title: tumor 35

description: tumor 35

value: NS+


title: UF0310_brep3

status: Public on May 04 2020

type: SRA

city: Gainesville

first: Matias

last: Kirst

state: FL

address: Newin-Ziegler, Room 320

country: USA

institute: University of Florida

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq FASTQ-files were quality and adapter trimmed using Trimmomatic v0.32
The pre-processed reads were aligned to v3.0 of the Populus thrichocarpa reference genome using STAR 2.5.2b
Picard v1.115 was used to remove duplicate reads and only unique alignments were kept for further analysis.
Three transcript assembly platforms were used to maximize the detection of novel genes: (1) Cufflinks version 2.2.1, (2) StringTie version 1.3.3 , and (3) Trinity version 2.3.2.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The master transcriptome was reformatted and annotated using gffcompare version 0.9.9c and subjected to expression filtering to remove artifacts generated by merging assemblies such that each transcript in the assembly was required to be expressed at FPKM >= 3 in at least two of the three biological replicates of at least three individuals and 50 observations.
Gene expression was measured using Cufflinks version 2.2.1
Supplementary_files_format_and_content: A single Comma separated (.csv) file includes a matirx with FPKM values for all samples (Matrix_fpkm_AllIndividuos.csv)

molecule: total RNA

organism: Populus deltoides

source_name: Xylem

growth_protocol: Plants were clonally propagated from apical green cuttings in a glasshouse at University of Florida as previously described (Fahrenkrog et al., 2017). Half of the population was grown in 2015 and the other half in 2016 in the same greenhouse, same conditions and time of the year (from April to August). Both experiments were set with three biological replicates, using a row-column design.

extract_protocol:
Total RNA was extracted according to the CTAB-LiCl protocol (Chang et al., 1993).
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina  following the manufacturerÕs instructions.

tag: age

value: 16 weeks


title: tumor 22

type: RNA

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

country: India

institute: CDFD

description: tumor 22

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

organism: Homo sapiens

source_name: Surgically removed tongue

label_protocol: 2 μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Sex

value: Female

tag: tissue

value: Squamous cell carcinoma of oral tongue

tag: Stage

tag: grade

value: I

tag: p53 status

source_name: pooled 11 cell line

tag: control type

value: Universal reference RNA


title: tumor 34

description: tumor 34


title: tumor 21

description: tumor 21

value: I-II


title: tumor 29

description: tumor 29

value: NS-


title: tumor 25

description: tumor 25

value: Male


title: tumor 28

description: tumor 28

value: II


title: tumor 36

description: tumor 36


title: tumor 32

description: tumor 32


title: tumor 40

description: tumor 40


title: UF0310_brep2


title: tumor 31

description: tumor 31


title: tumor 33

description: tumor 33


title: UF0310_brep1


title: tumor 39

description: tumor 39


title: tumor 30

description: tumor 30


title: tumor 38

description: tumor 38


title: tumor 26

description: tumor 26


title: tumor 24

description: tumor 24


title: tumor 23

description: tumor 23


title: tumor 20

description: tumor 20


title: tumor 19

description: tumor 19


title: UF0309_brep3


title: UF0309_brep2


title: tumor 17

description: tumor 17


title: UF0317_brep1


title: UF0308_brep3


title: UF0308_brep1


title: UF0299_brep3


title: UF0308_brep2


title: UF0299_brep2


title: tumor 15

description: tumor 15


title: UF0299_brep1


title: UF0298_brep3


title: UF0298_brep1


title: UF0298_brep2


title: UF0309_brep1


title: tumor 16

description: tumor 16


title: UF0297_brep3


title: tumor 14

description: tumor 14


title: UF0297_brep2


title: tumor 18

description: tumor 18


title: tumor 9

description: tumor 9


title: tumor 7

description: tumor 7


title: tumor 8

description: tumor 8


title: tumor 10

description: tumor 10


title: tumor 6

description: tumor 6


title: tumor 5

description: tumor 5


title: tumor 11

description: tumor 11

value: III


title: tumor 13

description: tumor 13


title: UF0297_brep1


title: tumor 12

description: tumor 12


title: UF0291_brep3


title: UF0291_brep2


title: left hippocampus, wildtype 3

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

data_processing:
Raw reads were trimmed using fastp
Trimmed reads were aligned to the reference genome using bowtie2
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

organism: Mus musculus

source_name: left hippocampus

growth_protocol: We housed the mice in an AAALAS-certified level three facility on a 14-hour light cycle with ad libitum access to standard chow and water.

extract_protocol:
We dissected the left hippocampi of 46-week-old, male, wild-type littermates. We immediately flash froze the tissue in liquid nitrogen and stored it temporarily at -80°C. We later homogenized the tissue in TRIzol Reagent (ThermoFisher Scientific) with the Polytron PT 10-35 GT (Kinematica). Lastly,we isolated the RNA by chloroform phase separation, precipitated it with 2-propanol, and washed it with 75% ethanol. We eluted the purified RNA in water.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: We used wild-type, male C57BL/6J mice (Jackson Lab)

tag: strain

tag: genotype

value: wild type

value: 46 weeks

value: left hippocampus


title: UF0291_brep1


title: UF0289_brep3


title: left hippocampus, wildtype 2


title: tumor 4

description: tumor 4


title: DENV_3

city: Albany

first: Cara

middle: T

last: Pager

state: NY

address: 1400 Washington Ave.

institute: University At Albany

data_processing:
Illumina bcl2fastq software (version 2.19.0)  used for basecalling.
Raw sequencing reads were analyzed for quality using FASTQC  (version 0.11.7)
Reads were aligned to the hg19 reference genome using STAR (version 2.7.0b)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated utilizing DESeq2 (version 1.25.0)
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file include FPKM values for each Sample

source_name: Neuroblastoma

extract_protocol:
RNA was harvested by lysing cells in uL 500 Trizol reagent. RNA-seq analysis libraries were prepared using the NEBNext® poly(A) magnetic isolation module (NEB E7490), NEBNext® Ultra™ Directional RNA library prep kit for Illumina® (NEB E7760) and NEBNext® Multiplex oligos for Illumina ® (NEB E7335S). 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Neuroblastoma

tag: experiment

value: DENV


title: tumor 3

description: tumor 3


title: left hippocampus, wildtype 1


title: tumor 1

description: tumor 1


title: tumor 2

description: tumor 2


title: UF0326_brep3


title: UF0289_brep1


title: PRVABC59_3


title: MR766_3


title: DENV_2


title: UF0276_brep2


title: UF0279_brep2


title: UF0279_brep1


title: PRVABC59_2


title: UF0276_brep3


title: UF0289_brep2


title: Mock_3

value: Mock


title: UF0276_brep1


title: UF0274_brep3


title: UF0274_brep2


title: MR766_2


title: Mock_2


title: PRVABC59_1


title: DENV_1


title: UF0274_brep1


title: UF0273_brep3


title: UF0273_brep2


title: Mock_1


title: UF0273_brep1


title: MR766_1


title: UF0272_brep3


title: Sepsis-8

city: Baltimore

first: Sheng

last: Wang

state: MD

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

data_processing:
Sequenced reads were first trimmed using Trim Galore software for adaptor sequence, and mapped to mouse genome (build mm9), genome-mappable reads were then mapped to mouse miRNA sequences (miRBase release 22.1) using the exceRpt Small RNA-Seq Pipeline.
Genome_build: hg38 and miRBase version 21
Supplementary_files_format_and_content: SV18447_exceRpt_miRNA_ReadCounts.txt

source_name: plasma

extract_protocol:
Blood samples were collected through venipuncture and then centrifuged immediately to prepapre cell-free plasma. Plasma RNA was extracted using Trizol LS supplemented with QIAseq miRNA Library QC Spike-ins.
Libraries were prepared for sequencing using Norgen small RNA library prep kit

tag: disease state

value: sepsis

value: plasma


title: Sepsis-10


title: Sepsis-9


title: UF0272_brep2

value: 16 weeks


title: Sepsis-7


title: UF0279_brep3


title: UF0272_brep1


title: UF0263_brep3


title: Sepsis-6


title: Sepsis-5


title: UF0263_brep2


title: Sepsis-3


title: UF0263_brep1


title: UF0259_brep3


title: Sepsis-2


title: UF0259_brep2


title: UF0259_brep1


title: Control-8

value: healthy control


title: Sepsis-1


title: Control-7


title: UF0258_brep3


title: UF0258_brep2


title: UF0258_brep1


title: Control-5


title: UF0255_brep3


title: Control-6


title: Control-4


title: UF0255_brep2


title: Control-3


title: UF0255_brep1


title: Control-2


title: UF0253_brep2


title: Calu3_smallRNA-untr-4h-B

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: Count File: Calu3_smallRNA_miRNAcounts.txt.gz

data_processing:
PolyA-RNA and total-RNA sequencing reads were mapped to the hg38 version of the human genome using STAR (version 2.7.1a) combined with the GENCODE (v30) annotation and the non-standard parameters (--sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000).
Small-RNA sequencing reads were preprocessed using cutadapt (version 2.9) in two passes, first trimming i) the Illumina TruSeq adaptor at the 3’ end, ii) all 3’ end bases with mean Phred score below 30 and iii) the three 5’end overhang nucleotides associated with the Clonetech library preparation protocol. In the second pass, poly(A)-tails were trimmed. Trimmed reads were mapped to hg38 using bowtie (version 1.2.2) and the non-standard parameters (-q -n 1 -e 80 -l 18 -a -m 5 --best --strata). The expression of known miRNAs (miRBase 22 annotation) was estimated using mirdeep2 (version 2.0.0.7) and standard parameters. Gene expression was estimated using FeatureCounts (version 1.5.1) and the non-standard parameters (-F GTF -t exon -g gene_id -C -M --fraction -p -s 2 -O -T 16 -B -Q 4).
For scRNA-seq, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123). Genomes used were hg19, AY310120 (SARS-CoV-1) and MN908947 (SARS-CoV-2)
Genome_build: hg38, hg19
Supplementary_files_format_and_content: tab separated values

source_name: small RNA from Calu3 cells, untr infected 4hpi, replicate B

growth_protocol: H1299, Caco-2 and Calu-3 cells were grown in DMEM/10%FCS/PenStrep/non-essential amino acids/L-glutamine/pyruvate

extract_protocol:
For polyA/total/small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods. For single-cell RNA-sequencing, cells were fixed in methanol and stored at -80 degrees until further processing. Rehydration was done as described in Alles et al. 2017 (doi: 10.1186/s12915-017-0383-5)
PolyA and total RNA-seq libraries were constructed using the NEB Ultra II Directional RNA Library Prep Kit. SmallRNA-seq libraries were constructed using the Clontech SMARTer smRNA-Seq Kit. Single-cell libraries were constructed using a a Nadia device (Dolomite Bio) according to version 1.8 of the manufacturer's protocol, except that the second-strand synthesis step as described in Hughes et al. 2019 (doi: doi.org/10.1101/689273) was included after the exonuclease step.

treatment_protocol: Infections were done by adding the appropriate amount of virus stock solution (produced in Vero E6 cells) at an MOI of 0.3  directly to the cells. For mock infections, supernatant from non-infected Vero E6 cells was used.

tag: infection

value: untreated

tag: time point

tag: molecule subtype

value: small RNA extracted from whole cells


title: Control-1


title: Sepsis-4


title: UF0252_brep3


title: UF0253_brep1


title: Calu3_smallRNA-S2-4h-B

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 4hpi, replicate B


title: UF0252_brep1


title: Calu3_smallRNA-S2-24h-B

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 24hpi, replicate B


title: Calu3_smallRNA-untr-4h-A

source_name: small RNA from Calu3 cells, untr infected 4hpi, replicate A


title: UF0252_brep2


title: Calu3_smallRNA-S2-24h-A

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 24hpi, replicate A


title: UF0248_brep2


title: Calu3_smallRNA-S2-12h-B

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 12hpi, replicate B


title: UF0248_brep1


title: Calu3_smallRNA-S2-12h-A

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 12hpi, replicate A


title: Calu3_smallRNA-S1-4h-B

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 4hpi, replicate B


title: UF0246_brep2


title: Calu3_smallRNA-S1-4h-A

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 4hpi, replicate A


title: UF0245_brep3


title: UF0253_brep3


title: UF0248_brep3


title: Calu3_smallRNA-S1-12h-B

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 12hpi, replicate B


title: UF0245_brep2


title: UF0245_brep1


title: UF0244_brep3


title: Calu3_smallRNA-S1-12h-A

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 12hpi, replicate A


title: Calu3_smallRNA-S1-24h-A

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 24hpi, replicate A


title: Calu3_smallRNA-S2-4h-A

source_name: small RNA from Calu3 cells, SARS-CoV-2 infected 4hpi, replicate A


title: UF0244_brep1

source_name: Xylem


title: UF0243_brep2


title: UF0244_brep2


title: Calu3_polyA_series2-8h-S2-2

description: Count File: Calu3_polyA_series2_readcounts.txt.gz

molecule: polyA RNA

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 8hpi, replicate 2

value: polyA RNA extracted from whole cells


title: Calu3_smallRNA-mock-24h-A

source_name: small RNA from Calu3 cells, mock infected 24hpi, replicate A

value: mock


title: Calu3_smallRNA-mock-4h-A

source_name: small RNA from Calu3 cells, mock infected 4hpi, replicate A


title: Calu3_smallRNA-mock-4h-B

source_name: small RNA from Calu3 cells, mock infected 4hpi, replicate B


title: UF0242_brep3


title: UF0242_brep2


title: UF0246_brep1


title: UF0242_brep1


title: Calu3_smallRNA-S1-24h-B

source_name: small RNA from Calu3 cells, SARS-CoV-1 infected 24hpi, replicate B


title: UF0241_brep3


title: UF0241_brep2


title: Calu3_smallRNA-mock-24h-B

source_name: small RNA from Calu3 cells, mock infected 24hpi, replicate B


title: UF0241_brep1


title: UF0239_brep2


title: UF0239_brep3


title: Calu3_polyA_series2-4h-S1-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 4hpi, replicate 1


title: Calu3_polyA_series2-4h-S2-2

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 4hpi, replicate 2


title: Calu3_polyA_series2-8h-S1-2

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 8hpi, replicate 2


title: Calu3_polyA_series2-4h-S2-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 4hpi, replicate 1


title: UF0243_brep3


title: Calu3_polyA_series2-4h-S1-2

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 4hpi, replicate 2


title: UF0243_brep1


title: Calu3_polyA_series2-4h-mock-1

source_name: polyA RNA from Calu3 cells, series2, mock infected 4hpi, replicate 1


title: Calu3_polyA_series2-4h-mock-2

source_name: polyA RNA from Calu3 cells, series2, mock infected 4hpi, replicate 2


title: Calu3_polyA_series2-8h-S1-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 8hpi, replicate 1


title: UF0239_brep1


title: UF0238_brep3


title: Calu3_polyA_series2-12h-S1-2

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 12hpi, replicate 2


title: UF0238_brep2


title: Calu3_polyA_series2-12h-S2-2

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 12hpi, replicate 2


title: Calu3_polyA_series2-12h-S1-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-1 infected 12hpi, replicate 1


title: UF0238_brep1

source_name: Xylem


title: Calu3_polyA_series2-8h-S2-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 8hpi, replicate 1


title: UF0236_brep2


title: UF0236_brep3


title: Calu3_polyA_series2-12h-mock-2

source_name: polyA RNA from Calu3 cells, series2, mock infected 12hpi, replicate 2


title: Calu3_polyA_series2-12h-mock-1

source_name: polyA RNA from Calu3 cells, series2, mock infected 12hpi, replicate 1


title: UF0246_brep3


title: UF0236_brep1


title: Calu3_polyA_series1-S2-24h-B-detachedcells

description: Count File: Calu3_polyA_series1_readcounts.txt.gz

source_name: polyA RNA from detached Calu3 cells, series1, SARS-CoV-2 infected 24hpi, replicate B


title: Calu3_polyA_series1-S2-24h-A-detachedcells

source_name: polyA RNA from detached Calu3 cells, series1, SARS-CoV-2 infected 24hpi, replicate A


title: Calu3_polyA_series1-S1-24h-A-detachedcells

source_name: polyA RNA from detached Calu3 cells, series1, SARS-CoV-1 infected 24hpi, replicate A


title: UF0232_brep3


title: UF0231_brep3


title: UF0231_brep2


title: Calu3_polyA_series2-12h-S2-1

source_name: polyA RNA from Calu3 cells, series2, SARS-CoV-2 infected 12hpi, replicate 1


title: Calu3_polyA_series1-S1-24h-B-detachedcells

source_name: polyA RNA from detached Calu3 cells, series1, SARS-CoV-1 infected 24hpi, replicate B


title: Calu3_polyA_series1-S2-24h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 24hpi, replicate B


title: Calu3_polyA_series1-S2-24h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 24hpi, replicate A


title: Calu3_polyA_series1-S2-12h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 12hpi, replicate A


title: UF0231_brep1


title: Calu3_polyA_series1-S2-4h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 4hpi, replicate B


title: UF0230_brep2


title: UF0229_brep3


title: UF0229_brep1


title: Calu3_polyA_series1-S2-4h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 4hpi, replicate A


title: UF0229_brep2


title: UF0230_brep3


title: UF0228_brep3


title: Calu3_polyA_series1-S1-12h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 12hpi, replicate B


title: Calu3_polyA_series1-S1-24h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 24hpi, replicate B


title: Calu3_polyA_series1-S1-24h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 24hpi, replicate A


title: Calu3_polyA_series1-S1-12h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 12hpi, replicate A


title: UF0228_brep2

source_name: Xylem


title: Calu3_polyA_series1-S1-4h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 4hpi, replicate B


title: UF0228_brep1


title: UF0232_brep2


title: UF0227_brep2


title: Calu3_polyA_series1-S1-4h-A

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-1 infected 4hpi, replicate A


title: UF0227_brep1


title: UF0230_brep1


title: UF0226_brep1


title: UF0224_brep3


title: UF0226_brep3


title: UF0224_brep2


title: UF0224_brep1


title: UF0226_brep2


title: UF0218_brep2


title: UF0218_brep1


title: UF0216_brep3


title: Calu3_polyA_series1-mock-24h-A

source_name: polyA RNA from Calu3 cells, series1, mock infected 24hpi, replicate A


title: Calu3_polyA_series1-untr-4h-A

source_name: polyA RNA from Calu3 cells, series1, untr infected 4hpi, replicate A


title: Calu3_polyA_series1-untr-4h-B

source_name: polyA RNA from Calu3 cells, series1, untr infected 4hpi, replicate B


title: Caco2_polyA-S2-4h-A

description: Count File: Caco2_polyA_readcounts.txt.gz

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 4hpi, replicate A


title: Caco2_polyA-S2-4h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 4hpi, replicate B


title: UF0227_brep3


title: Caco2_polyA-untr-4h-A

source_name: polyA RNA from Caco2 cells, untr infected 4hpi, replicate A


title: Calu3_polyA_series1-mock-4h-A

source_name: polyA RNA from Calu3 cells, series1, mock infected 4hpi, replicate A


title: Caco2_polyA-S2-24h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 24hpi, replicate B


title: Caco2_polyA-S2-12h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 12hpi, replicate B


title: Calu3_polyA_series1-mock-24h-B

source_name: polyA RNA from Calu3 cells, series1, mock infected 24hpi, replicate B


title: Calu3_polyA_series1-mock-4h-B

source_name: polyA RNA from Calu3 cells, series1, mock infected 4hpi, replicate B


title: UF0216_brep2


title: Caco2_polyA-S1-4h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 4hpi, replicate B


title: Caco2_polyA-untr-4h-B

source_name: polyA RNA from Caco2 cells, untr infected 4hpi, replicate B


title: UF0212_brep3


title: UF0216_brep1


title: Caco2_polyA-S1-4h-A

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 4hpi, replicate A


title: UF0212_brep2

source_name: Xylem


title: UF0218_brep3


title: Caco2_polyA-S2-24h-A

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 24hpi, replicate A


title: Caco2_polyA-S1-24h-A

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 24hpi, replicate A


title: Caco2_polyA-S1-24h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 24hpi, replicate B


title: UF0232_brep1


title: UF0212_brep1


title: UF0210_brep3


title: UF0210_brep2


title: Caco2_polyA-S1-12h-B

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 12hpi, replicate B


title: Caco2_polyA-mock-24h-B

source_name: polyA RNA from Caco2 cells, mock infected 24hpi, replicate B


title: UF0206_brep1


title: UF0207_brep2


title: UF0210_brep1


title: UF0207_brep3


title: Caco2_polyA-mock-24h-A

source_name: polyA RNA from Caco2 cells, mock infected 24hpi, replicate A


title: UF0205_brep1


title: Caco2_polyA-S2-12h-A

source_name: polyA RNA from Caco2 cells, SARS-CoV-2 infected 12hpi, replicate A


title: UF0207_brep1


title: Caco2_polyA-mock-4h-B

source_name: polyA RNA from Caco2 cells, mock infected 4hpi, replicate B


title: H1299_polyA_untr-4h-B

description: Count File: H1299_polyA_readcounts.txt.gz

source_name: polyA RNA from H1299 cells, untreated harvested 4hpi, replicate B


title: UF0204_brep3


title: UF0206_brep3


title: UF0206_brep2


title: H1299_polyA_S2-4h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 4hpi, replicate B


title: Caco2_polyA-mock-4h-A

source_name: polyA RNA from Caco2 cells, mock infected 4hpi, replicate A


title: UF0205_brep3


title: Caco2_polyA-S1-12h-A

source_name: polyA RNA from Caco2 cells, SARS-CoV-1 infected 12hpi, replicate A


title: H1299_polyA_S2-36h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 36hpi, replicate B


title: UF0204_brep1


title: H1299_polyA_S2-4h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 4hpi, replicate A


title: H1299_polyA_S2-24h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 24hpi, replicate B


title: H1299_polyA_S2-12h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 12hpi, replicate B


title: H1299_polyA_S2-36h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 36hpi, replicate A


title: H1299_polyA_S2-24h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 24hpi, replicate A


title: UF0203_brep3

source_name: Xylem


title: H1299_polyA_untr-4h-A

source_name: polyA RNA from H1299 cells, untreated harvested 4hpi, replicate A


title: UF0205_brep2


title: UF0204_brep2


title: UF0203_brep2


title: H1299_polyA_S2-12h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-2 infected harvested 12hpi, replicate A


title: H1299_polyA_S1-4h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 4hpi, replicate B


title: UF0203_brep1


title: UF0197_brep3


title: UF0196_brep1


title: H1299_polyA_S1-36h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 36hpi, replicate B


title: H1299_polyA_S1-12h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 12hpi, replicate B


title: H1299_polyA_S1-24h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 24hpi, replicate A


title: UF0196_brep3


title: UF0194_brep3


title: H1299_polyA_S1-12h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 12hpi, replicate A


title: UF0196_brep2


title: H1299_polyA_mock-4h-A

source_name: polyA RNA from H1299 cells, mock infected harvested 4hpi, replicate A


title: H1299_polyA_S1-24h-B

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 24hpi, replicate B


title: UF0194_brep1


title: H1299_polyA_mock-36h-B

source_name: polyA RNA from H1299 cells, mock infected harvested 36hpi, replicate B


title: UF0193_brep2


title: H1299_polyA_mock-36h-A

source_name: polyA RNA from H1299 cells, mock infected harvested 36hpi, replicate A


title: UF0193_brep3


title: UF0194_brep2


title: UF0197_brep2


title: UF0197_brep1


title: H1299_polyA_S1-4h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 4hpi, replicate A


title: H1299_polyA_S1-36h-A

source_name: polyA RNA from H1299 cells, SARS-CoV-1 infected harvested 36hpi, replicate A


title: AT011WT_RRBS

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

library_source: genomic

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with BCL2FASTQ v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCh38/hg38 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

molecule: genomic DNA

source_name: peripheral blood mononuclear cells

extract_protocol:
48 hours post-aspiration, all groups were euthanized for isolation of lung CD4+ T cells by magnetic bead pre-enrichment and fluorescence-activated cell sorting. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.5% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

value: peripheral blood mononuclear cells

tag: phenotype

value: Healthy control

tag: % phenotype criteria


title: AT012WT_RRBS

tag: age


title: UF0191_brep2


title: UF0193_brep1


title: UF0191_brep1


title: UF0190_brep3


title: UF0191_brep3


title: UF0186_brep3


title: UF0190_brep2


title: AT004_RRBS

value: Mild/variant AT


title: AT003_RRBS


title: UF0190_brep1


title: UF0185_brep2


title: AT006_RRBS

value: Classic AT


title: AT001_RRBS


title: AT008_RRBS


title: AT007_RRBS


title: UF0186_brep2


title: AT002_RRBS


title: AT012WT

data_processing:
Basecalls performed using Illumina RTA2 software.
BCL2FASTQ v2.17.1.14 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the hg38 reference genome using Tophat v.2.1.0, and SeqMonk v1.44.0 was used to generate gene and transcript expression levels.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.44.0.

extract_protocol:
PBMCs were isolated using the Ficoll-Paque Plus Method (GE Healthcare Bio-sciences AB) using a process that maintains the viability and a normalized distribution of B and T lymphocytes to account for relative lymphopenia among AT versus control participants. RNA and genomic DNA were obtained using the AllPrep DNA/RNA Micro Kit (Qiagen).
Libraries for RNA sequencing were prepared with the NEBNext Ultra I RNA Library Prep Kit for Illumina with poly(A) mRNA selection and sequenced using 1 x 75 single-end reads on an Illumina NextSeq 500 instrument using a NextSeq 500/550 V2 High Output reagent kit.


title: AT011WT


title: AT010WT_RRBS


title: AT009WT_RRBS


title: UF0185_brep1


title: UF0184_brep3


title: AT009WT


title: UF0186_brep1


title: UF0184_brep1


title: AT005_RRBS


title: UF0185_brep3


title: UF0183_brep3


title: UF0184_brep2


title: Calu3_polyA_series1-S2-12h-B

source_name: polyA RNA from Calu3 cells, series1, SARS-CoV-2 infected 12hpi, replicate B


title: AT010WT


title: AT008


title: UF0183_brep2


title: AT007


title: AT001


title: UF0183_brep1


title: UF0179_brep3


title: AT005


title: AT006


title: AT003


title: UF0179_brep1


title: UF0177_brep3


title: UF0177_brep2


title: AT002


title: UF0175_brep3


title: UF0177_brep1


title: JNsi481

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd 4200 CTRB

department: Dept of Pediatrics, Oncology Division

institute: Children's Hospital of Philadelphia

description:
processed data files:
raw_data.txt
filtered_data.txt

data_processing:
Libraries were sequenced using 2x75 bp sequencing on the Illumina NextSeq 500 platform at the Van Andel Research Institute.  Data were demultplexed using bcl2fastq v2.20.0.
Adapter removal performed using Trimgalore v0.4.4 with options --paired -q 20
Alignment to hg38 performed using STAR v2.5.2b with options --twopassMode Basic --quantMode GeneCounts
Data were filtered in R for a minimum of 10 counts per million in >0 samples to generate the filtered expression matrix
RNAseq differential expression analysis was performed using edgeR and DESeq2 standard workflow
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files; raw_data.txt contains the raw gene counts from STAR --quantMode; filtered_data.txt file contains the prefiltered data that was then used for differential expression analysis.

source_name: Desmoplastic Small Round Cell Tumor

growth_protocol: JN-DSCRT-1 and BER cells were grown in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gemini Bio-Products), 2 mM L-glutamine (Invitrogen), 100 U/mL penicillin and 100 μg/mL streptomycin (Invitrogen). Cell lines were maintained at less than 80% confluency at 37°C and 5% CO2 and confirmed to be mycoplasma negative every 6-months.

extract_protocol:
RNA was extracted with the RNeasy kit (Qiagen).
Sequencing libraries were prepared using the Kapa Biosystems stranded mRNA-Seq kit for the Illumina platform.

treatment_protocol: JN-DSCRT-1 and BER cells were treated with 20nM siNeg (control) OR (siEWS-WT1) for 48-hours then collected.

tag: treatment

tag: replicate


title: JNsi482


title: UF0175_brep2

source_name: Xylem


title: JNN483

value: siNeg


title: JNN482


title: UF0172_brep3


title: UF0175_brep1


title: UF0179_brep2


title: JNN481


title: UF0172_brep1


title: Bsi483

value: BER


title: Bsi482


title: UF0172_brep2


title: UF0169_brep2


title: Bneg383


title: Bsi481


title: UF0169_brep3


title: UF0167_brep2


title: Bneg482


title: UF0167_brep3


title: UF0169_brep1


title: Bneg481


title: ICAM1+/GP350-  Rep2

city: Boston

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). normalized reads

source_name: MUTU1 Burkitt Lymphoma cells

growth_protocol: MUTU I cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
Total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination
To construct RNA-seq libraries, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA).

treatment_protocol: MUTU I cells were transduced with lentiviruses expressing control or UHRF1 sgRNA. At day 8 post-transduction, cells were FACSorted for corresonding subpopulations.

tag: sgrna

value: Cells expressing UHRF1 sgRNA


title: UF0167_brep1


title: ICAM1+/GP350-  Rep3


title: AT004

tag: tissue


title: UF0166_brep2


title: ICAM1-/GP350+ Rep3


title: UF0166_brep1


title: ICAM1+/GP350-  Rep1


title: ICAM1-/GP350+ Rep2


title: UF0164_brep2


title: UF0164_brep3


title: ICAM1-/GP350+ Rep1


title: Control sgRNA Rep3

value: Cells expressing Control sgRNA


title: UF0164_brep1


title: Control sgRNA Rep2


title: Control sgRNA Rep1


title: UF0166_brep3


title: UF0163_brep2


title: UF0163_brep1


title: MUTU III Rep2

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively

source_name: MUTU III Burkitt Lymphoma cells

growth_protocol: MUTU I and MUTU III cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

treatment_protocol: No specific treatment

tag: cell type

value: MUTU III Burkitt Lymphoma cells


title: MUTU III Rep3


title: H1299_polyA_mock-4h-B

source_name: polyA RNA from H1299 cells, mock infected harvested 4hpi, replicate B


title: UF0163_brep3


title: UF0155_brep1


title: UF0153_brep3


title: ICAM1+ Rep2

data_processing:
Adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 5 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between experimental group and the control group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCh37.83
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj), normalized reads

source_name: RaeL Burkitt Lymphoma cells

growth_protocol: RaeL cells were cultured in GIBCO RPMI 1650 medium (Life Technologies) with 10% fetal calf serum (FCS) and 10 mM HEPES in a humidified chamber at 37 degrees Celcius with 5% CO2.

treatment_protocol: RaeL cells were transduced with lentiviruses expressing control or UHRF1 sgRNA. At day 8 post-transduction, cells were FACSorted for corresonding subpopulations.


title: UF0153_brep2


title: MUTU I Rep2

source_name: MUTU I Burkitt Lymphoma cells

value: MUTU I Burkitt Lymphoma cells


title: ICAM1+ Rep1


title: UF0151_brep2


title: UF0153_brep1


title: MUTU I Rep3


title: Control Rep1


title: UF0151_brep3


title: Control Rep2


title: UF0151_brep1


title: UF0155_brep2


title: NA18517 IP replicate

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

description: jointPeakReadCount.txt

data_processing:
Seequencing reads were aligned to reference genome by Tophat2 using WASP pipeline to avoid mapping bias due to SNPs.
Read count of connected bins was quantified by R package MeRIPtools.
Joint peak calling and read count quntification by R package MeRIPtools.
QTL mapping using beta-binomial regression by R package MeRIPtools
Genome_build: hg19
Supplementary_files_format_and_content: (1) Joint m6A peaks across 60 thousand genome YRI individuals in BED12 file and associated read count of input and IP samples.   (2) summary statistics of beta-binomial regression

source_name: Lymphoblastoid cell line

growth_protocol: Standard LCL culture protocol according to instruction downloaded from Coriell institute.

extract_protocol:
TRIzol (Invitrogen) + polyT beads
Kapa RNA hyperPrep kit for Illumina

tag: batch

tag: molecule

value: m6A enriched mRNA


title: UF0155_brep3

value: 16 weeks


title: NA18510 IP replicate

description: jointPeakReadCount.txt


title: UF0148_brep1


title: UF0148_brep2


title: MUTU III Rep1


title: NA18507 IP replicate

description: jointPeakReadCount.txt


title: UF0147_brep3


title: NA18502 IP replicate

description: jointPeakReadCount.txt


title: UF0147_brep2


title: NA18505 IP replicate

description: jointPeakReadCount.txt


title: NA18517 Input replicate

description: jointPeakReadCount.txt

value: mRNA


title: NA18504 IP replicate

description: jointPeakReadCount.txt


title: NA18510 Input replicate

description: jointPeakReadCount.txt


title: NA18507 Input replicate

description: jointPeakReadCount.txt


title: NA18505 Input replicate

description: jointPeakReadCount.txt


title: NA18504 Input replicate

description: jointPeakReadCount.txt


title: NA18510 IP

description: jointPeakReadCount.txt


title: NA18502 Input replicate

description: jointPeakReadCount.txt


title: UF0141_brep1


title: UF0143_brep1


title: UF0143_brep2


title: NA18507 IP

description: jointPeakReadCount.txt


title: UF0143_brep3


title: UF0140_brep1


title: UF0139_brep3


title: NA18505 IP

description: jointPeakReadCount.txt


title: NA18504 IP

description: jointPeakReadCount.txt


title: UF0147_brep1


title: UF0141_brep2


title: UF0141_brep3


title: UF0140_brep2


title: UF0140_brep3


title: NA18517 Input

description: jointPeakReadCount.txt


title: UF0139_brep1


title: UF0138_brep3


title: NA18517 IP

description: jointPeakReadCount.txt


title: UF0138_brep2


title: NA18507 Input

description: jointPeakReadCount.txt


title: UF0148_brep3


title: UF0138_brep1


title: NA18504 Input

description: jointPeakReadCount.txt


title: UF0137_brep3


title: NA18502 Input

description: jointPeakReadCount.txt


title: UF0137_brep2


title: UF0129_brep3


title: UF0129_brep1


title: UF0137_brep1


title: H3K27Ac.Y.NR.8.2

city: San Francisco

first: Louis

last: Ptacek

state: CA

institute: University of California San Francisco

data_processing:
Bowtie2 (v2.2.4) was used to align sequencing data to the mm10 genome with standard parameters. For each ChIP, peaks that enrich over the appropriate input were called using the HOMER findPeaks command with settings -style factor, -size 275, -fragLength 250. For scatter plots, heatmaps, box and whisker plots, tag-density for individual peaks for each replicate as described was quantified by HOMER annotatePeaks with setting -size given, and averaged. For histograms, the average tag-density across numerous peaks for each replicate was determined with annotatePeaks with the settings -hist 5, size -2000. For gene ontology analyses, sam files for both replicates were merged (samtools1.2 merge command) and peaks that enrich over the input were identified as above and compared across groups with HOMER mergePeaks. Gene ontology analysis of KEGG and Interpro databases was performed with HOMER findGO command using non-redundant genes annotated from identified peaks. For tornado plots, tag-density +/- 1kb from the center of the peak as described was generated from merged sam files using the HOMER annotatePeaks command with settings -ghist 25, and -size 2000. Tornado plots were z-score normalized and sorted from max-min signal according to old, NR-treated mice at ZT8.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were created using MACS2 (2.1.0) with options -B --SPMR --nomodel --extsize 300 -q 0.1 -g mm --broad

source_name: Liver

extract_protocol:
Liver was collected at the indicated time points and processed for ChIP-seq as previously published. Briefly, liver was fixed in disuccinimidyl glutarate (2mM in PBS + 1% DMSO, 30 min) and formaldehyde (1% in PBS, 10 min) prior to aliquoting and freezing at -80˚C. For BMAL1 (antibody produced in Bass Lab as in (43), Millipore ABE2599) and HSF1 (Cell Signaling 4356) ChIP-Seq, nuclei from a quarter of a liver were isolated in buffer (150 mM NaCl, 5 mM EDTA pH8, 50 mM Tris-HCl pH8, 0.35% NP-40) in the presence of protease inhibitors by needle, then sheared in 1% SDS buffer in a sonicator (diagenode) for 6 cycles 30on/30off at 4˚C. An aliquot for input samples was taken after shearing. Chromatin was diluted 1:10 in dilution buffer (.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 1.2 mM EDTA pH8, 1.67 mM Tris-HCl pH8), and immunoprecipitations with 15 µg of antibody were performed overnight at 4˚C, rotating. Secondary-conjugated, BSA-blocked paramagnetic beads were used to pull down protein/DNA complexes. Chromatin was de-crosslinked and purified by Qiagen MinElute column. Inputs were quantified by Qubit Fluorometer (Invitrogen) for each liver, and 2 ng of equimolar pools of the replicates per condition were processed into libraries.
Library prep with NEBNext Ultra II Library prep kit. Libraries were size-selected to 200-600 bp on the Sage Pippin Prep prior to PCR amplification. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

tag: strain

value: 10 months

tag: genotype

value: WT

tag: treatment time point

value: 6 months

tag: collection time point

value: Liver

tag: chip antibody


title: H3K27Ac.Y.NR.8.1


title: JNsi483

tag: cell line


title: UF0139_brep2


title: H3K9Ac.Y.NR.8.2


title: NA18502 IP

description: jointPeakReadCount.txt


title: H3K27Ac.Y.H2O.8.1


title: UF0129_brep2


title: H3K27Ac.Y.H2O.8.2


title: UF0128_brep3


title: H3K9Ac.Y.H2O.8.2


title: UF0128_brep2


title: H3K9Ac.Y.NR.8.1


title: NA18510 Input

description: jointPeakReadCount.txt


title: NA18505 Input

description: jointPeakReadCount.txt


title: H3K9Ac.Y.H2O.8.1


title: Ovi_TBP_tumor3_tumor4

city: Utrecht

first: Kadi

last: Lõhmussaar

state: -- Select State/Province --

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Total RNA was extracted from murine oviductal TBP-clone-derived tumor tissue using standard Trizol extraction method including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

data_processing:
Paired-end reads from Illumina sequencing were aligned to the mouse transcriptome genome by BWA
DESeq2 (v1.18.0) was used for read normalization and differential expression analysis.
Gene set enrichment anlysis (GSEA) was performed using GSEA software v3.0 beta2.
Genome_build: GRCm38
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts.

source_name: Mouse tumors

extract_protocol:
Total RNA was extracted using standard Trizol extraction method (tissues) or Qiagen RNeasy Mini Kit (organoids) according to manufacturer's instructions including DNaseI treatment.
RNA libraries were prepared for sequencing using Cel-Seq2 protocol. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: origin

value: oviduct

value: TBP-clone-derived tumor tissue

tag: sample type

value: Tumor3 and Tumor4


title: Ovi_TBP_tumor5_tumor6

value: Tumor5 and Tumor6


title: UF0128_brep1


title: UF0125_brep1


title: UF0122_brep3


title: UF0122_brep2


title: Ovi_TBP_tumor1_tumor2

value: Tumor1 and Tumor2


title: Ovi_tumor_org_T3mes_T4epi

description: Total RNA was extracted from organoids derived from murine oviductal TBP-clone-derived tumors using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse tumor-derived organoids

value: TBP-clone-derived tumor organoids

value: T3-mes and T4-epi


title: Ovi_tumor_org_T1mes_T2epi

value: T1-mes and T2-epi


title: UF0125_brep3


title: UF0125_brep2


title: Ovi_TBP_clones_Cas9_GFP

description: Total RNA was extracted from murine oviductal TBP-clones using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse oviduct TBP mutant clones

value: mutant organoids

value: 3 oviduct TBP mutants


title: UF0118_brep1


title: UF0116_brep2


title: UF0113_brep3


title: MUTU I Rep1

value: MUTU I Burkitt Lymphoma cells


title: UF0116_brep3

value: 16 weeks


title: UF0113_brep2


title: Oviiduct_organoids_Cas9GFP

description: Total RNA was extracted from murine wildtype oviductal organoids using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse oviduct organoids

value: bulk wildtype organoids from Cas9GFP mice

value: 3 oviduct Cas9GFP organoid samples


title: OSE_organoids

description: Total RNA was extracted from murine wildtype OSE organoids using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse OSE organoids

value: OSE

value: bulk wildtype organoids

value: 2 OSE organoid samples (the first lane was removed from analysis)


title: UF0113_brep1


title: OSE_bulk_tissue

description: Total RNA was extracted from murine bulk OSE epithelial tissue using standard Trizol extraction method including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse OSE tissue

value: bulk wildtype tissue

value: 3 OSE tissue samples


title: Oviduct_organoids

value: oviduct

value: 3 oviduct organoid samples


title: ATAC-BKO.8.4

data_processing:
Bowtie2 (v2.2.4) was used to align ATAC-Seq data to the mm10 genome with standard parameters and --local. Nucleosome-free reads were separated out with the R package ATACSeqQ. For each library, nucleosome free peaks that enrich over background were called using the HOMER findPeaks command with settings -size 150, -fragLength 41. For scatter plots, heatmaps, box and whisker plots, tag-density for individual peaks for each replicate as described was quantified by HOMER annotatePeaks with setting -size given, and averaged. For histograms, the average tag-density across numerous peaks for each replicate was determined with annotatePeaks with the settings -hist 5, size -2000.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files of nucleosome-free reads were created using MACS2(2.1.0) with options -f BAMPE -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --all-summits -g mm

extract_protocol:
100 mg of fresh liver was dounced in ice-cold PBS, passed through a 40 uM filter, and 50,000 cells were processed as described previously66. Briefly, samples were resuspended in ATAC-RSB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) containing 0.1% IGEPAL, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 3 min prior to 20x dilution in ATAC-RSB containing 0.01% Tween-20. Nuclear pellets were subjected to tagmentation at 37˚C for 30 min in Nextera TD buffer (Illumina) containing 33% PBS, 0.01% digitonin, 0.1% Tween-20, and 2.5 units Nextera transposase enzyme (Illumina). Following transposition reaction, DNA was purified using MinElute columns (Qiagen), subjected to 9 amplification cycles, size-selected by Sage Pippin Prep for fragments between 100-1000 bp, and sequenced by 42 bp paired-end sequencing to an average depth of ~50M aligned reads per sample.
library prep following the OMNIATAC protocol using NEXTERA transposase enzyme. Libraries were size-selected to 100-1000 bp on the Sage Pippin Prep prior after 9 cycles of PCR amplification. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

value: 4-6 months

value: Bmal1 ko/ko

tag: collection timepoint

value: Liver


title: ATAC-BKO.8.3

tag: age


title: UF0116_brep1


title: C57BL6-nur77-WT (Lyn +/+)

city: Vancouver

first: Ken

last: Harder

state: BC

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

description: wt_and_lynko_monocytes_raw_counts.csv.gz

data_processing:
The Cell Ranger Single Cell Software Suite, version 3.0.2 was used for de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome.
Specific details and instructions to run Cell Ranger can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Cell ranger output was imported in Seurat Version 3.1 and the data was normalized, scaled and monocytes were identified based on gene expression profiles.
Next, monocyte barcodes were subsetted and the data is provided as processed data files
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv and scaled_data.csv generated using Seurat Version 3.1

source_name: RBC lysed whole blood

extract_protocol:
Blood was collected from C57BL/6, Lyn-/-, Nr4a1-eGFP/cre and Nr4a1-eGFP/cre Lyn-/- mice using a cardiac puncture. Blood was RBC lysed and equal numbers of either C57BL/6 and Nr4a1-eGFP/cre WBCs (wt, Lyn+/+), or Lyn-/- and Nr4a1-eGFP/cre Lyn-/- cells (Lyn-/-) were pooled and sorted. 26,500 sorted cells were loaded on the 10X chromium system at a concentration of 530 cells/uL and data from 10,859 and 11,093 cells was obtained from wt and Lyn-/- samples, respectively.
The sequencing protocol is the 10x Genomics V3.1 NextGEM single cell 3' sequencing protocol.

value: Lyn +/+


title: UF0118_brep3

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq FASTQ-files were quality and adapter trimmed using Trimmomatic v0.32
The pre-processed reads were aligned to v3.0 of the Populus thrichocarpa reference genome using STAR 2.5.2b
Picard v1.115 was used to remove duplicate reads and only unique alignments were kept for further analysis.
Three transcript assembly platforms were used to maximize the detection of novel genes: (1) Cufflinks version 2.2.1, (2) StringTie version 1.3.3 , and (3) Trinity version 2.3.2.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The master transcriptome was reformatted and annotated using gffcompare version 0.9.9c and subjected to expression filtering to remove artifacts generated by merging assemblies such that each transcript in the assembly was required to be expressed at FPKM >= 3 in at least two of the three biological replicates of at least three individuals and 50 observations.
Gene expression was measured using Cufflinks version 2.2.1
Supplementary_files_format_and_content: A single Comma separated (.csv) file includes a matirx with FPKM values for all samples (Matrix_fpkm_AllIndividuos.csv)


title: UF0112_brep2


title: UF0110_brep3


title: UF0112_brep1


title: LYN-KO-nur77-lyn-KO (Lyn -/-)

description: wt_and_lynko_monocytes_scaled_data.csv.gz

value: Lyn -/-


title: Oviduct_bulk_tissue

description: Total RNA was extracted from murine bulk oviductal tissue using standard Trizol extraction method including DNaseI treatment. RNA libraries were prepared for sequencing using Cel-Seq2 protocol.

source_name: Mouse oviduct tissue

value: 3 oviduct tissue samples


title: UF0110_brep2


title: ATAC-BKO.8.1

tag: treatment


title: UF0122_brep1


title: ATAC-WT.8.1

value: WT


title: UF0112_brep3

value: 16 weeks


title: UF0108_brep2


title: UF0108_brep3


title: UF0108_brep1


title: ATAC-BKO.8.2


title: UF0106_brep2


title: UF0106_brep3


title: Input.O.NR.8

data_processing:
Bowtie2 (v2.2.4) was used to align sequencing data to the mm10 genome with standard parameters. For each ChIP, peaks that enrich over the appropriate input were called using the HOMER findPeaks command with settings -style factor, -size 275, -fragLength 250. For scatter plots, heatmaps, box and whisker plots, tag-density for individual peaks for each replicate as described was quantified by HOMER annotatePeaks with setting -size given, and averaged. For histograms, the average tag-density across numerous peaks for each replicate was determined with annotatePeaks with the settings -hist 5, size -2000. For gene ontology analyses, sam files for both replicates were merged (samtools1.2 merge command) and peaks that enrich over the input were identified as above and compared across groups with HOMER mergePeaks. Gene ontology analysis of KEGG and Interpro databases was performed with HOMER findGO command using non-redundant genes annotated from identified peaks. For tornado plots, tag-density +/- 1kb from the center of the peak as described was generated from merged sam files using the HOMER annotatePeaks command with settings -ghist 25, and -size 2000. Tornado plots were z-score normalized and sorted from max-min signal according to old, NR-treated mice at ZT8.
mm10
bigWig files were created using MACS2(2.1.0) with options -B --SPMR --nomodel --extsize 300 -q 0.1 -g mm --broad

extract_protocol:
Liver was collected at the indicated time points and processed for ChIP-seq as previously published. Briefly, liver was fixed in disuccinimidyl glutarate (2mM in PBS + 1% DMSO, 30 min) and formaldehyde (1% in PBS, 10 min) prior to aliquoting and freezing at -80˚C. For BMAL1 (antibody produced in Bass Lab as in (43), Millipore ABE2599) and HSF1 (Cell Signaling 4356) ChIP-Seq, nucleii from a quarter of a liver were isolated in buffer (150 mM NaCl, 5 mM EDTA pH8, 50 mM Tris-HCl pH8, 0.35% NP-40) in the presence of protease inhibitors by needle, then sheared in 1% SDS buffer in a sonicator (diagenode) for 6 cycles 30on/30off at 4˚C. An aliquot for input samples was taken after shearing. Chromatin was diluted 1:10 in dilution buffer (.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 1.2 mM EDTA pH8, 1.67 mM Tris-HCl pH8), and immunoprecipitations with 15 µg of antibody were performed overnight at 4˚C, rotating. Secondary-conjugated, BSA-blocked paramagnetic beads were used to pull down protein/DNA complexes. Chromatin was de-crosslinked and purified by Qiagen MinElute column. Inputs were quantified by Qubit Fluorometer (Invitrogen) for each liver, and 2 ng of equimolar pools of the replicates per condition were processed into libraries.
library prep with NEBNext Ultra II library prep kit. Libraries were size-selected to 200-600 bp on the Sage Pippin Prep prior to PCR amplification. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

value: 22 months

value: 6 months

value: Input


title: UF0106_brep1


title: Input.O.H2O.20


title: Input.O.H2O.8


title: Input.Y.NR.8

value: 10 months


title: Input.Y.H2O.20


title: Input.O.NR.20


title: UF0104_brep3


title: Input.Y.NR.20


title: UF0104_brep1


title: Input.Y.H2O.8


title: ATAC-WT.8.2


title: HSF1.O.NR.20.2


title: HSF1.O.NR.20.1


title: UF0110_brep1


title: UF0098_brep3


title: HSF1.O.NR.8.2


title: HSF1.O.NR.8.1


title: UF0098_brep1


title: UF0094_brep3


title: HSF1.O.H2O.20.2


title: HSF1.O.H2O.20.1


title: UF0094_brep2


title: HSF1.O.H2O.8.2


title: HSF1.O.H2O.8.1


title: UF0090_brep1


title: HSF1.Y.NR.8.2


title: UF0118_brep2


title: UF0094_brep1


title: UF0090_brep2


title: UF0090_brep3


title: HSF1.Y.NR.20.2


title: HSF1.Y.NR.8.1


title: UF0089_brep3


title: HSF1.Y.H2O.20.1


title: UF0088_brep2


title: HSF1.Y.H2O.8.2


title: UF0088_brep3


title: UF0089_brep2


title: UF0088_brep1


title: UF0089_brep1


title: HSF1.Y.H2O.20.2


title: HSF1.Y.H2O.8.1


title: UF0086_brep3


title: UF0098_brep2


title: UF0104_brep2


title: UF0086_brep2


title: UF0086_brep1


title: BMAL1.O.NR.8.2

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: BMAL1.O.NR.20.2


title: UF0085_brep3


title: HSF1.Y.NR.20.1


title: BMAL1.O.NR.8.1


title: UF0085_brep2


title: UF0085_brep1


title: BMAL1.O.H2O.20.1


title: BMAL1.O.H2O.8.2


title: UF0084_brep2


title: BMAL1.O.H2O.8.1


title: UF0084_brep3


title: BMAL1.Y.NR.20.2


title: UF0083_brep2


title: BMAL1.Y.NR.8.2


title: UF0083_brep1


title: BMAL1.Y.H2O.20.2


title: BMAL1.Y.H2O.20.1


title: UF0082_brep2


title: UF0082_brep1


title: BMAL1.Y.H2O.8.2


title: UF0082_brep3


title: BMAL1.Y.NR.20.1


title: BMAL1.O.NR.20.1


title: BMAL1.Y.H2O.8.1


title: UF0081_brep2


title: Input.BKO.NR.8.1

value: 2 months


title: BMAL1.O.H2O.20.2


title: UF0081_brep1


title: Input.WT.NR.8.1


title: UF0081_brep3


title: UF0080_brep3


title: Input.BKO.H2O.8.1


title: UF0080_brep2


title: Input.WT.H2O.8.1


title: UF0078_brep3


title: HSF1.BKO.NR.8.2


title: UF0084_brep1


title: BMAL1.Y.NR.8.1


title: HSF1.WT.NR.8.2


title: HSF1.WT.NR.8.1


title: UF0077_brep3


title: UF0077_brep2


title: HSF1.BKO.H2O.8.1


title: UF0075_brep3


title: HSF1.WT.H2O.8.1


title: UF0075_brep2


title: HSF1.WT.H2O.8.2


title: Input-LSKO.NMN.6.1

value: Alb-Cre; Sirt1 fx/fx

value: 4hr NMN (500 mg/kg i.p.)


title: UF0075_brep1


title: Input-LSKO.Sal.6.1

value: Saline


title: UF0074_brep3


title: UF0074_brep1


title: BMAL1-LSKO.NMN.6.2

value: 4-6 months


title: UF0074_brep2


title: HSF1.BKO.NR.8.1

value: Bmal1 ko/ko


title: Input-Ctrl.NMN.6.1

value: Sirt1 fx/fx


title: UF0080_brep1


title: UF0073_brep1


title: UF0073_brep3


title: Input-Ctrl.Sal.6.1


title: BMAL1-LSKO.Sal.6.2


title: UF0078_brep1


title: BMAL1-LSKO.NMN.6.1


title: UF0073_brep2


title: UF0078_brep2


title: BMAL1-LSKO.Sal.6.1


title: UF0072_brep3


title: UF0077_brep1


title: HSF1.BKO.H2O.8.2


title: UF0072_brep2


title: BMAL1-Ctrl.NMN.6.2


title: BMAL1-Ctrl.NMN.6.1


title: BMAL1-Ctrl.Sal.6.2


title: UF0068_brep3


title: UF0068_brep2


title: UF0067_brep3


title: UF0067_brep2


title: RNA-LSKO.NMN.6.4

data_processing:
Using standard parameters, sequences were aligned to the mm10 genome with STAR (v2.5.2) and assigned to Ensembl features (GRCm38.vM12) with subread:featureCounts (v1.5.1). Analysis of differential expression at each timepoint was performed with standard parameters in DESeq2 (v1.24.0) after removal of genes with 0 read counts. FDR-adjusted p-value cutoff for significance was set to 0.1. DESeq2-normalized counts were used for analysis of rhythmic expression with eJTK_Cycle (v3.1.R). Period lengths were allowed between 20 and 28 hours to account for sampling frequency (4 hours). Adjusted p-values of 0.1 and 0.9 were chosen for ‘rhythmic’ and ‘non-rhythmic’ genes respectively. Genes were classified as “unaffected” if they were similarly rhythmic in both conditions, as “gain” if they were non-rhythmic in the control condition and rhythmic in the experimental condition, as “loss” if they were rhythmic in the control condition and non-rhythmic in the experimental condition, and “phase-shift” if they were rhythmic in both conditions but were annotated with peak phases that were greater than 4 hours different. Heatmaps were sorted by peak phase for the control condition for loss, unaffected, and phase-shift reprogramming groups, while they were sorted by peak phase of the experimental condition for the gain reprogramming group. Gene ontology and promoter motif analysis were performed on genes from each reprogramming group that were sub-divided by phase. Gene ontology analysis of the KEGG term database was performed with the HOMER findGO command. Enrichment of known motifs +/- 2 kb of the TSS were determined using the HOMER findMotif command. The JASPAR vertebrate DNA binding motif database was used as the known motif set with a threshold set to 6.5.
mm10
tab delimited text files contain non-normalized counts per gene. Generated with subread:featurecounts

extract_protocol:
RNA was isolated from 10-20mg of liver tissue using trizol reagent and purified on the Zymo Direct-Zol RNA miniprep kit. RNA quality was assessed by Bioanalyzer (Agilent). RNAs with a RNA Integrity Number (RIN) greater than 8 were used for library prep.
Libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit from NEB. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.


title: RNA-LSKO.NMN.6.3


title: RNA-LSKO.NMN.6.2


title: UF0066_brep3

extract_protocol:
Total RNA was extracted according to the CTAB-LiCl protocol (Chang et al., 1993).
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina  following the manufacturerÕs instructions.


title: UF0067_brep1


title: RNA-LSKO.Sal.6.3


title: RNA-LSKO.Sal.6.2


title: RNA-LSKO.NMN.6.1


title: UF0063_brep3


title: UF0066_brep2


title: UF0063_brep2


title: BMAL1-Ctrl.Sal.6.1


title: RNA-Ctrl.NMN.6.3


title: RNA-Ctrl.NMN.6.4


title: UF0066_brep1


title: RNA-Ctrl.NMN.6.2


title: UF0072_brep1


title: RNA-LSKO.Sal.6.1


title: RNA-Ctrl.NMN.6.1


title: UF0063_brep1


title: RNA-Ctrl.Sal.6.3


title: RNA-Ctrl.Sal.6.4


title: UF0061_brep3


title: UF0061_brep1


title: UF0068_brep1


title: UF0060_brep3


title: RNA-Ctrl.Sal.6.1


title: RNA-Ctrl.Sal.6.2


title: UF0060_brep2


title: UF0057_brep3


title: RNA-BKO.NMN.6.2


title: RNA-BKO.NMN.6.1


title: UF0057_brep2


title: RNA-BKO.Sal.6.2


title: RNA-BKO.Sal.6.1


title: RNA-WT.NMN.6.2


title: UF0054_brep2


title: UF0057_brep1


title: UF0054_brep3


title: RNA-WT.Sal.6.3


title: UF0061_brep2


title: RNA-WT.NMN.6.1


title: UF0052_brep3


title: UF0052_brep1


title: RNA-WT.Sal.6.1


title: LNKO.RHYTHM.20.3

description: mice were fasted 18-hours prior to collection

value: 8 months

value: Alb-Cre; Namptfx/fx


title: LNKO.RHYTHM.20.2


title: UF0050_brep3


title: UF0052_brep2


title: RNA-WT.Sal.6.2


title: UF0060_brep1


title: UF0050_brep2


title: UF0050_brep1


title: UF0048_brep2


title: UF0048_brep1


title: ctrl.RHYTHM.20.4

value: Namptfx/fx


title: ctrl.RHYTHM.20.6


title: ctrl.RHYTHM.20.3

value: Alb-Cre; Nampt+/+


title: LNKO.RHYTHM.20.1


title: UF0048_brep3

value: 16 weeks


title: UF0047_brep3


title: UF0047_brep2


title: ctrl.RHYTHM.20.2


title: ctrl.RHYTHM.20.1


title: UF0044_brep3


title: UF0047_brep1


title: UF0044_brep1


title: ctrl.RHYTHM.16.5


title: LNKO.RHYTHM.16.1


title: UF0042_brep3


title: ctrl.RHYTHM.16.4


title: ctrl.RHYTHM.16.3


title: UF0042_brep1


title: ctrl.RHYTHM.16.2


title: ctrl.RHYTHM.16.1


title: ctrl.RHYTHM.20.5


title: UF0041_brep3


title: UF0041_brep1


title: LNKO.RHYTHM.12.2


title: UF0041_brep2


title: LNKO.RHYTHM.12.1


title: UF0040_brep3


title: ctrl.RHYTHM.12.4


title: LNKO.RHYTHM.16.2


title: UF0040_brep2


title: UF0044_brep2


title: UF0040_brep1


title: ctrl.RHYTHM.12.5


title: LNKO.RHYTHM.16.3


title: UF0039_brep3


title: ctrl.RHYTHM.12.3


title: ctrl.RHYTHM.12.6


title: UF0036_brep2


title: LNKO.RHYTHM.8.4


title: ctrl.RHYTHM.12.2


title: LNKO.RHYTHM.8.3


title: UF0039_brep1


title: UF0036_brep1


title: UF0036_brep3


title: ctrl.RHYTHM.12.1


title: LNKO.RHYTHM.8.1


title: UF0039_brep2


title: LNKO.RHYTHM.8.2


title: UF0035_brep3


title: ctrl.RHYTHM.8.6


title: ctrl.RHYTHM.8.5


title: UF0035_brep1


title: UF0035_brep2


title: UF0042_brep2


title: ctrl.RHYTHM.8.4


title: UF0033_brep3


title: UF0033_brep2


title: UF0033_brep1


title: ctrl.RHYTHM.8.3


title: iNeurons, Control 3

data_processing:
Raw reads were trimed using fastp
Trimmed reads were aligned to the reference genome using bowtie2
Samtools were used to sort, convert, and index alignment files
Deeptools were used to generate bigwig files
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: Excitatory neurons

growth_protocol: We used WA09 (H9; RRID:CVCL_9773, WiCell) female embryonic stem cells (ESCs) to generate human neurons as previously described (Jiang et al., 2017). We confirmed their identity by STR analysis and verified that they were free of mycoplasma. We differentiated neural progenitors into human neurons over three weeks, changing the media every 3 days. Afterwards, we passaged the neurons with trypsin. We infected the neurons with lentivirus three days after passaging. We then cultured the cells for 60 days after infection, changing the media three times per week.

extract_protocol:
After 60 days of culturing the infected neurons, we extracted RNA from shRNA-infected, human ESC-derived neurons in a 12-well plate. We lysed the neurons in the tissue-culture plate with TRIzol Reagent (ThermoFisher Scientific) and immediately transferred the lysate to microfuge tubes for trituration. We then isolated the RNA by chloroform phase separation, precipitation with 2-propanol, washing with 75% ethanol, and eluting in water.
We prepared sequencing libraries as previously described (Routh et al., 2017). We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. We then amplified the cDNA for 21 cycles with Universal primer and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 75 base-pair reads on a Nextseq 550 (Illumina).

treatment_protocol: Three days after passaging, we infected the neurons with lentiviruses containing the control pGIPZ non-silencing shRNA clone RHS4348 (Dharmacon) at a multiplicity of infection of 10. We verified the tropism and infectivity of the virus using the tGFP reporter signal. On day two after infection, we treated the cells with 1 µM 5-Fluoro-2′-deoxyuridine for one day to remove proliferating glia from the culture (Hui et al., 2016). At day 3, we treated the neurons with puromycin (0.75–1.25 g/ml) for 6 days to select for infected cells.

value: WA09 embryonic stem-cell derived excitatory neurons

tag: culture duration

value: 60 days

tag: shRNA

value: Scramble


title: iNeurons, Control 2


title: iNeurons, Control 1


title: ctrl.RHYTHM.8.2


title: UF0031_brep3

source_name: Xylem


title: ctrl.RHYTHM.8.1


title: UF0031_brep1


title: LNKO.RHYTHM.4.2


title: UF0030_brep3


title: UF0031_brep2


title: Genomic DNA from T-cell lymphoblastic lymphoma 47

type: genomic

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium 850K Human Methylation BeadChip using standard Illumina protocol.

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

data_processing:
DNA methylation data were analyzed using the methylation analysis module within BeadStudio software employing default parameters (Illumina, Inc., San Diego CA, USA).
normalized_data.txt: Tab-delimited text file includes Normalized (Beta-Mixture Quantile dilation method) Average Beta.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from T-LBL samples using Qiagen DNeasy Kit according to standard instructions.

tag: tissue

value: T-cell lymphoblastic lymphoma

tag: disease state

value: Relapse-free T-LBL


title: Genomic DNA from T-cell lymphoblastic lymphoma 43

value: Relapse T-LBL


title: UF0030_brep1


title: LNKO.RHYTHM.4.1


title: UF0030_brep2


title: ctrl.RHYTHM.4.5


title: UF0026_brep3


title: UF0026_brep1


title: UF0026_brep2


title: ctrl.RHYTHM.4.4


title: ctrl.RHYTHM.4.3


title: ctrl.RHYTHM.4.1


title: ctrl.RHYTHM.4.2


title: Genomic DNA from T-cell lymphoblastic lymphoma 30


title: LNKO.RHYTHM.0.5


title: LNKO.RHYTHM.0.4


title: UF0025_brep1


title: UF0025_brep2


title: LNKO.RHYTHM.0.3


title: LNKO.RHYTHM.4.3


title: UF0024_brep3


title: ctrl.RHYTHM.4.6


title: LNKO.RHYTHM.0.2


title: UF0023_brep2


title: UF0024_brep2


title: UF0023_brep3


title: LNKO.RHYTHM.0.1


title: UF0023_brep1


title: ctrl.RHYTHM.0.9


title: UF0025_brep3


title: UF0022_brep3


title: Genomic DNA from T-cell lymphoblastic lymphoma 9


title: UF0022_brep2


title: ctrl.RHYTHM.0.6


title: ctrl.RHYTHM.0.5


title: Genomic DNA from T-cell lymphoblastic lymphoma 7


title: UF0022_brep1


title: UF0020_brep3


title: ctrl.RHYTHM.0.3


title: UF0020_brep2


title: Genomic DNA from T-cell lymphoblastic lymphoma 5


title: UF0024_brep1


title: Genomic DNA from T-cell lymphoblastic lymphoma 2


title: ctrl.RHYTHM.0.8


title: Calu3_scRNAseq-S2-8h-B

description: Count File: Calu3_scRNAseq_morethan1000genes_rawcounts_tr.txt.gz

data_processing:
PolyA-RNA and total-RNA sequencing reads were mapped to the hg38 version of the human genome using STAR (version 2.7.1a) combined with the GENCODE (v30) annotation and the non-standard parameters (--sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000).
Small-RNA sequencing reads were preprocessed using cutadapt (version 2.9) in two passes, first trimming i) the Illumina TruSeq adaptor at the 3’ end, ii) all 3’ end bases with mean Phred score below 30 and iii) the three 5’end overhang nucleotides associated with the Clonetech library preparation protocol. In the second pass, poly(A)-tails were trimmed. Trimmed reads were mapped to hg38 using bowtie (version 1.2.2) and the non-standard parameters (-q -n 1 -e 80 -l 18 -a -m 5 --best --strata). The expression of known miRNAs (miRBase 22 annotation) was estimated using mirdeep2 (version 2.0.0.7) and standard parameters. Gene expression was estimated using FeatureCounts (version 1.5.1) and the non-standard parameters (-F GTF -t exon -g gene_id -C -M --fraction -p -s 2 -O -T 16 -B -Q 4).
For scRNA-seq, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123). Genomes used were hg19, AY310120 (SARS-CoV-1) and MN908947 (SARS-CoV-2)
Genome_build: hg38, hg19
Supplementary_files_format_and_content: tab separated values

source_name: single-cell RNA from Calu3 cells, S2 infected 8hpi, replicate B

tag: infection

tag: time point

tag: molecule subtype

value: polyA RNA extracted from single cells


title: ctrl.RHYTHM.0.7

tag: strain

tag: genotype


title: UF0020_brep1


title: UF0018_brep3


title: ctrl.RHYTHM.0.1

tag: collection time point


title: UF0018_brep2


title: Calu3_scRNAseq-S2-8h-A

source_name: single-cell RNA from Calu3 cells, S2 infected 8hpi, replicate A


title: NR.RHYTHM.20.3

value: WT

tag: treatment time point

value: 4 months

tag: chip antibody


title: Genomic DNA from T-cell lymphoblastic lymphoma 8


title: Calu3_scRNAseq-S2-4h-A

source_name: single-cell RNA from Calu3 cells, S2 infected 4hpi, replicate A

tag: cell line


title: Calu3_scRNAseq-S2-12h-B

source_name: single-cell RNA from Calu3 cells, S2 infected 12hpi, replicate B


title: UF0018_brep1


title: NR.RHYTHM.20.2


title: Calu3_scRNAseq-S2-12h-A

source_name: single-cell RNA from Calu3 cells, S2 infected 12hpi, replicate A


title: NR.RHYTHM.20.1


title: ctrl.RHYTHM.0.2


title: Calu3_scRNAseq-S1-8h-A

source_name: single-cell RNA from Calu3 cells, S1 infected 8hpi, replicate A


title: ctrl.RHYTHM.0.4

source_name: Liver


title: Calu3_scRNAseq-S1-8h-B

source_name: single-cell RNA from Calu3 cells, S1 infected 8hpi, replicate B


title: H2O.RHYTHM.20.3


title: UF0016_brep2


title: Calu3_scRNAseq-S1-4h-B

source_name: single-cell RNA from Calu3 cells, S1 infected 4hpi, replicate B


title: Calu3_scRNAseq-S2-4h-B

source_name: single-cell RNA from Calu3 cells, S2 infected 4hpi, replicate B


title: H2O.RHYTHM.20.2


title: H2O.RHYTHM.20.1


title: UF0014_brep3


title: Calu3_scRNAseq-S1-4h-A

source_name: single-cell RNA from Calu3 cells, S1 infected 4hpi, replicate A


title: RNA-BKO.Sal.6.3

value: 4-6 months

value: Saline


title: NR.RHYTHM.16.3


title: UF0014_brep2


title: Calu3_scRNAseq-S1-12h-B

source_name: single-cell RNA from Calu3 cells, S1 infected 12hpi, replicate B


title: Calu3_scRNAseq-S1-12h-A

source_name: single-cell RNA from Calu3 cells, S1 infected 12hpi, replicate A


title: NR.RHYTHM.16.2


title: UF0013_brep3


title: UF0014_brep1


title: UF0016_brep3


title: UF0013_brep2


title: Calu3_scRNAseq-mock-4h-B

source_name: single-cell RNA from Calu3 cells, mock infected 4hpi, replicate B

value: mock


title: UF0016_brep1


title: Calu3_scRNAseq-mock-4h-A

source_name: single-cell RNA from Calu3 cells, mock infected 4hpi, replicate A


title: UF0054_brep1


title: H2O.RHYTHM.16.3

value: 8 months


title: RAG-/-_day 28_ rep 1

city: Giessen

first: Thaqif

last: El Khassawna

address: Aulweg 128

department: Faculty of Medicine

institute: Justus Liebig University of Giessen

description: replicate 1

hyb_protocol: Illumina's MouseRef-8 v2.0 Expression BeadChips, standard protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using bead array and Bioconductor packages in R

label: biotin

source_name: Mice fractured callus

label_protocol: Not provided

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

treatment_protocol: RAG1-/- mice lack both mature B and T-cells. The differentiation of B and T-cells in these mice is arrested at an early stage due to their inability to perform V(D)J recombination.

value: fractured callus

value: C57BL/6N Recombination Activating Gene 1 homozygous knock out

value: 8 weeks old

tag: gender

value: male


title: H2O.RHYTHM.16.2


title: RAG-/-_day 28_ rep 3

description: replicate 3


title: RAG-/-_day 21_ rep 2

description: replicate 2


title: RAG-/-_day 28_ rep 2

description: replicate 2


title: Calu3_scRNAseq-mock-12h-B

source_name: single-cell RNA from Calu3 cells, mock infected 12hpi, replicate B


title: UF0013_brep1

source_name: Xylem

value: 16 weeks


title: H2O.RHYTHM.16.1


title: NR.RHYTHM.16.1


title: Calu3_scRNAseq-mock-12h-A

source_name: single-cell RNA from Calu3 cells, mock infected 12hpi, replicate A


title: UF0011_brep2


title: RAG-/-_day 21_ rep 3

description: replicate 3


title: NR.RHYTHM.12.2


title: UF0011_brep3


title: UF0011_brep1


title: H1299_scRNAseq-S2-36h-B

description: Count File: H1299_scRNAseq_morethan2000genes_rawcounts_tr.txt.gz

source_name: single-cell RNA from H1299 cells, S2 infected 36hpi, replicate B


title: RAG-/-_day 14_ rep 2

description: replicate 2


title: H1299_scRNAseq-S2-36h-A

source_name: single-cell RNA from H1299 cells, S2 infected 36hpi, replicate A


title: RAG-/-_day 14_ rep 3

description: replicate 3


title: NR.RHYTHM.12.3


title: H1299_scRNAseq-S2-24h-B

source_name: single-cell RNA from H1299 cells, S2 infected 24hpi, replicate B


title: H1299_scRNAseq-S2-24h-A

source_name: single-cell RNA from H1299 cells, S2 infected 24hpi, replicate A


title: H2O.RHYTHM.12.3

source_name: Liver


title: RAG-/-_day 21_ rep 1

description: replicate 1


title: NR.RHYTHM.12.1


title: RAG-/-_day 7_ rep 3

description: replicate 3


title: UF0010_brep3


title: RAG-/-_day 14_ rep 1

description: replicate 1


title: H1299_scRNAseq-S2-12h-B

source_name: single-cell RNA from H1299 cells, S2 infected 12hpi, replicate B


title: H1299_scRNAseq-S2-12h-A

source_name: single-cell RNA from H1299 cells, S2 infected 12hpi, replicate A


title: UF0010_brep1


title: RAG-/-_day 7_ rep 2

description: replicate 2


title: RAG-/-_day 7_ rep 1

description: replicate 1


title: UF0009_brep2


title: NR.RHYTHM.8.3


title: RAG-/-_day 3_ rep 2

description: replicate 2


title: H1299_scRNAseq-S1-36h-A

source_name: single-cell RNA from H1299 cells, S1 infected 36hpi, replicate A


title: H2O.RHYTHM.12.2


title: H1299_scRNAseq-S1-36h-B

source_name: single-cell RNA from H1299 cells, S1 infected 36hpi, replicate B


title: RAG-/-_day 3_ rep 3

description: replicate 3


title: UF0009_brep1


title: UF0008_brep3


title: UF0010_brep2


title: H1299_scRNAseq-S1-24h-A

source_name: single-cell RNA from H1299 cells, S1 infected 24hpi, replicate A


title: H2O.RHYTHM.12.1


title: NR.RHYTHM.8.1


title: RAG-/-_day 0_ rep 2

description: replicate 2


title: RAG-/-_day 0_ rep 3

description: replicate 3


title: UF0008_brep2


title: H2O.RHYTHM.8.2


title: H2O.RHYTHM.8.3


title: H1299_scRNAseq-S1-12h-B

source_name: single-cell RNA from H1299 cells, S1 infected 12hpi, replicate B


title: NR.RHYTHM.8.2


title: UF0008_brep1


title: H1299_scRNAseq-mock-4h-B

source_name: single-cell RNA from H1299 cells, mock infected 4hpi, replicate B


title: H1299_scRNAseq-S1-24h-B

source_name: single-cell RNA from H1299 cells, S1 infected 24hpi, replicate B


title: UF0007_brep3


title: H1299_scRNAseq-mock-4h-A

source_name: single-cell RNA from H1299 cells, mock infected 4hpi, replicate A


title: NR.RHYTHM.4.3


title: UF0007_brep2


title: UF0007_brep1


title: H1299_scRNAseq-mock-36h-B

source_name: single-cell RNA from H1299 cells, mock infected 36hpi, replicate B


title: RAG-/-_day 0_ rep 1

description: replicate 1

source_name: Mice fractured callus


title: wild type_day 28_ rep 3

description: replicate 3


title: wild type_day 28_ rep 2

description: replicate 2


title: wild type_day 28_ rep 1

description: replicate 1


title: NR.RHYTHM.4.1


title: wild type_day 21_ rep 3

description: replicate 3


title: H1299_scRNAseq-mock-36h-A

source_name: single-cell RNA from H1299 cells, mock infected 36hpi, replicate A


title: H2O.RHYTHM.4.3


title: UF0006_brep2

source_name: Xylem


title: wild type_day 21_ rep 2

description: replicate 2


title: H2O.RHYTHM.8.1


title: H1299_scRNAseq-S1-12h-A

source_name: single-cell RNA from H1299 cells, S1 infected 12hpi, replicate A


title: HeLa cells, YTHDC1_KD_B

city: Rome

first: Gaia

last: Di Timoteo

state: RM

address: piazza Aldo Moro 5

country: Italy

institute: University of Rome "La Sapienza"

data_processing:
bcl2fastq2 (Version 2.20) was used for base calling.
Trimmomatic was used to remove adapter sequences; minimum read length after trimming was set to 20.
Reads were then aligned to the human reference genome (GRCh38) using BWA-MEM with -T 19 option.
CircRNA detection in each sample was then carried out using CIRI2 software with -0 option. To identify circRNA host genes, the program was provided with Ensembl 90 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Sample-specific CIRI2 output files containing, for each circRNA, its genomic coordinates, the number of supporting reads, the host gene and other information.

source_name: adenocarcinoma of the cervix

growth_protocol: HeLa cells were cultured in DMEM with 10% FBS, L-Glutamine 2 mM and Penicillin/Streptomycin 1X.

extract_protocol:
Total RNA in this study was extracted with TRIazol reagent and the direct-zol RNA  Miniprep kit according to the manufacturer’s specifications (ZYMO RESEARCH).
Truseq Stranded Total RNA Prep kit with Ribo-Zero H/M/R treatment (Illumina) was used for the library construction.

treatment_protocol: Hela cells (150000) were plated in 35mm plates and transfected 12 hrs later with the siRNA indicated (30 nM) using Lipofectamine RNAiMAX Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions. After 48hrs from the first siRNA pulse, cells were harvested (single pulse) or treated with a second 48h hrs siRNA pulse (double pulse).

value: HeLa

tag: sirna used

value: YTHDC1 siRNA  [Catalog No. SI00882161] (Qiagen)

tag: sirna pulse

value: single


title: NR.RHYTHM.4.2

tag: age

tag: treatment


title: HeLa cells, YTHDC1_KD_A


title: UF0006_brep1


title: UF0004_brep3


title: UF0006_brep3


title: H2O.RHYTHM.4.2


title: UF0004_brep2


title: HeLa cells, YTHDC1_SCR_B

value: Control YTHDC1 [Catalog No. 1022076] (Qiagen)


title: HeLa cells, YTHDC1_SCR_A


title: wild type_day 14_ rep 3

description: replicate 3


title: wild type_day 14_ rep 2

description: replicate 2


title: H2O.RHYTHM.4.1


title: NR.RHYTHM.0.3


title: UF0004_brep1


title: wild type_day 21_ rep 1

description: replicate 1


title: HeLa cells, METTL3_KD_B

value: double


title: wild type_day 14_ rep 1

description: replicate 1


title: wild type_day 7_ rep 3

description: replicate 3


title: NR.RHYTHM.0.4


title: NR.RHYTHM.0.2


title: UF0003_brep3


title: RAG-/-_day 3_ rep 1

description: replicate 1


title: UF0003_brep2


title: HeLa cells, METTL_SCR_A

value: Control [Catalog No. 1022076] (Qiagen)


title: NR.RHYTHM.0.1

value: WT


title: H2O.RHYTHM.0.4

value: 4 months


title: UF0003_brep1


title: H2O.RHYTHM.0.3


title: wild type_day 7_ rep 2

description: replicate 2


title: UF0001_brep3


title: UF0009_brep3


title: wild type_day 3_ rep 2

description: replicate 2


title: H2O.RHYTHM.0.2


title: UF0001_brep2


title: wild type_day 7_ rep 1

description: replicate 1


title: wild type_day 3_ rep 3

description: replicate 3


title: H2O.RHYTHM.0.1


title: Invasive rhizomorphs below bark layer [ARCE], replicate 2

city: Szeged

first: Laszlo

middle: G.

last: Nagy

state: Csongrad

address: Temesvari krt 62

department: Institute of Biochemistry, Synthetic and Systems Biology Unit

country: Hungary

institute: Biological Research Centre, Hungarian Academy of Sciences

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0.2). Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: JGI Mycocosm: Armillaria cepistipes B5 (Armcep1)
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Armillaria cepistipes

source_name: mycelium

growth_protocol: Cultures of Armillaria cepistipes B2 were inoculated on Malt extract agar (MEA) and incubated at 25oC in dark for a week. 4-5 cm long, autoclaved sterilized spruce roots were introduced to the week-old cultures of A. cepistipes and were again kept at 25oC in the dark for 2-3 weeks until they were colonized by the fungi

extract_protocol:
Total RNA was extracted from the four tissue types in three biological replicates, using the Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol.
Ribo-Zero rRNA removal Kit (Yeast) was used to deplete rRNA from total RNA. Subsequently, samples were processed with Illumina TruSeq V2 library preparation protocol. (cDNA synthesis with random hexa primers resulting in a non-strand specific library)

treatment_protocol: After colonization, roots were dissected to collect mycelium from below the outer bark layer and rhizomorphs emerging out of the colonized wood. Cultures of Armillaria without the addition of sterilized spruce roots were used as non-invasive controls. Tissues were flash frozen in liquid nitrogen and kept at -80oC until futher extraction.

tag: group


title: UF0001_brep1

city: Gainesville

first: Matias

last: Kirst

institute: University of Florida


title: Invasive rhizomorphs below bark layer [ARCE], replicate 3


title: Invasive rhizomorphs below bark layer [ARCE], replicate 1


title: Invasive rhizomorphs emerging out of bark [ARCE], replicate 3


title: PATU-8988T_P115_043

first: Zainab

middle: Murtaza

last: Doctor

state: MA

address: 360 Longwood Ave, LC-2106

institute: Dana Farber Cancer Institute

data_processing:
Data processing of fastq files to  counts was performed by Invitrogen using the Ion Torrent software suite.
Supplementary_files_format_and_content: The csv file contains mapped count values for each transcript for all samples in the study.

extract_protocol:
Cells were lysed in the dish using QIGEN Buffer RLT Plus. RNA was extracted using QIAGEN RNEasy Plus Mini Kit according to protocol.
RNA libraries were prepared for sequencing by Invitrogen

treatment_protocol: Cells were plated on Day 0, treated 24 hours later with the indicated compound or DMSO for 4h.

tag: cell type

value: pancreatic cancer cell line

tag: treatment time


title: wild type_day 3_ rep 1

description: replicate 1

tag: tissue


title: PATU-8988T_P115_042


title: Invasive rhizomorphs emerging out of bark [ARCE], replicate 1


title: PATU-8988T_P115_041


title: Invasive rhizomorphs emerging out of bark [AROC18], replicate 2

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0.2). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0.2). Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Count paired reads as two=no, Expression value= Total counts.
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: FUEG00000000.1
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool

organism: Armillaria ostoyae

growth_protocol: Cultures of Armillaria ostoyae C18 were inoculated on Malt extract agar (MEA) and incubated at 25oC in dark for a week. 4-5 cm long, autoclaved sterilized spruce roots were introduced to the week-old cultures of A. ostoyae and were again kept at 25oC in the dark for 2-3 weeks until they were colonized by the fungi


title: Invasive rhizomorphs emerging out of bark [AROC18], replicate 3


title: h3-sih2az_mnase32_x_chip_rep1

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

institute: Sun Yat-sen University

data_processing:
ChIP-seq clean reads were mapped to mm9 by Bowtie2 with default parameters.
Data were filtered by samtools with "-q 10"to retain high quality reads.
Enriched peaks were detected using MACS14 or MACS2 with input.
Genome_build: mm9
Supplementary_files_format_and_content: bed file with four tab-delimited fields, representing chromosome name, start, end and peak score.

source_name: mouse embryonic stem cell

growth_protocol: Mouse ES cells were cultured in the medium with 80% DMEM (EmbryoMax, SLM-220-B), 15% FBS (Hyclone, SH30070.03), Nonessential amino acids (EmbryoMax, TMS-001-C), 2-Mercaptoethanol (EmbryoMax, ES-007-E), L-glutamine (EmbryoMax, TMS-002-C), Nucleosides (EmbryoMax, ES-008-D), Pen/Strep (EmbryoMax, TMS-AB-2C) and 1000U/ml leukemia inhibitory factor (LIF) (ESGRO, ESG1107) in standard incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then digested with Mnase, then sonicated in N-lauroyl-sarcosine containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with agarose conjucated with antibodies.
Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova-seq.

value: mouse embryonic stem cell line

value: H3 (Abcam, ab1791)

value: siH2A.Z (siRNA targetting H2A.Z)


title: h3-sih2az_mnase32_x_chip_rep2


title: wild type_day 0_ rep 2

description: replicate 2

value: fractured callus


title: wild type_day 0_ rep 1

description: replicate 1


title: wild type_day 0_ rep 3

description: replicate 3


title: Non-invasive rhizomorphs [ARCE], replicate 3


title: h33-HA-sih2az_mnase32_x_chip_rep2

value: HA (Sigma, H3663)


title: Non-invasive rhizimorphs [AROC18], replicate 3


title: h33-HA-sih2az_mnase32_x_chip_rep1


title: PATU-8988T_BJP_005_042


title: Non-invasive rhizomorphs [ARCE], replicate 2


title: Non-invasive rhizimorphs [AROC18], replicate 2


title: Non-invasive mycelium [ARCE], replicate 3


title: h33-HA-siNC_mnase32_x_chip_rep1

value: siNC (negative control siRNA)


title: Non-invasive rhizomorphs [ARCE], replicate 1


title: PATU-8988T_BJP_005_041


title: Invasive rhizomorphs emerging out of bark [AROC18], replicate 1


title: Non-invasive mycelium [AROC18], replicate 3


title: PATU-8988T_DMSO_03

value: DMSO


title: Non-invasive mycelium [AROC18], replicate 2


title: Non-invasive mycelium [ARCE], replicate 2


title: HeLa cells, METTL3_KD_A


title: Non-invasive mycelium [AROC18], replicate 1


title: h33-HA-siNC_mnase32_x_chip_rep2


title: KO2_P63

city: Seoul

first: Jonghyo

last: Lim

address: Yonsei-ro 50

department: Biochemistry

country: South Korea

institute: Yonsei university

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10

source_name: skin

extract_protocol:
Skins were removed and dispase treated 30mins in 37℃, 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 for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

tag: tag

value: Back skin

value: post natal day 63

tag: genotype/variation


title: PATU-8988T_DMSO_02


title: PATU-8988T_BJP_005_043


title: Non-invasive mycelium [ARCE], replicate 1

tag: strain


title: Invasive mycelium below bark layer [AROC18], replicate 3


title: PATU-8988T_DMSO_01


title: Invasive mycelium below bark layer [ARCE], replicate 2


title: Invasive mycelium below bark layer [AROC18], replicate 2


title: WT2_P63

value: wild type