title: Osteosarcoma cell line p53R245/O GLmr_14WSi_1

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: Osteosarcoma cell line p53R245/O

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-deliminated data matrix of raw read counts

source_name: Cell lines from primary murine osteosarcoma

extract_protocol:
Frozen primary osteosarcomas were crushed and stored in Trizol. RNA was extracted using Zymo Direct-zol (Catalog Number: R2071) and Qiagen Rneasy (Catalog Number: 74004) kits as per standard instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cell line

value: Primary cell line

tag: p53 status

value: p53 siRNA knockdown


title: normal colon tissue from CRC patient [1008179]

status: Public on Mar 23 2022

type: genomic

city: Philadelphia

first: Carmen

last: Sapienza

state: PA

address: 3307 N Broad Street, Room 300 PAHB

department: Fels Cancer Institute for Personalized Medicine

country: USA

institute: Temple University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudios
matrix processed value definition: Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: colon mucosa biopsy

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from colon samples according to SOP

tag: age

tag: Sex

value: F

tag: race

value: CA

tag: disease state

value: Cancer

tag: tissue type

value: normal colon tissue from CRC patient


title: RNA-seq_Ocun_fibro_5aza0_1

type: SRA

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
Reads were aligned to the corresponding genome with HISAT2 v2.0.5 using default parameters and Ensembl transcriptome index.
For data visualization, BigWig files of normalized read counts per base were generated with bamToBed from bedtools and bedGraphToBigWig from UCSC using only reads that map uniquely in the genome.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide bigWig files for visualization of RNA-seq tracks.

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: Primary dermal fibroblasts

growth_protocol: Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
RNA samples were prepared using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-seq libraries were prepared from 150 to 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina), according to the manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The depleted RNA was fragmented using divalent cations at 94°C and cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were blunted, adenylated and ligated to adapters using T4 DNA Ligase. The cDNA libraries were generated with 12 cycles of PCR amplification, purified using AMPure XP beads (Beckman-Coulter) and checked for quality and quantified using capillary electrophoresis

treatment_protocol: Fibroblasts were treated with 1 µM final concentration of 5-AzadC (Sigma A3656) for 72 hours and the medium was renewed every day.

value: Female

tag: genome build

tag: treatment

value: Control (not treated)

tag: tissue

value: Primary dermal fibroblasts


title: RRBS_Ocun_fibro_5aza1

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were digested 5 hours by MspI (Thermo Scientific), end-repaired and A-tailed with Klenow fragment exo- (Thermo Scientific), and ligated to methylated adapters with T4 DNA ligase (Thermo Scientific) in Tango 1X buffer. Size selection was performed by gel excision from a 3% agarose 0.5X TBE gel to select fragments ranging from 150 to 400 bp. DNA was purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice with the EpiTect bisulfite kit (Qiagen), following the manufacturer’s instructions. Final libraries were amplified using the Pfu Turbo Cx hotstart DNA polymerase (Agilent) with 12 to 14 PCR cycles. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

value: Treated 5-AzadC 1 microM


title: normal colon tissue from CRC patient [1007888]

value: AA


title: normal colon tissue from CRC patient [1007884]

value: M


title: Osteosarcoma cell line p53R245/O GLmr_14Wctl

city: Houston

state: TX

description: Osteosarcoma cell line p53R245/O

organism: Mus musculus

tag: strain

value: p53 heterozygous mutant with LOH


title: normal colon tissue from CRC patient [1016765]


title: normal colon tissue from CRC patient [1015423]


title: normal colon tissue from CRC patient [1007546]


title: normal colon tissue from CRC patient [1015212]


title: normal colon tissue from CRC patient [1007544]


title: WT TAC rep 1 [99349]

city: Ann Arbor

first: David

middle: B

last: Lombard

state: Michigan

address: 3015 BSRB, 109 Zina Pitcher Place

department: Pathology

institute: University of Michigan Ann Arbor

data_processing:
Basecalling was performed by the Illumina HiSeq4000
FastQC was used for FASTQ file quality control
Sequences were aligned to the mm10 transcriptome using Kallisto v0.43.1 with parameters -b 100 --single -l 200 -s 20
Transcripts were counted and converted to genes using Tximport v1.8.0
Assembly: mm10
Supplementary files format and content: Spreadhseet for normalized counts (TPM: transcript per million counts) is included

source_name: Mouse heart

extract_protocol:
Hearts were removed from mice, flash-frozen, pulverized, resuspended in Trizol. RNA was extracted as per the manufacture, and ribodepleted.
RNA libraries were prepared using standard Illumina protocols

tag: genotype

value: WT

tag: surgery

value: TAC

tag: mouse heart

value: Mouse heart


title: WGBS_Ocun_fibro

data_processing:
Low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 and adapter sequences were trimmed with Trim Galore v0.4.4 (parameters -q 20 --clip_R1 5 --clip_R2 10 --stringency 2).
Reads were mapped to the corresponding genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50
Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark v0.22.1 with the parameters --minimum_count 5 and --percentage_cutoff 50
Methylation calls were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 5X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. Bisulfite conversion was performed with the EZ DNA Methylation-Gold kit (Zymo), and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA library Kit (Swift Biosciences) following the manufacturer’s instructions. 4 to 6 cycles were used for the final PCR amplification of the WGBS libraries. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

value: No treatment


title: Osteosarcoma from p53R270H/+ GIGI_RNAm726_752

description: Osteosarcoma from p53R270H/+

source_name: Primary murine osteosarcomas

value: C57BL/6J and 129S/SvJae mix

value: Primary tumor

value: p53 heterozygous mutant


title: Ceapin-3

city: Wuhan

first: Faming

last: Zhao

state: Hubei

address: Hangkong road 13

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

description: Sample_12-PCa-3.Aligned.sortedByCoord.out.bam

data_processing:
The pseudocounts generated by Salmon are represented as normalized TPM (transcripts per million) counts and map to transcripts
Genome_build: hg38
tab-delimited text file containing raw read counts for all samples
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: DU145 cells were cultured in regular growth medium (DMEM + 10% FBS + 1%P/S)

extract_protocol:
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For samples 1-6, cells were transfected with either Allstar control siRNA or ATF6-specific siRNA, and then cultured for 24 hrs. For samples 7-12, cells were treated with either DMSO or Ceapin-A7 (10μM) for 12hrs. For all samples, Tg (30 nM) was treated for 3 hrs before harvested.

tag: cell line

tag: cell type

value: human PCa cell line

tag: transfected with

value: ATF6-specific siRNA


title: normal colon tissue from CRC patient [1005460]

value: CA

value: Cancer

value: normal colon tissue from CRC patient


title: normal colon tissue from CRC patient [1005934]

value: F


title: normal colon tissue from CRC patient [1006969]


title: Osteosarcoma from p53R270H/+ GIGI_RNAm726_750

description: Osteosarcoma from p53R270H/+


title: Ceapin-2

description: Sample_11-PCa-2.Aligned.sortedByCoord.out.bam


title: normal colon tissue from CRC patient [1005074]


title: Osteosarcoma from p53R270H/+ GIGI_RNAm726_433

description: Osteosarcoma from p53R270H/+


title: Ceapin-1

description: Sample_10-PCa-1.Aligned.sortedByCoord.out.bam


title: Osteosarcoma from p53R270H/+ GIGI_RNAm726_296

description: Osteosarcoma from p53R270H/+


title: normal colon tissue from CRC patient [1005006]


title: normal colon tissue from CRC patient [1004526]


title: normal colon tissue from CRC patient [1003900]


title: DMSO-3

description: Sample_9-PCa-3.Aligned.sortedByCoord.out.bam

value: Allstar control siRNA


title: normal colon tissue from CRC patient [1010070]

value: AA


title: Osteosarcoma from p53R270H/+ GIGI_RNAm726_155

description: Osteosarcoma from p53R270H/+


title: normal colon tissue from CRC patient [1003884]

value: M


title: WT sham rep 1 [99356]

value: sham


title: DMSO-2

description: Sample_8-PCa-2.Aligned.sortedByCoord.out.bam


title: normal colon tissue from CRC patient [1003838]


title: normal colon tissue from CRC patient [1003680]


title: Osteosarcoma from p53R245W/+ GIGI_R245W_20_8

description: Osteosarcoma from p53R245W/+


title: DMSO-1

description: Sample_7-PCa-1.Aligned.sortedByCoord.out.bam


title: normal colon tissue from CRC patient [1003661]


title: Osteosarcoma from p53R245W/+ GIGI_R245W_18_113

description: Osteosarcoma from p53R245W/+


title: siATF6-3

description: Sample_6-PCa-3.Aligned.sortedByCoord.out.bam


title: normal colon tissue from CRC patient [1003077]


title: normal colon tissue from CRC patient [1003588]


title: normal colon tissue from CRC patient [1002980]


title: Osteosarcoma from p53R245W/+ GIGI_R245W_16_22

description: Osteosarcoma from p53R245W/+


title: normal colon tissue from CRC patient [1002979]


title: siATF6-2

description: Sample_5-PCa-2.Aligned.sortedByCoord.out.bam


title: Osteosarcoma from p53R172H/+ GIGI_R172H_28_no_18

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1002971]


title: Osteosarcoma from p53R172H/+ GIGI_R172H_27_no_5

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1002928]


title: normal colon tissue from CRC patient [1002923]


title: siCtrl-3

description: Sample_3-PCa-3.Aligned.sortedByCoord.out.bam


title: normal colon tissue from CRC patient [1002915]


title: siATF6-1

description: Sample_4-PCa-1.Aligned.sortedByCoord.out.bam


title: Osteosarcoma from p53R172H/+ GIGI_R172H_26_H232

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1002878]


title: normal colon tissue from CRC patient [1002746]


title: siCtrl-2

description: Sample_2-PCa-2.Aligned.sortedByCoord.out.bam


title: Osteosarcoma from p53R172H/+ GIGI_R172H_25_no_3

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1002335]


title: normal colon tissue from CRC patient [1002200]


title: siCtrl-1

description: Sample_1-PCa-1.Aligned.sortedByCoord.out.bam


title: Osteosarcoma from p53R172H/+ GIGI_R172H_24_H202F

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1001772]


title: normal colon tissue from CRC patient [1001527]


title: Osteosarcoma from p53R172H/+ GIGI_R172H_23_H225F

description: Osteosarcoma from p53R172H/+


title: normal colon tissue from CRC patient [1001503]


title: PKM2_IP_2

first: Dong

last: Chen

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

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of PKM2 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HeLa cell

growth_protocol: HeLa cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from PKM2-RNA complexes and another for the western blotting assay for PKM2 immunoprecipitation.The PKM2-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

value: HeLa

tag: antibody


title: PKM2_IP_1


title: normal colon tissue from CRC patient [1001323]


title: Osterosarcoma from p53+/- GIGI_P53_Eu_X24

description: Osterosarcoma from p53+/-

tag: p53 status

value: p53 heterozygous


title: normal colon tissue from CRC patient [1001204]

tag: age


title: Osterosarcoma from p53+/- GIGI_P53_332

description: Osterosarcoma from p53+/-


title: normal colon tissue from CRC patient [1001186]

tag: Sex


title: normal colon tissue from CRC patient [1001153]

tag: race


title: Osterosarcoma from p53+/- GIGI_P53_30_23

description: Osterosarcoma from p53+/-


title: normal colon tissue from CRC patient [1001063]

tag: disease state


title: Osterosarcoma from p53+/- GIGI_P53_29_ET5

description: Osterosarcoma from p53+/-


title: normal colon tissue from CRC patient [1000979]

tag: tissue type


title: normal colon tissue from CRC patient [1001125]


title: Hep3B_KO_1

city: Beijing

first: Jun

last: Liang

state: Beijing

address: 1 Life Park Road, Life Science Park of Zhongguancun, Changping

department: Department of Oncology

institute: Peking University International Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts, clean data (clean reads) were obtained by removing reads containing adapter, reads1containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
mm9
Matrix table with raw gene counts for every gene and every sample
tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hepatocellular carcinoma cell line

value: PSTK-/-


title: normal colon tissue from CRC patient [1000822]


title: normal colon tissue from CRC patient [1000168]


title: Hep3B_KO_2


title: normal colon tissue from CRC patient [1000048]


title: Mouse1, miR-181-injected side

city: Iowa City

first: Ethan

middle: J.

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

data_processing:
Reads were aligned using Kallisto version 0.43.1 using default settings, with specific input parameters of 100 bootstraps and 16 threads. The average mapping rate across samples was ~87% and read depth was ~ 15M reads per GFP sample, and ~ 40M reads per miR sample.
Differential gene expression was quantified using Sleuth version 0.30.0, aggregating abundance on Ensemble genes, with a two-step Likelihood Ratio Test and Wald Test
Genome_build: Ensemble transcriptome release 98 (119215 transcript targets), ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: ALL-RESULTS*txt files report normalized gene expression based on TPM values.

source_name: substantia nigra

extract_protocol:
Regions of substantia nigra were dissected, snap-frozen in liquid nitrogen and stored at -80 until processing. Tissue pieces were homogenized in 150-200 ul ice-cold lysis buffer (50 mM Tris, 120 mM NaCl, 5 mM EDTA, 1% triton-X100) with protease and phosphatase inhibitors (Sigma-Aldrich or Thermo Fisher Scientific) using disposable pellet pestles. Approximately 75-100 ul of lysate was transferred to 1-ml of TRIzol (Thermo Fisher Scientific) and stored at -80 till processing. Total RNA was isolated from TRIzol according to the manufacturer’s instructions (Thermo Fisher Scientific) and dissolved in TE (IDT) and quantified by nano-drop. RNA was DNase treated using DNA-free kit (Thermo Fisher Scientific). Total RNA samples isolated as described above were put over GeneJET RNA clean-up micro columns (cat# K0841, Thermo Fisher Scientific).
RNA quality assessment and sequencing were performed by the Iowa Institute of Human Genetics, Genomics Division, at the University of Iowa. RNA quality and concentrations were determined with the Agilent 2100 Bioanalyzer, and Dropsense or Little Lunatic (Unchained Labs, Pleasanton, CA) reads. RIN values for samples were all >7.5. Illumina TruSeq® Stranded mRNA Library Prep kits (Illumina, San Diego, CA) were used to prepare sequencing libraries from mRNA, followed by reverse transcription to cDNA, fragment purification and ligation to indexed (barcoded) adaptors.
Indexed libraries from AAV:miR-181 samples were prepared as a set and pooled for multiplex sequencing across two lanes on the Illumina HiSeq 4000 sequencer with 75-base paired-end reads. Indexed libraries from AAV:GFP samples were prepared as a set and pooled for multiplex sequencing across two lanes on the Illumina NovaSeq 6000 sequencer for 100 cycles with 50-base paired-end reads.

treatment_protocol: RNAseq was performed on RNA isolated from injected and non-injected SN regions harvested 3 weeks after stereotaxic injection of either AAV-hSYN1-miR-181 (1.65e10 vg; n=3 mice) or AAV-hSYN1-GFP (1e10 vg; N=5 mice).

value: substantia nigra

value: injection of AAV-hSYN1-miR-181

value: microRNA-181 overexpression


title: Mouse3, miR-181-injected side


title: Mouse2, miR-181-injected side


title: Hep3B_3

value: wild type


title: Hep3B_2


title: Mouse3, Uninjected side (control for miR-181)

value: uninjected

value: uninjected control for microRNA-181 overexpression


title: Hep3B_1


title: Mouse2, Uninjected side (control for miR-181)


title: normal colon tissue from CRC patient [1001383]

value: CA

value: Cancer


title: 398_T1_2

description:
SNU-398.txt
PCR product

data_processing:
The abundance of sgRNAs was counted by Bowtie2
TKOv3_guide_sequence
Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Genomic DNA was extracted from screen cell  using  TIANamp Genomic DNA Kit (TIANGEN) according to manufacturer's instructions.
Sequencing libraries were preparaed by amplifying gRNA inserts via a 2-step PCR using primers that include Illumina TruSeq adaptors with i5 and i7 indices


title: PKM2_input_2


title: Mouse1, Uninjected side (control for miR-181)


title: TRAP_IAA_AZD_4

city: Heidelberg

first: Alexis

last: Maizel

address: Im Neuenheimer Feld 230

department: Center for Organismal Studies

country: Germany

institute: Heidelberg University

description:
total RNA - RiboZero
TRAP_25

data_processing:
Reads were mapped onto the Arabidopsis thaliana genome (TAIR10) and numbers of reads per transcripts computed using STAR (version 2.5.2b) with options: --runThreadN 36 --quantMode TranscriptomeSAM GeneCounts
Subsequent analysis of differentially expressed genes was performed in R using the DEseq2 package (Love, M. I. et al. Genome Biology 15, (2014))
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include counts values per transcript for each Sample

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Seeds were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 7d after germination under 16h light/8h dark conditions.

extract_protocol:
Root tissues were  dissected after 6h. All sampling were performed in triplicate. For each sample, about 1500 segments of the lower two-thirds of the seedling roots were pooled, flash frozen in liquid nitrogen and later homogenised with a polysome-extraction buffer (Thellmann et al, 2020). The suspension was centrifuged for 15 min (16 000 g, 4°C). An aliquot of the homogenate was used for Bulk-RNA-extraction by use of TRIzol reagent (Invitrogen). The remaining supernatant was incubated with GFP-Trap® Magnetic Agarose beads (Chromotek, Munich, Germany). Ribosomal bound RNA was obtained by immunoprecipitation with magnetic anti-GFP beads in accordance with the manufacturer’s instructions and subsequently purified by use of TRIzol reagent (Invitrogen).
Illumina NextSeq libraries were prepared from 2 µg of total RNA (bulk) or 100ng (Ribosome bound) after depleting the rRNA via Ribo-Zero Plus rRNA Depletion Kit (Illumina) and sequencing performed on NextSeq 500 flow cells (12 samples per cell).

treatment_protocol: At 7 DAG, samples were treated for 16h with either with 10 µM AZD8055 or DMSO control media before being transferred to DMSO, 10 µM IAA, 10 µM AZD8055 or 10 µM AZD8055 + 10 µM IAA.

value: transgenic line ubiquitously expressing a GFP-tagged RPL35

tag: assay

value: TRAP

value: roots

tag: replicate


title: 398_T1_1

description:
SNU-398.txt
PCR product

tag: tissue


title: PKM2_input_1


title: squamatic acid 25 μM + TMZ 100 μM

type: RNA

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

description: squamatic acid

hyb_protocol: Biotin-labeled fragments of cDNA (5.5 μg) were hybridized to Human Gene 2.1 ST ArrayStrip (20 h, 292 48 °C).

scan_protocol: Microarrays were washed and stained according to the technical protocol, using AffymetrixGeneAtlasFuidics Station. The array strips were scanned employing Imaging Station of GeneAtlas System.

data_processing: Obtained CEL files were subjected for background correction and normalization using RobustMultiarrayAveraging (RMA) algorithm implemented in affy package of BioConductor.

label: biotin

source_name: T98G spheroids

label_protocol: The protocol involving transcription in vitro, biotin labelling and cDNA fragmentation for further hybridization was carried out using the Affymetrix GeneChip IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: T98G cell line were cultured in ultra-low attachment microplates (Corning® , NY, USA) (1000 cell per well) to form spheroids. The standard medium was supplemented with Corning® Matrigel® Matrix for Organoid Culture (3.5%) (Corning® , NY, USA) and epidermal growth factor – EGF (10 ng/ml) (Stemcell Technologies, Vancouver, Canada). Both 2D and 3 D cell culture were grown in a standard humidified incubator (Memmert, Schwabach, Germany) at 182 37 °C in 5% CO2, and 95% air atmosphere. Eagle’s Minimum Essential Medium (EMEM), Dulbecco’s modified Eagle medium (DMEM), and all other media components, including antibiotics solution (10,000 units penicillin and 10 mg streptomycin/mL), glutamine, nonessential amino acids (NEAA), and sodium pyruvate (NaP) were obtained from Merck (Darmstadt,Germany). Fetal bovine serum (FBS) was obtained from Biowest (Nuaillé, France). Other compounds used in the study, e.g. dimethylsulfoxide (DMSO), ribonuclease A (RNase A), 3-(4,5- dime- thylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), trypsin, Tris, PKF118–310, te- mozolomide (TMZ) and others were purchased from Merck (Darmstadt, Germany).

extract_protocol: The total RNA was extracted using TRI Reagent (Sigma-Aldrich, St. Louis, MO, USA) then purified on columns (NucleoSpin Total RNA Isolation, Qiagen GmbH, Hilden, Germany). The amount of total RNA was determined by optical density at 260 nm and its purity was estimated by 260/280 nm absorption ratio (higher than 1.8) (NanoDrop spectrophotometer, Thermo Scientific, Waltham, MA, USA). The RNA integrity and quality were checked in a Bioanalyser 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). The resulting RNA integrity numbers (RINs) were between 8.5 and 10 with an average of 9.2. Each sample was diluted to the RNA concentration of 100 ng/μl, at the OD260/OD280 ratio of 1.8/2.0. From each RNA sample, 100 ng of RNA was taken for microarray experiments.

treatment_protocol: 5 days were needed to form spheroids. After this period spheroids were treatment with: clear medium (control) (1), TMZ 100 μM (2), atranorin 25 μM + TMZ 100 μM (3), caperatic acid 50 μM + TMZ 100 μM (4), physodic acid 25 μM + TMZ 100 μM (5), squamatic acid 25 μM + TMZ 100 μM (6), salazinic acid 50 μM + TMZ 100 μM (7) and lecanoric acid 100 μM + TMZ 100 μM (8) . All subsequent analyses were performed 48 h after treatment.

value: spheroids from human glioblastoma cell line

tag: treatment

value: squamatic acid 25 uM + TMZ 100 uM


title: lecanoric acid 100 μM + TMZ 100 μM

description: lecanoric acid

value: lecanoric acid 100 uM + TMZ 100 uM


title: caperatic acid 50 μM + TMZ 100 μM

description: caperatic acid

value: caperatic acid 50 uM + TMZ 100 uM


title: physodic acid 25 μM + TMZ 100 μM

description: physodic acid

value: physodic acid 25 uM + TMZ 100 uM


title: control

description: control

value: control


title: Kidney, IRI

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

description:
Single cell RNA
Named "IRI" or "inj" in the combined processed data

data_processing:
Cell Ranger version 3.0.0 was used to process Chromium single cell 3’ RNA-seq output and align the Read to the mouse reference transcriptome (mm9).
A downstream data analysis was performed using Seurat v3.2 R package
Cells with transcriptome < 200 (likely cell fragments) or > 3,500 (potentially cell duplets) and cells with mitochondrial gene percentage > 50% were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: models_counts.txt (combined counts)
Supplementary_files_format_and_content: models_data.txt (combined normalized data)
Supplementary_files_format_and_content: models_scale_data.txt (combined scaled data)

source_name: Kidney

extract_protocol:
Injured kidneys were harvested, minced into approximately 1 mm3 cubes, and digested using Liberase™ (100 µg/mL) and DNase I (10 µg/mL) (Roche Diagnostics) for 25 min at 37 °C. Reaction was deactivated by adding chilled DMEM with 10% FBS. The solution was then passed through a 40-µm cell strainer. After centrifugation at 1,000 RPM for 10 min at 4 °C, the cell pellet was resuspended in chilled DMEM with 10% FBS and passed through another 40-µm cell strainer. Cell number and viability were analyzed using trypan blue staining (Invitrogen). This method generated single cell suspension with greater than 75% viability.
The scRNA-seq library and sequencing were performed at the Yale Center for Genome Analysis (YCGA).

tag: strain

value: Kidney

value: 9-week old

tag: genotype

value: Wild-type

value: Unilateral IRI with contralateral nephrectomy


title: Hep3B_KO_3

value: Hepatocellular carcinoma cell line

value: PSTK-/-


title: 398_T0_2

description:
SNU-398.txt
PCR product


title: TRAP_DMSO_4

description:
total RNA - RiboZero
TRAP_19

value: transgenic line ubiquitously expressing a GFP-tagged RPL33

value: DMSO


title: salazinic acid 50 μM + TMZ 100 μM

description: salazinic acid

value: salazinic acid 50 uM + TMZ 100 uM


title: atranorin 25 μM + TMZ 100 μM

description: atranorin

value: atranorin 25 uM + TMZ 100 uM


title: TRAP_IAA_AZD_3

description:
total RNA - RiboZero
TRAP_16

value: transgenic line ubiquitously expressing a GFP-tagged RPL32

value: TRAP

value: roots


title: Kidney, CTRL

description:
Single cell RNA
Named "CTRL" or "cont" in the combined processed data

value: Normal control


title: 398_T0_1

description:
SNU-398.txt
PCR product


title: TRAP_IAA_3

description:
total RNA - RiboZero
TRAP_13

value: transgenic line ubiquitously expressing a GFP-tagged RPL31

value: IAA


title: TRAP_IAA_AZD_2

description:
total RNA - RiboZero
TRAP_07

value: transgenic line ubiquitously expressing a GFP-tagged RPL29


title: Wild_type_3_S3

city: San Francisco

first: Lihui

last: Duan

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: UCSF

data_processing:
Sequences were aligned to the mm10 genome with STAR
HTseq was used to count the mapped reads of each gene .
DESeq2 was used for the gene differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: csv table with raw gene counts for every gene and every sample

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: type-2 conventional dendritic cells (cDC2s)

value: WT


title: TRAP_DMSO_3

description:
total RNA - RiboZero
TRAP_10

value: transgenic line ubiquitously expressing a GFP-tagged RPL30


title: 398_Sorafenib_2

description:
SNU-398.txt
PCR product

value: Hepatocellular carcinoma cell line


title: TRAP_IAA_2

description:
total RNA - RiboZero
TRAP_04

value: transgenic line ubiquitously expressing a GFP-tagged RPL28


title: Wild_type_2_S2


title: TMZ 100 μM

description: TMZ

value: spheroids from human glioblastoma cell line

value: TMZ 100 uM


title: 398_Sorafenib_1

description:
SNU-398.txt
PCR product


title: TRAP_DMSO_2

description:
total RNA - RiboZero
TRAP_01

value: transgenic line ubiquitously expressing a GFP-tagged RPL27

value: DMSO


title: BULK_IAA_AZD_4

description:
total RNA - RiboZero
Bulk_25

value: transgenic line ubiquitously expressing a GFP-tagged RPL26

value: BULK


title: Wild_type_1_S1


title: TRAP_IAA_4

description:
total RNA - RiboZero
TRAP_22

value: transgenic line ubiquitously expressing a GFP-tagged RPL34

value: TRAP

value: roots


title: 398_Regorafenib_2

description:
SNU-398.txt
PCR product


title: ArhGEF1_KO_3


title: BULK_DMSO_4

description:
total RNA - RiboZero
Bulk_19

value: transgenic line ubiquitously expressing a GFP-tagged RPL24


title: BULK_IAA_AZD_3

description:
total RNA - RiboZero
Bulk_16

value: transgenic line ubiquitously expressing a GFP-tagged RPL23


title: 398_Regorafenib_1

description:
SNU-398.txt
PCR product


title: BULK_IAA_3

description:
total RNA - RiboZero
Bulk_13

value: transgenic line ubiquitously expressing a GFP-tagged RPL22

value: IAA


title: 398_Palbociclib_2

description:
SNU-398.txt
PCR product


title: ArhGEF1_KO_2

value: spleen

value: type-2 conventional dendritic cells (cDC2s)


title: BULK_DMSO_3

description:
total RNA - RiboZero
Bulk_10

value: transgenic line ubiquitously expressing a GFP-tagged RPL21


title: BULK_IAA_AZD_2

description:
total RNA - RiboZero
Bulk_07

value: transgenic line ubiquitously expressing a GFP-tagged RPL20


title: 398_Palbociclib_1

description:
SNU-398.txt
PCR product

value: Hepatocellular carcinoma cell line


title: BULK_IAA_2

description:
total RNA - RiboZero
Bulk_04

value: transgenic line ubiquitously expressing a GFP-tagged RPL19


title: BULK_DMSO_2

description:
total RNA - RiboZero
Bulk_01

value: transgenic line ubiquitously expressing a GFP-tagged RPL18


title: Wild_type_3 S15

value: WT


title: Wild_type_2 S14


title: Col-0_IAA_3

growth_protocol: Seeds were germinated on Nitex membranes (Sefar) on 0.5X MS medium and transferred 7d after germination under 16h light/8h dark conditions to 10µM NPA for 24h.

extract_protocol:
Root samples were flash frozen in liquid nitrogen, RNA was extracted with the Universal RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were then transfered either to 10 µM NPA and 10 µM Estradiol (NPA_Es) or DMSO control (NPA) for additional 24 h before being shifted to either 10 µM IAA + 10 µM Estradiol (IAA_Ees) or DMSO (IAA) for LR induction or maintained on the same plates. Root tissue was harvested after 6 h. All sampling points were performed in triplicate.then transferred to plates containing 10µM IAA, and 10µM DEX and DMSO control. Root tissue was harvested at 0, 2, 4 and 6 h after transfer onto auxin plates. All sampling points were performed in triplicate. For each sample, app. 200 segments of the lower two-thirds of the seedling roots were pooled.


title: UB10pro_amiR-TOR_NPA_3

value: NPA


title: 398_Lenvatinib_2

description:
SNU-398.txt
PCR product


title: Col-0_NPA_3


title: Col-0_NPA_2


title: 398_Lenvatinib_1

description:
SNU-398.txt
PCR product


title: UB10pro_amiR-TOR_IAA_3


title: UB10pro_amiR-TOR_NPA_2


title: UB10pro_amiR-TOR_IAA_Es_3


title: 398_Erastin_2

description:
SNU-398.txt
PCR product


title: IRF4_KO_3


title: 398_Erastin_1

description:
SNU-398.txt
PCR product


title: UB10pro_amiR-TOR_IAA_2


title: 398_Abemaciclib_2

description:
SNU-398.txt
PCR product


title: Col-0_NPA_Es_3


title: BULK_IAA_4

description:
total RNA - RiboZero
Bulk_22

value: transgenic line ubiquitously expressing a GFP-tagged RPL25

value: BULK


title: UB10pro_amiR-TOR_IAA_Es_1


title: UB10pro_amiR-TOR_IAA_Es_2


title: Col-0_IAA_2


title: IRF4_KO_1


title: 3B_T1_2

description:
Hep3B.txt
PCR product


title: 398_Abemaciclib_1

description:
SNU-398.txt
PCR product


title: Col-0_NPA_1


title: ArhGEF1_KO_1


title: Wild_type_3


title: Col-0_IAA_Es_3


title: Col-0_IAA_Es_2


title: 3B_T1_1

description:
Hep3B.txt
PCR product


title: 3B_T0_2

description:
Hep3B.txt
PCR product


title: Col-0_IAA_1


title: UB10pro_amiR-TOR_IAA_1


title: UB10pro_amiR-TOR_NPA_Es_3


title: Wild_type_1


title: CD97_KO_3

value: CD97 KO


title: UB10pro_amiR-TOR_NPA_Es_2

value: roots


title: CD97_KO_2


title: Wild_type_1 S13


title: Col-0_IAA_Es_1


title: 3B_Sorafenib_2

description:
Hep3B.txt
PCR product


title: Col-0_NPA_Es_2


title: UB10pro_amiR-TOR_NPA_1


title: UB10pro_amiR-TOR_NPA_Es_1


title: CD97_KO_1


title: Col-0_NPA_Es_1


title: 3B_Sorafenib_1

description:
Hep3B.txt
PCR product


title: G13_KO_2

value: Adgre5-/- and CD11c-cre x Gna13fl/f


title: 3B_Regorafenib_2

description:
Hep3B.txt
PCR product


title: IRF4_KO_2


title: G13_KO_3


title: G13_KO_1


title: 3B_Regorafenib_1

description:
Hep3B.txt
PCR product


title: RRBS_Ggal_sperm

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
Assembly: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
Supplementary files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

organism: Gallus gallus

source_name: Sperm

value: Male

tag: genome build

value: No treatment

value: Sperm


title: 3B_Palbociclib_2

description:
Hep3B.txt
PCR product

tag: cell line


title: Wild_type_2

value: spleen

tag: cell type


title: 3B_Palbociclib_1

description:
Hep3B.txt
PCR product


title: RRBS_Mmus_fibro_5aza0

value: Female

value: Control (not treated)

value: Primary dermal fibroblasts


title: PEA2 ctrl replicate 3

city: Foggia

first: Annamaria

last: Piscazzi

address: Viale Pinto 1

country: Italy

institute: Università di Foggia

description: replicate 3

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol using HiScan system

data_processing: The data were normalised using neqc() quantile normalization with limma in R

source_name: poorly differentiated ovarian adenocarcinoma cell line

label_protocol: Standard Illumina label protocol

growth_protocol: PEA1 and PEA2 cell lines were grown in RPMI-1640 medium with 10% FBS, 1% L-glutamine and 1% pen/strep, at 37 °C/5% CO2.

extract_protocol: Total RNA was extracted with Invitrogen PureLink RNA Mini Kit, in accordance with the provided protocol. Quality control on extracted RNA was performed with Agilent Bioanalyzer.

treatment_protocol: The cells were treated with IGFBP6 (1ug/ml) for 2 hours.

value: derived from MK patient with OC after chemoterapy

tag: therapy response

value: peritoneal actites

value: Platinum-resistant no treated


title: PE10: preeclampsia placenta tissue circRNA 5

city: shenyang

first: ziwei

last: li

address: nanjingstreet 155

department: obstetric

institute: China medical university

description: circRNA expression preeclampsia placenta tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: preeclampsia placenta tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Preeclampsia and natural pregnancy placenta tissues

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

treatment_protocol: Tissues from caesarean surgery and promptly frozen in liquid nitrogen.

value: preeclampsia placenta tissue

tag: gender

value: female

tag: molecule subtype

value: circRNA


title: PEA2 +IGFBP6 replicate 2

description: replicate 2

value: Platinum-resistant treated with IGFBP6


title: PEA2 +IGFBP6 replicate 3

description: replicate 3


title: 3B_Lenvatinib_2

description:
Hep3B.txt
PCR product

value: Hepatocellular carcinoma cell line


title: PEA2 +IGFBP6 replicate 1

description: replicate 1


title: 3B_Lenvatinib_1

description:
Hep3B.txt
PCR product


title: 3B_T0_1

description:
Hep3B.txt
PCR product


title: PE9: preeclampsia placenta tissue circRNA 4


title: RNA-seq_Mmus_fibro_5aza1_3

value: Treated 5-AzadC 1 microM


title: 3B_Erastin_2

description:
Hep3B.txt
PCR product


title: RNA-seq_Mmus_fibro_5aza1_2


title: PEA2 ctrl replicate 2

description: replicate 2


title: RNA-seq_Mmus_fibro_5aza1_1


title: 3B_Erastin_1

description:
Hep3B.txt
PCR product


title: PE8: preeclampsia placenta tissue circRNA 3


title: PE2: preeclampsia placenta tissue circRNA 2


title: PEA2 ctrl replicate 1

description: replicate 1


title: 3B_Abemaciclib_2

description:
Hep3B.txt
PCR product


title: PEA1 +IGFBP6 replicate 3

description: replicate 3

value: derived from MK patient with OC prior to therapy

value: pleural effusion

value: Platinum-sensitive treated with IGFBP6


title: PEA1 +IGFBP6 replicate 2

description: replicate 2


title: PEA1 +IGFBP6 replicate 1

description: replicate 1


title: PE1: preeclampsia placenta tissue circRNA 1


title: NP7: natural pregnancy placenta tissue circRNA 5

description: circRNA expression data from Homo sapiens placenta

source_name: natural pregnancy placenta tissue

value: natural pregnancy placenta tissue


title: 3B_Abemaciclib_1

description:
Hep3B.txt
PCR product


title: RRBS_Mmus_fibro_5aza1


title: RNA-seq_Mmus_fibro_5aza0_1


title: KO_ribo

city: Guangzhou

first: Jie

address: No. 58, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-sen University

description:
polyA RNA
Ribo-seq

data_processing:
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the mouse reference genome (mm10) using bowtie with a maximum one mismatch allowed.
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
scRNA-seq data generated from the 10× Genomics platform were processed using CellRanger (version 3.1.0) pipeline. Gene expression matrix was created by using Seurat (V3.1.5) pipeline.
Genome_build: hg38, GRCH38，mm10
Supplementary_files_format_and_content: matrix table with raw gene counts

molecule: polyA RNA

source_name: HNSCC

growth_protocol: SCC15 cells were cultured in DMEM/F12 (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) . Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).

extract_protocol:
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).  HNSCC samples were harvested from the tongue of mice and single cell suspensions were prepared for 10× genomics processing.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set. scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to manufacturer’s protocol.

treatment_protocol: SCC15 cells were  transfected with sgRNAs for knockout of METTL1. SCC15 cells with normal expression of METTL1 were used as control. Mettl1-/- and wild type mice were induced with 4NQO to establish murine HNSCC model.

value: HNSCC cells

value: To immobilize initiating ribosomes, harringtonine was added to cell culture medium to a final concentration of 2 µg/ml. Cells were Incubated for 120 s with harringtonine in the incubator. Next, to block translational elongation, cycloheximide was added to cell culture medium to a final concentration of 100 µg/ml. Cells were mixed well and proceeded immediately to cell lysis.


title: NP5: natural pregnancy placenta tissue circRNA 4


title: KO_RNA-seq

description:
polyA RNA
Ribo-seq


title: WGBS_Mmus_muscle

source_name: Psoas muscle

value: Female

value: No treatment

value: Psoas muscle


title: M3St_mel

city: Lexington

first: Kinga

middle: B.

last: Graniczkowska

state: KY

address: 675 Rose St

department: Biology

institute: University of Kentucky

description: K. aerogenes 1nM rep3

data_processing:
Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012) was used for aligning clean reads to reference genome
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq R package (1.18.0).The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched
Supplementary_files_format_and_content: Excel file including FPKM values for each Sample

organism: Klebsiella aerogenes

source_name: planctonic culture

growth_protocol: Overnight culture of K. aerogenes was inoculated in 1:100 ratio into TSB media with either 0 nM or 1 nM melatonin. Bacteria were grown in a shaking incubator at 37C and 150 rpm. Exponential cells were collected when OD of culture reached 0.3, and stationary cells were harvested when OD=3.0.

extract_protocol:
RNA was extracted using hot phenol method.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Half of replicates were treated with 1 nM melatonin.

tag: growth stage

value: stationary

value: 1 nm melatonin


title: WGBS_Mmus_fibro

tag: Sex

value: Primary dermal fibroblasts


title: NP4: natural pregnancy placenta tissue circRNA 3

value: female


title: M2St_mel

description: K. aerogenes 1nM rep2


title: WT_ribo

description:
polyA RNA
Ribo-seq

value: normal


title: PEA1 ctrl replicate 2

description: replicate 2

value: Platinum-sensitive no treated


title: RRBS_Sscr_fibro_5aza1

data_processing:
Reads were trimmed with Trim Galore v0.4.4 to remove adapter sequences and low-quality ends with a Phred score below 20. Trim Galore was run in –non_directional and –rrbs mode to remove two additional bases artificially introduced at the MspI restriction sites.
Reads were aligned to the corresponding genome with Bismark v0.18.2 with default parameters.
A maximum of two mismatches and an insertion size for paired-end sequences of between 30 and 400 bp were allowed.
Methylation scores were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 10X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 10X sequencing depth.

organism: Sus scrofa

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were digested 5 hours by MspI (Thermo Scientific), end-repaired and A-tailed with Klenow fragment exo- (Thermo Scientific), and ligated to methylated adapters with T4 DNA ligase (Thermo Scientific) in Tango 1X buffer. Size selection was performed by gel excision from a 3% agarose 0.5X TBE gel to select fragments ranging from 150 to 400 bp. DNA was purified using the MinElute gel extraction kit (Qiagen) and bisulfite-converted twice with the EpiTect bisulfite kit (Qiagen), following the manufacturer’s instructions. Final libraries were amplified using the Pfu Turbo Cx hotstart DNA polymerase (Agilent) with 12 to 14 PCR cycles. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).


title: PEA1 ctrl replicate 1

description: replicate 1


title: NP2: natural pregnancy placenta tissue circRNA 1

value: circRNA


title: M1St_mel

description: K. aerogenes 1nM rep1


title: Rootstock anac071,096 rep3

city: Uppsala

first: Ai

last: Zhang

state: Uppsala

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
0.5 mm below hypocotyl around graft junction
BA3

data_processing:
adapter and low-quality sequences were removed using the fastp software
The cleaned reads were mapped to the Arabidopsis reference TAIR10 using hisat2
The number of reads was counted using htseq
Differentially expressed genes were identified using the DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each gene and each sample

source_name: Rootstock

growth_protocol: Seeds were surface sterilized with 75% ethanol for 20 minutes, then 99.5% ethanol for 5 minutes. Sterilized seeds were sown on 1/2MS with 1% (w/v) plant agar. After 2 days of stratification at 4 °C, seeds were moved to the growth chamber (8 hours of light/16 hours of dark, ~110 μmol m-2 s−1, 20°C). All seeds were grown vertically.

extract_protocol:
Total RNA was extracted using the ROTI®Prep RNA MINI (Roth) kit.
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® for paired end sequencing.The final PCR was for 13 cycles.

treatment_protocol: 7 day-old-seedlings were placed on one layer of 2.5x4cm sterile Hybond N membrane on top of two 8.5cm circles of sterile 3 Chr Whatman paper moisten with sterile distilled water in a 9cm petri dish. In a laminar flow hood using a dissecting microscope, one cotyledon was removed (intact treatment) and, in grafting treatment, a transverse cut was also made through the hypocotyl using a vascular dissecting knife. Plants were were assembled by aligning two cut halves of different plants and joining them together (grafted treatment), after which, petri dishes was sealed with parafilm and placed vertically under short day conditions at 20°C.

tag: time

value: 24 hours after grafting


title: Rootstock anac071,096 rep2

description:
0.5 mm below hypocotyl around graft junction
BA2


title: RRBS_Sscr_fibro_5aza0

source_name: Primary dermal fibroblasts

value: Control (not treated)


title: T3St_con

description: K. aerogenes 0nM rep3

value: control


title: RNA-seq_Mmus_fibro_5aza0_3

data_processing:
Reads were aligned to the corresponding genome with HISAT2 v2.0.5 using default parameters and Ensembl transcriptome index.
For data visualization, BigWig files of normalized read counts per base were generated with bamToBed from bedtools and bedGraphToBigWig from UCSC using only reads that map uniquely in the genome.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide bigWig files for visualization of RNA-seq tracks.

extract_protocol:
RNA samples were prepared using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-seq libraries were prepared from 150 to 350 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina), according to the manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The depleted RNA was fragmented using divalent cations at 94°C and cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were blunted, adenylated and ligated to adapters using T4 DNA Ligase. The cDNA libraries were generated with 12 cycles of PCR amplification, purified using AMPure XP beads (Beckman-Coulter) and checked for quality and quantified using capillary electrophoresis


title: NP-E-5

first: gaocai

state: HuBei

address: JIefang Avenve 1277, Jianghan District

department: Department of Orthopeadics

institute: wuhan union hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qualified using FastQC and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh38.94 whole genome
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Feng, Jianxing et al.  Bioinformatics (Oxford, England) vol. 28,21 (2012): 2782-8. 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: Homo_sapiens.GRCh38.94
Supplementary_files_format_and_content: FPKM of all sample sequencing data

source_name: human intervetebral disc

extract_protocol:
Cells are centrifuged and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to  instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly,RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer.  cDNA was synthed using   dNTPs, DNA polymeraseI and  RNaseH. Then cDNA was purified using  AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols.

treatment_protocol: Nucleus pulposus tissues were digested with 0.2% collagenase Ⅱ for 8 hours

value: nucleus pulposus cells

tag: Stage

value: degenerated


title: Rootstock anac071,096 rep1

description:
0.5 mm below hypocotyl around graft junction
BA1


title: RNA-seq_Mmus_fibro_5aza0_2


title: RNA-seq_Sscr_fibro_5aza1_3

value: Treated 5-AzadC 1 microM


title: RNA-seq_Sscr_fibro_5aza1_2


title: NP-E-4


title: T2St_con

description: K. aerogenes 0nM rep2


title: Scion anac071,096 rep3

description:
0.5 mm above hypocotyl around graft junction
TA3

source_name: Scion


title: T1St_con

description: K. aerogenes 0nM rep1


title: PEA1 ctrl replicate 3

description: replicate 3

value: derived from MK patient with OC prior to therapy

value: pleural effusion


title: NP-E-3


title: RNA-seq_Sscr_fibro_5aza1_1

value: Female


title: Scion anac071,096 rep2

description:
0.5 mm above hypocotyl around graft junction
TA2


title: M3E_mel

description: K. aerogenes 1nM rep3

value: exponential


title: NP-E-2


title: NP-E-1


title: M2E_mel

description: K. aerogenes 1nM rep2


title: Scion anac071,096 rep1

description:
0.5 mm above hypocotyl around graft junction
TA1


title: RNA-seq_Sscr_fibro_5aza0_2


title: Intact anac071,096 rep3

description:
1 mm hypocotyl
IA3

source_name: Intact


title: M1E_mel

description: K. aerogenes 1nM rep1


title: NP-C-8


title: NP3: natural pregnancy placenta tissue circRNA 2

value: natural pregnancy placenta tissue


title: Intact anac071,096 rep2

description:
1 mm hypocotyl
IA2


title: RNA-seq_Sscr_fibro_5aza0_1


title: T3E_con

description: K. aerogenes 0nM rep3


title: NP-C-7


title: WGBS_Sscr_fibro

data_processing:
Low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 and adapter sequences were trimmed with Trim Galore v0.4.4 (parameters -q 20 --clip_R1 5 --clip_R2 10 --stringency 2).
Reads were mapped to the corresponding genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50
Reads with incomplete bisulfite conversion were removed using the filter_non_conversion tool in Bismark v0.22.1 with the parameters --minimum_count 5 and --percentage_cutoff 50
Methylation calls were extracted as the ratio of the number of Cs over the total number of Cs and Ts using the Bismark_methylation_extractor. CGs were filtered to have a minimum sequencing depth of 5X.
genome build: hg38, mm10, oryCun2, canFam3, bosTau8, susScr11, galGal6
processed data files format and content: We provide IGV files containing methylation scores for all CGs with at least 5X sequencing depth.

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
100 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. Bisulfite conversion was performed with the EZ DNA Methylation-Gold kit (Zymo), and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA library Kit (Swift Biosciences) following the manufacturer’s instructions. 4 to 6 cycles were used for the final PCR amplification of the WGBS libraries. The libraries were purified using Agencourt AmpureXP beads (Beckman-Coulter).

value: No treatment


title: Intact anac071,096 rep1

description:
1 mm hypocotyl
IA1


title: T2E_con

description: K. aerogenes 0nM rep2


title: WT_RNA-seq

description:
polyA RNA
Ribo-seq

value: HNSCC cells


title: NP-C-4


title: Rootstock erf114,115 rep3

description:
0.5 mm below hypocotyl around graft junction
BE3


title: T1E_con

description: K. aerogenes 0nM rep1


title: Rootstock erf114,115 rep2

description:
0.5 mm below hypocotyl around graft junction
BE2


title: NP-C-3


title: Skin_biopsy_Healthy_Leg_Margin5 (spontaneous canine cutaneous lupus erythematosus control)

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: re-used GSM4661976

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing:
Data were analyzed with nSolver software version 4.0
raw counts for our analysis

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Healthy (leg margin)


title: Control plasmid_3rd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM and read count values for each Sample

growth_protocol: SRA01/04 cells were grown in DMEM with 10% fetal bovines serum (FBS), penicillin (100 U/μl) and streptomycin (100 μg/ml)  with 5% CO2 at 37 °C in DMEM

extract_protocol:
Total RNA was extracted with Trizol according to the manufacturer’s instructions, the RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase to remove DNA. To assess the quantity and quality of RNA, absorbance at 260 nm/280 nm was detected by Agilent Bioanalyzer 2100.
Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: a CELF1-overexpressing plasmid was transfected into SRA01/04 using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. After 48 h, the transfected cells were harvested for RT-qPCR analysis.

value: SRA01/04 cell

tag: transfection

value: control plasmid


title: Skin_biopsy_Healthy_Leg_Margin4 (spontaneous canine cutaneous lupus erythematosus control)

description: re-used GSM4661975


title: Rootstock erf114,115 rep1

description:
0.5 mm below hypocotyl around graft junction
BE1


title: Skin_biopsy_Healthy_Leg_Margin3 (spontaneous canine cutaneous lupus erythematosus control)

description: re-used GSM4661974


title: Control plasmid_2nd


title: Control plasmid_1st


title: Scion erf114,115 rep3

description:
0.5 mm above hypocotyl around graft junction
TE3


title: gMDSC_Napabucasin_3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 24 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

source_name: MDSC generated from whole bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Whole bone marrow from C57BL/6 mice was isolated after sacrificing mice. After ACK lysis cells were filtered through a 40 µM cell strainer and incubated for four days with IL-6 and GM-CSF (40 ng/ml each).

extract_protocol: Total RNA was isolated by RNeasy Mini Kit (Qiagen) including DNase digest.

treatment_protocol: Cells were washed and incubated for 24 hours with DMSO (control) or 1 µM Napabucasin.

value: in vitro generated myeloid-derived suppressor cells

value: STAT3 inhibitor


title: RNA-seq_Sscr_fibro_5aza0_3

city: Illkirch

first: Michael

address: 300 Bd Sebastien Brant

institute: CNRS

value: Control (not treated)

value: Primary dermal fibroblasts


title: gMDSC_DMSO_3

value: Ctrl


title: Scion erf114,115 rep2

description:
0.5 mm above hypocotyl around graft junction
TE2

value: 24 hours after grafting


title: CELF1_SRA_3rd

value: CELF1 overexpression


title: CELF1_SRA_2nd


title: Skin_biopsy_MLE_case1

value: MLE


title: Intact erf114,115 rep3

description:
1 mm hypocotyl
IE3


title: Intact erf114,115 rep2

description:
1 mm hypocotyl
IE2


title: gMDSC_DMSO_2


title: Skin_biopsy_DLE_case7

value: DLE


title: RRBS_Ggal_fibro_5aza0

value: Female


title: gMDSC_Napabucasin_1


title: Skin_biopsy_DLE_case6


title: RRBS_Ggal_fibro_5aza1

value: Treated 5-AzadC 1 microM


title: gMDSC_DMSO_1


title: RNA-seq_Ggal_fibro_5aza1_3


title: MPI MT 2

city: New York

first: Jaime

last: Chu

state: NY

address: 1 Gustave L. Levy Place, Annenberg 14-12

department: Pediatrics

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger
Genome_build: danRer11

organism: Danio rerio

source_name: Adult zebrafish liver dissection

growth_protocol: Adult fish were maintained on a 14:10 light/dark cycle at 28°C.

extract_protocol:
Livers were dissected from 18-month-old adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols, and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads.
Library construction was performed as per 10X Genomics v3 chemistry kit.
10X chromium

value: mpi+/- (mss7)

value: Liver


title: Skin_biopsy_DLE_case5


title: Rootstock dof quadruple rep2

description:
0.5 mm below hypocotyl around graft junction
BD2

value: dof quadruple


title: Rootstock dof quadruple rep3

description:
0.5 mm below hypocotyl around graft junction
BD3


title: RNA-seq_Ggal_fibro_5aza1_2

last: Weber

department: UMR7242 Biotechnology and Cell Signalling


title: WT 3

value: WT


title: Skin_biopsy_DLE_case3


title: Rootstock dof quadruple rep1

description:
0.5 mm below hypocotyl around graft junction
BD1


title: Skin_biopsy_Healthy_Leg_Margin2 (spontaneous canine cutaneous lupus erythematosus control)

description: re-used GSM4661973

value: Healthy (leg margin)


title: WT 2


title: RNA-seq_Ggal_fibro_5aza1_1


title: Scion erf114,115 rep1

description:
0.5 mm above hypocotyl around graft junction
TE1


title: Scion dof quadruple rep3

description:
0.5 mm above hypocotyl around graft junction
TD3


title: Skin_biopsy_Healthy_Leg_Margin1 (spontaneous canine cutaneous lupus erythematosus control)

description: re-used GSM4661972


title: Skin_biopsy_DLE_case2


title: WT 1


title: RNA-seq_Ggal_fibro_5aza0_3


title: gMDSC_Napabucasin_2


title: Scion dof quadruple rep2

description:
0.5 mm above hypocotyl around graft junction
TD2


title: CELF1_SRA_1st

first: Dong

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

institute: ABLife, Inc.

value: SRA01/04 cell


title: A549-ACE2 NIPBL SARS-CoV-2 rep2 ChIP-Seq

city: HOUSTON

first: Ruoyu

last: Wang

state: Texas

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
Hi-C: Hi-C reads were primarily processed using HiC-Pro (v.2.11.0) with minor modifications. The Hi-C validPairs files were converted into cool/mcool format for further visualization purpose.
ChIP-seq: All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10. Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Assembly: hg19
Supplementary files format and content: mcool files for Hi-C samples.
Supplementary files format and content: bigWig files for ChIP-seq samples.

growth_protocol: Human lung adenocarcinoma cells A549 expressing human ACE2 (A549-ACE2, #NR53821) was acquired from BEI Resources, Manassas, VA. They were maintained in DMEM/F-12 (1:1, Corning) medium supplemented with 10% FBS (GeneDepot) and blasticidin (100uM).

extract_protocol:
Lysates were clarified from sonicated nuclei and biotin-labelled DNA were isolated with C1 beads.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for Illumina according to manufacturer's instructions.

treatment_protocol: SARS-CoV-2 isolate USA-WA1/2020 (NR-52281; BEI Resources, Manassas, VA) was employed to infect human A549-ACE2 cells (NR53821; Bei Resources, Manassas, VA). For viral infections, serum/antibiotics-free Eagle’s MEM medium supplemented with 1mM HEPES was used. Briefly, cells grown in 10-cm culture dishes at about 70-80% confluency were washed with the serum free medium, viral inoculum was added at 0.1 MOI for 1 hr. After that, non-adsorbed viral particles were gently aspirated out and the monolayers were replenished with 10% FBS containing MEM supplemented with 1mM HEPES. Infected cells were incubated at 37°C with 5% CO2 for 6hr or 24hr post-infection for experiments.

value: epithelial cell

value: SARS-CoV-2 isolate USA-WA1/2020

tag: chip antibody

value: NIPBL (Bethyl, A301-779A lot#4)


title: RNA-seq_Cfam_fibro_5aza0_3

value: Control (not treated)

tag: tissue

value: Primary dermal fibroblasts


title: Skin_biopsy_DLE_case1


title: Scion dof quadruple rep1

description:
0.5 mm above hypocotyl around graft junction
TD1

value: 24 hours after grafting


title: RNA-seq_Ggal_fibro_5aza0_1

tag: treatment


title: A549-ACE2 NIPBL Mock rep2 ChIP-Seq

treatment_protocol: Mock

value: mock


title: MPI MT 3


title: RNA-seq_Cfam_fibro_5aza0_2

treatment_protocol: Fibroblasts were treated with 1 µM final concentration of 5-AzadC (Sigma A3656) for 72 hours and the medium was renewed every day.


title: Intact dof quadruple rep3

description:
1 mm hypocotyl
ID3


title: WGBS_Ggal_fibro

value: No treatment


title: A549-ACE2 NIPBL SARS-CoV-2 rep1 ChIP-Seq


title: Intact erf114,115 rep1

description:
1 mm hypocotyl
IE1


title: RNA-seq_Cfam_fibro_5aza0_1


title: MPI MT 1


title: A549-ACE2 NIPBL Mock rep1 ChIP-Seq


title: WGBS_Cfam_fibro


title: Skin_biopsy_DLE_case4

description: 13yo_neuteredMale_GermanShorthairPointer

value: DLE


title: A549-ACE2 H3K9me3 SARS-CoV-2 rep2 spiChIP-Seq


title: 2.0 mm FA_rep2

city: Stanford

first: Xue

last: Zhou

address: 371 Serra Mall

institute: Stanford University

description: Fixed anthers

data_processing:
Paired-end RNA-seq Read1 contained a 10 bp unique molecular identifier (UMI) and sample barcodes, and Read2 contained the transcript sequence. Each UMI was processed and attached to the Read2 metadata using fastp
Barcodes were used to demultiplexed Read2 into a separate file for each library using fastq-multx
After trimming the adapters by Trim Galore, the reads were mapped to version 4 of the B73 maize genome using Hisat2
Genome_build: Version 4 of the B73 maize genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Zea mays

source_name: Anthers

growth_protocol: Maize (Zea mays) W23 bz2 inbred line plants were grown in Stanford, CA, USA under greenhouse conditions (31 ℃/21 ℃, 14 h day/10 h night light cycle with supplemental LED and UV-A lamps providing ~50% of summer sun conditions).

extract_protocol:
Total RNA was isolated from three different LCM cell samples and FA samples at 1.5 mm and 2.0 mm using the RNAqueous™-Micro Kit
RNA-seq libraries were prepared using CEL-seq2

treatment_protocol: Anthers were dissected from tassels and then measured using a micrometer (Fisher Scientific).

tag: develpmental stage

value: Wild type_W23


title: Intact dof quadruple rep2

description:
1 mm hypocotyl
ID2

tag: genotype


title: A549-ACE2 H3K9me3 Mock rep2 spiChIP-Seq


title: aosmc.progerin3

city: St Louis

first: Susana

last: Gonzalo

state: MO

address: 1100 S Grand Blvd

department: Biochemistry and Molecular Biology

institute: Saint Louis University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52.
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: Excel with DE analysis

source_name: primary aortic smooth muscle cells

extract_protocol: Samples were prepared according to the library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovoSeq 6000.

tag: lentiviral transduction

value: Flag-progerin


title: Intact dof quadruple rep1

description:
1 mm hypocotyl
ID1


title: aosmc.progerin4


title: 2.0 mm FA_rep1

description: Fixed anthers


title: A549-ACE2 H3K4me3 SARS-CoV-2 rep2 spiChIP-Seq

tag: cell line


title: Rootstock Col-0 rep1

description:
0.5 mm below hypocotyl around graft junction
BC1


title: Rootstock Col-0 rep3

description:
0.5 mm below hypocotyl around graft junction
BC3


title: Rootstock Col-0 rep2

description:
0.5 mm below hypocotyl around graft junction
BC2


title: A549-ACE2 H3K4me3 Mock rep2 spiChIP-Seq

tag: cell type


title: 2.0 mm OSC_rep2

description: Other somatic cells


title: A549-ACE2 poly-IC rep2 Hi-C

treatment_protocol: A549-hACE2 cells were transfected with poly(I:C) (66ng/ml, Sigma, P9582) for 6 hours.

value: poly(I:C) for 6 hours


title: aosmc.control4

value: Flag


title: aosmc.progerin1


title: RNA-seq_Ggal_fibro_5aza0_2

value: Female

tag: genome build


title: Scion Col-0 rep3

description:
0.5 mm above hypocotyl around graft junction
TC3


title: aosmc.control2


title: 2.0 mm TAP_rep1

description: Tapetum


title: A549-ACE2 poly-IC rep1 Hi-C


title: 2.0 mm TAP_rep2

description: Tapetum


title: aosmc.control3


title: 2.0 mm OSC_rep1

description: Other somatic cells


title: Scion Col-0 rep2

description:
0.5 mm above hypocotyl around graft junction
TC2


title: aosmc.control1


title: Scion Col-0 rep1

description:
0.5 mm above hypocotyl around graft junction
TC1


title: A549-ACE2 Mock3 rep1 Hi-C


title: A549-ACE2 Mock3 rep2 Hi-C


title: 2.0 mm ME_rep2

description: Meiocytes


title: SF8628 6Gy Radiation Control 02

city: Aurora

first: Bridget

last: Sanford

state: CO

institute: University of Colorado

data_processing:
For RNA-seq: 1. adaptor trimming with trimmomatic 2. alignment with gsnap 3. FPKM produced with cufflinks
For shRNA library screening: 1. count generation with MAGeCK 2. normalization to read depth with MAGeCK 3. statistical testing by student's ttest with p value and adjusted pvalue
Assembly: hg38

source_name: Brain Tumor Cells

growth_protocol: SF8628 cells were routinely generated by replating adherent cells typically 1.5-2x106 cells on a tissue culture dish in DMEM media supplemented with 10% FBS, 1% AB/AM and 1% NEAA.

extract_protocol:
1. RNA-seq samples: Total RNA was extracted by ethanol precipiation in ddH2O. 2. Genomic DNA samples: Genomic DNA was extracted with AL Buffer and Ethanol precipitation in AE Buffer.
1. RNA-seq samples: Total RNA was extracted using Qiagen miRNeasy Mini kit. 2. Genomic DNA samples: Genomic DNA was extracted with Qiagen DNeasy Blood and Tissue Mini Kit.
RNA-Seq: Libraries were prepared by using the TruSeq Library Preparation Kit v2 (Agilent). Directional mRNA sequencing was performed at the University of Colorado Anschutz Medical Campus Genomics and Microarray Core on a HiSeq 2500 sequencing system (Illumina) using single-pass 125 bp reads (1 × 125) and approximately 50 million reads per sample. DNA Repair shRNA screen: Sample library preparation was performed using primers from transomic (TRP60001) and KOD HOT Start DNA polymerase kit (Millipore 17086).

treatment_protocol: 1. RNA-seq samples: 2x106 SF8628 Cells were plated in a tissue culture dish on day 0 in triplicate for each group (6Gy Radiation and Unirradiated). On Day 1, cells were exposed to 6Gy radiation or no radiation. Cells were collected at 6hrs after radiation in Qiazol and the total RNA was extracted. 2. DNA Repair shRNA Screen samples: SF8628 Cells were plated on day 0 and was transduced with a human lentiviral pooled shRNA library on day 1. On day 3, cells were treated with puromycin for selection. Then, on day 5, cells were split into 4 plates. Two of the plates received 6Gy radiation and two plates did not receive any further treatments. Cells were passaged regularly to maintain an MOI of 0.3. 21 days after radiation, cells were collected and the genomic DNA was extracted from the 2 samples in duplicates.

value: Diffuse Midline Glioma

tag: gene characteristics

value: H3.3K27M, WEE1 Amplified, BRAF WT, TP53 Mutant

value: 6Gy Radiation


title: Intact Col-0 rep2

description:
1 mm hypocotyl
IC2


title: Intact Col-0 rep3

description:
1 mm hypocotyl
IC3


title: SF8628 6Gy Radiation Control 03


title: 2.0 mm ME_rep1

description: Meiocytes


title: aosmc.progerin2


title: 1.5 mm FA_rep3

description: Fixed anthers


title: SF8628 6Gy Radiation Control 01


title: A549-ACE2 HCoV-OC43 rep2 Hi-C

treatment_protocol: A549-hACE2 cells were treated with 0.5 MOI common cold coronavirus HCoV-OC43 (ATCC, VR-1558) for 24 hours.

value: epithelial cell

value: common cold coronavirus HCoV-OC43


title: Intact Col-0 rep1

description:
1 mm hypocotyl
IC1


title: A549-ACE2 HCoV-OC43 rep1 Hi-C


title: SF8628 Unirradiated Control 02

value: Untreated


title: A549-ACE2 HI-WA1 rep1 Hi-C

treatment_protocol: A549-hACE2 cells were treated with equivalent number of the heat-inactivated SARS-CoV-2 (BEI resources, NR-52286) to 0.1 MOI (calculated based on genomic equivalence), for 24 hours.

value: heat-inactivated SARS-CoV-2


title: 1.5 mm OSC_rep2

description: Other somatic cells


title: SF8628 Unirradiated Control 01


title: 1.5 mm OSC_rep1

description: Other somatic cells


title: Rat6_TKA

city: Stony Brook

first: Martin

last: Kaczocha

address: Health Sciences Center, L4-077

institute: Stony Brook University

data_processing:
Pair-end reads were aligned to the rat genome using HISAT2
transcript counts were quantified with FeatureCounts, and differentially expressed genes (DEGs) were identified with DESeq2 package (Usegalaxy.org)
Gene expression fold-change ≥ 1.5 and false discovery rate (FDR) < 0.05 were set as the threshold values for subsequent analysis
Gene set enrichment analysis with ClusterProfiler was performed in R (https://learn.gencore.bio.nyu.edu)
Genome_build: rat genome (RGSC 6.0/rn6)

organism: Rattus norvegicus

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (#12183018A, Invitrogen/Thermo Fisher Scientific) following the manufacturer’s instructions, and treated on column to degrade contaminating DNA with PureLink DNase (#12185-010, Invitrogen/Thermo Fisher Scientific).  Purified total RNA was eluted from the column with RNase-free water.
mRNA-Seq was performed by Novogene (Davis Lab, Sacramento CA), sequencing libraries were generated and subsequently tested for their quality (Library QC) with Qubit, real-time PCR for quantification and BioAnalyzer for size distribution detection.  The Illumina NovaSeq platforms were used for a paired-end 150 bp sequencing strategy to sequence the cDNA libraries.

treatment_protocol: Naïve (no procedures), sham (anesthesia, skin incision, sutures), and TKA (anesthesia and complete TKA surgery)

tag: strain

value: Sprague Dawley

value: TKA

tag: tissue/cell type

value: DRGs collected from the left side at levels L3 and L4


title: SF8628 Unirradiated Control 03


title: Rat4_TKA

tag: Sex


title: A549-ACE2 HI-WA1 rep2 Hi-C


title: A549-ACE2 Mock2 rep1 Hi-C

value: mock


title: Rat2_TKA

value: Male


title: Rat1_TKA


title: Rat6_Sham

value: sham


title: Rat5_TKA


title: USP18 knockdown differentiation repl. 2

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”. The gene annotation used for quantification was Ensembl version 104.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

source_name: Skeletal muscle cell line

growth_protocol: Immortalized human skeletal muscle cells (7304.1) were cultured in growth medium (F10 (Gibco) medium supplemented with 15% FCS, 1 ng/ml bFGF, 10 ng/ml EGF and 0.4 ug/ml Dexamethasone). Differentiation was induced using differentiation medium (DMEM (Gibco), without any supplements) for 24h

extract_protocol:
RNA was extracted using Qiazol, precipitated using chloroform followed by RNA isolation using the PureLink™ RNA Mini Kit (Invitrogen) according to the manual.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA). The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions

treatment_protocol: Cell cultures, at roughly 50% confluence, were transfected with 10 nM siRNA using Lipofectamine RNAiMAX transfection reagent and grown for 48h in transfection medium (80% proliferation medium and 20% OptiMEM). Subsequently, medium was replaced with either normal proliferation or differentiation medium.

value: 7304.1 Skeletal muscle cell line

value: USP18 Knockdown (siRNA)


title: USP18 knockdown differentiation repl. 1


title: Rat3_TKA


title: 1.5 mm FA_rep1

description: Fixed anthers

value: Wild type_W23


title: A549-ACE2 Mock2 rep2 Hi-C


title: 1.5 mm ME_rep1

description: Meiocytes


title: 1.5 mm TAP_rep2

description: Tapetum


title: USP18 knockdown proliferation repl. 2


title: GM12878-Fixed-20k-Nextera_TD-55C-Homemade_Tn5-Rep4

city: Tucson

first: Hao

state: AZ

address: 1230 N Cherry Ave

department: CMM

institute: The University of Arizona

data_processing:
The paired-end reads were preprocessed using Trimmomatic v0.36 to trim the Nextera adaptors and low quality reads with the parameter setting as “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:20”.
The trimmed reads were mapped to either the hg19 human genome or mm10 mouse genome reference contigent upon the sample source using Bowtie2 v2,2.9 with the parameter setting as “-X 2000 -3 1” to restrict the maximum fragment length of 2000 bp and trim 1 base from the 3’ end of each read before alignment. Following mapping, only the reads confidently (MAPQ ≥ 10) mapped to assembled nuclear chromosomes, and in proper pairs (we used the “-f3” and “-F12” options in SAMtools v1.4) were preserved for downstream analysis.
Picard v2.20.2 “MarkDuplicates” was used to remove duplicate reads and estimate library complexity.
Peaks were called by MACS2 v2.1.2 using deduplicated bed files and considering a 200 bp window centered on the read start using the parameters “--nomodel --keep-dup all --extsize 200 --shift -100”. Because each peak may have multiple summits (and will therefore be listed multiple times in the resulting peak bed file), the peaks output from MACS2 were then merged into a single peak set for each sample using bedtools “merge”.
Genome_build: Data from GM12878 were mapped to hg19 and data from mouse lungs were mapped to mm10
Supplementary_files_format_and_content: Matrix of the number of reads overlapping each peak for each GM12878 sample was generated by "multiBamSummary" (deepTools v3.5.1) using deduplicated bam files and a non-overlapping peak set that combined the peaks identified from each condition. The first column contains the coordinates for each peak.
Supplementary_files_format_and_content: Matrix with deviation scores for each motif and each GM12878 sample was computed by chromVAR v1.12.0. The first column shows the human motif ID from JASPAR CORE database.

growth_protocol: The GM12878 cell line was cultured at 37°C with 5% CO2 in RPMI 1640 medium (GIBCO, cat. no. 11875-093) containing 15% FBS (GIBCO, cat. no. 10437-028), 100 U/ml Penicillin Streptomycin (GIBCO, cat. no. 15140-122). Cells were counted and split to 300,000 cells/ml three times a week

extract_protocol:
1) Nuclei isolation from native GM12878:  ~2 million native cells were collected and washed using 4 ml 1X PBS (pH 7.4, Gibco, cat. no. 10-010-023) supplemented with 0.04% BSA (PBSB), and then resuspended in 200 μl of ATAC-seq lysis buffer. Lysis buffer was made by supplementing ATAC resuspension buffer (RSB) with detergents. RSB buffer is 10 mM Tris-HCl (pH 7.5, Invitrogen, cat. no. 15567027), 10 mM NaCl (Invitrogen, cat. no. AM9759) and 3 mM MgCl2 (Invitrogen, cat. no. AM9530G) in nuclease free water. RSB was made in bulk and stored at 4°C long-term. On the day of the experiment, the ATAC lysis buffer was made by adding 0.1% IGEPAL (Sigma, cat. no. I3021), 0.01% digitonin (Invitrogen, cat. no. BN2006), and 0.1% Tween-20 (Bio-Rad, cat. no. 1610781) to RSB. Detergent percentages reported are final concentrations. After resuspending cell pellets in the lysis buffer, they were incubated on ice for 3 min, and then the lysis was stopped by adding 1 ml RSB containing 0.1% Tween-20. Nuclei were then centrifuged at 500 r.c.f for 10 min at 4 °C and resuspended in 200 ul of PBSB. The nuclei were counted and diluted to 3,100 nuclei/μl with PBSB. Then, 6.6 μl of diluted nuclei (20,460 total nuclei) were transferred to 12.4 μl of transposition reaction (10 μl of 2X Tagmentation buffer, 0.2 μl of 1% digitonin, 0.2 μl of 10% Tween-20, and 2 μl of H2O). We then added 1 μl of transposase to the transposition mix containing nuclei. Tagmentation was carried out on a thermocycler at either 37°C or 55°C for 30 min. Tagmented DNA was cleaned up using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer (Zymo, cat. no. D4004). 2) Nuclei isolation from fixed GM12878: the frozen, fixed cells (~ 2 million) were incubated in a 37°C water bath until thawed (~ 1 min). After thawing, the cells stored in 1 ml freezing buffer were diluted with 3 ml of PBSB. The fixed cells were collected by centrifuging at 500 r.c.f for 10 min at 4°C, resuspended again in 1 ml PBSB, and then centrifuged at 500 r.c.f for 5 min at 4°C to wash the cells. Following washing, the nuclei were isolated and tagmented as described in the ATAC-seq protocol for native samples described above. After tagmentation, crosslinks were then reversed for the fixed, tagmented nuclei by adding 60 μl of reverse-crosslinking buffer containing 0.067% SDS and 1.33 mg/ml Proteinase K (Qiagen, cat. no. 19133) in Qiagen Buffer EB (final concentration of 0.05% SDS and 1 mg/ml Proteinase K) directly to the tagmentation reactions, and incubating the samples at 65°C for 15 hours in a thermomixer with shaking at 1,000 r.p.m. Following crosslink reversal, tagmented DNA was purified using Zymo DNA Clean and Concentrator-5 columns with 5X binding buffer. 3) The isolation of mouse lung nuclei was performed following the single-nucleus isolation protocol described by Joshi Nikita and Misharin Alexander. In brief, we cut a ~0.1-0.2 g piece from the lung sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min, and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution, Sigma-Aldrich, Cat. 11836153001) in Nuclei EZ prep buffer (Sigma-Aldrich, Cat. NUC101), into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube (Miltenyi Biotec, Cat. 130-096-334). An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with Trypan blue in the presence of 2X Omni buffer (20 mM Tris HCl (pH 7.5), 10 mM MgCl2 and 20% Dimethyl Formamide), and then collected by centrifugation at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei to a concentration of 4-5 million nuclei/ml in a nuclei freezing buffer containing 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat .no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), and 2% protease inhibitor (Sigma, cat. no. P8340). 1 ml aliquots of the nuclei were flash frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
5 μl of purified DNA out of 10 μl purified product was amplified in a 25 μl PCR reaction containing NEBNext PCR master mix (1X final), 0.5X SYBR Green and 1.25 μM of Ad1 primer from Buenrostro JD. et al., 2013 and 1.25 μM of an N7 primer containing custom barcodes. Samples were amplified on a Bio-Rad CFX Connect Real-time cycler using the following program: 72°C for 5 min; 98°C for 30s; cycling at 98°C for 10 s, 63°C for 30 s, 72°C for 1 min; samples were monitored and stopped when it appeared that their exponential amplification was leveling off. At this point the samples were allowed to incubate at 72°C for an additional minute to fully extend the library. All native samples were stopped after 9 cycles and fixed samples were stopped after 10 cycles. PCR products were cleaned up with Ampure XP beads. A double size selection was performed to remove DNA fragments larger than ~1500 bp (with 0.4X AMPure XP beads) and smaller than ~100 bp (with 1.5X AMPure XP beads). To do this, we added 25 μl of Qiagen Buffer EB to each PCR reaction to bring the volume to 50 μl, and then added 20 μl of beads (homogenizing the mixture well by pipetting), followed by a 5 min incubation at RT. The samples were then put on a magnet stand to bind the beads. 68 μl of the supernatant was transferred to a new 1.5 ml tube and an additional 53 μl of beads were added to the supernatant and resuspended thoroughly (we estimated that 19.4 μl of the 68 μl transferred was bead buffer and 48.6 μl was sample, so to get to 1.5X beads for the second selection we needed to add an additional 72.9 - 19.4 μl of beads, which we rounded off to 53 μl). After another 5 min at RT, the samples were placed on the magnet to clear the beads and the supernatant was discarded. Beads were washed twice with 200 μl of 80% EtOH (made fresh for each experiment). After the second wash, the beads were briefly spun, and any residual ethanol was removed. The beads were then put back on the magnet stand and air dried for 1 min. Then, beads were removed from the magnet and resuspended in 22 μl of Buffer EB, incubated for 2 min at RT and then placed on the magnet stand again. 20 μl of supernatant was transferred to a new tube. The 96 ATAC-seq libraries of the GM12878 cell line and 72 libraries of mouse lungs were pooled separately and sequenced with 2x76 bp reads in two independent runs on an NextSeq 550 Platform using the High Output Kits.

treatment_protocol: For fixation, cells were washed and resuspended in 9.2 ml of RPMI medium without additives, then crosslinked with 270 μl of 37% formaldehyde (1% final, VWR, cat. no. MK501602) for 10 min at room temperature. The fixation reaction was quenched by adding 500 μl of 2.5 M glycine (0.125 M final, Sigma, 50046-50G) and incubated for 5 min at room temperature, and then on ice for 15 min. The fixed cells were collected and resuspend in the freezing buffer, which contains 50 mM Tris-HCI (pH 8.0, Invitrogen, cat. no. 15568025), 5 mM Magnesium Acetate (Sigma, cat. no. 63052), 25% glycerol (VWR, cat. no. RC3290-32), 0.1 mM EDTA (Fisher, cat. no. AM9260G), 5 mM DTT (Fisher, cat. no. P2325), 2% protease inhibitor (Sigma, cat. no. P8340). Then, 2 million cells per aliquot were flash frozen in liquid nitrogen for long-term storage.

value: lymphoblastoid

tag: nuclei state

value: Fixed

tag: nuclei input


title: Rat5_Sham

value: Female


title: 1.5 mm TAP_rep1

description: Tapetum


title: 1.5 mm ME_rep2

description: Meiocytes


title: GM12878-Fixed-20k-THS_TD-55C-Homemade_Tn5-Rep4


title: GM12878-Fixed-20k-Omni_TD-55C-Nextera_Tn5-Rep4


title: RRBS_Btau_fibro_5aza1

organism: Bos taurus

growth_protocol: Primary dermal fibroblasts were grown in DMEM-GlutaMax supplemented with 10% fetal bovine serum and 50U/mL penicillin-streptomycin in a humidified atmosphere containing 5% CO2 at 37°C.

value: Treated 5-AzadC 1 microM

value: Primary dermal fibroblasts


title: GM12878-Fixed-20k-THS_TD-55C-Nextera_Tn5-Rep4


title: Rat4_Sham


title: USP18 knockdown differentiation repl. 3


title: GM12878-Fixed-20k-Omni_TD-55C-Homemade_Tn5-Rep4


title: Rat3_Sham


title: USP18 knockdown proliferation repl. 3


title: Rat2_Sham


title: RNA-seq_Btau_fibro_5aza1_3


title: GM12878-Fixed-20k-Nextera_TD-55C-Nextera_Tn5-Rep4


title: RNA-seq_Btau_fibro_5aza1_2


title: GM12878-Fixed-20k-THS_TD-37C-Homemade_Tn5-Rep4


title: Rat6_Naive

value: naïve


title: Rat1_Sham


title: USP18 knockdown proliferation repl. 1


title: RNA-seq_Btau_fibro_5aza0_3

value: Control (not treated)


title: GM12878-Fixed-20k-Nextera_TD-37C-Homemade_Tn5-Rep4


title: GM12878-Fixed-20k-THS_TD-37C-Nextera_Tn5-Rep4


title: RNA-seq_Btau_fibro_5aza0_2


title: Control differentation repl. 2

value: Untreated


title: GM12878-Fixed-20k-Omni_TD-37C-Homemade_Tn5-Rep4


title: GM12878-Fixed-20k-Omni_TD-37C-Nextera_Tn5-Rep4


title: Rat4_Naive

value: Sprague Dawley


title: Rat2_Naive