title: myocardial tissue, DJ-1 treated mice, n1

city: Barcelona

first: Lina

last: Badimon

address: St Antoni M Claret, 167

department: ICCC-Cardiovascular Program

institute: Research Institut- HSCSP

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion after DJ-1 pre-treatment
S15

hyb_protocol: Hybridization controls from the Hybridization, Wash and Stain Kit (Affymetrix) were added to the sample. Every sample was hybridized to GeneChip Mouse Gene 1.0 ST array during 16 h at 45°C and 60 rpm, according to manufacturer’s instruccions. Hybridization, washing and staining of microarrays were performed using the Affymetrix GeneChip 3000 7G System (645 Hybridization Oven, 450 Fluidic Station and GeneChip 3000 7G Scanner).

scan_protocol: Scanning of microarrays was performed using the Affymetrix GeneChip 3000 7G System (645 Hybridization Oven, 450 Fluidic Station and GeneChip 3000 7G Scanner).

data_processing: Raw data were pre-processed (background correction, normalization and median polish summarization of the probes) with Robust Multiarray Average (RMA) method. Bioinformatics was used to analyze the extracted log2 expression data.

source_name: myocardial tissue from mice, recombinant DJ-1 protein pre-treatment 1h before LAD coronary artery ligation for 45 minutes followed by 2 hours of reperfusion

label_protocol: 5.5 ug of single strand DNA were fragmented and labeled with biotin using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Male CH3 mice 8-10 weeks old weighing 25-30g

extract_protocol: Frozen tissue was grinded using mortar and pestle. Total RNA was extracted using a combined organic extraction and silica-membrane columns method (RNesasy Mini Kit, Qiagen; Valencia, CA, USA). RNA quantification was determined spectrophotometrically using the Nanodrop ND-1000 (Thermo Fisher Scientific; Whaltham, MA, USA). RNA quality was measured using Agilent 2100 Bioanalyzer technology (Agilent Technologies; Santa Clara, CA, USA) with the Agilent RNA 6000 Nano Kit (Agilent Technologies). Only RNA samples with RIN > 7 values (RNA integrity number) were chosen for microarray experiments. Using the Ambion WT Expression Kit (Ambion, Life Tecnologies, Carlsbad, CA, USA) 100 ng of total RNA (mixed with poly-A controls; Affymetrix) were converted to double strand DNA, in two steps, in order to obtain cRNA by an in vitro transcription. Single strand DNA was obtained from 10 ug of cRNA.

treatment_protocol: 45 minutes LAD coronary artery occlusion followed by 2 hours of reperfusion. Afterwards hearts were carefully excised.

value: myocardial tissue

value: male

tag: strain

value: 8-10 weeks old

tag: weight


title: myocardial tissue, DJ-1 treated mice, n2

status: Public on Dec 20 2020

type: RNA

country: Spain

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion after DJ-1 pre-treatment
S13

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: Sex

tag: age


title: myocardial tissue, placebo treated mice, n4

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion without DJ-1 pre-treatment
S10

source_name: myocardial tissue from mice, PBS pre-treatment 1h before LAD coronary artery ligation for 45 minutes followed by 2 hours of reperfusion


title: 5027_S4

type: SRA

city: Durham

first: Aashutosh

last: Vihani

state: NC

address: 264 CARL Building

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
STAR read alignment
RSEM read quantification
EdgeR differential expression
Intact olfactory receptor subsetting
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV files with differential expression statistics and rounded read counts

source_name: Whole olfactory mucosa

extract_protocol:
Whole olfactory mucosa was dissected and sequenced
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole olfactory mucosa

value: f

tag: genotype

value: wt

value: sex-combined


title: myocardial tissue, placebo treated mice, n2

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion without DJ-1 pre-treatment
S11


title: myocardial tissue, placebo treated mice, n1

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion without DJ-1 pre-treatment
S12


title: PreB_RNAseq_shRen_3

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

country: China

institute: Sichuan University

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
processed data files format and content: txt files with gene TPM

molecule: polyA RNA

source_name: PreB cells

growth_protocol: preB cells were cultured in RPMI 1640 medium supplemented with 20% gibco FBS, 1% Pen/Strep and 10ng/ml mouse IL7.

extract_protocol: RNA was extracted with Trizol

treatment_protocol: 24h after isolation and culture, preB cells were transducted with eMLM-shRen or eMLM-shPhf23 through retroviral infection. 48h after infection, the transducted cells labelled with GFP were sorted out by FACS AriaIII. Immediately after sorting, the cells were centrifugated to obtain cell pellets, followed by Trizol addition.

value: PreB cells

tag: plasmids

tag: replicates


title: CB_CB35

city: Oxford

first: Adam

last: Mead

address: Headington

department: WIMM

country: United Kingdom

institute: UNiversity of Oxford

data_processing:
Alignment to hg19 with CellRanger (2.0.0).
Raw UMI counts and cells were filtered and scaled by Seurat (2.0.1)
Genome_build: hg19
Supplementary_files_format_and_content: scaled UMI

organism: Homo sapiens

source_name: CD34+ HSPCs

extract_protocol:
FACS sorted CD34+ HSPCs were processed according to 10x genomics protocol
Library construction was preformed according to 10X genomics protocol

tag: cell type

value: CD34+ hematopoietic stem and progenitor cells (HSPCs)

value: cord blood


title: 276_TNF: CAGE-seq, Primary FLS, TNF stimulated

city: Manchester

first: Xiangyu

middle: Jack

last: Ge

address: Oxford road

institute: University of Manchester

description: processed_data_file: Knee_TNF_clusters_tpm.txt

data_processing:
CHiC were mapped to GRCh38 using HICUP, CHiCAGO was applied to the stimulatory conditions, treating each sample as a replicate. Interactions with CHiCAGO score over 5 were picked up and corresponding counts data were extracted from CHiCAGO results, for downstream differential interaction analysis using DESeq2.
Individual ATAC-seq reads were mapped to GRCh38 by Bowtie2. Duplicates were removed by Picard. Bam files of the stimulatory conditions were merged and MACS2 were applied to call peaks on each merged bam file.
RNA-seq data were mapped to GRCh38 by STAR. Gene expression quantification was done by RSEM, downstream normalizatioin and differential analysis was performed by DESeq2.
Hi-C reads were mapped to GRCh38 and processed by the HiC-Pro pipeline, the .hic files produced were then used for downstream TAD analysis using the R package TADCompare.
Hi-C reads were mapped to GRCh38 by HiCUP and then converted to HOMER format, runHiCpca.pl and findHiCCompartments.pl from HOMER were used to identify A/B compartments.
Genome_build: GRCh38
Supplementary_files_format_and_content: HGNC_FLS_norm_exp.txt: RNA-seq expression counts normalized by DESeq2.
Supplementary_files_format_and_content: narrowPeak/broadPeak: ATAC/ChIP-seq peaks as identified by MACS2 (chromosome, start, end, id, score, strand, signalValue, pValue, qValue, peak point-source)
Supplementary_files_format_and_content: allValidPairs.hic : Hi-C data processed by HiC-Pro.
Supplementary_files_format_and_content: Chicago_washU_text.txt : Significant Chi-C interactions (bait location, prey location, ChiCAGO score)
Supplementary_files_format_and_content: 18_segment.sorted.bed : ChromHMM state inference from 18 states based on 6 histone marks. (Segment_chr, segment_start, Segment_end, Inferred state)
Supplementary_files_format_and_content: All_stim/unstim_A/B.bed : Merged A/B compartments as identified by HOMER. (A/B compartment chr, A/B compartment start, A/B compartment end)
Supplementary_files_format_and_content: All_TADs_extended.sorted.bed : TADs identified with TADCompare, and their differential TAD status. (TAD chr, TAD start, TAD end, basal TAD score, stim TAD score, differential TAD score, differential status, enriched in condition, differential TAD type)

source_name: Primary FLS

extract_protocol:
Cultured human FLS from RA patients were treated with 10 ng/ml TNF, 24h or were left untreated (Supplementary table 2). RNA was isolated using the Quick RNA MicroPrep Kit (Zymo Research).
CAGE libraries were prepared and sequenced as previously described in Kodzius et al.

tag: sample id

tag: stimulation

value: 10 ng/ml TNF for 24 hours

tag: joint

value: knee

tag: disease state

value: Rheumatoid Arthritis


title: 460: CAGE-seq, Primary FLS, unstimulated

description: processed_data_file: MCP_clusters_tpm.txt

value: MCP


title: PreB_RNAseq_shPhf23.877_2


title: myocardial tissue, DJ-1 treated mice, n4

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion after DJ-1 pre-treatment
S16


title: myocardial tissue, placebo treated mice, n3

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion without DJ-1 pre-treatment
S9


title: myocardial tissue, DJ-1 treated mice, n3

description:
Gene expression data from myocardial tissue subjected to ischemia and reperfusion after DJ-1 pre-treatment
S14


title: PreB_RNAseq_shPhf23.877_1


title: 4998_S5

value: bax ko

value: sex-separated


title: 276: CAGE-seq, Primary FLS, unstimulated

description: processed_data_file: Knee_clusters_tpm.txt


title: 460_TNF: CAGE-seq, Primary FLS, TNF stimulated

description: processed_data_file: MCP_TNF_clusters_tpm.txt


title: 415B_TNF: CAGE-seq, Primary FLS, TNF stimulated


title: JMML_ID1

value: Juvenile Myelomonocytic Leukemia (JMML)


title: 4998_S4


title: CB_CB37


title: 4331_S10

extract_protocol:
Whole olfactory mucosa was dissected and either sequenced or subjected to pS6-IP-Seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: experimental

value: ebFarnesene


title: 415B: CAGE-seq, Primary FLS, unstimulated


title: PreB_RNAseq_shPhf23.338_2


title: CK

city: Lin'an

first: Jianhui

last: Li

state: Zhejiang

address: Jincheng Street

institute: Zhejiang A & F University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed.software CutAdapter,parameters -o 5 -p 100
Genome_build: Trinity_gene.fasta
Supplementary_files_format_and_content: tab-delimited text files include count and RPKM values for each Sample

organism: Cunninghamia lanceolata

source_name: Root

growth_protocol: 1/4 Hoagland nutrient solution was applied for cultivating strong plantlets for one month.

extract_protocol:
Total roots RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chinese fir were treated by low phosphorus (LP，the phosphorus present in distilled water, which was determined to be less than 0.01mM) and phosphorus sufficient (CK，phosphorus concentration of 1mM)for four months.

tag: phosphorus concentration

tag: treatment time

value: four months

value: root


title: PreB_RNAseq_shPhf23.338_3


title: LP


title: 4998_S3

value: Whole olfactory mucosa

value: m


title: 420_TNF: CAGE-seq, Primary FLS, TNF stimulated

description: processed_data_file: Shoulder_TNF_clusters_tpm.txt

value: shoulder


title: JMML_ID5


title: PreB_RNAseq_shPhf23.338_1

value: PreB cells


title: 4998_S1


title: 420: CAGE-seq, Primary FLS, unstimulated

description: processed_data_file: Shoulder_clusters_tpm.txt


title: Lymphoma_RNAseq_DMSO-3-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
DMSO-3-12h

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with gene counts, txt file with gene TPM

source_name: Lymphoma

growth_protocol: The lymphoma was developed on recipient mice after transplantation through tail vein injection.

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Myc-driven shPhf23 or control shRen lymphoma cells were harvested from enlarged lymph nodes of recipient mice.

value: Lymphoma cells


title: 424_TNF: CAGE-seq, Primary FLS, TNF stimulated


title: 4575_S6

value: f

value: wt


title: Lymphoma_RNAseq_DMSO-2-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
DMSO-2-12h


title: ZZ_3

city: Xinyang

first: pengpeng

last: Zhang

state: Henan

address: No.237 Nanhu Road Shihe District

institute: Xinayang Normal University

description:
circRNA
circRNA-seq
processed data file: circRNA_prediction_all.txt

data_processing:
For all raw sequencing data of each sample, adapter reads and low-quality reads were removed using Seqtk.
The filtered data were aligned to reference genome GRCm38.p4 (mm10) using BWA-MEM.
Identification of circRNAs was performed using CIRI.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: circRNA_prediction_all.txt: Tab-delimited text file.

source_name: myoblast

growth_protocol: The C2C12 mouse myoblasts were maintained in growth medium consisting of DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was isolated from C2C12 cells at the following time points: proliferating (70-80% confluence, D0), 3 days (D3), and 6 days (D6) after induction of differentiation. Total RNA was isolated using TRIzol according to the manufacturer’s instructions. To enrich circRNAs, the total RNAs was treated with RNAClean XP Kit (Cat# A63987, Beckman Coulter, Inc., Kraemer Boulevard, Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) following the manufacturer’s instructions.
1000 ng RNA was used as the input for the VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina ® (Vazyme, Inc., Piscataway, NJ, USA), and sequencing libraries were created according to the manufacturer's protocol.

treatment_protocol: Once confluent, the medium was switched to DMEM supplemented with 2% horse serum to promote myoblasts differentiation into myocytes and subsequent fusion to myotubes.

tag: cell line

value: myoblast cell line

tag: tissue origination

value: skeletal muscle

tag: time point

value: proliferation


title: 4575_S5


title: ZZ_2


title: ZZ_1


title: 4575_S4


title: Lymphoma_RNAseq_DMSO-1-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
DMSO-1-12h


title: 4998_S6

value: bax ko


title: 4998_S2

value: sex-separated


title: FH6d_3

value: differentiation 6 days


title: 427_TNF: CAGE-seq, Primary FLS, TNF stimulated

value: 10 ng/ml TNF for 24 hours

value: knee

value: Rheumatoid Arthritis


title: 4575_S3


title: Lymphoma_RNAseq_Drug_67-3-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
67-3-12h


title: FH6d_2


title: Lymphoma_RNAseq_Drug_67-2-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
67-2-12h


title: 427: CAGE-seq, Primary FLS, unstimulated


title: FH6d_1

description:
circRNA
circRNA-seq
processed data file: circRNA_prediction_all.txt
FH6_1


title: Lymphoma_RNAseq_Drug_67-1-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
67-1-12h


title: 4429_S1


title: 4429_S2


title: PreB_RNAseq_shPhf23.877_3


title: 429: CAGE-seq, Primary FLS, unstimulated


title: 4319_S11


title: 4319_S12


title: 217_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 217_TNF.txt

extract_protocol:
Cultured FLS were treated with 10 ng/ml human recombinant TNF (Roche) for 24 h or were left untreated. Total RNA was isolated using the RNeasy Mini kit (Qiagen) including on-column DNAase I digestion.
RNA-seq libraries were generated using the Illumina TruSeq Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit


title: Lymphoma_RNAseq_Drug_264-2-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
264-2-12h


title: FH3d_3

value: differentiation 3 days


title: Lymphoma_RNAseq_Drug_264-3-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
264-3-12h


title: FH3d_2


title: 4319_S10

value: Whole olfactory mucosa


title: 217: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 217_control.txt


title: Ba/F3_Input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using STAR_2.6.0a
Bam files were transformed to bigwig files by Deeptools
peaks were called using macs2 2.1.1
processed data files format and content: bigWig  and peak files

molecule: genomic DNA

source_name: Ba/F3 cells

growth_protocol: Ba/F3 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% Pen/Strep and 2ng/ml mouse IL3.

extract_protocol:
The ChIP DNA was purified with Qiagen MinElute PCR Purification Kit
ChIP DNA was prepared according to the protocol provided in Methods.

treatment_protocol: Ba/F3 cells were transducted with mCherry labelled and flag tagged mouse Phf23 (pMIC-mPhf23-flag) through retroviral infection. 48h after infection, the mCherry positive cells were sorted out by FACS AriaIII and cultured in vitro.

value: Ba/F3 cells


title: 4319_S9

value: m


title: FH3d_1


title: 427_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 427_TNF.txt


title: ali1 - oxo_rep3

city: Braunschweig

first: Abhishek

last: Shrestha

address: Messeweg 11/12

country: Germany

institute: Julius-Kuehn Institute

description: Col0_ace vs Col0_oxo.tabular

data_processing:
Base calling performed by BGI TECH SOLUTIONS (HONGKONG) CO., LIMITED
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis TAIR10 reference genome using  RNAStar with default settings except strand field flag XS was included (Version 2.4.0d-2) (Dobin et al. 2013)
Transcript assembly, abundance estimation and test for differential expression was performed using default settings of cufflinks (Version 2.2.1.0) , cuffmerge (Version 2.2.1.0) and cuffdiff (Version 2.2.1.5) (Trapnell et al. 2010)
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: tabular file containing gene differential expression after cuffdiff analysis between two treatments in Col-0 and ali1 mutant

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis seeds were surface sterilized with sterilization mix of 12% bleach: deionized water: 100% EtOH (1:3:4) for 10 min and further rinsed twice with 100% EtOH for one minute. Seeds were dried and germinated on ½-strength MS (Murashige & Skoog) agar plates under sterile conditions for two weeks.

extract_protocol:
RNA was isolated from Arabidopsis seedlings using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s recommendations.
One μg of total RNA was taken for DNAse digestion using the PerfeCTa DNAse I (Quanta Biosciences). Oligo dT based mRNA enrichment was carried out. RNA fragment and reverse transcription was performed after which end repair, add A-tailing and bubble adaptor ligation was carried out. PCR amplification was followed by single strand separation and cyclization to from DNA nanoball synthesis. Sequencing on DNBseq platform was then performed.

treatment_protocol: Arabidopsis seedlings grown on ½-strength MS medium under sterile conditions were transferred to square Petri dishes or six-well plates containing ½-strength MS medium with different AHL molecule N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) at a final concentration of 6 μM. Acetone was used as a solvent control. Seedlings were challenged with 100 nM flg22, three days after the AHL pretreatment and harvest after 2h of flg22 challenge.

tag: ecotype

value: 2 weeks and 3 days seedlings

tag: treatment

value: 6 microM oxo-C14-HSL

tag: challenged

value: 100 nM flg22


title: 429_TNF: CAGE-seq, Primary FLS, TNF stimulated

value: shoulder


title: 424: CAGE-seq, Primary FLS, unstimulated

description: processed_data_file: MCP_clusters_tpm.txt

value: MCP


title: 4319_S7

tag: tissue

tag: Sex

value: wt

tag: age


title: 4319_S8

tag: genotype


title: Ba/F3_Phf23-ChIP-2

tag: plasmids

tag: replicates

tag: antibody

value: FLAG M2 agarose beads(Sigma, A2220)


title: Ba/F3_Hdac1-ChIP-3


title: 4319_S6

value: f


title: Ba/F3_Phf23-ChIP-1


title: Lymphoma_RNAseq_Drug_264-1-12h

description:
Drug_Hdac_RNAseq_count.txt
Drug_Hdac_RNAseq_TPM.txt
264-1-12h

tag: cell type

value: Lymphoma cells


title: ali1 - oxo_rep1

description: Col0_ace vs Col0_oxo.tabular


title: ali1 - ace_rep1

description: Col0_ace vs Col0_oxo.tabular

value: acetone control


title: Ba/F3_Hdac1-ChIP-2


title: ali1 - ace_rep2

description: Col0_ace vs Col0_oxo.tabular


title: ali1 - ace_rep3

description: Col0_ace vs Col0_oxo.tabular


title: ali1 - oxo_rep2

description: Col0_ace vs Col0_oxo.tabular


title: 427: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 427_control.txt

tag: sample id

tag: stimulation

tag: joint

tag: disease state


title: Col-0 - oxo_rep3

description: ali1_ace vs ali1_oxo.tabular

value: wildtype


title: 466: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 466_control_CTGAGCCGGT-TTCTCGTGCA.txt


title: 438: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 438_control.txt


title: 430_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 430_TNF.txt

value: 10 ng/ml TNF for 24 hours


title: Ba/F3_H3K4me3-ChIP-2

value: H3K4me3(abcam, ab8580)


title: Col-0 - oxo_rep2

description: ali1_ace vs ali1_oxo.tabular


title: Ba/F3_H3K4me3-ChIP-1


title: 438_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 438_TNF.txt

value: Rheumatoid Arthritis


title: 430: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 430_control.txt


title: 466_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 466_TNF.txt


title: Ba/F3_H3K27ac-ChIP-2

value: H3K27ac(abcam, ab4729)


title: Col-0 - oxo_rep1

description: ali1_ace vs ali1_oxo.tabular


title: Col-0 - ace_rep3

description: ali1_ace vs ali1_oxo.tabular


title: Ba/F3_H3K27ac-ChIP-1

value: Ba/F3 cells


title: Ba/F3_Hdac1-ChIP-1


title: 4319_S2

value: Whole olfactory mucosa

value: m

value: sex-separated


title: 4319_S5


title: 4319_S3


title: 4319_S4


title: 4319_S1


title: 4237_S12


title: Col-0 - ace_rep2

description: ali1_ace vs ali1_oxo.tabular

value: 2 weeks and 3 days seedlings

value: 100 nM flg22


title: 4237_S11


title: Col-0 - ace_rep1

description: ali1_ace vs ali1_oxo.tabular


title: Lymphoma_RNAseq_shRen_210R

data_processing:
Sequenced reads were mapped to GRCm38 whole genome using STAR_2.6.0a
processed data files format and content: txt files with gene counts

source_name: lymph node

value: lymph node


title: 331_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 331_TNF.txt

value: shoulder


title: 331: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 331_control.txt


title: Lymphoma_RNAseq_shRen_125R


title: 379_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 379_TNF.txt

value: finger


title: 285_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 285_TNF_AACGAGGCCG-CACGGAACAA.txt

value: wrist


title: 4237_S10

value: f

value: wt


title: 4237_S9


title: 285: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 285_control_TGGACCGCCA-CGTCTCATAT.txt


title: 4237_S8


title: 379: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 379_control.txt


title: Lymphoma_RNAseq_shRen_125B


title: FPV-3

city: Beijing

first: Lingling

address: Yuanmingyuan West Road No.2

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Felis catus

growth_protocol: F81 cells were obtained from the Cell Resource Center of the Shanghai Institute for Biological Science, Chinese Academy of Science, and maintained in Dulbecco′s Modified Eagle Medium (DMEM) (Gibco, CA) containing 5% fetal bovine serum and 1% penicillin-streptomycin at 37 ℃ with 5% CO2. FPV strain (FPV-BJ04) is a strain of FPV originally isolated from feces of infected cats in a pet′s hospital, Beijing, China. Initially, the full genome of this strain has been sequenced accurately in our laboratory.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare six small RNA libraries (N1, N2, N3, P1,P2, P3) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: For construction of small RNA libraries, F81 cells were cultured in 75 cm² cell flasks and divided into two groups (3 flasks per group). One group was infected with FPV-BJ04 at a dose of 1×106 TCID50, the control group left uninfected. At 48h post-infection, FPV-BJ04 infected (FPV) and uninfected cells (Ctrl) were treated using Trizol reagent (Invitrogen, CA, USA) for the following total RNA extraction.

tag: cell line

value: feline kidney cell line

value: Feline Panleukopenia Virus infected

tag: cell culture

value: 48 hours after treatment


title: FPV-2


title: Lymphoma_RNAseq_shPhf23_126R


title: 387_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 387_TNF_GCTGACGTTG-GATAGGCCGA.txt

value: 10 ng/ml TNF for 24 hours

value: Rheumatoid Arthritis


title: Lymphoma_RNAseq_shPhf23_126L


title: 4237_S7


title: 387: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 387_control.txt


title: ApcMin.PCdel [QC10]

city: Dallas

first: Ezra

last: Burstein

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Internal Medicine

institute: University of Texas Southwestern Medical Center

data_processing:
CLC Genomics Workbench 7 was used for RNA-seq alignment and statistical analysis
two-step normalization and associative analysis were implemented in MatLab using the algorithm available in R package (diffGeneAnalysis)
Supplementary_files_format_and_content: gene abundance in tab-delimited format

source_name: adenoma polyp

extract_protocol:
guanidine-isothiocyanate lysis with silica-membrane purification
TruSeq RNA Kit

tag: strain

value: C57BL/6 background

value: age>42 days


title: Ctrl-2

tag: treatment

value: uninfected


title: Esrp1-KO rep4

city: Nanjing

first: Luping

last: Yu

address: Nanjing Medical University, 101 Longmian Rd, Jiangning, Nanjing

institute: State Key Laboratory of Reproductive Medicine (SKLRM)

data_processing:
The samples were collected in tubes with lysis component and ribonuclease inhibitor. Then we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA andmagbeadspurification step to clean up the production. Then the cDNA production waschecked by Qubit® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp.Then the cDNA was sheared randomly by ultrasonic wavesfor Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation.After library preparation, PerkinElmer LabChip®GX TouchandStepOnePlus™ Real-Time PCRSystem were introduced for library quality inspection.Qualifiedlibraries were then loaded on IlluminaHiseq platform for PE150 sequencing.
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: ovary

extract_protocol:
Every fifteen oocytes were collected in tubes with ribonuclease inhibitor and lysis component. The directly lysed oocytes were used for cDNA synthesis using Smart-seq2.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: oocyte

value: post natal day 42


title: 230_TNF: RNA-seq, Primary FLS, TNF stimulated

description: processed_data_file: 230_TNF_GTTGGATGAA-TCATAGATTG.txt


title: 230: RNA-seq, Primary FLS, unstimulated

description: processed_data_file: 230_control_CTTATTGGCC-TTAAGACAAG.txt


title: Lymphoma_RNAseq_shPhf23_126B


title: ApcMin.PCdel [QC8]


title: Ctrl-3


title: Ctrl-1


title: ApcMin [QC6]


title: Esrp1-KO rep2


title: Esrp1-KO rep3


title: FPV-1


title: Esrp1-KO rep1


title: ApcMin [QC4]


title: ahl13-1 +HrcC 3rd rep

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Reads were quality checked using FASTQC.
Sequenced reads were passed through trimmomatic0.36 to remove adapter contents and low quality sequences.
Trimmed sequences were checked for quality again using FASTQC.
Trimmed sequences were aligned to Arabidopsis thaliana genome using Tophat V2.1.1
FPKM values for each sample and differential expression between samples were calculated using Cufflinks V2.2.1
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel; FPKM values

growth_protocol: 14 days-old seedlings were grown under long-day conditions on sugar-free MS (Murashige and Skoog) plates at 23oC

extract_protocol:
The whole 14 days-old seedlings were used for total RNA extraction.
mRNA library generation followed by paired end sequencing (Hiseq4000)

treatment_protocol: Spray inoculated treatment with Pst hrcC bacterial suspension at an OD600=0.002 for 24 hours

tag: genotype/variation

value: Pst hrcC treated

value: whole seedlings

value: 14 days-old seedlings


title: WT rep4

tag: tissue

value: wild type


title: FPV-3

description: lncRNA sequencing

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the total RNA was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
Transcripts that overlapped with known mRNAs and shorter than 200 bp were discarded. Then we utilized CPC,CNCI to predict transcripts with coding potential. All novel transcripts with CPC score ≤-1 and CNCI score ≤0 and class code (I, j, o, u, x) were conside red as lncRNAs.  StringTie and edgeR was used to estimate the expression levels of all mRNA and lncRNA

source_name: feline kidney cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ Magnetic Gold Kit (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the . TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing ( 2 x 150 bp) on an Illumina Hiseq 4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: For construction of the six RNA-seq libraries, F81 cells were cultured in 75 cm² cell flasks and divided into two groups (3 flasks per group). One group was infected with FPV-BJ04 at a dose of 1×106 TCID50, the control group left uninfected. At 48h post-infection, FPV-BJ04 infected (FPV) and uninfected cells (Ctrl) were treated using Trizol reagent (Invitrogen, CA, USA) for the following total RNA extraction.

tag: infection

tag: tine


title: ApcMin [QC5]

tag: age


title: FPV-1

description: lncRNA sequencing


title: ApcMin.PCdel  [QC3]


title: FPV-2

description: lncRNA sequencing


title: Ctrl-3

description: lncRNA sequencing

value: Feline Panleukopenia Virus uninfected


title: ahl13-1 ctrl 2nd rep

value: control


title: WT rep3

tag: genotype


title: ahl13-1 +HrcC 2nd rep


title: CE

city: beijing

first: wenyu

last: ding

address: 15 Datun Road Chaoyang District

institute: University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.1.0 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: cerebral cortex

extract_protocol:
The embryonic cortical VZ/SVZ  areas were microdissected from coronal slices that were vibratome-sectioned  in ice-chilled ACSF and total RNA was harvested. Then the total RNA was used for mRNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: embryonic stage

tag: brain structure

value: ventricular zone/subventricle zone


title: Ctrl-2

description: lncRNA sequencing

tag: cell type

value: feline kidney cell line


title: WT rep1


title: ahl13-1 ctrl 1st rep


title: Ctrl-1

description: lncRNA sequencing


title: WT


title: ahl13-1 ctrl 3rd rep


title: US45103023_252665519151_S01_GE1-v5_95_Feb07_1_2

status: Public on Dec 19 2020

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

country: Italy

institute: University of Firenze

description: gene expression profile

hyb_protocol: Hybridization was performed on human whole genome 44,000 (Agilent-014850) oligonucleotide microarrays using reagents and protocols provided by the manufacturer (Agilent Technologies, Manual Part Number G4140-90042) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: uterus

label_protocol: cDNA synthesis and Cy3 labeling were performed with 500 ng of total RNA by Agilent’s Quick Amp Labeling Kit.

extract_protocol: Total RNA was isolated by Trizol reagent according to the manufacturer’s protocol (Invitrogen S.R.L, Italy). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). High quality quantified RNA was purified on silica gel columns using the RNeasy MinElute Cleanup kit (QIAGEN S.p.A., Italy).

tag: gender

value: F

value: 17 months

value: WT

value: uterus


title: US45103023_252665519151_S01_GE1-v5_95_Feb07_1_4

description: gene expression profile

value: hLHR overexpressed


title: US45103023_252665519151_S01_GE1-v5_95_Feb07_1_3

description: gene expression profile


title: US45103023_252665519150_S02_GE1-v1_95_Feb07_1_4

description: gene expression profile

value: 6 months


title: US45103023_252665519151_S01_GE1-v5_95_Feb07_1_1

description: gene expression profile


title: US45103023_252665519150_S02_GE1-v1_95_Feb07_1_2

description: gene expression profile


title: US45103023_252665519150_S02_GE1-v1_95_Feb07_1_3

description: gene expression profile


title: US45103023_252665519150_S02_GE1-v1_95_Feb07_1_1

description: gene expression profile


title: ahl13-1 +HrcC 1st rep


title: Day 11 H3K4me3 ChIP rep1

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description:
Chromatin IP against H3K4me3
H3K4me3_D11.island.txt.gz

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were mapped using BOWTIE aligner program (version 0.11.3) (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.). All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) algorithm (Xu et al, 2014).
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: PeakName        ChIP_island_read_count  CONTROL_island_read_count

growth_protocol: Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Two replicates were prepared for each treatment. Cells were obtained from Sigma and were maintained for not more than 4 passages before collection for ChIP-seq analysis.

extract_protocol:
ChIP was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101), followed by Ampure XP Beads purification before library construction.
SwiftChIP with GTC-Prep adaptor

treatment_protocol: 1x106 cells was seeded per a p100 plate. Day 0 cells were plated 2 days before collection. Day 11 cells were plated 11 days before collection, and erlotinib was added when the cells attached to the plate. 10 μL of 2 mM erlotinib (prepared in DMSO) were added to each plate containing 10 mL of media to obtain the final concentration of 2 µM. The medium was changed every 3 days, with the 9th day being the last day.

tag: agent

value: 2 microM erlotinib for 11 days

tag: replicate number

value: biological replicate 1

tag: chip antibody

value: 07-473 (Upstate Tech.)


title: Day 0-2

data_processing:
Alignment: Sequencing reads were mapped using TopHat (version 2.1.1) (Trapnell et al., 2009). After read quality assessment by FastQC program, identified short reads were uniquely aligned allowing at best two mismatches to the reference genome. Sequences that matched more than one place with equally quality were discarded. The reads that were not mapped to the genome were utilized to map against the transcriptome. Any residual mapping bias was checked using RSEQtools (Habegger et al., 2011)
After mapping, we used SubRead packagefeatureCount (version 2.21; Liao Y, etal 2013) to calculate absolute readabundance (read count. rc) for each transcript/gene associated toEnsEMBL (v74) genes. First strand cDNA was synthesized from random hexamers,which required read count reweighting scheme to eliminate sequencingbias  (Hansenet al., 2010).Therefore, we calculated weighted counts (wc) usingthe R/Bioconductor package Genominator (version1.2.4).With genes >9 counts, we appliedR/Bioconductor  (Gentlemanet al., 2004)package DESeq (version 2)  (Anderset al., 2013),for differentialexpression analysis using the negative binomial model.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: WeightedCount.txt.gz

growth_protocol: Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells were obtained from Sigma and were maintained for not more than 4 passages before collection for RNA-seq analysis.

extract_protocol:
Total cellular RNA was isolated by TRIzol (Invitrogen), which was followed by QIAGEN Rneasy Micro purification.
Illumina TruSeq Stranded Total RNA Ribo-Zero

value: untreated

value: biological replicate 2


title: Day 11 input

description: input DNA

tag: cell line


title: Day 11-1

value: 2 microM erlotinib

tag: time point

value: 11 days


title: Day 11 H3K4me3 ChIP rep2


title: Day 11-2


title: Day 0-1


title: WT rep2

tag: strain

value: oocyte

value: wild type

value: post natal day 42


title: Day 3 osimertinib+crizotinib

description: Single cell RNA-seq was performed using Drop-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against genome version GRCh37.p13 hg19 (From Ensembl) and corresponding gene model is extracted from Ensembl version 74.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

source_name: PC9-derived tumor xenografts

growth_protocol: 5x106 cells were injected subcutaneously into the right side flank of female athymic nude (nu/nu) 6-weeks-old mice. The cells have been transduced with pLenti PGK Blast V5-LUC (w528-1) (Addgene) lentiviruses for tumor imaging. The mice have reached tumor volume between 200 mm3 and 240 mm3 , which occurred between 10 and 15 days after the implantation. Osimertinib (AZD-9291, LC Laboratories) and crizotinib (PF02341066, LC Laboratories) were prepared in 0.5% hydroxypropyl methylcellulose and 0.5% polysorbate 80. Mice were dosed daily by oral gavage for 3 days with 0.1 ml of vehicle, the combination of osimertinib (5 mg/kg/day) and crizotinib (20 mg/kg/day), single drugs, or vehicle (0.5% hydroxypropyl methylcellulose and 0.5% polysorbate 80). Tumor cells were loaded on the Drop-seq instrument 50 minutes after the mouse euthanasia.

extract_protocol:
Drop-seq on the single cell suspension
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)

treatment_protocol: The tumor tissue was chopped in a drop of 200 µL of the Enzyme Mix of the human Tumor Dissociation Kit (Miltenyi Biotec) (50 μL Enzyme H, 25 μL Enzyme R and 6.25 μL of Enzyme A diluted in 1119 µL DMEM) on ice and transferred using a 1000-µL Gilson pipet with cut-off tip to a 2 mL tube. Then, the sample was incubated for 15 minutes at 37°C with a vigorous rotation, pipetting it up and down (3x) using a 1000-µL Gilson pipet tip (without cut off) for 2 min. every 5 minutes until there is no macroscopic chunks. The cell suspension was passed through a 40 μm strainer, collecting the cells by passing 20 mL of DMEM through the strainer at RT. Counting with trypan blue and immunofluorescent labeling (after cell fixation in 4 % paraformaldehyde) was performed at each experimental checkpoint. After passing through the strainer, the cell suspension was centrifuged at 300×g for 7 min at RT. 0.6 mL of ACK lysing buffer was added to 1 mm3 of pellet and the pellet was resuspended by gentle pipetting using a 1000-µL pipet tip (with a cut-off). The lysis was performed on ice for up to 2 min, after which the tube was filled with 14 mL of PBS/0.04% BSA and centrifuged at 300×g for 5 min. The ACK treatment was repeated if the pellet was still red. The cell pellet was resuspended in 300 µL PBS/0.04% BSA, cells from each of the two mice were counted separately, mixed 1:1 and used for scRNA-seq.

tag: treatment

value: treated with combination of osimertinib 5 mg/kg/day + crizotinib 20 mg/kg/day

tag: timepoint

value: three days

tag: replicates

value: Mix 1:1 of dissociated cells from two experimental mice per Drop-seq sample


title: Day 3 control

value: treated with vehicle


title: Day 3 osimertinib

value: treated with osimertinib 5 mg/kg/day


title: Day 3 crizotinib

value: treated with crizotinib 20 mg/kg/day


title: PC9D3-CRI-ERL2 scRNA-seq

source_name: PC9, Day 3 erlotinib + crizotinib rep2

growth_protocol: Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for not more than 5 passages before collection for scRNA analysis.

treatment_protocol: 1x106 cells were seeded on a p100 plate. Next day, a respective drug was added to each plate containing 10 mL of media: 12.5 µL of 20 mM etoposide (prepared in DMSO) were added to obtain the final concentration of 25 µM; 10 μL of 2 mM erlotinib (prepared in DMSO) were used to obtain the final concentration of 2 µM; and for the drug combination, 10 μL of 1 mM erlotinib and crizotinib (both prepared in DMSO) were used to obtain the final concentration of 1 µM each. Medium was changed again next day, on new medium containing respective drug. Total treatment time was 3 days. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

value: treated with 1 µM erlotinib combined with 1 µM crizotinib


title: PC9D3-ERL2 scRNA-seq

source_name: PC9, Day 3 erlotinib rep2

value: treated with 2 µM erlotinib


title: PC9D3-ERL1  scRNA-seq

source_name: PC9, Day 3 erlotinib rep1

value: biological replicate 1


title: Day00b scRNA-seq

source_name: PC9 untreated (Day 0)

tag: replicate


title: PC9D3-CRI-ERL1 scRNA-seq

source_name: PC9, Day 3 erlotinib + crizotinib rep1


title: Day11b scRNA-seq

source_name: PC9 treated with 2 µM erlotinib (Day 11)

value: eleven days


title: P8127011

data_processing:
Illumina Casava1.7 software used for base calling.
Illumina paired end raw FastQ files were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. Mapping was performed using STAR aligner (version 2.5.2a) and sequencing reads were aligned to human reference genome/transcriptome version GRCh37.p13 using Ensembl gene model (release 74) (Cunningham et al., 2014).
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The aligned libraries for Drop-seq were further processed into Digital Gene Expression (DGE) matrix using the Drop-seq program DigitalExpression tool (integrated in Drop- seq_tools-1.13). The number of cells that were extracted from aligned BAM file was based on the knee plot procedure, which extracts the number of reads per cell, then plots the cumulative distribution of reads and selects the knee of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as counts) of each gene for each extracted cell

source_name: NSCLC

treatment_protocol: Fresh resected human tumors were obtained from the UIC Head & Neck/Thoracic Cancer Disease Department and immediately processed for single cell dissociation. The tissue (~3-5 mm3) was supplied in 5 mL of Tissue Storage Solution (Miltenyi Biotec) on ice and was loaded for the flow on Drop-seq instrument not later than 6 hrs after the surgery. Fat, fibrous and necrotic areas were removed. The tumor tissue was chopped in a drop of 200 µL of the Enzyme Mix of the human Tumor Dissociation Kit (Miltenyi Biotec) (50 μL Enzyme H, 25 μL Enzyme R and 6.25 μL of Enzyme A diluted in 1119 µL DMEM) on ice and transferred using a 1000-µL Gilson pipet with cut-off tip to a 2 mL tube. Then, the sample was incubated for 15 minutes at 37°C with a vigorous rotation, pipetting it up and down (3x) using a 1000-µL Gilson pipet tip (without cut off) for 2 min. every 5 minutes until there is no macroscopic chunks. The cell suspension was passed through a 40 μm strainer, collecting the cells by passing 20 mL of DMEM through the strainer at RT. Counting with trypan blue and immunofluorescent labeling (after cell fixation in 4 % paraformaldehyde) was performed at each experimental checkpoint. After passing through the strainer, the cell suspension was centrifuged at 300×g for 7 min at RT. 0.6 mL of ACK lysing buffer was added to 1 mm3 of pellet and the pellet was resuspended by gentle pipetting using a 1000-µL pipet tip (with a cut-off). The lysis was performed on ice for up to 2 min, after which the tube was filled with 14 mL of PBS/0.04% BSA and centrifuged at 300×g for 5 min. The ACK treatment was repeated if the pellet was still red. The cell pellet was resuspended in 300 µL PBS/0.04% BSA, cells were counted and used for scRNA-seq.

tag: oncogenic driver mutation

value: EGFR exon19, p.746_A750del and PD-L1 no expression

tag: Stage

value: TMN pT1c,N0,Mx and Stage Ic

tag: primary/metastaic

value: primary

tag: smoking history

value: A non-smoker


title: Day 0 H3K4me3 ChIP rep2

description:
Chromatin IP against H3K4me3
H3K4me3_D00.island.txt.gz

value: untreated

value: biological replicate 2

value: 07-473 (Upstate Tech.)


title: HCC827 Day 0

data_processing:
Illumina Casava1.7 software used for base calling.
Illumina paired end raw FastQ files were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. Mapping was performed using STAR aligner (version 2.5.2a) and sequencing reads were aligned to human reference genome/transcriptome version GRCh37.p13 using Ensembl gene model (release 74) (Cunningham et al., 2014).
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The aligned libraries for Drop-seq were further processed into Digital Gene Expression (DGE) matrix using the Drop-seq program DigitalExpression tool (integrated in Drop- seq_tools-1.13). The number of cells that were extracted from aligned BAM file was based on the knee plot procedure, which extracts the number of reads per cell, then plots the cumulative distribution of reads and selects the knee of the distribution.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

growth_protocol: Non-small cell lung carcinoma cell line HCC827/ATCC® CRL-2868 (American Type Culture Collection) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for not more than 5 passages before collection for scRNA analysis.

treatment_protocol: 2.5x106 cells was seeded on a p100 plate. Treatment was initiated 24 h after seeding by adding 10 μL of 3µM erlotinib (prepared in DMSO) to respective p100 plate containing 10 mL of media. Media of treated cells were changed next day, 48 hours before cell collection for Drop-seq. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

tag: tissue

value: Day 0


title: P8127005

value: TMN cT1c,N2,M1B and Stage IVB

value: brain resection with metastatic carcinoma to brain from lung

value: A smoker, 5 cig/day for 50 years


title: HCC827 Day 3

value: Non-small cell lung carcinoma cell line HCC827

value: treated with 3 nM erlotinib

value: Day 3


title: Day 0 H3K4me3 ChIP rep1


title: Day 0 input

description: input DNA


title: PC9Day3-Eto scRNA-seq

source_name: PC9, Day 3 etoposide

value: treated with 25 µM etoposide

value: three days


title: P8126999

source_name: Adenocarcinoma with focal squamous differentiation

value: KRAS codon12, c.34G>T, p.G12C and PD-L1 low expression

value: TMN pT1b,N0,Mx and Stage not available

value: A smoker, 22 pk/year for 22 years quit 2013


title: DMSO_4hr_2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
The first 12 nucleotides were trimmed according to QuantSeq 3' mRNA-Seq library for Illumina FWD guidelines, Truseq adapters were also trimmed.
To detect T>C conversion events from the RNA-seq data sets, reads were processed using SlamDunk v.0.2.4.
Reads were first mapped to the human genome (GRCh38), read length was set to 75 (-rl option), trimming from 12 bp from the 5' end (-5 12 option), reporting up to 100 alignments per read (-n 100 option) and activating the multi-mapper retention strategy (-m option). Variants were called and filtered out with a variant fraction of 0.2 (-mv option) and default filtering for base-quality cutoff of ¡Ý27 (-mbq option). Reads were filtered for having ¡Ý1 T>C conversions (-c 1 option), remaining parameters were left to their defaults.
For each T-position in a given 3' UTR, the number of reads covering this position and the number of reads with T to C conversion at this position were recorded; both values were summed over all T-positions in the UTR, and the conversion rate for the UTR was computed as the percentage of reads with T>C conversion relative to the total number of reads
For gene-level analysis, raw reads mapped to different UTR annotations of the same gene were summed up by gene. Size factors were estimated on total mRNA reads for global normalization with DESeq2 (version 1.26.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated total raw counts from SlamDunk, tab separated T>C converted counts from SlamDunk, tab separated normalized younts from DESeq2.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen #74134).
Total RNA was subjected to alkylation by iodoacetamide (10mM, Sigma #I1149) for 15 min.
500ng alkylated RNA was used as input for generating 3'-end mRNA sequencing libraries using a commercially available kit (QuantSeq 3_mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen #015.24).
We then performed a Nextera XT library prep according to Illumina protocol 15031942 Rev. E. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation 4200. We performed single end 75nt sequencings on NextSeq 500.

treatment_protocol:
RPMI-8402 cells were treated with a final concentration of 1uM CB103 for 1hr, 4hr or 24hrs or 0.04% DMSO control.
Newly synthesized RNA was labeled for each indicated time span at a final concentration of 100µM 4-thiouridine (4sU, Sigma #T4509).

tag: cell type

value: DMSO

tag: time

tag: batch


title: DMSO_4hr_1


title: DMSO_4hr_3


title: DMSO_24hr_3


title: CTRL-Input3

data_processing:
Illumina bcl2fastq 2.19.1 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed.
Reads were aligned to mouse genome build mm10 using BWA (v.0.7.15-r1140) using bwa mem -M.
Properly paired good quality reads were filtered with samtools (v1.5) using samtools view -b -h -f 0x2 -q 2.
Peaks were called using MACS2 (2.1.1.20160309) using macs2 callpeak -t -f BAMPE -g mm -B --nomodel --nolambda -q 0.05 --keep-dup all --call-summits (RBPH) or --broad --broad-cutoff 0.1 (H3K27ac).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each ChIP sample- generated by MACS2

source_name: CLL splenocytes (CD19+B220-)

extract_protocol:
Cells were isolated from sorted CLL spenocytes (CD19+B220-) and fixed with 1% methanol-free 16% formaldehyde (Pierce Life Technologies) for 10 min at room temperature. Then 0.125M glycine was used to quench fixation, and incubated for 5 min at room temperature. Fixed cells were washed twice with 1x PBS (Gibco Life Technologies) with 1x EDTA-free protease inhibitor cocktail (Pierce Life Technologies).
ChIP reaction was performed with Diagenode iDeal ChIP-seq kit for Transcription Factors (Diagenode) with modifications of the manual detailed below. Lysed samples were sonicated in 100 uL of complete Shearing buffer iS1b for 30 cycles 30sec ON/30sec OFF using Diagenode Bioruptor NextGen (Diagenode). Sheared chromatin was immunoprecipitated with 2ug anti-RBPJ antibody (ab25949, Abcam) or 1ug anti-H3K27ac (ab4729,  Abcam). One percent of total chromatin was set aside to be used as input control. Eluted and decross-linked DNA was purified with Diagenode MicroChIP DiaPure columns (Diagenode) and eluted in 30L of Nuclease-Free water.
ChIP and input libraries for sequencing were prepared with Swift Biosciences Accel-NGS 2S Plus DNA Dual Indexing Library Kit (Swift Biosciences). Size selection steps were performed with Agencourt AMPure XP magnetic beads (Beckman Coulter). Library amplification was performed following DNA quantification with Invitrogen Qubit Fluorometer. Subsequently, ChIP-seq library was quantified with KAPA Library Quantification Kit (Roche) and Agilent Fragment Analyzer. Prepared libraries were sequenced using the sequencing platforms at GENEWIZ with Illumina HiSeq 4000 150 bp paired-end reads generating 65-90 million paired reads per library.

value: CLL splenocytes (CD19+B220-)

tag: transgene

value: IgH.TEμ;RNIC lox/+ mib1-Cre

tag: group

value: CTRL

tag: protein target

value: Input


title: DMSO_24hr_1


title: RNIC-Input2

value: NICD

tag: chip antibody


title: RBPJ_RNIC_rep2

tag: strain

value: RBPJ


title: RBPJ_RNIC_rep1


title: CTRL-Input1


title: RNIC-Input1


title: RNIC-Input3


title: DMSO_24hr_2

tag: treatment


title: Day11c scRNA-seq

tag: cell line

value: treated with 2 µM erlotinib

tag: timepoint

value: eleven days

value: biological replicate 2


title: DMSO_1hr_2

tag: replicate


title: RBPJ_CTRL_rep1

value: IgH.TEμ;RNIC lox/+


title: RBPJ_CTRL_rep3


title: DMSO_1hr_3


title: RBPJ_CTRL_rep2


title: CTRL-Input2


title: H3K27ac_RNIC_rep3


title: CB103_4hr_1


title: CB103_4hr_2


title: DMSO_1hr_1


title: H3K27ac_RNIC_rep1


title: H3K27ac_RNIC_rep2


title: H3K27ac_CTRL_rep3


title: CB103_4hr_3


title: CB103_24hr_3


title: H3K27ac_CTRL_rep2


title: CB103_24hr_1


title: CB103_24hr_2


title: H3K27ac_CTRL_rep1


title: CB103_1hr_3


title: EpCAM-positive

source_name: PC9 U937 mix

growth_protocol: Non-small cell lung carcinoma cell line PC9 (Sigma) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin (1% PS) in 5% CO2 at 37ºC. Cells obtained from vendor were maintained for 8 passages before collection for scRNA analysis. U937 cells were grown in RPMI, 10% FBS (HyClone), 1% PS, in 5% CO2 at 37ºC.

treatment_protocol: 1.5x106 PC9 cells was seeded on a p150 plate. 2.5x105 U937 cells were seeding per ml in 30 mL of media in a 162 cm2 flask, and 3 uL of 1 mM of TPA was added to induce differentiation. Cells were trypsinized, centrifuged and resuspended in RPMI with FBS, counted, and processed further for separation with Milteny microbeads and Drop-seq.

value: PC9 U937 mix

value: 4.725x106 mixed cells were separated with EpCAM beads. EpCAM+ fraction containing epithelial cells was collected and used for Drop-seq

value: Cells selected using CD326 (EpCAM) MicroBeads (Miltenyi Biotec, cat#130-061-101).


title: CD45-negative

value: 4.725x106 mixed cells were separated with CD45 beads. CD45- fraction containing epithelial cells was collected and used for Drop-seq

value: Cells selected using CD45 MicroBeads (Miltenyi Biotec, cat#130-045-801).


title: PC9 U937 mix

value: whole cell mixture:9.45x106 PC9 cells were mixed with 9.45x106 U937 cells (50% each). 4.725x106 of this mixed cell suspension cells were used for Drop-seq

value: untreated


title: CB103_1hr_2


title: REH_CBFA2T3

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

data_processing:
ChIP-seq reads were aligned to the reference human genome version GRCh37 (hg19)
The .sam files were converted to .bam files using SAMtools
The .bam files were then processed to yield .wig files using MACS
Genome_build: hg19
Supplementary_files_format_and_content: wig

growth_protocol: REH cells were maintained in RPMI 1640 medium (Gibco, Thermo Fisher Scientific) containing 10% heat-inactivated fetal calf serum (FCS) (Eurobio) supplemented with antibiotics (100 U/mL penicillin-G and 100 U/mL streptomycin, Gibco).

extract_protocol:
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min. Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer’s protocol.

value: REH

value: Pre-B lymphoblast cells

value: Peripheral blood

value: CBFA2T3 (ab33072, Abcam)


title: REH_RUNX1_rep2

value: RUNX1 (ab23980, Abcam)


title: PC9 Day 11

treatment_protocol: 1x106 cells was seeded on a p100 plate. Treatment was initiated when the cells attached by adding 10 μL of 2 mM erlotinib (prepared in DMSO) to respective p100 plate containing 10 mL of media. Cells were treated for 11 days and then removed from the drug for six days and either re-treated for 2 more days (D19_ERL), or not treated (D19_DMSO). Media was changed every three days, and ~48 hours before cell collection for Drop-seq. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

value: treated with erlotinib for eleven days


title: REH_H3K27ac

value: H3K27ac (ab4729, Abcam)


title: PC9 Day 2

value: treated with 2 µM erlotinib

value: treated with erlotinib for two days


title: DLD1_PYCARD+Tet_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in DLD1-PYCARD cell line with tetracycline

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DLD1, PYCARD+Tet, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two cell lines derived from prostate cancer and colorectal cancer, LNCaP_PYCARD and  DLD1_PYCARD, were grown in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: The RNAs from LNCaP_PYCARD and DLD1_PYCARD cells with (4 days tetracycline treatment) or without tetracycline were prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: LNCaP_PYCARD and DLD1_PYCARD cells were treated with or without 1 μg/ml tetracycline for 4 days.

tag: sample type

value: colorectal cancer cell line

value: colon


title: LNCaP_PYCARD+Tet_exp1

description: Gene expression in LNCaP-PYCARD cell line with tetracycline

source_name: LNCaP, PYCARD+Tet, experiment 1

value: prostate cancer cell line

value: prostate


title: DNA Remission Sample 6

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

data_processing:
Reads were adpter-trimmed and aligned using Meth10X (github.com/luuloi/Meth10X).
Alignement to the refrence genome was done using bwa-meth (github.com/brentp/bwa-meth).
QC was conducted using Qualimap 2.
Differentially methylated regions were identified using MethPipe. Data from two lanes have been pooled for a single set of fastq files per sample.
Genome_build: hg38
Supplementary_files_format_and_content: bigTable.tsv contains CpG coverage and methylation data
C = count methylated
cov = total coverage
dup.C = count methylated (2nd lane)
dup.cov = total coverage (2nd lane)

source_name: PBMCs

extract_protocol:
Illumina’s “Whole- Genome Bisulfite sequencing for Methylation Analysis” protocol
Library preparation was performed using  Illumina’s Paired-end DNA Sample Prep Kit

value: PBMCs

tag: disease state

value: Chronic Myeloid Leukemia

tag: Stage

value: remission

tag: age

value: adult


title: DNA Remission Sample 7

tag: tissue


title: DNA Remission Sample 8


title: DNA Remission Sample 5


title: DNA Remission Sample 9


title: DNA Remission Sample 4


title: REH_H3K4me3

value: REH

tag: cell type

value: H3K4me3 (04-745, Merck Millipore)


title: CB103_1hr_1

tag: time


title: REH_H3K4me1

value: Pre-B lymphoblast cells

value: Peripheral blood

value: H3K4me1 (07-436, Merck Millipore)


title: DNA Remission Sample 3


title: PC9 D19 ERL

value: treated with erlotinib for eleven days, followed by 6 days with no treatment and then two days with ERL


title: PC9 D19 DMSO

value: treated with erlotinib for eleven days, followed by eight days with DMSO


title: DNA Remission Sample 2


title: DLD1_PYCARD-Tet_exp1

description: Gene expression in DLD1-PYCARD cell line without tetracycline

source_name: DLD1, PYCARD-Tet, experiment 1


title: Day 11 PC9 erlotinib

treatment_protocol: 1x106 cells was seeded on a p100 plate. Treatment was initiated when the cells attached by adding 10 μL of 2 mM erlotinib (prepared in DMSO) to respective p100 plate containing 10 mL of media. Media was changed every three days, and ~48 hours before cell collection for Drop-seq. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

value: treated with 2 µM erlotinib

value: eleven days


title: DNA Remission Sample 11


title: KOPT-K1_CB-103.3: CB-103 treatment, rep3

description: Gene expression data from CB103 treated KOPT-K1

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at 45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The data was normalized using Robust Multichip Average method (Bioconductor package  oligo, R version 3.0.1).

source_name: Human T-ALL cell line KOPT-K1

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5μg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit (Affymetrix Cat.no. 900671, Santa Clara, USA).

growth_protocol: Human T-ALL cell line KOPT-K1 (kindly provided by Iannis Aifantis, NYU School of Medicine) were grown in flasks RPMI 1640 medium supplemented with 10% FCS.

extract_protocol: Cells were collected 24h post-treatment and lysed in RLT buffer (Qiagen). Total RNAs from 5 x 105 cells were isolated and purified with RNeasy® kit (Qiagen). RNA quantities were assessed by NanoDrop®ND-1000 spectrophotometer and the RNA quality was assessed using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA).

treatment_protocol: Cells were treated with 10µM CB-103 or 0.1% DMSO as control for 24h.  Cells were collected 6 hours post-transfection by trypsin-treatment, and seeded at confluency (50’000 cells/cm2) on chamber slides pre-coated with 3 µg/cm2 fibronectin.

value: Human T-ALL cell line KOPT-K1


title: Day 9 PC9 erlotinib

value: nine days


title: PC9 Day 0

value: untreated


title: Day 4 PC9 erlotinib

value: four days


title: LNCaP_PYCARD-Tet_exp1

description: Gene expression in LNCaP-PYCARD cell line without tetracycline

source_name: LNCaP, PYCARD-Tet, experiment 1

value: prostate cancer cell line

value: prostate


title: KOPT-K1_CB-103.1: CB-103 treatment, rep1


title: DNA Diagnosis Sample 9

value: PBMCs

value: Chronic Myeloid Leukemia

value: chronic phase


title: Day 1 PC9 erlotinib

value: one day


title: Day 2 PC9 erlotinib

value: two days


title: DNA Diagnosis Sample 11

value: adult


title: Day 0 PC9 erlotinib


title: DNA Diagnosis Sample 7


title: DNA Diagnosis Sample 6


title: M14Day3_Vem

growth_protocol: M14 (NCI-FREDERICK CANCER DCTD TUMOR/CELL LINE REPOSITORY) was grown in RPMI, 5% FBS (HyClone) media containing penicillin and streptomycin in 5% CO2 at 37ºC. Cells obtained from NCI were maintained for not more than 5 passages before collection for scRNA analysis.

treatment_protocol: 2.5x106 cells was seeded on a p100 plate. Treatment was initiated 24 h after seeding by adding 10 μL of 1 mM vemurafenib (prepared in DMSO) to respective p100 plate containing 10 mL of media. Media of treated cells were changed next day, 48 hours before cell collection for Drop-seq. Cells were trypsinized, centrifuged and resuspended in DMEM (no FBS), counted, and processed further for Drop-seq.

value: treated with 1 µM vemurafenib

value: three days


title: KOPT-K1_DMSO.3: Control vehicle, rep3

description: Gene expression data from DMSO treated KOPT-K1


title: prx-5 2

city: Ulsan

first: Stéphane

middle: G.

last: Rolland

address: UNIST-Gil 50, Eonyang-eup, Ulju-gun

country: South Korea

institute: IBS Center for Genomic Integrity

data_processing:
Basecalling: Illumina Casava Pipeline.
The RNA-Seq reads are aligned to the reference genome cel235 using Bowtie generating genome alignments.
Operating on the RNA-Seq alignments and Cufflinks processing, Cuffdiff was used to track the mapped reads and to determine the fragment per kilobase per million mapped reads (FPKM) for each transcript in all the samples. Primary transcripts and gene FPKMs were then computed by adding up the FPKMs of each gene group.
Genome_build: cel235
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: control_group_vs_case_group.gene_expression_table.tsv: Table with differential expression for each gene.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Strain was maintained on NGM plates at 20°C.

extract_protocol:
RNA was extracted using commercial kits with modified and optimized protocols. The integrity and quantity of the starting material were determined by appropriate methods, e.g. volume and concentration measurement.
Library preparation has been performed with an optimized protocol and standard Illumina adapter sequences have been used.

treatment_protocol: L4 larvae were treated by RNAi by feeding on NGM plates supplemented with 6mM IPTG. Adults of the next generation were collected and worm pellets were stored at -80°C until RNA extraction.

value: Bristol N2

tag: genotype

value: Wild type

tag: developmental stage

value: Adult

value: Whole body


title: prx-5 3

description: control_group_vs_case_group.gene_expression_table.tsv


title: Nalm6_CBFA2T3

value: Pre-B lymphoblast cells

value: Peripheral blood

value: CBFA2T3 (ab33072, Abcam)


title: M14Day0

value: untreated


title: tag-208 3


title: tag-208 1


title: DNA Diagnosis Sample 5


title: PC9D3Erl

description: Single cell RNA-seq was performed using 10x Genomics

data_processing:
Fastq files from Illumina was processed using the function "count" (chemistry=SC3Pv3) in 10X Genomics Cellranger version 3.0. with default paramaters.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Three types of tab-delimited text files: barcodes.tsv, features.tsv and matrix.mtx. features, barcodoes and matrix from Cellranger version 3.0

extract_protocol: 10x Genomics on the single cell suspension

value: treated with 2 µM erlotinib


title: HPB-ALL_CB-103.2: CB-103 treatment, rep2

description: Gene expression data from CB103 treated HPB-ALL

source_name: Human T-ALL cell line HPB-ALL

value: Human T-ALL cell line HPB-ALL

value: HPB-ALL


title: HPB-ALL_CB-103.3: CB-103 treatment, rep3


title: deep senescent cells - H3K27me3_rep2

city: Jinan

first: Xianglin

state: Shandong

address: 247 Beiyuan Street

department: The Second Hospital of Shandong University

institute: Shandong University

data_processing:
mapping to hg19 with bowtie2
deduplication by Picard
macs2 callpeak --SPMR, and get pileup files
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, normalized pileup files

source_name: foreskin fibroblast

extract_protocol: ChIP experiment was carried out as previously described (Hawkins et al., 2010) with H3K9me3 (Abcam, ab8898) and H3K27m3(CST, 9733s) antibodies.

value: BJ

value: bleomycin (40 ug/ml; Biorbyt) for 2 hours and culture for 28 days

tag: cell state

value: DS


title: deep senescent cells - H3K27me3_rep1


title: HPB-ALL_DMSO.1: Control vehicle, rep1

description: Gene expression data from DMSO treated HPB-ALL


title: KOPT-K1_DMSO.1: Control vehicle, rep1

value: Human T-ALL cell line KOPT-K1


title: HPB-ALL_DMSO.2: Control vehicle, rep2


title: DNA Diagnosis Sample 8

value: PBMCs

value: Chronic Myeloid Leukemia

value: chronic phase

value: adult


title: HPB-ALL_CB-103.1: CB-103 treatment, rep1


title: KOPT-K1_DMSO.2: Control vehicle, rep2


title: HPB-ALL_DMSO.3: Control vehicle, rep3


title: tag-208 2

value: Bristol N2

value: Wild type

value: Adult


title: DNA Diagnosis Sample 4


title: PC9D0


title: DNA Remission Sample 1

value: remission


title: quiescent cells - H3K27me3_rep2

value: 0.1% fetal bovine serum for 4 days

value: Q


title: quiescent cells - H3K27me3_rep1


title: prx-5 1

value: Whole body


title: DNA Diagnosis Sample 2


title: DNA Diagnosis Sample 3


title: growing cells - H3K27me3_rep1

value: untreated

value: G


title: senescent cells - H3K27me3_rep2

value: BJ

value: bleomycin (40 ug/ml; Biorbyt) for 2 hours and culture for 12 days

value: S


title: deep senescent cells - H3K9me3_rep1

value: bleomycin (40 ug/ml; Biorbyt) for 2 hours and culture for 28 days

value: DS


title: XRN-1(+) rep3

city: Xiamen

first: Fei

last: Qi

address: 4221 South Xiang'an Road

department: School of Life Sciences

institute: Xiamen University

data_processing:
Only read pairs starting with the expected adapter sequences were used. The adapters were trimmed using cutadapt, and pairs with either read shorter than 50 nucleotides after the trimming were discarded
The processed read pairs were mapped to the human reference genome (GRCh37/hg19) using bowtie2. Only unique alignments with genomic distances shorter than 1000 nt between read 1 and 2 were kept. Genomic positions of the first nucleotides of the reads 1 of each aligned read pair were used for further analysis.
For s168-P sample, Reads 1 of the read pairs containing the sequence corresponding to the ligated RNA oligo were selected for further analysis. They were trimmed for 5′- and 3′-end adapters using cutadapt
For s168-P sample, processed Reads 1 were mapped to the sequence of the 168 nt fragment using bowtie, allowing no mismatch in the first 10 nucleotides to achieve a precise 5′-end alignment.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedgraph files containing counts 5'-end of sequenced fragments at each genomic position
Supplementary_files_format_and_content: For s168-P sample, bed files containing coordinates of Reads 1 of sequenced fragments on the 168 nt sequence of hovlinc ribozyme

growth_protocol: Human chronic myeloid leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (Thermo Fisher Scientific) and 1% (v/v) pen-strep (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol:
Human genomic DNA was isolated from the K562 cell line and fragmented with DNase. After heating at 75°C for 10 min, digested DNA was purified and the desired size range of 200–1000 bp was confirmed by agarose gel electrophoresis. The DNA was then incubated with T4 DNA Polymerase in presence of dNTPs to repair the ends. The fragmented genomic DNA was then ligated to the two annealed adapters using T4 DNA ligase. All of the purified DNA was then used for PCR amplification. The amplified DNA was then used as a template for IVT by T7 RNA polymerase. The IVT products were denatured and renatured. The cleavage reaction was performed by incubating the renatured IVT products in 2 mM MgCl2, 100 mM KCl and 30 mM Tris-HCl pH 7.0 for 1 h at 37°C. One microgram of RNA (either treated with RppH and XRN-1 enzymes or the untreated control) was reversed transcribed. TdT and dCTP were added to the denatured cDNA and incubated at 37°C for 30 min. Then ddCTP was added to the reaction mixture and incubated at 37°C for additional 30 minutes to block free 3′-OH ends, followed by incubation at 70°C for 10 minutes to inactivate TdT. For s168-P sample, an RNA oligo containing a monophosphate moiety on both 5′ and 3′ ends was ligated to the self-cleavage products of the 168 nt fragment of hovlinc ribozyme in the presence of the RtcB ligase.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cleaved RNA (5–10 µg) was subjected to successive treatments with RppH 5′ pyrophosphohydrolase (NEB, M0356) and XRN-1 exoribonuclease (NEB, M0338). First, the cleaved RNA was incubated with RppH (1 U per 1 µg RNA) in 1X NEBuffer 2 in 20 µl at 37°C for 1 h to convert the 5′ triphosphates to monophosphates, purified with 2X volumes of VAHTS RNA Clean Beads and eluted in 10 µl water. Second, all of the RppH-treated RNA was incubated with XRN-1 (1 U per 1 µg RNA) in 1X NEBuffer 3 in 20 µl at 37°C for 2 h, purified with 2X volumes of VAHTS RNA Clean Beads and eluted in 7 µl water. In parallel, 1 µg of cleaved RNA was put through all the treatments but with the omission of the RppH and XRN-1 enzymes.

value: chronic myelogenous leukemia cell line

value: treated with RppH and XRN-1


title: XRN-1(-)2 rep3


title: self-cleavage products ligated to an RNA oligo

organism: synthetic construct

tag: product


title: senescent cells - H3K9me3_rep1

tag: chip antibody


title: quiescent cells - H3K9me3_rep2


title: quiescent cells - H3K9me3_rep1


title: senescent cells - H3K27me3_rep1


title: DNA Control Sample 4

value: PBMCs

value: Healthy Control

value: adult


title: DNA Control Sample 3


title: growing cells - H3K9me3_rep1


title: XRN-1(-)2 rep2


title: DNA Diagnosis Sample 1

value: Chronic Myeloid Leukemia

value: chronic phase


title: XRN-1(+) rep2


title: XRN-1(-)1 rep3


title: DNA Control Sample 2


title: XRN-1(-)1 rep2


title: XRN-1(+) rep1


title: deep senescent cells - H3K9me3_rep2


title: DNA Control Sample 6


title: DNA Control Sample 1


title: senescent cells - H3K9me3_rep2


title: XRN-1(-)2 rep1


title: L3290166145

city: Dubai

first: Ruchi

last: Jain

address: Al jaddaf

department: Genomics

country: United Arab Emirates

institute: Al jalila Children's Specialty Hospital

data_processing:
High quality reads (Q ≥ 30) were first mapped to rRNA sequences to remove potential rRNA reads using hisat v2-2.1.0.
fastq files were then aligned to GRCh37 (hg19) of Human reference genome
The unmapped reads were then mapped to the SARS-CoV-2 genome (GenBank Accession number: NC_045512.2) using BWA v0.7.17
PCR duplicates were removed with Picard MarkDuplicates program v2.18.17
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm in the SubReads package v2.0.1
Differentially expressed genes (1.5-fold and 5% false discovery rate) were identified by DeSeq2 v1.28.1
Genome_build: Homo sapiens (human) genome assembly GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

source_name: Nasopharyngeal swabs

extract_protocol:
RNA was extracted from nasopharyngeal swabs using the QIAamp Viral RNA Mini or the 213 EZ1 DSP Virus Kits (Qiagen, Hilden, Germany)  according to the manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA Library kit from Illumina (San Diego, CA, USA) , according to the manufacturer’s instructions.
RNA-seq NovaSeq SP Reagent kit (2 X 150 cycles) from Illumina (San Diego, CA, USA)

tag: disease

tag: disease severity

value: Asymptomatic/Mild


title: L3290166436


title: L3290166079


title: L3290164996

value: Moderate


title: L3290164968


title: L3290165435


title: L3290164790


title: Patient 9 replicate 3

city: Seattle

first: Robert

middle: K.

last: Bradley

state: Washington

address: 1100 Fairview Ave N

department: Public Health Sciences/Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Mutations were introduced into the endogenous UPF1 locus using CRISPR/Cas9

data_processing:
Gene annotations from UCSC knownGene track, Ensembl71, and MISO v2.0 were merged.
RNA-seq reads were mapped to the transcriptome with RSEM v1.2.4, modified to invoke Bowtie v1.0.0 with the ‘-v 2’ option.
Remaining unaligned reads were mapped to the genome as well as a database of possible splice junctions, consisting of all possible combinations of 5' and 3' splice sites annotated for each gene, using TopHat v2.0.8b.
Isoform ratios were quantified with MISO v2.0.
The abundance of NMD(+) isoforms was determined for each sample.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel files containing differentially spliced isoforms for HEK 293T cell lines carrying mutations for Patient 1 and Patient 9.

source_name: Human embryonic kidney

growth_protocol: HEK 293T cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, and 100 mg/mL Streptomycin (PenStrep, GIBCO). Cells were cultured at 37°C and 5% CO2. Cells were split at a ratio of 1:10 once they reached 90-100% confluency as needed.

extract_protocol:
RNA was extracted using RNeasy columns (Qiagen) per manufacturer’s instructions.
RNA was Poly(A)-selected, and unstranded Illumina libraries were prepared with the standard TruSeq protocol.

treatment_protocol: Ultramers for homology directed repair (HDR) were designed using previously described strategies (Richardson, Ray, DeWitt, Curie, & Corn, 2016) and synthesized by IDT, Inc. HEK 293T cells were transiently transfected with 1 μg/mL sgRNA/pX459 Cas9 expression plasmid and 20 nM HDR Ultramer using Lipofectamine 2000 that was diluted in Opti-MEM Reduced Serum Medium (ThermoFisher). Cells were incubated at 37°C for 24 hours, at which time the transfection medium was replaced with DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, 100 mg/mL Streptomycin (PenStrep, GIBCO), and 2 mg/mL puromycin. Cells were then incubated for 48-72 hours in DMEM media (GIBCO) supplemented with 10% FBS (GIBCO), 100 IU Penicillin, 100 mg/mL Streptomycin (PenStrep, GIBCO), and 2 mg/mL puromycin, at which time genomic DNA was extracted and regions of interest were amplified using the appropriate oligos. Monoclonal cell lines carrying the desired mutations were obtained via flow cytometry.

tag: cell line

value: HEK 293T

tag: clonality

value: monoclonal

tag: mutated gene

tag: mutation

tag: method mutagenesis

value: CRISPR/Cas9 homology directed repair


title: ATAC_NICD_rep4

data_processing:
Illumina bcl2fastq 2.19.1 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed.
Reads were aligned to mouse genome build mm10 using BWA (0.7.13-r1126) using bwa mem -M.
Properly paired good quality reads were filtered with samtools (v1.3.1) using samtools view -b -h -f 0x2 -q 2.
Peaks were called using MACS2 (2.1.1.20160309) using macs2 callpeak -t -f BAMPE -g mm -B --nomodel --nolambda -q 0.05 --keep-dup all --broad --broad-cutoff 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file for each ChIP sample- generated by MACS2

extract_protocol:
50'000 CLL cells were isolated from sorted spenocytes (CD19+B220-) and processed as in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Library was amplify using NEBNext High-Fidelity 2X PCR Master Mix and size selection was performed using Agencourt AMPure XP beads. The primer list can be found in Current Protocol in Molecular Biology by Buenrostro et al. in 2015 ATAC-Seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Prepared libraries were sequenced on the Illumina NextSeq 500 with paired-end 2x79nt reads.

tag: strain

tag: gender

value: f

value: CLL splenocytes (CD19+B220-)

tag: transgene

value: IgH.TEμ;RNIC{delta}/+ mb1-Cre

tag: group

value: NICD

tag: replicate

tag: batch


title: L3290164717


title: XRN-1(-)1 rep1

tag: cell type

tag: treatment

value: untreated


title: ATAC_NICD_rep3

value: m


title: L3290160143


title: Patient 9 replicate 1


title: ATAC_NICD_rep2


title: L3290162047


title: growing cells - H3K27me3_rep2

value: BJ

tag: cell state

value: G


title: L1758


title: ATAC_NICD_rep1


title: Patient 1 replicate 3


title: L3290161092


title: L5621


title: L9440


title: L7355


title: Wild-type control replicate 3


title: L4184


title: ATAC_WT_rep4

value: IgH.TEμ;RNIC+/+ mb1-Cre

value: CTRL


title: L3280


title: Wild-type control replicate 2


title: Patient 9 replicate 2


title: KOPT-K1_CB-103.2: CB-103 treatment, rep2

tag: tissue

value: Human T-ALL cell line KOPT-K1


title: ATAC_WT_rep2


title: Patient 1 replicate 2


title: L8477

tag: disease


title: L1014

tag: disease severity


title: L1076


title: L8386

value: Severe/Critical


title: Wild-type control replicate 1

tag: cell line


title: L7100

value: Asymptomatic/Mild


title: ATAC_WT_rep1


title: L9768


title: 2_HAEC_2.50

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003).
To evaluate sequencing quality, FastQC (0.11.7) was used both before and after adapter trimming via TrimGalore (0.4.4).
The bisulfite-reduced and sequenced reads were then aligned to the CT- and GA-converted human hg38 (GRCh38.p12) genome assembly via Bismark (v0.20.0) to quantify relative alignment of methylated and unmethylated CpGs, respectively.
Genome_build: hg38 (GRCh38.p12.genome.fa)
Supplementary_files_format_and_content: Differential DNA methylation was generated and exported as .xlsx

source_name: aortic endothelial cells (HAECs)

extract_protocol:
Genomic DNA was isolated from HEACs treated with 125 mg/dL and 250 mg/dL D-glucose using DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s instructions. DNA concentration and purity were determined using NanoDrop 2000 (Thermo Scientific). DNA integrity was verified using elecrophoresis on 1% agarose gel.
Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).

treatment_protocol: After cell attachment, human aortic endothelial cells were treated with culture medium containing 125 mg/dL and 250 mg/dL D-Glucose. After 48 h, the D-glucose containing culture medium was refreshed for another 24 h (total treatment 72 h). Each experiment was conducted in duplicate following the third passage.

value: aortic endothelial cells (HAECs)

tag: glucose concentration (mg/ml)


title: ATAC_WT_rep3


title: L6867


title: mb1_NICD.4

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.9.1 as needed. Reads were aligned to mouse genome build mm10 using HISAT2, v2.0.3beta aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR(3.28.0) TMM method and log2 transformed with voom (limma3.42.0).
Batch effect was removed using ComBat (sva3.34.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID.

extract_protocol:
Cells were isolated from sorted CLL spenocytes (CD19+B220-) and RNA was harvested using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) according to manufacturer’s instructions
We performed cDNA library prep starting from 5 ng RNA (CD19 samples) or 8 ng RNA (mb1 samples) per sample with the "SMART-seq v4 Ultra Low Input RNA Kit for Sequencing", according to Clontech protocol (mb1 samples). For CD19 samples, we applied the modification recommended by Clontech in the SMART-seq v4 protocol: starting Nextera XT with an input of 150pg instead of the 1ng indicated by Illumina. Final AMPure bead purification with 0.9x ratio, to enrich for longer fragments.
We then performed a Nextera XT library prep according to Illumina protocol 15031942 Rev. E. We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation 4200. We performed paired-end 2x79nt (CD19 samples) or single end 75nt (mb1 samples) sequencings on NextSeq 500.

value: female

value: IgH.TEμ;RNIC lox/+ mb1-Cre

tag: cre


title: 2_HAEC_1.25


title: mb1_NICD.3


title: L0184


title: L5970


title: mb1_NICD.2

value: male


title: L6627


title: L3779


title: 1_HAEC_1.25


title: DNA Control Sample 5

value: PBMCs

tag: disease state

value: Healthy Control

tag: Stage

tag: age

value: adult


title: L0231

value: Moderate


title: mb1_NICD.1

tag: strain

tag: gender

value: NICD


title: L4682


title: 2_HAEC_0.00


title: L0068


title: L6599


title: 1_HAEC_2.50


title: 1_HAEC_0.00


title: mb1_CTRL.3

tag: transgene

value: IgH.TEμ;RNIC lox/+

tag: group


title: L2409


title: L9766


title: L9928


title: mb1_CTRL.2

tag: replicate

tag: batch


title: L2185


title: L0904


title: L3290165790


title: L1802


title: CD19_NICD.2

value: IgH.TEμ;RNIC lox/+ CD19-Cre


title: L3715


title: L2771


title: L4280


title: L0509


title: MDA-MB-231 - vehicle rep. 2

city: Odense C

first: morten

last: gjerstorff

state: FYN

address: J.B. Winslows Vej 25, 3.

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequenced reads were trimmed for adaptor sequence and then mapped to the hg19 genome using STAR 2.3.1z_r395 with standard parameters.
Reads in exons were counted using the iRNA-seq pipeline from Madsen et al., Nucleic Acids Research, 2015.
Diferential gene expression analysis was performed using DeSeq2 (Love et al., Genome Biology, 2014).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for every sample and DeSeq2 output

source_name: Breast adenocarcinoma

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich) supplemented with 10 % fetal bovine serum (FBS, Sigma-Aldrich) and 1 % penicillin-streptomycin. The cells were kept at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using guanidiumthiocyanate
Purified RNA was prepared for sequencing using the TruSeq RNA sample preparation kit according to manufacturer’s instructions (Illumina) and sequenced using the Illumina HiSeq 1500 system.

treatment_protocol: MDA-MB-231 cells were treated for 96 hours with 1 µM guadecitabine and then left untreated for another 24 hours before harvest

value: Breast adenocarcinoma


title: MDA-MB-231 - vehicle rep. 3


title: growing cells - H3K9me3_rep2

last: Zhang

value: BJ

tag: treatment

value: untreated

value: G

tag: chip antibody


title: L0484


title: CD19_NICD.1


title: MDA-MB-231 - vehicle rep. 1

tag: tissue


title: MDA-MB-231 - SGI-110 rep. 1


title: MDA-MB-231 - SGI-110 rep. 3


title: CD19_CTRL.2

value: CTRL