samples (6 PBMCs and 2 tumor cells suspensions) were labeled by Sample Tag and pooled for single-cell capture with the BD Rhapsody Single-Cell Analysis system (BD Bioscience, USA). 1,700 cells from each sample were included in the pool. Single-cell suspensions with PBS were loaded into microfluidic devices using the BD Rhapsody Single-Cell Analysis System (BD Bioscience, USA). Subsequently, the scRNA-seq libraries were constructed according to the protocol of the Immune Response Targeted Panel (Human) Single Cell RNA Library Kit (BD Bioscience, USA). Individual libraries were diluted and pooled according to the manufacturer’s recommendations. Finally, Illumina NextSeq 2000 sequencing was performed using NextSeq 2000 P2 reagents (100 cycles).

treatment_protocol: Both patients received 2-4 courses of adriamycin with cyclophosphamide followed by 4 NAC courses of taxanes before surgery. Samples were collected from both TNBC patients at three time points: before NAC and on days 3 and 21 after the administration of the 1st NAC course

tag: Sex

value: F

value: Before NAC, After NAC (day 3 or day 21)


title: K98314,Currumbin,Testis,oxidized,rep2

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

data_processing:
We first removed the adapter sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGT) from all small RNA-seq reads using cutadapt (version 1.15). Reads shorter than 18nt or longer than 32nt were filtered out prior to alignment. Subsequently, reads mapping to rRNAs, miRNAs, snoRNAs, snRNAs, and tRNAs were excluded. rRNA and miRNA annotations were obtained from our previous study using RNAmmer and miRDeep2, respectively. The remaining small RNA-seq reads were independently mapped to the reference koala genome, transposon consensus sequences, and spike-in sequences using Bowtie (version 1.1.0) with parameters “-v 1 -a --best --strata”. PCR duplicates were removed using Umitools with default parameters. Finally, unoxidized and oxidized replicate libraries are merge for each koala tissue to calculate the piRNA (24-32nt smallRNAs after filtering) signal track.
Assembly: phaCin_unsw_v4.1
Supplementary files format and content: bigWig files include the density of piRNAs across the watson strand of the koala genome.
Supplementary files format and content: bigWig files include the density of piRNAs across the crick strand of the koala genome.

organism: Phascolarctos cinereus

source_name: Testis

extract_protocol:
Total RNA samples were treated with Turbo DNase (Invitrogen) and RNA cleanup was done following manufacturer’s instructions using the RNeasy Mini Kit (Qiagen).
Small RNA sequencing libraries were prepared as previously described (Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., et al. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521.). Briefly, total RNA was isolated from flash frozen koala tissue using the mirVana miRNA Isolation Kit (Ambion/Life Technologies). Small RNAs were sized selected and purified from a 15% denaturing polyacrylamide-urea gel using the ZR small-RNA™ PAGE Recovery Kit (Zymo Research). For oxidized RNA library preparations, purified RNA was oxidized with 25 mM NaIO4 in 30 mM borax, 30 mM boric acid, pH 8.6, for 30 min at room temperature followed by ethanol precipitation. 3′ pre-adenylated adapter was ligated to oxidized or un-oxidized small RNAs. The 3´ ligated product was purified from a 15% denaturing polyacrylamide-urea gel. 5′ RNA adapter ligation was performed and the ligated product was purified from a 10% denaturing polyacrylamide-urea gel and used to synthesize cDNA. The resulting cDNA was PCR amplified and run on a 2% Certified Low Range Ultra Agarose (Bio-Rad) gel with subsequent extraction using the QIAquick® Gel Extraction Kit (Qiagen). ERCC spike-ins and UMI tags are added to all libraries.

value: Testis

tag: Stage

value: adult

tag: location

value: Currumbin

tag: koala id


title: mixed sample [1_S1]

description:
Library name: 1_S1
Immune Response Targeted Panel (Human)

value: Peripheral blood mononuclear cells or tumor


title: SHY5Y cell line, TDP43 fluorescent aggregates treatment, replicate 1

description: Library name: Atto_1

value: SHY5Y cell line

value: TDP-43 aggregates


title: KRas7dControl_P16

value: Mouse total pancreas

value: Pdx1-Cre;LSL-KrasG12D (termed KrasG12D/PEC )

value: CTR 7 days after injection


title: WT7dControl_P14


title: KRas7dControl_P15


title: K98314,Currumbin,Testis,rep3


title: K98314,Currumbin,Testis,rep2


title: WT7dControl_P7


title: K98314,Currumbin,Testis


title: KRas3dControl_P13

value: CTR 3 days after injection


title: KRas3dCeru_P11

value: Cerul 3 days after injection


title: KRas3dControl_P2

value: CTR 3 days after injection


title: K98224,Currumbin,Testis


title: A-498, VHL, Rep3

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

library_source: other

data_processing:
Raw sequencing reads were first aligned to the reference human transcriptome (hg19) using bowtie2 (v 2.3.4.3). Reads that failed to map to the human transcriptome were subsequently aligned to the reference ERV genome. Paired-end reads where both ends perfectly matching to at least one ERV reference sequence (PM), or those with no more than one mismatch across both reads (1MM), were preserved. Single ends from read pairs that met the following criteria were also kept for downstream analysis: (i) perfect match to an ERV reference sequence; (ii) not part of any paired-end PM or 1MM matches to any ERV reference sequence; (iii) no matches to the human transcriptome. Duplicated reads were identified and removed using PicardMarkDuplicates. Quantification was performed using HTSeq (v 0.11.0),and the final expression was defined as 2× number of paired-end matches (PM & 1MM) + number of single-end matches to the ERV reference database.The expression of each ERV was normalized by the library size of the corresponding sample as well as the length of the ERV. These normalized ERV counts were used in downstream analyses.
Assembly: hg19
Supplementary files format and content: An excel file, which contains normalized ERV counts for 3173 ERVs (defined by Vargiu et al, Retrovilogy, 2016) under all conditions

molecule: other

growth_protocol: 786-O and A-498 cells were obtained from American Type Culture Collection and were cultured in DMEM (Gibco 11995073) supplemented with FBS (GeminiBio 100-106), 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
1×10^7-2×10^7 adherent cells were washed once with ice-cold PBS and subsequently lysed/scraped directly from the plates on ice using a polysome extraction buffer [(25 mM HEPES pH 7.5, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 1% Triton X-100, 0.1 mg/ml cycloheximide, 0.05 U/l RNase inhibitor (Invitrogen AM2696), and 1× Roche-complete EDTA-free protease inhibitor cocktail (Roche 4693132001)]. The lysates were homogenized with 5-6 strokes in a glass Dounce homogenizer on ice, then cleared at 10,000xg for 5 min at 4°C. Cleared lysates were loaded on top of 10-50% linear sucrose gradients (mixed using a BioComp gradient mixer gradients containing 25 mM HEPES pH 7.5, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 0.1 mg/ml cycloheximide, and 1× Roche-complete EDTA-free protease inhibitor cocktail) and centrifuged in a Beckman Coulter ultracentrifuge at 40,000 rpm for 3 h at 4°C in a SW41Ti rotor. After centrifugation, gradients were fractionated and analyzed using a BioComp fractionator monitoring absorbance at 260 nm. Polysome profiles were manually inspected to determine fractions containing polysomes, and these fractions were pooled for RNA purification (polysome-containing fractions were identified as all fractions heavier than the monosome peak which was excluded). RNA was purified from pooled polysome sucrose gradient fractions using Trizol LS (Invitrogen 10296028) followed by sequential isopropanol and ethanol precipitations. RNA quality was analyzed using an Agilent RNA TapeStation (RIN values all > 9).
Libraries were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara 634873). The sequencing libraries were quantified using Qubit HS DNA assays and an Agilent High Sensitivity TapeStation. The final pool was sequenced with paired-end 100 bp reads (for 786-O samples) and paired-end 150 bp reads (for A-498 samples) on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: 786-O and A-498 cells were infected with bicistronic vectors (pLX304-EV-IRES-GFP or pLX304-VHL-IRES-Tdtomato), GFP or Tdtomato positive cells were isolated by FACS.

value: ccRCC

value: Infected with pVHL protein (VHL)


title: A-498, VHL, Rep2


title: KRas3dControl_P5


title: K98214,Currumbin,Ovary

source_name: Ovary

value: Ovary


title: WT3dControl_P4


title: K-ras/off

description: Control

value: control

value: 6 hours


title: A-498, VHL, Rep1


title: K94276,SunshineCoast,Testis,oxidized

value: Testis

value: SunshineCoast


title: A-498, EV, Rep2

value: Infected with empty vector (EV)


title: Krascells_ChIP_input_EzhKO_Clone2 b

library_source: genomic

molecule: genomic DNA

source_name: Mouse PDAC cell line

value: Mouse PDAC cell line

value: KrasG12D; Ezh2KO

value: CRISPR/Cas9 EZH2KO


title: A-498, EV, Rep1


title: K98314,Currumbin,Testis,oxidized

value: adult

value: Currumbin


title: K94276,SunshineCoast,Testis


title: K94283,SunshineCoast,Ovary


title: Krascells_ChIP_input_EzhKO_Clone2


title: Krascells_ChIP_input_Control_Clone1 b


title: K71362,SunshineCoast,Testis,rep2


title: 786-O, VHL, Rep2


title: 786-O, VHL, Rep3


title: Krascells_ChIP_input_Control_Clone1


title: K94276,SunshineCoast,Testis,rep2


title: K98214,Currumbin,Ovary,oxidized


title: Krascells_ChIP_H3K4me3_EzhKO_Clone1


title: Krascells_ChIP_H3K4me3_EzhKO_Clone2


title: K71362,SunshineCoast,Testis


title: 786-O, EV, Rep2


title: 786-O, EV, Rep3


title: Mutant, SA + Glucose, Replicate 3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description:
Library name: LSG_3
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + SA

data_processing:
All paired-end FASTQ files were processed through the same pipeline. Reads were trimmed using Trimmomatic version 0.3  with the default settings except for a HEADCROP of 5, LEADING of 3, TRAILING of 3, SLIDINGWINDOW of 3:30, and MINLEN of 36. After trimming, the reads were aligned to the N. aromaticivorans DSM12444 genome sequence (GenBank accession GCF_000013325.1) using bwa-mem (version 0.7.17-h5bf99c6_8)  with default settings. Alignment files were further processed with Picard-tools (version 2.26.10) (https://broadinstitute.github.io/picard/) (CleanSAM and AddOrRepleaceReadGroups commands) and samtools (version 1.2)  (sort and index commands). Paired aligned reads were mapped to gene locations using HTSeq version 0.6.0. The R package edgeR (version 3.30.3) with default settings was used to identify significantly differentially expressed genes from pairwise analyses, using Benjamini and Hochberg false discovery rate (FDR) less than 0.05 as a significance threshold (57). Raw sequencing reads were normalized using the fragments per kilobase per million mapped reads method (FPKM).
Assembly: GCF_000013325.1
Supplementary files format and content: Rodríguez-Castro_HTseq_counts.txt contains the RAW gene counts for the experiments as determined by Htseq-count
Supplementary files format and content: Rodríguez-Castro_FPKM_Results.txt contains FPKM normalized gene counts for all experiments.

organism: Novosphingobium aromaticivorans DSM 12444

source_name: bacterial

growth_protocol: N. aromaticivorans DSM12444 and DSM12444Δ14285 were cultured overnight in SMB medium supplemented with 10 mM glucose and 5 mM of PCA. The next day the cells were harvested and resuspended in SMB medium with 10 mM glucose and 5 mM of an aromatic compound (PCA, 4-CA, VA or SA) to reach a cell concentration of 30 Klett units. The cells were cultured until mid-log phase. A culture supplemented only with glucose was also included for further comparisons.

extract_protocol:
The RNA was extracted with acid phenol:chloroform, following the manufacture´s instructions (Thermo Fisher Scientific; Waltham, USA). The cells were pelleted by centrifugation (4,300 x g for 10 minutes) at 4°C and stored at -80°C. Cell pellets were resuspended in 1 mL of lysis solution (2 % SDS, 16 mM EDTA) and heated at 65˚C for 5 minutes. Samples were mixed with 1 mL of hot acid phenol:chloroform and incubated at 65˚C for 5 minutes. To separate the RNA from other biomolecules, the samples were centrifuged at room temperature for 15 minutes at 20,000 g. The aqueous phase was transferred to a new tube and washed two more times with hot acid phenol:chloroform. The aqueous phase was mixed with 1 mL of chloroform and centrifuged for 15 minutes at 20,000 g. To precipitate the RNA, the samples were mixed with 100 µL of 3 M sodium acetate and 1 mL of isopropanol and incubated at -20oC for at least 1 h. Samples were centrifugated at 4˚C for 30 minutes at 16,000 g. The pellet was washed twice with 1 mL of cold 75 % EtOH. Once residual ethanol was removed by pipetting and evaporation, the pellet was resuspended in 40 μL of RNase-free water. Remaining DNA was removed with the TURBO DNA-free Kit (Thermo Fisher Scientific; Waltham, MA, USA), according to the manufacturer´s instructions. Finally, the RNA was cleaned using the RNeasy Mini Kit (Qiagen, Hilden, Germany), following the manufacturer’s recommendations.
RNA-seq library preparation and sequencing was performed by the Joint Genome Institute (JGI) using default parameters. rRNA in the samples was depleted using the QIAseq FastSelect kit (Qiagen, Hilden, Germany). Libraries were constructed using the TruSeq stranded mRNA kit (Illumina) following standard JGI protocols.

treatment_protocol: Growth was stopped by the addition of ice cold 5% acid phenol:chloroform (5:1) in dry ice.

value: bacterial

value: delta SARO_RS09410 (sacB) delta SARO_RS14285 (LysR-type transcription factor)


title: Krascells_ChIP_H3K4me3_Control_Clone2


title: K71362,SunshineCoast,Testis,oxidized


title: 786-O, VHL, Rep1


title: 786-O, EV, Rep1


title: Krascells_ChIP_H3K4me3_Control_Clone1


title: Mutant, SA + Glucose, Replicate 2

description:
Library name: LSG_2
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + SA


title: A-498, EV, Rep3


title: Krascells_ChIP_H3K27ac_EzhKO_Clone2


title: Mutant, SA + Glucose, Replicate 1

description:
Library name: LSG_1
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + SA


title: Mutant, VA + Glucose, Replicate 3

description:
Library name: LVG_3
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + VA


title: MCF7 10^-8M E2 1h replicate 1 RNA-seq

city: Aurora

first: Kiran

last: Vinod Paul

institute: University of Colorado-Anschutz medical campus

description: RNA-seq

data_processing:
Adapter trimming was done using cutadapt
Alignment was done using STAR
raw reads were generated using Rsubread
expression values (TPM) were generated using Salmon
Assembly: GRCh38
Supplementary files format and content: tab seperated text file was generated having the raw reads

source_name: MCF7 cell line

growth_protocol: MCF7 cells were maintained in DMEM/High glucose (4.5g/L) supplemented with 10% fetal bovine serum.

extract_protocol:
Zymo Direct-zol RNA Mini Prep
RNA libraries were prepared for sequencing using standard Illumina protocols at the University of Colorado Denver Genomics and Microarray Core facility.

treatment_protocol: Cells were estrogen withdrawn (MEM, no glutamine, no phenol red + 10% Dextran Coated Charcoal stripped fetal bovine serum + glutagro supplement) for at least 72 hours and then treated 1hr with indicated E2 concentration or ethanol vehicle.

value: estrogen


title: MCF7 10^-8M E2 1h replicate 2 RNA-seq

description: RNA-seq


title: Krascells_ChIP_H3K27ac_EzhKO_Clone1


title: Krascells_ChIP_H3K27ac_Control_Clone2


title: P10_8h

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
processed data files:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.14). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue < = 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM or raw count values for each Sample

source_name: Passage 10 BMSCs at 8h post-irradiation

growth_protocol: The BMSCs were cultured in human mesenchymal stem cell growth medium (ScienCell, Carlsbad, CA) at 37 °C in a humidified atmosphere containing 5% CO2

extract_protocol:
Total RNA was harvested from the BMSCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. The total RNA was treated with the RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using the SmartsSpec Plus spectrophotometer (BioRad). The RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 5μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen). The purified mRNAs were fragmented at 95 ℃, followed by end repair and 5' adaptor ligation. Then RNA reverse transcription was performed with an RT primer harbouring a 3' adaptor sequence and randomized hexamers. The cDNAs were purified and amplified with the RNA-Seq Library Preparation Kit (Gnomegen). PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing.

treatment_protocol: When the cultured P6 and P10 BMSCs reached 80% confluence, they were irradiated with 9 Gy by Co-60 at a dose rate of 700 cGy/min. The control group cells were placed in the same location but not exposed to irradiation. The BMSCs were sequentially cultured and were collected at 2h and 8h post-irradiation

value: Bone marrow stromal cells (BMSCs)

tag: passage

tag: radiation status

value: 8h post-irradiation


title: WT3dControl_P6

value: Mouse total pancreas

value: CTR 3 days after injection


title: MCF7 10^-10M E2 1h replicate 3 RNA-seq

description: RNA-seq


title: Mutant, VA + Glucose, Replicate 1

description:
Library name: LVG_1
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + VA


title: Krascells_ATAC_EzhKO_Clone2


title: P10_2h

source_name: Passage 10 BMSCs at 2h post-irradiation

value: 2h post-irradiation


title: K63855,Currumbin,Testis


title: Mutant, 4-CA + Glucose, Replicate 3

description:
Library name: L4G_3
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + 4-CA


title: P10_0h

source_name: Passage 10 BMSCs without irradiation (control)

value: without irradiation


title: MCF7 10^-10M E2 1h replicate 2 RNA-seq

description: RNA-seq


title: Krascells_ATAC_EzhKO_Clone1


title: MCF7 10^-10M E2 1h replicate 1 RNA-seq

description: RNA-seq


title: Mutant, 4-CA + Glucose, Replicate 2

description:
Library name: L4G_2
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + 4-CA


title: P6_8h

source_name: Passage 6 BMSCs at 8h post-irradiation


title: Krascells_ATAC_Control_Clone2

value: KrasG12D; CTR

value: CRISPR/Cas9 CTR


title: MCF7 10^-8M E2 1h replicate 3 RNA-seq

description: RNA-seq


title: P6_2h

source_name: Passage 6 BMSCs at 2h post-irradiation


title: MCF7 10^-12M E2 1h replicate 3 RNA-seq

description: RNA-seq


title: Krascells_ATAC_Control_Clone1


title: MCF7 10^-12M E2 1h replicate 2 RNA-seq

description: RNA-seq


title: Mutant, 4-CA + Glucose, Replicate 1

description:
Library name: L4G_1
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + 4-CA


title: P6_0h

source_name: Passage 6 BMSCs without irradiation (control)


title: Mutant, VA + Glucose, Replicate 2

description:
Library name: LVG_2
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + VA


title: Mutant, PCA + Glucose, Replicate 3

description:
Library name: LPG_3
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + PCA


title: Krascells_ChIP_H3K27ac_Control_Clone1


title: MCF7 10^-12M E2 1h replicate 1 RNA-seq

description: RNA-seq


title: S18 BoHV-1 challenged

city: Grange, Dunsany

first: Stephanie

last: O'Donoghue

state: Meath

address: Animal Bioscience Research Centre

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
Sequenced reads  were assessed for quality using FastQC (version 0.11.8).
Reads were trimmed at the 3’ end using cutadadapt (version 1.18) (Martin, 2011) for the removal of short reads (< 10 bases), ambiguous nucleotides and ploy-G-artefacts.
Sequenced reads were aligned to the ARS-UCD1.2 bovine reference genome and counts generated using STAR alignment tool (verison 2.6.1b)
Assembly: ARS UCD1.2
Supplementary files format and content: TXT file of raw counts table fo sequenced reads

organism: Bos taurus

source_name: mediastinal lymph node

extract_protocol:
Total RNA was extracted using the Qiagen Universal plus mini kit (Bio-scieneces LTD, Dublin, Ireland) according to the manufacturers instructions
RNA-Seq library preparation was performed using the TruSeq stranded mRNA Kit (Illumina, San Diego, California, USA).

value: mediastinal lymph node

tag: breed

value: Holstein-Friesian

value: BoHV-1 challenged


title: MCF7 ETOH 1h replicate 3 RNA-seq

description: RNA-seq

value: ethanol vehicle


title: ONT1, CENH3-OX

city: Bunkyo-ku

first: Sayuri

last: Tsukahara

state: Tokyo

address: Hongo 7-3-1

country: Japan

institute: The University of Tokyo

description: Library name: ONT1

data_processing:
ChIP-seq reads were mapped on the Col-CEN genome using Bowtie2 (ver. 2.4.4). The read count for each 10 kb bins was calculated using the coverage function of BEDTools (ver. 2.26.0).
For ONT, R9 reads were filtered for length and accuracy using Filtlong (Version 0.2.0) (--min_mean_q 90, --min_length 5000). Methylation prediction for the CG, CHG, and CHH contexts were called using DeepSignal-plant (v1.6.1) using the model: model.dp2.CNN.arabnrice2-1_120m_R9.4plus_tem.bn13_sn16.both_bilstm.epoch6.ckpt.
Assembly: Col-CEN_v1.2
Supplementary files format and content: bedgraph for ChIP-seq, tsv for ONT
Library strategy: DNA methylation data examined by Nanopore sequencing

organism: Arabidopsis thaliana

source_name: 3-week-old seedlings

extract_protocol:
For ChIP-seq, Ground tissue samples were fixed with 1% formaldehyde for 10 min. After quencing and cell lysis, chromatin was sonicated using a bioruptor pico (Diagenode). For ONT, DNA was extracted using NucleoBond HMW DNA kit (MACHEREY-NAGEL).
ChIP-seq libraries were constructed using ThruPLEX DNA-seq Kit (Clontech). ONT library was prepared using LSK-110 ligation kit.
For ONT, DNA was extracted using NucleoBond HMW DNA kit (MACHEREY-NAGEL).
ONT library was prepared using LSK-110 ligation kit.

value: 3-week-old seedlings

value: ONT


title: WT Monocyte-derived macrophage 10 days post LPC_131

city: Edinburgh

first: Veronique

last: Miron

address: 49 Little France Crescent

department: UK DRI

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Alignment to mouse genome (GRCm38):  STAR aligner v2.5.2a
Number of mapped read pairs/gene:  GENCODE vM12
Normalization (TMM):  R v3.3.2, edgeR v3.16.5
Transformation (VOOM):  R v3.3.2, limma v3.30.8
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel files with raw gene counts for each sample, and normalized data as log2 CPM

extract_protocol:
Mice were perfused with ice cold PBS with 10% sodium citrate. Lesions were isolated, manually dounced, and cells isolated by Percoll gradient. Microglia and monocyte-derived macrophages were FACS isolated, first excluding dead cells, then gating on Cd11b+ Ly6G- CD3- Cd45lo (microglia) CD45hi (MDM) cells.
[Details] Mice were perfused with ice cold phosphate buffered saline with 10% sodium citrate. The lesioned corpus callosum was dissected and manually homogenised using a 2 ml Dounce and filtered (250 µm filter; Pierce). Cells were centrifuged at 600 g for 5 min (with brake), then resuspended in 100 % fetal bovine serum (FBS) and 33 % Percoll (1:10), with 1 ml of 10 % FBS overlaid, and centrifuged for 15 min at 800 g at 4 °C without brake. The cell pellet was washed in FACS buffer and centrifuged for 10 min at 600 g at 4 °C, and incubated with anti-mouse CD16/32 Fc-block (Clone 93, BioLegend, 1:200) on ice for 10 min. Cells were incubated with fluorescently-conjugated antibodies against CD11b-PeCy7 (Clone M1/70, Invitrogen, 1:100), CD45-BV605 (Clone 30D11, Biolegend, 1:200), Ly6G-PerCP Cy5 (Clone 1A8, BioLegend, 1:200), and CD3-APC (Clone 17A2, BioLegend, 1:200) on ice for 30 min. Following centrifugation and filtration (30 ?m), cells were sorted by flow cytometry into FBS-coated Eppendorf tubes on ice. Cells were spun at 800 g for 5 min, resuspended in RLT Plus buffer with ?-mercaptoethanol, and centrifuged at 10,000 rpm for 2 min using QIAshredder tubes (Qiagen). RNA was extracted using the AllPrep DNA/RNA/miRNA kit (Qiagen) as per the manufacturer?s instructions, and quantity/quality analysed using the Bioanalyser 2100 (Agilent) and RNA 6000 Pico kit (Agilent) as per the manufacturer?s instructions. Isolated cells were centrifuged at 800 g for 5 min and resuspended in 350 ?l RLT Plus buffer with ?-mercaptoethanol and centrifuged at 10,000 rpm for 2 min using QIAshredder tubes (QIAGEN). RNA was extracted using the AllPrep DNA/RNA/miRNA kit (QIAGEN) as per the manufacturer?s instructions. Quantity and quality of RNA was determined using the Bioanalyser 2100 (Agilent) and RNA 6000 Pico kit (Agilent) as per the manufacturer?s instructions. cDNA production and library preparation were performed by BGI (Hong Kong).
cDNA production and library preparation were performed by BGI (Hong Kong). Briefly, double stranded cDNA was prepared according to OvationÂ® RNA Seq System V2 (NuGEN), as per manufacturerâ€™s instructions. The amplified cDNA was combined with End Repair Mix, incubated at 20 â„ƒ for 30 min. End-repaired DNA was purified with AxyPrep Mag PCR clean up kit (Axygen), and then combined with A-Tailing Mix (Enzymatic) at 37 â„ƒ for 30 min. Adpators (Invitrogen) were ligated to the Adenylate 3â€™ ends DNA, and incubated at 16 â„ƒ for 16 h, and purified with AxyPrep Mag PCR clean up kit. The adapter-ligated DNA fragments were selected as based on the insert size. The adapter-ligated DNA fragments were enriched by PCR amplification using PCR Primer cocktail (Invitrogen) and PCR Master Mix (New England Biolabs), and the PCR products (final library) were purified with AxyPrep Mag PCR clean up kit (Axygen). The final library was quantitated in two ways: the average molecule length was determined using the Bioanalyser 2100 using the DNA 1000 kit (Agilent), and the library was quantified by real-time quantitative PCR (qPCR) (TaqMan Probe). The qualified libraries were amplified using cBot (Illumina) to generate the cluster on the Flow Cell (HiSeq 4000, Illumina). An average of 40 million clean 100 paired-end reads (read length approximately 100 bp) were obtained per sample. Data was processed to remove adaptors and low-quality reads were removed from raw reads.

treatment_protocol:
LPC stereotaxic injection into the corpus callosum and recovered 10 days post injection.
10 week-old male C57Bl/6J mice were anaesthetized with isoflurane before stereotaxic injection of 2 μl of 1% lysolecithin (LPC; vol/vol) into the corpus callosum (WT microglia n=3; Ccr2-/- microglia n=3; WT monocyte-derived macrophages n=2; Ccr2-/- monocyte-derived macrophages n=1).

value: male

tag: age

value: 10 weeks

value: WT

value: corpus callosum

value: Monocyte-derived macrophages

value: injection of lysolecithin (LPC) into the corpus callosum

value: 10 days post LPC


title: WT Monocyte-derived macrophage 10 days post LPC_130


title: Mutant, PCA + Glucose, Replicate 1

description:
Library name: LPG_1
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + PCA

value: bacterial

value: delta SARO_RS09410 (sacB) delta SARO_RS14285 (LysR-type transcription factor)


title: MCF7 ETOH 1h replicate 2 RNA-seq

description: RNA-seq


title: Mutant, Glucose, Replicate 2

description:
Library name: LG_2
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose


title: S17 BoHV-1 challenged


title: MCF7 ETOH 1h replicate 1 RNA-seq

description: RNA-seq


title: WT Microglia 10 days post LPC_128

source_name: WT Microglia 10 days post LPC

value: Microglia


title: Mutant, Glucose, Replicate 1

description:
Library name: LG_1
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose


title: S16 BoHV-1 challenged


title: Healthy.Controls.TCR.VDJ

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

description: 10x Genomics-TCR.VDJ

data_processing:
The 10X Cell Ranger package (10X Genomics, v6.0.1) was used to process data and align to human genome (GRCh38-2020-A).
The filtered feature-barcode matrices were imported into R for downstream analysis using the Seurat package (v4.1.0) (Hao et al., 2021). Doublets and dead cells were filtered out by quality control. Cells with the number of detected genes between 200 to 3500 and the proportion of mitochondrion gene reads less than 10% were selected for further analysis. All gene expression count data were carried out with SCTransform (V2, regulation) for the normalization and variance stabilization (Choudhary and Satija., 2022). Antibody hashtag data were normalized by centered log-ratio (CLR) transformation, and cells with double and negative labels were removed.
3085 cells from active tattoo uveitis, 3142 cells from convalescent tattoo uveitis, 5153 cells from sarcoidosis and 3804 cells from healthy donors were submitted for the integration analysis to compare the samples between different groups (Stuart et al., 2019).
Filtered contig annotations assembled by the Cell Ranger was used for TCR clonotypes analysis by ScRepertoire package (v1.3.5) (Borcherding et al., 2021). Cells with same VDJC gene segments and the CDR3 region for TCRA and TCRB chains were viewed as same clonotype. The unique clonotype proportions between different samples were calculated, and the same clonotypes between two groups was analyzed by the scatterClonotype function.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files for gene expression
Supplementary files format and content: Comma-separated values for VDJ sequencing

source_name: Blood

extract_protocol:
PBMCs were collected by gradient centrifugation using Ficoll-Paque Plus tubes (GE Healthcare). Live 7AAD- PBMCs were sorted by flow into 1.5-ml Eppendorf tubes with FACS buffer.
Single cell gene expression and VDJ libraries were prepared by Biomolecular Resource Facility at ANU using Chromium Next GEM Single Cell 5' Kit v2 Dual Index and Single Cell Human TCR Amplification Kit (10x Genomics) according to the manufacturer’s instructions. The library was sequenced in S1 flow cell with 2 x 50 bp paired-end reads by NovaSeq 6000 sequencer (Illumina).

value: Blood

tag: disease state

value: healthy

value: PBMCs

value: No treatment


title: S15 BoHV-1 challenged

value: mediastinal lymph node

value: Holstein-Friesian

value: BoHV-1 challenged


title: w1118 Drosophila brain_Spermidine Food_Rep3

city: Berlin

first: Stephan

middle: J

last: Sigrist

state: Berlin

address: Takustr. 6, 2OG, AG Sigrist

department: Biology, Chemistry and Pharmacy,

country: Germany

institute: Freie Universität Berlin

description:
15-day-old
Tian_spd_3

data_processing:
The count data were based on the HTSeq package from the Huber lab
Supplementary_files_format_and_content: FPKM values were based on Cufflinks as well as Fold Change and p-values from DESeq

organism: Drosophila melanogaster

source_name: w1118 Drosophila brain Spermidine Food

growth_protocol: Wild type w1118 fly strains were reared at normal food with or without spermidine

extract_protocol:
RNA was harvested using Trizol reagent. Truseq stranded mRNA sequencing kit was used with 100ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fly brains were manually dissected and snapfrozen on liquid nitrogen

tag: organ/tissue

value: Dissected fly brains

value: Normal food with spermidine


title: Active.Sarcoidosis.TCR.VDJ

description: 10x Genomics-TCR.VDJ

value: active sarcoidosis

tag: cell type


title: WT, SA + Glucose, Replicate 2

description:
Library name: NSG_2
Parent (∆SARO_RS09410) grown in Glucose + SA

tag: genotype

value: delta SARO_RS09410 (sacB)


title: WT Microglia 10 days post LPC_127

tag: strain

value: male

value: 10 weeks

value: WT

value: corpus callosum

tag: treatment


title: S13 BoHV-1 challenged


title: WT, VA + Glucose, Replicate 2

description:
Library name: NVG_2
Parent (∆SARO_RS09410) grown in Glucose + VA

value: bacterial


title: Mutant, PCA + Glucose, Replicate 2

description:
Library name: LPG_2
Mutant (∆SARO_RS09410 ∆SARO_RS14285) grown in Glucose + PCA

value: delta SARO_RS09410 (sacB) delta SARO_RS14285 (LysR-type transcription factor)


title: WT, SA + Glucose, Replicate 1

description:
Library name: NSG_1
Parent (∆SARO_RS09410) grown in Glucose + SA


title: w1118 Drosophila brain_Spermidine Food_Rep2

description:
15-day-old
Tian_spd_2


title: Inactive.Tattoo.Uveitis.TCR.VDJ

description: 10x Genomics-TCR.VDJ

value: Blood

value: inactive tattoo uveitis


title: w1118 Drosophila brain_Spermidine Food_Rep1

description:
15-day-old
Tian_spd_1


title: S14 BoHV-1 challenged


title: Active.Tattoo.Uveitis.TCR.VDJ

description: 10x Genomics-TCR.VDJ

value: active tattoo uveitis

value: PBMCs


title: S12 BoHV-1 challenged

value: mediastinal lymph node


title: WT, VA + Glucose, Replicate 1

description:
Library name: NVG_1
Parent (∆SARO_RS09410) grown in Glucose + VA


title: w1118 Drosophila brain_Normal Food_Rep3

description:
15-day-old
Tian_normal_3

source_name: w1118 Drosophila brain Normal Food

value: Normal food


title: Healthy.Controls.GEX

description: 10x Genomics-gene expresssion

value: healthy

value: No treatment


title: WT, 4-CA + Glucose, Replicate 2

description:
Library name: N4G_2
Parent (∆SARO_RS09410) grown in Glucose + 4-CA


title: WT Microglia 10 days post LPC_129

value: Microglia

value: injection of lysolecithin (LPC) into the corpus callosum

value: 10 days post LPC


title: w1118 Drosophila brain_Normal Food_Rep2

description:
15-day-old
Tian_normal_2

value: Dissected fly brains


title: Active.Sarcoidosis.GEX

description: 10x Genomics-gene expresssion

value: active sarcoidosis


title: S10 BoHV-1 challenged

value: Holstein-Friesian

value: BoHV-1 challenged


title: w1118 Drosophila brain_Normal Food_Rep1

description:
15-day-old
Tian_normal_1


title: WT, 4-CA + Glucose, Replicate 1

description:
Library name: N4G_1
Parent (∆SARO_RS09410) grown in Glucose + 4-CA

value: bacterial

value: delta SARO_RS09410 (sacB)


title: S9 BoHV-1 challenged


title: WT, PCA + Glucose, Replicate 2

description:
Library name: NPG_2
Parent (∆SARO_RS09410) grown in Glucose + PCA


title: Inactive.Tattoo.Uveitis.GEX

description: 10x Genomics-gene expresssion

value: Blood


title: balb_f3_none

first: Linden

last: Hu

address: 136 Harrison Avenue

department: Microbiology

institute: Tufts University School of Medicine

data_processing:
Reads were mapped to P. leucopus (GCF_004664715.2) or the M. musculus (GRCm39) genome using STAR version 2.6.1 and gene expression was summarized using RSEM version 1.3.1.
Assembly: GCF_004664715.2, GRCh39
Supplementary files format and content: output .genes.results file from RSEM

source_name: skin

extract_protocol:
After all rodent samples were collected, samples were thawed on ice, transferred to QIAzol, and bead beaten with a 6.35 mm chrome steel bead (Biospec Products) for two cycles of two minutes each at an oscillation frequency of 30/second using a TissueLyser II (Qiagen). RNA was extracted using the miRNeasy mini kit (Qiagen), with the modification that two RWT washes were performed. gDNA was digested using TURBO DNase (Invitrogen) and RNA was repurified using the RNeasy MinElute Cleanup Kit (Qiagen).
Purified RNA was submitted to Azenta Life Sciences/Genewiz for library preparation and sequencing (Illumina HiSeq 2x150bp).

value: skin

value: Female

tag: condition

value: no tickbite


title: Active.Tattoo.Uveitis.GEX

description: 10x Genomics-gene expresssion

tag: tissue

value: active tattoo uveitis

value: PBMCs


title: S8 BoHV-1 challenged

value: mediastinal lymph node


title: WT, PCA + Glucose, Replicate 1

description:
Library name: NPG_1
Parent (∆SARO_RS09410) grown in Glucose + PCA


title: balb_f2_tick

value: tickbite


title: S7 BoHV-1 challenged


title: UCD12 10^-10M E2 1h replicate 1 IgG CUT&RUN

description: IgG CUT&RUN

data_processing:
Adapter trimming was done using cutadapt
Alignment was done using Bowtie2
Peak calling was done using custom python script
Peak clustering was done using Kmeans clustering
Assembly: GRCh38
Supplementary files format and content: BED files were generated for each cell line and condition. No peak calling was done for the anti-IgG samples.  The anti-IgG samples were aligned and used to subtract the IgG samples from the other samples to get the pure signals.
Library strategy: CUT&RUN

source_name: UCD12 cell line

growth_protocol: MCF7 cells were maintained in DMEM/High glucose (4.5g/L) supplemented with 10% fetal bovine serum. UCD12 cells were maintained in DMEM/Hams F12 50:50 Mix supplemented with 10% fetal bovine serum.

extract_protocol:
ERα or IgG CUT&RUN
CUT&RUN libraries were made with Tecan Ovation® Ultralow V2 DNA-Seq Library Prep Kit

tag: cell line

value: estrogen

tag: chip antibody

value: anti-IgG


title: S11 BoHV-1 challenged


title: WT, Glucose, Replicate 2

description:
Library name: NG_2
Parent (∆SARO_RS09410) grown in Glucose


title: balb_m1_tick

tag: Sex

value: Male


title: WT, Glucose, Replicate 1

description:
Library name: NG_1
Parent (∆SARO_RS09410) (∆SARO_RS09410) grown in Glucose


title: S6 control

value: control


title: balb_f2_none


title: S5 control


title: balb_m1_none


title: MCF7 10^-10M E2 1h replicate 1 IgG CUT&RUN

description: IgG CUT&RUN


title: MCF7 10^-10M E2 1h replicate 2 IgG CUT&RUN

description: IgG CUT&RUN


title: UCD12 10^-8M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_8_peak.bed

value: anti-ER


title: S4 control

value: Holstein-Friesian


title: S3 control


title: balb_f1_tick


title: clyta planula acme 4

city: Villefranche-sur-mer

first: Richard

last: Copley

address: 181 chemin du lazaret

country: France

institute: CNRS UMR7009

description: Library name: ACME4

data_processing:
Mapping to genome builds using STARsolo
Assembly: Clytia v3 / Astroides v1 / Pocillopora ASM370409v1
Supplementary files format and content: STARsolo data matrices

organism: Clytia hemisphaerica

source_name: planula larva

extract_protocol:
ACME/methanol as described
10X genomics libraries

value: planula larva


title: clyta planula acme 5

description: Library name: ACME5


title: UCD12 10^-8M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_8_peak.bed


title: clyta planula acme 3

description: Library name: ACME3


title: clyta planula methanol

description: Library name: METH


title: balb_f3_tick


title: S2 control


title: balb_f1_none


title: S1 control


title: clyta planula acme 2

description: Library name: ACME2


title: UCD12 10^-10M E2 1h replicate 2 IgG CUT&RUN

description: IgG CUT&RUN


title: MEC-29

city: KUNMING

first: Ruiqing

last: LONG

state: YUN NAN PROVINCE

address: XICHANG ROAD

institute: the first affiliated hospital of Kunming medical university

data_processing:
Data from PacBio Sequel were exported in the BAM format, and circular consensus sequencing (CCS) files were exported using SMRT Link v8.0. Data from different samples were identified according to their barcode sequences and converted to the FastQ format.
After exporting the PacBio downlink data to a CCS file (the CCS sequence was obtained using SMRT Link v8.0, provided by PacBio), the data were pre-processed in three main steps: (i) CCS identification: raw CCS sequence data obtained by barcode identification using Lima v1.7.0; (ii) CCS filtering, identification, and removal of primer sequences; and (iii) length filtering using Cutadapt 1.9.1 to obtain clean CCS sequences that did not contain primer sequences. UCHIME v8.1 was used to identify and remove chimeric sequences and obtain effective CCS sequences.
Assembly: Silva.138
Supplementary files format and content: See the Method.pdf and Result.pdf in the src-en folder for details.

organism: human metagenome

source_name: Middle-ear lesion tissues

extract_protocol:
The nucleic acid was extracted by TGuide S96 magnetic bead method soil/feces genomic DNA extraction kit. Remarks: Manufacturer: Tiangen Biochemical Technology (Beijing) Co., Ltd., model: DP812. Extraction kit: TGUIDE S96 Magnetic SOIL/STOOL DNA Kit (Tiangen Biotechnology (Beijing) Co., Ltd., China)
DNA was isolated from the specimens and processed for microbiome analysis by 16S rRNA gene sequencing. Genomic DNA was extracted using a PowerSoil® DNA Isolation Kit following the manufacturer’s instructions. The extracted total DNA was subjected to PCR using specific primers with barcodes synthesised based on the full-length primer sequences (27F: 5’-AGRGTTTGATYNTGGCTCAG-3’ and 1492R:5’- TASGGHTACCTTGTTASGACTT-3’). The PCR conditions were as follows: 95 °C for 5 min, 25/30 cycles of 95 °C for 30 s, 50 °C for 30 s, and 72 °C for 60 s/1 kb, and 72 °C for 7 min). The PCR products were purified, quantified, and homogenised to form a sequencing library (SMRT Bell).

value: middle ear cholesteatoma (MEC)


title: UCD12 10^-10M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_10_peak.bed


title: S18

source_name: pharyngeal tonsil

value: pharyngeal tonsil

value: BoHV-1 challenged


title: UCD12 10^-10M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_10_peak.bed


title: S17


title: MEC-28


title: Pocillopora planula larva C6-2

description: Library name: A-1_C6_pocillopora-acuta-2

organism: Pocillopora acuta


title: clyta planula acme 1

description: Library name: ACME1


title: MEC-27


title: S16


title: UCD12 10^-10M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_10_peak.bed


title: MEC-26


title: UCD12 10^-12M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_12_peak.bed


title: Pocillopora planula larva C3

description: Library name: 4-1_C3_pocillopora-acuta


title: MEC-25


title: Pocillopora planula larva C6-1

description: Library name: A-1_C6_pocillopora-acuta-1


title: UCD12 10^-12M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_12_peak.bed


title: S14


title: Astroides planula larva, facs sorted d

description: Library name: Houliston_Astroides_Facs2

organism: Astroides calycularis


title: UCD12 10^-8M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_8_peak.bed


title: UCD12 ETOH 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed

value: ethanol vehicle


title: Astroides planula larva, facs sorted c

description: Library name: Astraoides_Facs1


title: MEC-23


title: Astroides planula larva, facs sorted b

description: Library name: Houliston_Astroides_Facs1


title: S12


title: MEC-22


title: UCD12 10^-12M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_10_12_peak.bed


title: S15


title: UCD12 ETOH 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed


title: S13


title: MEC-24


title: Astroides planula larva a

description: Library name: Astroides7000


title: S10


title: UCD12 ETOH 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed


title: MEC-21


title: MEC-20


title: MCF7 10^-8M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_8_peak.bed

source_name: MCF7 cell line


title: S9


title: Clytia planula cells, 52 hpf

description: Library name: P4-1


title: MCF7 10^-8M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_8_peak.bed


title: MEC-18


title: S8


title: MCF7 10^-8M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_8_peak.bed


title: Clytia planula cells, 66 hpf bis

description: Library name: P2-2bis


title: MEC-17


title: S7


title: Clytia planula cells, 66 hpf

description: Library name: P2-2


title: MCF7 10^-10M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_10_peak.bed


title: S6


title: S11


title: MEC-16


title: S5


title: MCF7 10^-10M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_10_peak.bed


title: Six2_E185_T1_visiumHD

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Library name: Sample 1

data_processing:
Fastq files were processed using the spaceranger count pipeline in SpaceRanger v3.0.1 with the “refdata-gex-mm10-2020-A” mm10 index files provided by 10x.
A custom probe was designed to target the mutant allele of Mllt1. To include the custom probe in the SpaceRanger workflow, the “Visium_Mouse_Transcriptome_Probe_Set_v2.0_mm10-2020-A.csv” file provided by 10x was appended with an extra row to specify the sequence of the custom probe (TGAGCTTCTCACAGCGCAGGTGGTTCAGGTGGTTGACAGGAGGGTTGCCC), filling in gene ID and name fields to differentiate it from the native Mllt1 probes.
Assembly: mm10
Supplementary files format and content: *-fiducials-image-registration.json - JSON file produced by manual alignment of CytAssist and H&E images in 10x Loupe Browser
Supplementary files format and content: *_cytassist.tif - CytAssist image
Supplementary files format and content: *_brightfield.tif - H&E stained high-resolution, brightfield image
Supplementary files format and content: *_outs.tar.gz - The outs/ folder from the SpaceRanger pipeline
Library strategy: Spatial Transcriptomics

source_name: kidney

extract_protocol:
FFPE tissue sections were placed on slides, stained, and imaged according to manufacturer’s instructions in the Visium HD FFPE Tissue Preparation Handbook (10X Genomics, Rev A).
Slides were further processed with the 10X Visium Mouse Transcriptome Probe Kit v2 (10X Genomics, Rev A) according to the manufacturer’s instruction, including probe transfer to the Visium HD slide (6.5 mm) using the Visium CytAssist (10x Genomics, Pleasanton, CA).

value: kidney


title: MCF7 10^-10M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_10_peak.bed


title: Clytia planula cells, 52 hpf bis

description: Library name: P4-1bis


title: MEC-14


title: S3


title: MCF7 10^-12M E2 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_12_peak.bed


title: Inner cell mass of E3.5 blastocyst, male, rep12

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

description: hic single E3.5 ICM male 12

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Inner cell mass

extract_protocol:
Embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).

value: Inner cell mass

value: wild type

value: C57BL/6N X PWK/PhJ


title: MEC-13


title: MEC-19


title: Inner cell mass of E3.5 blastocyst, male, rep11

description: hic single E3.5 ICM male 11


title: MCF7 10^-12M E2 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_12_peak.bed


title: S2


title: Inner cell mass of E3.5 blastocyst, male, rep10

description: hic single E3.5 ICM male 10


title: MCF7 10^-12M E2 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_MCF7_E2_10_12_peak.bed


title: S1


title: MCF7 ETOH 1h replicate 3 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed


title: MEC-11


title: 13_NFRKRAS48

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

institute: WEILL CORNELL MEDICINE

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Assembly: Mus musculus - mouse (GRCm38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: pancreas

extract_protocol:
pancreata were removed, flash frozen in liquid nitrogen, and RNA was extracted from liver tissue  using RNeasy Plus Mini kit (Qiagen Cat#74134).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: regular chow fed mice

value: pancreas


title: Inner cell mass of E3.5 blastocyst, male, rep8

description: hic single E3.5 ICM male 8


title: Inner cell mass of E3.5 blastocyst, male, rep9

description: hic single E3.5 ICM male 9


title: Foxd1_E185_T1_visiumHD

description: Library name: Sample 2

value: Foxd1GC/+;Enl+/+ and Foxd1GC/+;EnlT1/+


title: MEC-15


title: MEC-10


title: 12_NFRKRAS16


title: S4


title: MEC-9


title: 11_NFRKRAS12


title: Inner cell mass of E3.5 blastocyst, male, rep7

description: hic single E3.5 ICM male 7


title: MCF7 ETOH 1h replicate 1 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed


title: Inner cell mass of E3.5 blastocyst, male, rep6

description: hic single E3.5 ICM male 6


title: MEC-8


title: 10_KRAS41


title: Inner cell mass of E3.5 blastocyst, male, rep5

description: hic single E3.5 ICM male 5


title: MEC-7


title: MEC-6


title: 09_KRAS11


title: MEC-12


title: Inner cell mass of E3.5 blastocyst, male, rep4

description: hic single E3.5 ICM male 4


title: Pocillopora planula larva aboral end, C5 colony

description: Library name: Pocillopora-aboral-C5

data_processing:
Mapping to genome builds using STAR
Assembly: Clytia v3 / Astroides v1 / Pocillopora ASM370409v1
Supplementary files format and content: STAR mapping counts per gene, format: genename,count

extract_protocol:
Total RNA was extracted using the RNAqueous™ Total RNA Isolation Kit (Ambion, Thermo Fisher). Treatment with DNase I (Q1 DNAse, Promega) for 20 min at 37 °C (2 units per sample) was followed by purification using the RNeasy minElute Cleanup kit (Qiagen). RNA quality of all samples was checked using the Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit.
Library preparation and sequencing were outsourced (BGI, DNBseq), generating 30 million 100-base paired end reads per replicate.


title: 08_KRAS10


title: Pocillopora planula larva oral end, C5 colony

description: Library name: Pocillopora-oral-C5


title: Pocillopora planula larva oral end, C3 colony

description: Library name: Pocillopora-oral-C3


title: MCF7 ETOH 1h replicate 2 ERα CUT&RUN

description:
ER CUT&RUN
06_UCD12_EtOH_peak.bed


title: MEC-5


title: Pocillopora planula larva aboral end, C3 colony

description: Library name: Pocillopora-aboral-C3


title: 07_NRF46

value: Nrf2Act-PEC:Pancreas specific Nrf2 activated mice


title: MEC-4


title: Inner cell mass of E3.5 blastocyst, male, rep2

description: hic single E3.5 ICM male 2


title: Inner cell mass of E3.5 blastocyst, male, rep3

description: hic single E3.5 ICM male 3


title: 06_NRF8


title: MEC-3


title: 05_NRF36


title: Inner cell mass of E3.5 blastocyst, male, rep1

description: hic single E3.5 ICM male 1


title: Clytia planula larva oral end 2

description: Library name: Clytia-oral-2


title: Inner cell mass of E3.5 blastocyst, female, rep14

description: hic single E3.5 ICM female 14


title: Uncut Clytia planula 1

description: Library name: Clytia-ctrl-1


title: MEC-1


title: Inner cell mass of E3.5 blastocyst, female, rep13

description: hic single E3.5 ICM female 13


title: MEC-2


title: Uncut Clytia planula 2

description: Library name: Clytia-ctrl-2


title: Clytia planula larva oral end 1

description: Library name: Clytia-oral-1


title: 03_CTR5

value: Wild type B6 mice


title: Clytia planula larva aboral end 2

description: Library name: Clytia-aboral-2


title: CSOM-12

value: chronic suppurative otitis media (CSOM)


title: 02_CTR3


title: Inner cell mass of E3.5 blastocyst, female, rep12

description: hic single E3.5 ICM female 12


title: Inner cell mass of E3.5 blastocyst, female, rep11

description: hic single E3.5 ICM female 11


title: Clytia planula larva aboral end 1

description: Library name: Clytia-aboral-1


title: CSOM-11


title: EedKO_rep2 (KC_EEDKO#4)

data_processing:
Data were checked for quality with FASTQC (v0.11.9) and aligned to the mm10 version of the mouse genome (mm10_UCSC_GRCm38.p3) with STAR (v2.7.3a).
Gene expression quantification was achieved within the STAR alignment step, with the parameter --quantMode GeneCounts. Data normalization and differential expression analysis was carried out with DESeq2 (v1.34.0), within the R environment (v4.1.3)
Counts data from all conditions were filtered based on their raw count, keeping only those where the sum of the counts for all samples was higher than 10, then normalised and logged with DESeq2 v1.34.0 rlog function (Love et al., 2014)
Assembly: Mus musculus - mouse (GRCm38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.

source_name: Mouse PDAC cell line

extract_protocol:
RNA was extracted from liver tissue  using RNeasy Plus Mini kit (Qiagen Cat#74134).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

value: Mouse PDAC cell line

value: KrasG12D; EedKO

value: CRISPR/Cas9 EEDKO


title: CSOM-9


title: CSOM-10


title: 761_2_1

city: Daejeon

first: Yeong Seok

last: Kim

state: Yuseong

address: 141, Gajeong-ro

country: South Korea

institute: Korea Research Institute of Chemical Technology

description:
Library name: Sample 5
761_2_1

data_processing:
To check the quality of data before processing with analysis on raw data, FastQC (v0.11.7) was used.
Trimming was performed with various parameters for illumina paired-end or single-end using trimmomatic 0.38.
The reference genome sequences were aligned using Bowtie 1.1.2
The abundance of the filtered genes was calculated from the number of mapped reads using HTseq version 0.10.0
Assembly: CFBP1430
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Erwinia amylovora

growth_protocol: E. amylovora was maintained on mannitol glutamate yeast extract medium (MGY) at 28 ºC

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (Qiagen).
The RNA-seq library was generated using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina) followint manufacturer's protocols.

treatment_protocol: Edodine was treated at IC50 on bacterial inoculation, and incubated at 0.6 of optical density.

value: Bacterial cell

value: Edodine


title: 761_3_1

description:
Library name: Sample 6
761_3_1


title: Inner cell mass of E3.5 blastocyst, female, rep9

description: hic single E3.5 ICM female 9


title: EedKO_rep1 (KC_EEDKO#1)


title: CSOM-8


title: 761_1_1

description:
Library name: Sample 4
761_1_1


title: CSOM-7


title: Ezh2KO_rep2 (KC_EZH2KO#3)

value: KrasG12D; Ezh2KO

value: CRISPR/Cas9 EZH2KO


title: NO_3_1

description:
Library name: Sample 3
NO_3_1

value: non-treatment


title: Inner cell mass of E3.5 blastocyst, female, rep7

description: hic single E3.5 ICM female 7


title: Inner cell mass of E3.5 blastocyst, female, rep8

description: hic single E3.5 ICM female 8


title: 04_NRF6


title: Ezh2KO_rep1 (KC_EZH2KO#2)


title: NO_2_1

description:
Library name: Sample 2
NO_2_1


title: Inner cell mass of E3.5 blastocyst, female, rep6

description: hic single E3.5 ICM female 6


title: Ctrl_rep2 (KC_CTR#2)

value: KrasG12D; CTR

value: CRISPR/Cas9 CTR


title: Inner cell mass of E3.5 blastocyst, female, rep5

description: hic single E3.5 ICM female 5

value: Inner cell mass

value: wild type


title: 01_CTR2

value: pancreas


title: Inner cell mass of E3.5 blastocyst, female, rep10

description: hic single E3.5 ICM female 10

value: C57BL/6N X PWK/PhJ


title: Ctrl_rep1 (KC_CTR#1)


title: CSOM-5


title: NO_1_1

description:
Library name: Sample 1
NO_1_1


title: CSOM-4


title: LA#15  (KPC_EZH2KO#2)

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Genes with 0 counts in all the samples were removed.
Assembly: Mus musculus - mouse (GRCm38)
Supplementary files format and content: Counts matrix with gene expression value for all samples.


title: LA#14 (KPC_EZH2KO#1)


title: Inner cell mass of E3.5 blastocyst, female, rep2

description: hic single E3.5 ICM female 2


title: Inner cell mass of E3.5 blastocyst, female, rep3

description: hic single E3.5 ICM female 3


title: Pero-M-1_tick

organism: Peromyscus leucopus

value: skin

value: Male

value: tickbite


title: Inner cell mass of E3.5 blastocyst, female, rep1

description: hic single E3.5 ICM female 1


title: Pero-F-3_tick

value: Female


title: CSOM-6

value: chronic suppurative otitis media (CSOM)


title: LA#12 (KPC_CTR#2)

value: Mouse PDAC cell line


title: Pero-F-1_tick


title: Uncut Astroides planula 2

description: Library name: astr_ctrl_2

value: planula larva


title: Pero-F-2_tick


title: CSOM-1


title: LA#11 (KPC_CTR#1)


title: Inner cell mass of E3.5 blastocyst, female, rep4

description: hic single E3.5 ICM female 4


title: M.tuberculosis H37Rv, drug exposure of Linezolid for 24 hr,rep2

city: Delhi

first: Mandira

last: Varma Basil

address: University of Delhi

department: Department of Microbiology

country: India

institute: Vallabhbhai Patel Chest Institute

description: Library name: AN-3-1

data_processing:
Redcliffe Labs processed the transcriptome samples using in-house pipelines, including Adapter Removal v2.3.2 and HISAT2 v2.1.0.
QC method Qubit and TapeStation 4150
Gene expression was estimated with FeatureCounts v2.0.1
differential gene expression analysis was conducted  using edgeR
The clean data were aligned to the M. tuberculosis H37Rv reference genome HISAT2 v2.1.0. Gene expression estimation was performed using FeatureCounts v2.0.1, and differential gene expression was analyzed using edgeR
Assembly: M. tuberculosis H37Rv reference genome ASM19595v2
Supplementary files format and content: Expression_Estimation Linezolid.xlsx

organism: Mycobacterium tuberculosis

source_name: Bacterial Cell

growth_protocol: H37Rv culture was maintained in Lowenstein Jensen (LJ) medium and Middle brook 7H9 broth containing 0.2 percent glycerol, 0.05 percent Tween 80, and OADC (oleic acid, albumin bovine, fraction V, dextrose catalase); and incubated at 37°C

extract_protocol:
RNA from both exposed (sub-inhibitory concentration of ¼ MIC) and unexposed cultures was extracted using the TRIZOL method
RNA samples extracted from log phase cultures of H37Rv after exposure to ¼ MIC of linezolid, and unexposed control sample, that met the quality criteria were used for library preparation with the NEB RNA Library Prep Kit and then sequenced

treatment_protocol: M. tuberculosis H37Rv culture maintained in Middlebrook 7H9 liquid medium was exposed to different subinhibitory concentrations of linezolid (1/2MIC, 1/4MIC and 1/8MIC) at mid log phase . The unexposed culture was taken as control.

value: Bacterial Cell

value: Linezolid exposed culture

tag: time

value: 24 hrs


title: M.tuberculosis H37Rv, drug exposure of Linezolid for 24 hr,rep3

description: Library name: AN-3-2


title: Pero-M-2_none

value: no tickbite


title: LA#10 (KC_EZH2KO#3)

value: KrasG12D; Ezh2KO

value: CRISPR/Cas9 EZH2KO


title: M.tuberculosis H37Rv, drug exposure of Linezolid for 24 hr,rep1

description: Library name: AN-3


title: Pero-M-2_tick


title: Astroides planula larva oral end 2

description: Library name: astr_oral_2


title: Pero-M-1_none


title: LA#9 (KC_EZH2KO#2)


title: Astroides planula larva oral end 1

description: Library name: astr_oral_1


title: M.tuberculosis H37Rv, unexposed culture, Control, rep3

description: Library name: AN-1-2

value: Unexposed culture


title: Pero-F-3_none


title: CSOM-3


title: LA#8 (KC_CTR#3)

value: KrasG12D; CTR

value: CRISPR/Cas9 CTR


title: CSOM-2


title: LA#13 (KPC_CTR#3)


title: Astroides planula larva aboral end 2

description: Library name: astr_aboral_2


title: Pero-F-2_none


title: LA#7 (KC_CTR#2)


title: M.tuberculosis H37Rv, unexposed culture, Control, rep1

description: Library name: AN-1

value: wild type


title: Astroides planula larva aboral end 1

description: Library name: astr_aboral_1


title: Uncut Astroides planula 1

description: Library name: astr_ctrl_1


title: 2 w-HI biol rep 7

status: Public on Feb 19 2025

city: Gainesville

first: Zhihua

last: Jiang

state: FL

address: 1600 SW Archer Rd

institute: University of Florida

description: Library name: 2 w-HI-7

data_processing:
To ensure quality, multi-QC Analysis was conducted for each sequence run using Illumina’s Dragen RNA software (Illumina). Once sequencing was completed, the raw sequence base call files (BCL) were converted to FASTQ files using Illumina’s bcl2fastq conversion software (Illumina, CA) as input for downstream bioinformatics analysis. The raw sequencing reads were quality controlled using FastQC and mapped to the mouse GRCm39 genome assembly as well as Gencode M32 annotations using STAR aligner. RSEM were applied to summarize gene counts.
Assembly: GRCm39
Supplementary files format and content: Processed data includes tab-delimited text files (.SJ.out.tab) containing splice junction information, such as chromosomal coordinates, junction types, and read counts, generated by STAR aligner.

source_name: ascending aorta

extract_protocol:
Total RNAs were extracted using a TRIzol plus RNA Purification kit (12183555, Invitrogen) following manufacturer’s instructions. An aliquot was collected for every sample and analyzed with an RNA 6000 Pico Kit (5067-1513, Agilent) on an Agilent 2100 Bioanalyzer (Agilent, CA). All RNA samples produced a RIN > 8.0 while those entering next step had a RIN ³ 8.5.
Illumina Stranded mRNA Prep and Ligation Kit

value: ascending aorta

tag: time point

value: 2 w

value: mixed

tag: batch


title: 2 w-HI biol rep 4

description: Library name: 2 w-HI-4


title: Pero-F-1_none

city: Boston

value: skin

value: Female


title: 2 w-HI biol rep 5

description: Library name: 2 w-HI-5


title: 2 w-HI biol rep 6

description: Library name: 2 w-HI-6


title: 2 w-HI biol rep 1

description: Library name: 2 w-HI-1


title: 2 w-HI biol rep 3

description: Library name: 2 w-HI-3


title: 2 w-A biol rep 3

description: Library name: 2 w-A-4


title: 2 w-A biol rep 5

description: Library name: 2 w-A-6


title: 2 w-A biol rep 4

description: Library name: 2 w-A-5


title: 2 w-HI biol rep 2

description: Library name: 2 w-HI-2


title: 1 w-HI biol rep 7

description: Library name: 1 w-HI-7

value: 1 w


title: 2 w-A biol rep 6

description: Library name: 2 w-A-7


title: 1 w-HI biol rep 6

description: Library name: 1 w-HI-6


title: 2 w-A biol rep 2

description: Library name: 2 w-A-3


title: 2 w-A biol rep 1

description: Library name: 2 w-A-2


title: 1 w-HI biol rep 3

description: Library name: 1 w-HI-3


title: 1 w-HI biol rep 5

description: Library name: 1 w-HI-5


title: M.tuberculosis H37Rv, unexposed culture, Control, rep2

description: Library name: AN-1-1


title: 1 w-A biol rep 6

description: Library name: 1 w-A-6


title: 1 w-HI biol rep 2

description: Library name: 1 w-HI-2


title: 1 w-A biol rep 4

description: Library name: 1 w-A-4


title: 1 w-A biol rep 5

description: Library name: 1 w-A-5


title: 1 w-A biol rep 3

description: Library name: 1 w-A-3


title: 1 w-A biol rep 2

description: Library name: 1 w-A-2


title: B biol rep 6

description: Library name: B-6


title: B biol rep 4

description: Library name: B-4


title: B biol rep 5

description: Library name: B-5


title: B biol rep 1

description: Library name: B-1


title: H2009 cell line, Vehicle control, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Library name: H2009_Vehicle_n3_S9

data_processing:
Fastq generation performed with BaseSpace DRAGEN analysis version 1.2.1.
Quality control of fastq sequences performed using FastQC (v0.10.1).
Sequences alinged to the hg38.p12 human genome using STAR (v2.6).
Read counts were obtained from the STAR alignment files using htseq-count (v0.10.0) and the Ensembl v93 gene annotations with ribosomal genes removed.
Assembly: hg38.p12
Supplementary files format and content: tab-delimited file containing raw reads determined from htseq-count

growth_protocol: Cells were maintained in RPMI-1640 (Gibco-ThermoFisher, Waltham, MA, USA), supplemented with 10% FBS, and grown at 37C in a humidified 5% CO2 incubator.

extract_protocol:
Following incubation, RNA was isolated from LUAD cells using EZNA Total RNA Kit (Omega, Norcross, GA, USA).
Libraries were prepared from 1µg RNA using the Universal Plus mRNA-Seq with NuQuant® (Tecan, Switzerland), and Universal Plus UDI S02622 was used to barcode the libraries.  Size, purity, and quantitation of libraries was performed using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Libraries were quantified by Qubit dsDNA HS kit (ThermoFisher, Q33231) and size analysis done with the HS NGS Fragment Kit (Agilent, DNF-474-0500) on the Agilent Fragment Analyzer.  Libraries were diluted to 2nM with Illumina Resuspension Buffer (RSB), equivolume pooled, then further diluted to 750pM with Resuspension buffer with Tween. PhiX positive control was spiked in to a final concentration of 2%. Denaturation and final dilution was done onboard instrument and libraries sequenced on a P2 100 cycle kit (Illumina, 20046811) with 101 sequencing cycles and 2 index reads of 8bp each on the NextSeq 2000 instrument.

treatment_protocol: For our bacterially supplemented media, E. coli were grown in 2mL lysogeny broth (LB) media for 24 hours on a shaker at 37C.  Afterwards, E. coli were added to RPMI-1640 supplemented with 10% FBS and 1% L-glutamine at a final OD of 0.1 and allowed to grow overnight. Following incubation, E. coli cells were removed from the media by centrifugation (12,000 x g for 10 minutes) and filter sterilization (0.2µ).  For inhibition of TLR4, cells were incubated in C34 (MedChemExpress, NJ, USA) at a final concentration of 5µM for 2 days.   Bacterially supplemented media was treated in 3 separate manners: filtered dialysis, charcoal stripping and RNAse supplementation.  14mL of bacterially supplemented media was filter dialyzed using Ultracel®-3K (Amicon, Burlington, MA, USA) at a centrifugal force of 4000 x g for 1 hour.   Charcoal stripping was performed by 0.28g of Dextran Coated Charcoal (Sigma Aldrich, Burlington, MA, USA) into 14mL of bacterially supplemented media and incubated rocking overnight at 4oC.  Media was then centrifuged at 2000 x g for 15 minutes to remove charcoal.  Bacterially supplemented media was also treated with RNAseA at a final concentration of 100µg/mL prior to administration to LUAD cells. Human LUAD cell lines, A549 and H2009, were incubated in bacterially supplemented RPMI-1640 media for 48 hours.

value: 1:1 RPMI:PBS


title: B biol rep 3

description: Library name: B-3


title: B biol rep 2

description: Library name: B-2


title: H2009 cell line, Vehicle control, replicate 2

description: Library name: H2009_Vehicle_n2_S8


title: H2009 cell line, Bacterially supplemented media, replicate 3

description: Library name: H2009_Bacteria_n3_S12

value: 1:1 RPMI; bacterially supplemented media


title: H2009 cell line, Bacterially supplemented media, replicate 2

description: Library name: H2009_Bacteria_n2_S11


title: H2009 cell line, Bacterially supplemented media, replicate 1

description: Library name: H2009_Bacteria_n1_S10


title: H2009 cell line, Vehicle control, replicate 1

description: Library name: H2009_Vehicle_n1_S7


title: A549 cell line, Bacterially supplemented media, replicate 2

description: Library name: A549_Bacteria_n2_S5


title: 1 w-HI biol rep 4

description: Library name: 1 w-HI-4


title: A549 cell line, Vehicle control, replicate 3

description: Library name: A549_Vehicle_n3_S3


title: A549 cell line, Bacterially supplemented media, replicate 1

description: Library name: A549_Bacteria_n1_S4


title: A549 cell line, Bacterially supplemented media, replicate 3

description: Library name: A549_Bacteria_n3_S6


title: 1 w-HI biol rep 1

description: Library name: 1 w-HI-1


title: A549 cell line, Vehicle control, replicate 2

description: Library name: A549_Vehicle_n2_S2


title: K562,EC100-GFP;RAD21-AID,IAA,rep2,MYC

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Library name: sample24

data_processing:
4C-seq reads were mapped to the hg38 reference genome and processed using pipe4C (https://github.com/deLaatLab/pipe4C).
Normalized 4C coverage was calculated using R (rproject.org). Counts at non-blind fragments were adjusted to 1 million intra-chromosomal mapped reads after exclusion of the two highest-count fragments.
Count data was smoothed using a running mean with a window size of 21 fragments using the R package caTools v1.18.2.
Assembly: hg38
Supplementary files format and content: wig, bed
Library strategy: 4C-seq

growth_protocol: EC100-GFP RAD21-AID and EC100-GFP LDB1-FKBP  K562 cells were cultured in RPMI 1640 (Gibco) supplemented with 10% FBS (Sigma) and 1% pen–strep (Gibco). Cells were grown at a maximal density of 5x10^5 cells/ml. Experiments were performed maximum 1 week after FACS sorting cells GFP positive for 2 consecutive weeks with gating based on non-GFP expressing K562 cells.

extract_protocol:
4C templates preparation was performed as described in PMID: 31351925. In short, 5-10M cells were crosslinked with 2% formaldehyde for 10 minutes and quenched with 0.125M final concentration glycine on ice. Pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 7.5, 0.5% NP-40, 1% TritonX-100, 150 mM NaCl, 5 mM EDTA) for 20 minutes on ice. Then, SDS (0.3% final concentration) was added, followed by TritonX-100 (2.5% final concentration), and chromatin was digested in situ using 100U Csp6I (ThermoFisher Cat#ER0211). DNA was then ligated using T4 ligase (Roche Cat#10799009001), decrosslinked by overnight ProtK treatment (Roche Cat#3115801001), and purified using isopropanol precipitation. Samples were then digested using 50U NlaIII (NEB Cat#R0125), ligated at a concentration of 5ng template/ul, and final 4C templates were purified with P-Beads (Macherey Nagel Cat#744100.34). 4C PCRs were performed in a two-step manner using the Expand Long Template PCR system (Roche Cat#11759060001).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using ELT PCR System (Roche, cat. no. 11681842001).

treatment_protocol: To deplete RAD21, cells were treated with 1μM 5-Ph-IAA (MedChemExpress, Cat#HY-134653) for 2 hours.To deplete LDB1, dTAG-7 (TOCRIS, Cat#6912) was added to the medium in a final concentration of 500nM for 4 hours.

value: IAA

tag: replicate

tag: viewpoint

value: MYC


title: K562,EC100-GFP;RAD21-AID,IAA,rep2,MS4A3

description: Library name: sample23


title: S2 cells, ChIP INPUT, replicate 2

first: Stephen

last: Gisselbrecht

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

description: Library name: Input-R2

data_processing:
bcl2fastq is used for base calling.
Trim galore (v. 0.6.6) was used to remove adaptor sequences and bases with sequencing quality below 30.
Reads were then mapped to dm3 using bowtie2 (v. 2.5.1) with the settings “--sensitive-local --no-discordant --no-mixed”. PCR duplicates were called using Picard MarkDuplicates. Libraries were filtered for alignments above mapq 30.
Peak calling was performed using MACS2 (v. 2.1.1.20160309) with the corresponding input reads as control and the settings “--broad -g dm -f BAMPE”.
Following ENCODE guidelines, we used the irreproducible discovery rate (IDR) framework to identify peaks that are consistent between the two replicate samples that used the same antibody. For calling peaks found to be reproducible by IDR analysis, a more relaxed threshold of “-p 1e3” was used to call peaks in each library before running IDR (v. 2.0.2).
Assembly: dm3
Supplementary files format and content: broadPeak (except for input samples)
Supplementary files format and content: bedfiles of consistent peaks between replicates called by IDR (except for input samples)

extract_protocol:
Cells were fixed for 10 minutes in 1% formaldehyde, quenched, and frozen. Chromatin was sonicated with a Bioruptor Plus (Diagenode) at high power for 30 seconds on and 30 seconds off. Sixty cycles was chosen to fragment DNA with a peak of fragments ~200 - 600 bp.
100 µg chromatin as measured from the decrosslinked sample was aliquoted to each ChIP reaction. Eluted DNA was decrosslinked and purified using Monarch PCR and DNA Cleanup Kit (New England Biolab T1030S). DNA was quantified using Qubit HS dsDNA and High Sensitivity D5000 DNA ScreenTape assays (Agilent). Sequencing libraries were generated using NEBNext Ultra II (E7645S) with NEBNext multiplex oligos for Illumina (E7335S). The number of PCR cycles was selected according to manufacturer’s recommendations for the mass of DNA in each library. Input, H4K20me1 libraries using Abcam 9051 antibodies, and H3K27me3 libraries were amplified with 3 cycles of PCR, while H4K20me1 libraries using the Active Motif or Thermo antibodies required 6 cycles of PCR. QC of sequencing libraries was performed using Qubit High Sensitivity dsDNA assays for DNA concentration and High Sensitivity D1000 and D5000 DNA ScreenTape assays (Agilent)  for fragment length distributions. Libraries generated using the Active Motif or Thermo H4K20me1 antibodies were size-selected them with SPRISelect beads (Beckman Coulter B23317) prior to sequencing, using a right-side size selection with 0.4x bead ratio to remove large fragments.


title: S2 cells, ChIP INPUT, replicate 1

description: Library name: Input-R1


title: K562,EC100-GFP;RAD21-AID,IAA,rep2,LMO2

description: Library name: sample22


title: 1 w-A biol rep 1

description: Library name: 1 w-A-1


title: S2 cells, H4K20me1 ChIP with Thermo Fisher MA5-18067 antibody, replicate 2

description: Library name: H4K20me1-Thermo-R2

value: Thermo Fisher MA5-18067


title: K562,EC100-GFP;RAD21-AID,IAA,rep1,MYC

description: Library name: sample21


title: S2 cells, H4K20me1 ChIP with Thermo Fisher MA5-18067 antibody, replicate 1

description: Library name: H4K20me1-Thermo-R1


title: K562,EC100-GFP;RAD21-AID,IAA,rep1,MS4A3

description: Library name: sample20


title: S2 cells, H4K20me1 ChIP with Active Motif AB_2615074 antibody, replicate 1

description: Library name: H4K20me1-AM-R1_R1

value: Active Motif AB_2615074


title: S2 cells, H4K20me1 ChIP with Active Motif AB_2615074 antibody, replicate 2

description: Library name: H4K20me1-AM-R1_R2


title: K562,EC100-GFP;RAD21-AID,IAA,rep1,LMO2

description: Library name: sample19


title: A549 cell line, Vehicle control, replicate 1

description: Library name: A549_Vehicle_n1_S1


title: S2 cells, H4K20me1 ChIP with Abcam ab9051 antibody, replicate 2

description: Library name: H4K20me1-Abcam9051-R2

value: Abcam ab9051


title: K562,EC100-GFP;RAD21-AID,DMSO,rep2,MYC

description: Library name: sample18

value: DMSO


title: S2 cells, H3K27me3 ChIP, replicate 2

description: Library name: H3K27me3-R2

value: Epicypher 13-0055