title: SHAPE-map_delta_denatured

description:
processed data file:
SUPPORTING_TABLE_01_SHAPE_SEQUENCING_STATS.csv
SUPPORTING_TABLE_02_SHAPE_DATA.csv

data_processing:
library strategy: SHAPE-Map
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
PoreCupine samples were basecalled with  live basecalling and processed with minimap2, Python and R
SPLASH samples were mapped with bwa-mem (version 0.7.17); chimeric reads were detected using the pipelie from Aw et al (2016)
NmSeq: the adaptor were trimmed by cutadapt (version 1.8.1); duplicational reads were remove according to UMI; Nmseq samples were mapped with bwa-aln (version 0.7.17); the accumulation depth of 3' end of reads were normalized by the read counts of each gene, subtracted to the background of input control; the enrichment of 2'OM was calculated with Z-test with the conditions FDR <0.05, DOED >=10, DOED/Dinput > 1.5.
Genome_build: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_414378 (SARS-CoV-2 Delta382); ChlSab1.1.102
Supplementary_files_format_and_content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary_files_format_and_content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT & Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_03_Delta382_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_04_WT_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_05_PORECUPINE.csv: Pore-Cupine reactivity data
Supplementary_files_format_and_content: SUPPORTING_TABLE_06_Delta382_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_07_WT_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_08_NMseq_HOST_ALL.tsv: 2'O-methylation on host RNA
Supplementary_files_format_and_content: SUPPORTING_TABLE_09_NMseq_SARS-CoV-2.tsv: 2'O-methylation on virus RNA


title: SHAPE-map_delta_dmso

status: Public on Jul 05 2021

type: SRA

city: Singapore

first: Roland

middle: G

last: Huber

address: 30 Biopolis Street

department: Bioinformatics Institute (BII)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

library_source: transcriptomic

molecule: total RNA

organism: Chlorocebus

source_name: Vero cell infected with SARS COV2 EPI_ISL_414378 strain

growth_protocol: Vero E6 cells were infected with/without SARS-CoV viruses (WX56 wild-type and CA001 d382 mutant) at an multiplicity of infection (MOI) = 0.01 for 48 h.

extract_protocol:
SHAPE-MaP Structure probing: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
SHAPE-MaP libraries were made similar to the published protocol Smola et al. (2015)
SPLASH: The total RNA was extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
SPLASH libraries were made similarly to the published protocol in Aw et al.(2016)
NmSeq: The total RNA was then extracted from the cells using E.Z.N.A. Total RNA Kit I (Omega bio-tek)
NmSeq libraries were constructed and multiplexed following the published method in Hsu, P.J., et al. (2019).

treatment_protocol:
SHAPE-MaP Structure probing and PORE-cupine were performed by using 1:20 the volume of 1M NAI (03-310, Merck, 25 µl of NAI in 500 µl of infected cells) and incubated the reaction for 15 min at 37 °C for structure probing; we added 1:20 volume of dimethyl sulfoxide (DMSO) as negative control; aside a third portion of the virus as for the denaturing control in the downstream library preparation process.
We performed SPLASH libraries similarly to the published protocol in Aw et al.(2016). The cells were then incubated with 200 µM biotinylated psoralen and 0.01% digitonin in PBS for 10 min at 37 °C. The cells were spread onto a 10cm dish and irradiated at 365 nm of UV on ice for 20 min. the total RNA was extracted using E.Z.N.A. Total RNA Kit I (Omega bio-tek) according to the manufacturer’s instructions.
NmSeq was performed following the published method in Hsu, P.J., et al. (2019). In brief, 8 rounds of oxidation-elimination-dephosphorylation (OED) plus an extra oxidation-elimination step were performed to cause enrichment of the 3' read ends at the 2’OM sites. 10 ug of each samples were used following NmSeq protocol. For input control library without OED, 1ug of RNA were used. The libraries were constructed using NEBNext Small RNA library kit with customized adaptors as mentioned in the published protocol.

tag: cell type

value: Vero cell

tag: treatment


title: ca_NM_10d_rep1 [H06447]

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

country: Germany

institute: University Hospital Schleswig-Holstein

description:
H06447
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

library_source: genomic

data_processing:
Library strategy: 16S rRNA sequencing
16S rRNA: After assembling the reads using SeqPrep, subsequent identification of chimera with ChimeraSlayer and manual verification, chimera were removed from the data set. The sequences were further analyzes using QIIME 1.9.0.
RNA-Seq: After quality filtering (fastq_illumina_filter, prinseq-lite, cutadapt), sequencing reads were mapped against the Drosophila melanogaster reference BDGP6 using TopHat v2.1.0 with sensitive option. The read counts per transcript were calculated with the Python script HTSeq v0.6.1p1 using the mode ‘intersection-strict’.
Genome_build: Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files include read counts per gene for each sample.
Supplementary_files_format_and_content: otu_table_mc50_w_tax_wochimera_ctrl_50filtered.txt: Tab-delimited text file includes read counts per OTU for each sample.

molecule: genomic DNA

organism: insect gut metagenome

source_name: midguts of 5 Drosophila melanogaster individuals

growth_protocol: We used homozygous flies containing esg-Gal4, UAS-GFP, tubulin-Gal80ts on the 2nd chromosome, and UAS-Luciferase on the 3rd chromosome and crossed them to homozygous UAS-RAFgof flies to obtain the F1 generation with a temperature inducible tumor phenotype. As a control we crossed EGT;Luc2 to w1118 wildtype flies. All fly lines were raised on a cornmeal based standard medium at 20 °C. The F1 generation was shifted to 29 °C 5-7 days post eclosion to induce the expression of UAS-dependent genes.

extract_protocol:
DNA for 16S rRNA sequencing was extracted with the DNeasy Blood & Tissue Kit (Qiagen, #69504) following the manufacturer´s protocol for Pretreatment for Gram-Positive Bacteria, followed by the protocol for Purification of Total DNA from Animal Tissues. For RNA isolation 15 midguts per treatment were dissected in S2 medium, immediately transferred to a 2 ml screw cap tube containing 1 ml RNA Magic (Bio-Budget, #56-1000-100) and homogenized for 2 min at 3.25 m/sec using a bead mill homogenizer with 3 zirconium beads per tube. The homogenate was incubated for 5 min at RT and stored at -20 °C until further processing. Samples were thawed on ice for subsequent RNA isolation. 200 μl chloroform were added into each tube. Tubes were inverted (not vortexed) several times to provide homogenous mixing and incubated for 5 min at RT prior to 15 min centrifugation at 12.000 xg and 4 °C. The upper aqueous phase was transferred into a new tube (about 500 μl) and 500 μl 99% EtOH were added. The samples were centrifuged for 45 min at 17.000 xg and 4 °C after vigorously inverting the tubes for 30 sec. The supernatant was carefully removed and the RNA containing pellet was washed by adding 200 μl 99% EtOH and centrifuging for 5 min at 12.000 xg and 4 °C. The supernatant was completely removed and the pellet was air-dried for 3 min. The pellet was subsequently resuspended in 13 ml RNase-free ddH2O.
The bacterial variable regions 1 and 2 of 16S rRNA genes were amplified as described by Rausch et al. (2016). RNA-Seq libraries were created with the TruSeq Stranded mRNA Library Kit (Illumina, San Diego, USA).

treatment_protocol: We used a standard corn meal based medium for all stock flies and crossings. All assays were conducted on low-melt fly food containing 1.5% agar, 2% bacto yeast extract and 7% corn syrup (NM). The medium was boiled and supplemented with 0.1% propionic acid and 0.3% nipagin to prevent microbial growth. For dietary restriction (DR) the amount of bacto yeast was reduced to 0.1%. The recurrent diet consisted of an alternating regimen of four days DR followed by feeding on NM for three days.

tag: tissue

value: Midguts

tag: disease state

value: Cancer

tag: diet

value: NM

tag: feeding time

value: 10 days


title: post-RASP stress dataset #2 sample 29

type: RNA

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

country: USA

institute: USACEHR

description: post-RASP stress samples 29  of 43

hyb_protocol: The slides were hybridized at 60ºC for 16 h (for cDNA microarrays and Trizol® isolated RNA)

scan_protocol: Hybridized slides were scanned and recorded using a GenePix® Pro 4000B (Axon Instruments Inc., Union City, CA) optical scanner, and the images were digitized using GenePix® 6.0 software (Axon Instruments Inc, Union City, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Homo sapiens

source_name: pooled whole human tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Micromax Tyramide Signal Amplification (TSA) Labeling and Detection Kit (Perkin Elmer, Inc., Waltham, MA) following the manufacturer’s protocol.

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

treatment_protocol: RASP trainees underwent extreme stressor condtions which simulated an intense battlefield scenario for more than 8 weeks.  Yersinia pestis treatment: leucocytes from whole blood were diluted with 1x balanced salt solution (BSS) without divalent cations (Invitrogen-Gibco, CA) & centrifuged at 350 x g, for 15 minutes.  A total of 2 ml culture fluid consisting of RPMI 1640 (Invitrogen-Gibco, CA) and 10 % human AB serum (Sigma) and was incubated with Y. pestis for 30 minutes, then diluted and centrifuged as before. Cells were re-suspended in 7 ml of culture media (RPMI 1640 and 10 % human AB serum) and plated in wells.  These were treated with Y. pestis to a final multiplicity of infection of 1 (MOI) or 1 bacterium per cell, and then incubated at 37 C and 5% CO2 for 4 hours.  Dengue virus treatment: isolated leukocytes were incubated with dengue virus serotype 2 (DENV-2) for 2 hours pre-plate incubation, and then 4 hours in plates to a final MOI of 1 (one viral particle per cell). Incubation was done in RPMI 1640 and 10 % human AB serum media at 37 ˚C and 5% CO2.  SEB exposure: SEB toxin was added to leukocytes to a final concentration of 100 ng/mL and incubated at 37 °C for 6 hours with 5% CO2.  At the end of the incubation period, treated leucocytes were centrifuged at 350 x g for 15 minutes. The pellets obtained from spinning of each well were treated with 2 ml TRIzolTM (Invitrogen, CA) reagent, and kept at –80 C for RNA isolation.

tag: sample type

value: Strategen universal reference RNA Cat. No. 740000

source_name: leukocytes

value: WBCs (leukocytes)


title: PORE-cupine_wt_mod

description:
processed data file:
SUPPORTING_TABLE_05_PORECUPINE.csv

data_processing:
library strategy: PORE-cupine
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
PoreCupine samples were basecalled with  live basecalling and processed with minimap2, Python and R
SPLASH samples were mapped with bwa-mem (version 0.7.17); chimeric reads were detected using the pipelie from Aw et al (2016)
NmSeq: the adaptor were trimmed by cutadapt (version 1.8.1); duplicational reads were remove according to UMI; Nmseq samples were mapped with bwa-aln (version 0.7.17); the accumulation depth of 3' end of reads were normalized by the read counts of each gene, subtracted to the background of input control; the enrichment of 2'OM was calculated with Z-test with the conditions FDR <0.05, DOED >=10, DOED/Dinput > 1.5.
Genome_build: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_414378 (SARS-CoV-2 Delta382); ChlSab1.1.102
Supplementary_files_format_and_content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary_files_format_and_content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT & Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_03_Delta382_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_04_WT_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_05_PORECUPINE.csv: Pore-Cupine reactivity data
Supplementary_files_format_and_content: SUPPORTING_TABLE_06_Delta382_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_07_WT_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_08_NMseq_HOST_ALL.tsv: 2'O-methylation on host RNA
Supplementary_files_format_and_content: SUPPORTING_TABLE_09_NMseq_SARS-CoV-2.tsv: 2'O-methylation on virus RNA

source_name: Vero cell infected with SARS COV2 EPI_ISL_407987 strain


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 49)

type: genomic

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description: Fig 7 and 9

hyb_protocol: Serum, BALF and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing:
Spot and background intensities were measured using an annotated grid (.gal) file. Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis, A one-way ANOVA was performed. A P value below 0.05 was considered significant. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA).
The graphs generated in the publication associated to this document were done using the raw data. Therefore, there are no differences between the raw data and processed data.

molecule: other

organism: Mus musculus

source_name: Serum

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

value: d14 dpc

tag: mouse id

value: Serum


title: post-RASP stress dataset #2 sample 33

description: post-RASP stress samples 33  of 43


title: ca_DRNM_6d_rep5 [H06446]

description:
H06446
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: DRNM

value: 6 days


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 53)

description: Fig 7 and 9


title: post-RASP stress dataset #2 sample 28

description: post-RASP stress samples 28  of 43


title: SHAPE-map_delta_NAI

value: infected with SARS COV2 EPI_ISL_414378 strain


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 50)

description: Fig 7 and 9


title: SHAPE-map_wt_dmso

value: infected with SARS COV2 EPI_ISL_407987 strain


title: SHAPE-map_wt_denatured


title: ca_DRNM_6d_rep4 [H06445]

description:
H06445
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengePBSd14 dpc (SAMPLE 45)

description: Fig 7 and 9

value: PBS


title: prime/boost challengePBSd14 dpc (SAMPLE 47)

description: Fig 7 and 9


title: prime/boost challengePBSd14 dpc (SAMPLE 46)

description: Fig 7 and 9


title: ca_DRNM_6d_rep3 [H06444]

description:
H06444
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengePBSd14 dpc (SAMPLE 48)

description: Fig 7 and 9


title: PLC-shUSP22-2

city: Hangzhou

first: Sunbin

last: Ling

state: Zhejiang

address: 79 Qingchun Road

country: China

institute: Zhejiang University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.1.0 with default parameters. The number of reads mapped to each gene was calculated by Htseq.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: PLC/PRF/5 cells

growth_protocol: PLC/PRF/5 cells were in DMEM media with high glucose

extract_protocol:
Samples were immediately frozen in liquid nitrogen and stored at  -80℃ until further use.RNA was harvested using Trizol reagent.  NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNAs were isolated from Total RNA and fragmented to approximately 200bp.Subsequently, the purified  RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).

treatment_protocol: Lentivirus-mediated gene interference of USP22 and hypoxic conditioning was performed in a bis-gas incubator with 1% O2/5% CO2/balance N2 for 48 hours.

tag: cell line

value: PLC/PRF/5 cells

value: hepatocellular carcinoma cells

tag: genotype/variation

value: USP22 knockdown


title: prime/boostcaLend20 dpb (SAMPLE 44)

description: Fig 5 and 9

value: prime/boost

value: caLen

value: d20 dpb


title: ca_DRNM_6d_rep1 [H06442]

description:
H06442
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Midguts

value: Cancer


title: post-RASP stress dataset #2 sample 26

description: post-RASP stress samples 26  of 43

value: Strategen universal reference RNA Cat. No. 740000

value: WBCs (leukocytes)


title: SHAPE-map_wt_NAI

value: Vero cell


title: post-RASP stress dataset #2 sample 24

description: post-RASP stress samples 24  of 43


title: prime/boostcaLend20 dpb (SAMPLE 43)

description: Fig 5 and 9

value: Serum


title: post-RASP stress dataset #2 sample 25

description: post-RASP stress samples 25  of 43


title: ca_DRNM_6d_rep2 [H06443]

description:
H06443
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: DRNM


title: ca_DR_6d_rep5 [H06441]

description:
H06441
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: DR

value: 6 days


title: post-RASP stress dataset #2 sample 22

description: post-RASP stress samples 22  of 43


title: prime/boostcaLend20 dpb (SAMPLE 42)

description: Fig 5 and 9


title: post-RASP stress dataset #2 sample 23

description: post-RASP stress samples 23  of 43


title: ca_DR_6d_rep4 [H06440]

description:
H06440
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 39)

description: Fig 5 and 9


title: PLC-NC-1

value: control


title: post-RASP stress dataset #2 sample 21

description: post-RASP stress samples 21  of 43


title: ca_DR_6d_rep3 [H06439]

description:
H06439
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: PLC-shUSP22-1


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 40)

description: Fig 5 and 9


title: prime/boostcaLend20 dpb (SAMPLE 41)

description: Fig 5 and 9


title: post-RASP stress dataset #2 sample 20

description: post-RASP stress samples 20  of 43


title: post-RASP stress dataset #2 sample 19

description: post-RASP stress samples 19  of 43


title: ca_DR_6d_rep1 [H06437]

description:
H06437
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 38)

description: Fig 5 and 9


title: com_24h

city: Guangzhou

first: Xi

last: Sun

state: Guangdong

address: Zhongshan 2nd road

department: Department of parasitology

institute: Sun yat-sen university

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: abundance measurements

source_name: Bone marrow

growth_protocol: Bone marrow cells were cultured with M-CSF (20 ng/mL) in complete medium [DMEM High Glucose, 100 U/ml of penicillin-streptomycin and 10% heat-inactivated (56 °C, 30 min) FBS] for 7 days.

extract_protocol:
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.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase(RNase H- ). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were  converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were  ligated to prepare for hybridization. In order to select cDNA fragments of  preferentially 250~300 bp in length, the library fragments were purified with AMPure  XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA)  was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5  min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA  polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products  were purified (AMPure XP system) and library quality was assessed on the Agilent  Bioanalyzer 2100 system.

treatment_protocol: BMDMs treated with PBS (ctr), free (AC L4 exofree), IL-4, com (IL-4+AC L4 exofree) for 6h, 12h, and 24 h

tag: strain

value: BALB/c

value: Bone marrow-derived macrophages

value: treated with IL4 and exofree for 24h


title: free_24h

value: treated with exofree for 24h


title: ca_NM_6d_rep5 [H06436]

description:
H06436
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: NM


title: ca_DR_6d_rep2 [H06438]

description:
H06438
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: PLC-NC-2

value: PLC/PRF/5 cells

value: hepatocellular carcinoma cells


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 37)

description: Fig 5 and 9

value: prime/boost

value: d20 dpb


title: post-RASP stress dataset #2 sample 18

description: post-RASP stress samples 18  of 43

value: Strategen universal reference RNA Cat. No. 740000


title: ca_NM_6d_rep4 [H06435]

description:
H06435
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Midguts

value: Cancer


title: prime/boostPBSd20 dpb (SAMPLE 36)

description: Fig 5 and 9

value: PBS

value: Serum


title: IL4_24h

value: treated with IL4 for 24h


title: ctr_24h

value: treated with PBS for 24h


title: com_12h

value: treated with IL4 and exofree for 12h


title: ca_NM_6d_rep3 [H06434]

description:
H06434
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: 6 days


title: IL4_12h

value: BALB/c

value: Bone marrow-derived macrophages

value: treated with IL4 for 12h


title: prime/boostPBSd20 dpb (SAMPLE 34)

description: Fig 5 and 9


title: free_12h

value: treated with exofree for 12h


title: ca_NM_6d_rep1 [H06432]

description:
H06432
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: NM


title: post-RASP stress dataset #2 sample 16

description: post-RASP stress samples 16  of 43

value: WBCs (leukocytes)


title: ctr_12h

value: treated with PBS for 12h


title: post-RASP stress dataset #2 sample 15

description: post-RASP stress samples 15  of 43


title: com_6h

value: treated with IL4 and exofree for 6h


title: post-RASP stress dataset #2 sample 17

description: post-RASP stress samples 17  of 43

value: Strategen universal reference RNA Cat. No. 740000


title: prime/boostPBSd20 dpb (SAMPLE 33)

description: Fig 5 and 9

value: prime/boost

value: d20 dpb


title: prime/boost challengecaLend14 dpc (SAMPLE 32)

description: Fig. 6 and 9

value: prime/boost challenge

value: caLen

value: d14 dpc


title: prime/boost challengecaLend14 dpc (SAMPLE 31)

description: Fig. 6 and 9

value: Serum


title: post-RASP stress dataset #2 sample 14

description: post-RASP stress samples 14  of 43


title: free_6h

value: treated with exofree for 6h


title: IL4_6h

value: treated with IL4 for 6h


title: post-RASP stress dataset #2 sample 12

description: post-RASP stress samples 12  of 43


title: post-RASP stress dataset #2 sample 13

description: post-RASP stress samples 13  of 43


title: post-RASP stress dataset #2 sample 27

description: post-RASP stress samples 27  of 43


title: ca_DR_3d_rep3 [H06429]

description:
H06429
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: Midguts

value: Cancer

value: DR

value: 3 days


title: prime/boost challengecaLend14 dpc (SAMPLE 30)

description: Fig. 6 and 9


title: ca_DR_3d_rep4 [H06430]

description:
H06430
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boostPBSd20 dpb (SAMPLE 35)

description: Fig 5 and 9

value: PBS


title: ca_DR_3d_rep2 [H06428]

description:
H06428
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP stress dataset #2 sample 10

description: post-RASP stress samples 10  of 43

value: WBCs (leukocytes)


title: prime/boost challengecaLend14 dpc (SAMPLE 29)

description: Fig. 6 and 9


title: post-RASP stress dataset #2 sample 9

description: post-RASP stress samples 9  of 43


title: ca_NM_6d_rep2 [H06433]

description:
H06433
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

value: NM

value: 6 days


title: ca_DR_3d_rep5 [H06431]

description:
H06431
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 28)

description: Fig. 6 and 9


title: ca_DR_3d_rep1 [H06427]

description:
H06427
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: ca_NM_3d_rep5 [H06426]

description:
H06426
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengecaLend14 dpc (SAMPLE 26)

description: Fig. 6 and 9


title: prime/boost challengecaLend14 dpc (SAMPLE 27)

description: Fig. 6 and 9


title: ctr_6h

value: BALB/c

value: Bone marrow-derived macrophages

value: treated with PBS for 6h


title: prime/boost challengecaLend14 dpc (SAMPLE 25)

description: Fig. 6 and 9

value: prime/boost challenge


title: ca_NM_3d_rep3 [H06424]

description:
H06424
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: post-RASP stress dataset #2 sample 11

description: post-RASP stress samples 11  of 43

value: Strategen universal reference RNA Cat. No. 740000


title: human_7_or_more_lymph_rep10

city: Shanghai

first: yu

middle: zhi

last: long

state: Shanghai

address: NO.100 Haining Road

department: General Surgery

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University

description: The expression of miRNA in cancer tissues,7 or more lymph nodes

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.

source_name: Tissue Micriarray,7 or more lymph nodes,10

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

treatment_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: gastric cancer

tag: gender

value: male

tag: age


title: post-RASP stress dataset #2 sample 6

description: post-RASP stress samples 6  of 43


title: ca_NM_3d_rep1 [H06422]

description:
H06422
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 24)

description: Fig. 6 and 9

value: d14 dpc

value: Serum


title: human_7_or_more_lymph_rep9

source_name: Tissue Micriarray,7 or more lymph nodes,9


title: post-RASP stress dataset #2 sample 8

description: post-RASP stress samples 8  of 43


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 23)

description: Fig. 6 and 9


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 22)

description: Fig. 6 and 9


title: human_7_or_more_lymph_rep8

source_name: Tissue Micriarray,7 or more lymph nodes,8

value: female


title: human_7_or_more_lymph_rep6

source_name: Tissue Micriarray,7 or more lymph nodes,6


title: human_7_or_more_lymph_rep7

source_name: Tissue Micriarray,7 or more lymph nodes,7


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 21)

description: Fig. 6 and 9


title: Lept-3_rep3 [G2021_22_18]

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

data_processing:
Base calling in illumina HiSeq X
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
reads mapping to annotated genes were counted using featureCounts
differential gene expression analysis using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were cultured in DMEM-F12 supplemented with 15% FBS, 2 mM L-glutamine, Insulin-transferrin-selenium (1x), 450 µM 1-Thioglycerol, and 50 µg/ml Ascorbic acid. Cells are maintained on Collagen-treated plates.

extract_protocol: RNAs from various cells were purified by the Direct-zol RNA kit (Zymo). RNA-seq libraries were prepared using NEBNext Ultra II RNA-Seq Kit (NEB) as per the manufacturer’s instruction with duel indexing. Quality of libraries was assessed in Tapestation (Agilent technologies) using D1000 Tape. Libraries were quantified using a well plate reader (Bio Tek) and pooled at a concentration of 12nM. Pooled libraries were quantified using the Droplet PCR system (Bio-Rad), and pooled libraries were sequenced in one lane Nova-Seq S4 as 150 bp Paired-end reads.

value: Patient-derived primary HER2+ Leptomeningeal carcinomatosis (Lepto)


title: human_7_or_more_lymph_rep5

source_name: Tissue Micriarray,7 or more lymph nodes,5


title: post-RASP stress dataset #2 sample 5

description: post-RASP stress samples 5  of 43


title: post-RASP stress dataset #2 sample 3

description: post-RASP stress samples 3  of 43


title: post-RASP stress dataset #2 sample 4

description: post-RASP stress samples 4  of 43


title: post-RASP stress dataset #2 sample 2

description: post-RASP stress samples 2  of 43


title: Lept-3_rep2 [G2021_22_17]


title: human_7_or_more_lymph_rep4

source_name: Tissue Micriarray,7 or more lymph nodes,4


title: post-RASP stress dataset #2 sample 1

description: post-RASP stress samples 1  of 43


title: human_7_or_more_lymph_rep3

source_name: Tissue Micriarray,7 or more lymph nodes,3


title: Lept-3_rep1 [G2021_22_16]


title: T15D-3

city: Nan Jing

first: pinghua

last: Fan

state: CHINA

address: Long Pan Lu 159

institute: Nanjing Forestry University

data_processing:
Raw reads obtained from the sequencing machines were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
GO enrichment analysis provides all GO terms that significantly enriched in DEGs comparing to the genome background, and filter the DEGs that correspond to biological functions. Firstly all DEGs were mapped to GO terms in the Gene Ontology database (http://www.geneontology.org/), gene numbers were calculated for every term, significantly enriched GO terms in DEGs comparing to the genome background were defined by hypergeometric test. KEGG is the major public pathway-related database. Pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways in DEGs comparing with the whole genome background. The calculating formula is the same as that in GO analysis.
Genome_build: Carya illinoinensis (GigaDB), release date 2019/02/13.
Supplementary_files_format_and_content: pecan_drought_fpkm.txt: Matrix table with FPKM values for every gene and every sample.

organism: Carya illinoinensis

source_name: leaf

extract_protocol:
The leaves were flash frozen with liquid nitrogen, and the total RNA of leaves was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: leaf

value: drought treated for 15 days


title: T15D-2


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 20)

description: Fig. 6 and 9


title: Lept-2_rep3 [G2021_22_15]


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 19)

description: Fig. 6 and 9


title: T15D-1


title: Lept-2_rep1 [G2021_22_13]


title: Lept-2_rep2 [G2021_22_14]


title: Lept-1_rep2 [G2021_22_11]


title: T12D-3

value: drought treated for 12 days


title: prime/boost challengePBSd14 dpc (SAMPLE 16)

description: Fig. 6 and 9

value: PBS


title: human_no_lymph_rep10

description: The expression of miRNA in cancer tissues,no lymph node

source_name: Tissue Micriarray,no lymph node,10


title: human_7_or_more_lymph_rep1

source_name: Tissue Micriarray,7 or more lymph nodes,1


title: T12D-2


title: human_no_lymph_rep9

source_name: Tissue Micriarray,no lymph node,9


title: prime/boost challengePBSd14 dpc (SAMPLE 14)

description: Fig. 6 and 9


title: Lept-1_rep3 [G2021_22_12]


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 18)

description: Fig. 6 and 9


title: ca_NM_3d_rep4 [H06425]

description:
H06425
16S rRNA
processed data file: otu_table_mc50_w_tax_wochimera.txt

source_name: midguts of 5 Drosophila melanogaster individuals

value: Midguts

value: Cancer

value: NM

value: 3 days


title: post-RASP stress dataset #2 sample 7

description: post-RASP stress samples 7  of 43

source_name: pooled whole human tissue cell line

source_name: leukocytes

value: WBCs (leukocytes)


title: prime/boost challengePBSd14 dpc (SAMPLE 15)

description: Fig. 6 and 9

source_name: Serum

value: prime/boost challenge


title: T9D-3

value: drought treated for 9 days


title: T12D-1


title: human_no_lymph_rep8

source_name: Tissue Micriarray,no lymph node,8

value: gastric cancer


title: prime/boostcaLend20 dpb (SAMPLE 12)

description: Fig. 6 and 9

value: prime/boost

value: caLen

value: d20 dpb


title: Lept-1_rep1 [G2021_22_10]


title: T6D-3

value: drought treated for 6 days


title: BT474_rep1 [G2021_22_7]

value: breast cancer cell line

tag: cell subtype

value: HER2 positive


title: human_7_or_more_lymph_rep2

source_name: Tissue Micriarray,7 or more lymph nodes,2

value: female


title: human_no_lymph_rep7

source_name: Tissue Micriarray,no lymph node,7

value: male


title: prime/boost challengePBSd14 dpc (SAMPLE 13)

description: Fig. 6 and 9

value: PBS

value: d14 dpc

value: Serum


title: T6D-2

value: leaf


title: human_no_lymph_rep6

source_name: Tissue Micriarray,no lymph node,6


title: T9D-2


title: T6D-1


title: MDA-MB-231_rep2 [G2021_22_5]

tag: cell type

value: Basal


title: BT474_rep3 [G2021_22_9]


title: T9D-1

tag: treatment


title: prime/boostcaLend20 dpb (SAMPLE 11)

description: Fig. 4 and 9


title: BT474_rep2 [G2021_22_8]


title: MDA-MB-231_rep3 [G2021_22_6]


title: T3D-3

tag: tissue

value: drought treated for 3 days


title: prime/boostcaLend20 dpb (SAMPLE 9)

description: Fig. 4 and 9


title: human_no_lymph_rep1

source_name: Tissue Micriarray,no lymph node,1


title: MDA-MB-231_rep1 [G2021_22_4]


title: human_no_lymph_rep5

source_name: Tissue Micriarray,no lymph node,5


title: T3D-2


title: prime/boost challengeIGIP-H1attd14 dpc (SAMPLE 17)

description: Fig. 6 and 9

value: prime/boost challenge


title: human_no_lymph_rep4

source_name: Tissue Micriarray,no lymph node,4


title: bone marrow RsCDX2::Mx1Cre mouse 3

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

description: Sample 6: MO68

data_processing:
The base-calling was done with bcl2fastq (v2.17.1.14).
The reads were aligned with STAR (v2.5) with default parameters.
The read count per gene were obtained with HTSeq (v0.6.1) with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: read count per gene

source_name: Bonne marrow Cdx2 expression replicate

extract_protocol:
total RNA extracted from mouse bone marrow in Trizol (Life Technologies)
Illumina TruSeq stranded mRNA

treatment_protocol: intraperitoneal injection of pI:pC at 10µg/g once a day for 3 days

value: 3 times intraperitoneally pI:PC at 10µg/g

value: bone marrow


title: T47D_rep3 [G2021_22_3]

value: Luminal


title: human_no_lymph_rep2

source_name: Tissue Micriarray,no lymph node,2

value: gastric cancer


title: bone marrow RsCDX2::Mx1Cre mouse 2

description: Sample 5: MO59


title: T47D_rep2 [G2021_22_2]


title: prime/boostcaLend20 dpb (SAMPLE 10)

description: Fig. 4 and 9

value: prime/boost

value: caLen

value: d20 dpb


title: bone marrow RsCDX2::Mx1Cre mouse 1

description: Sample 4: MO48


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 7)

description: Fig. 4 and 9


title: T3D-1

source_name: leaf


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 8)

description: Fig. 4 and 9


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 6)

description: Fig. 4 and 9


title: CK-3

value: untreated


title: human_no_lymph_rep3

source_name: Tissue Micriarray,no lymph node,3


title: prime/boostIGIP-H1attd20 dpb (SAMPLE 5)

description: Fig. 4 and 9


title: bone marrow wild type mouse

description: Sample 3: MO75

source_name: Bone marrow control

value: wild type


title: T47D_rep1 [G2021_22_1]

value: breast cancer cell line


title: TgN3840_nCATS

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: nCATS-released fragments

data_processing:
All scripts are available at https://github.com/lldelisle/scriptsForWilleminEtAl2021.
Fastq was generated from fast5 files using Guppy version 3.1.5+781ed57
Reads were mapped on mm10 or TgN3840_postTLA using minimap2 version 2.15
Non primary alignments were discarded.
bam was converted to bed with bedtools 2.27.1
Genome_build: mm10 or TgN3840_TLAderived (https://github.com/lldelisle/scriptsForWilleminEtAl2021/blob/master/minION_nCATS/TgN3840_TLAderived.fa)
Supplementary_files_format_and_content: bed file where each line is an alignment

source_name: headless and tailless embryo

extract_protocol:
High molecular weight genomic DNA (HMW gDNA) was prepared as described hereafter. The sample was proteinase K digested in digestion buffer (50 mM Tris-HCl pH 8, 10 mM EDTA pH 8, 200 mM NaCl, 0.5% SDS) at 55°C while shaking for 48 hours. HMW gDNA was purified with two successive rounds of phenol-chloroform extraction, followed by ethanol precipitation. A size selection was carried out using 0.8x vol. of SPRI beads and magnetic separation. gDNA dephosphorylation was performed using Quick Calf Intestinal Phosphatase (CIP) (NEB, M0525) in 1X CutSmart Buffer (NEB). In two independent reactions corresponding to the two different pools of sgRNAs, cleavage and A-tailing was performed using the Cas9 RNPs (for cleavage) together with Taq DNA Polymerase (for A-tailing) (NEB, M0273) in the presence of dATP within the same reaction mix.
The products from both Cas9-mediated release reactions were pooled together and adapter ligation was performed using the AMX adapters from the Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK109), following the manufacturer’s instructions. The resulting library was then purified using SPRI beads and the Long Fragment Buffer (LFB) from the kit.

tag: genotype

tag: embryonic day


title: prime/boostPBSd20 dpb (SAMPLE 4)

description: Fig. 4 and 9

value: PBS


title: bone marrow Mx1Cre mouse

description: Sample 2: MO65


title: CK-1


title: CK-2


title: bone marrow RsCDX2 mouse

description: Sample 1: MO47


title: prime/boostPBSd20 dpb (SAMPLE 3)

description: Fig. 4 and 9


title: ZSTK474

city: London

middle: J

last: Pennington

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Cell Ranger v3.0 (10X Genomics) analysis pipeline was used to demultiplex sequenced libraries to generate fastq files. Subsequently, fastq files were aligned, filtered and feature-barcode matrices were generated. Fastq files were mapped to the reference mouse genome mm10 (UCSC).
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: foetal thymic lobes

growth_protocol: Foetal thymic lobes from 15-day old C57BL/6 embryos (E15) were cultured for 8 days in the presence of pan-PI3K inhibitor (ZSTK474) or under control conditions, prior to cell isolation.

extract_protocol:
Single-cell suspensions of foetal thymocytes were obtained by gently homogenizing thymic lobes followed by straining through nylon strainers. Cells were stained for cell surface markers, followed by sorting of total γδ T cells from each sample, control and ZSTK474-treated.
Single cell RNA sequencing libraries were generated using the Chromium™ Single Cell 5' Library and Gel Bead Kit (10X Genomics) according to the manufacturer's instructions. Uniquely indexed libraries were pooled for paired-end sequencing (Illumina NextSeq).

treatment_protocol: Foetal thymic lobes were cultured under control conditions or in the presence of pan-PI3K inhibitor ZSTK474.

tag: background strain

value: wild-type

value: treated with ZSTK474 for 8 days

value: foetal thymic lobes


title: Nmseq host infected with SARS-CoV-2

description: processed data file:

data_processing:
library strategy: NmSeq
SHAPE-MaP samples were processed using Bowtie2 and ShapeMapper 2.1.5
PoreCupine samples were basecalled with  live basecalling and processed with minimap2, Python and R
SPLASH samples were mapped with bwa-mem (version 0.7.17); chimeric reads were detected using the pipelie from Aw et al (2016)
NmSeq: the adaptor were trimmed by cutadapt (version 1.8.1); duplicational reads were remove according to UMI; Nmseq samples were mapped with bwa-aln (version 0.7.17); the accumulation depth of 3' end of reads were normalized by the read counts of each gene, subtracted to the background of input control; the enrichment of 2'OM was calculated with Z-test with the conditions FDR <0.05, DOED >=10, DOED/Dinput > 1.5.
Genome_build: EPI_ISL_407987 (SARS-CoV-2 WT); EPI_ISL_414378 (SARS-CoV-2 Delta382); ChlSab1.1.102
Supplementary_files_format_and_content: SUPPORTING_TABLE_01_SEQUENCING_STATS.csv: Sequencing alignment statistics
Supplementary_files_format_and_content: SUPPORTING_TABLE_02_SHAPE_DATA.csv: SHAPE reactivity data WT & Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_03_Delta382_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_04_WT_SPLASH_INTRAMOLECULAR.csv: SPLASH intramolecular crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_05_PORECUPINE.csv: Pore-Cupine reactivity data
Supplementary_files_format_and_content: SUPPORTING_TABLE_06_Delta382_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking Delta382
Supplementary_files_format_and_content: SUPPORTING_TABLE_07_WT_SPLASH_VIRUS_HOST_INTERACTIONS.csv: SPLASH virus-host crosslinking WT
Supplementary_files_format_and_content: SUPPORTING_TABLE_08_NMseq_HOST_ALL.tsv: 2'O-methylation on host RNA
Supplementary_files_format_and_content: SUPPORTING_TABLE_09_NMseq_SARS-CoV-2.tsv: 2'O-methylation on virus RNA

source_name: Vero cell infected with SARS COV2 EPI_ISL_407987 strain

value: Vero cell


title: prime/boostPBSd20 dpb (SAMPLE 2)

description: Fig. 4 and 9

tag: sample type

value: Serum


title: E9.5 Erythroid Myeloid Progenitors

city: Rochester

first: James

last: Palis

state: NY

address: 601 Elmwood Ave.

department: Pediatrics

institute: University of Rochester

data_processing:
CellRanger v2.1.1 was used to demultiplex and and CellRanger v3.2.0 was used to prcoess to gene counts per cell using default settings
Genome_build: mg38
Supplementary_files_format_and_content: 3 filtered_gene_bs_matrices files

molecule: polyA RNA

source_name: yolk sac

growth_protocol: Primary E9.5 yolk sac cell

extract_protocol:
Qiagen Rneasy PLUS Micro
10X Genomics recommended library construction protocol

treatment_protocol: Collagenase dissocitation FACS

value: Erythroid Myeloid Progenitors

tag: developmental stage

tag: markers

value: CD-1 outbred (Charles River)


title: Control


title: Nmseq host

description: processed data file:

source_name: Vero cell


title: prime/boostPBSd20 dpb (SAMPLE 1)

description: Fig. 4 and 9

source_name: Serum

tag: vaccine regimen

tag: vaccine

tag: time point


title: scD45LN_L004

status: Public on Jul 04 2021

city: Lebanon

first: Aleksey

last: Molodtsov

state: NH

address: 1 Medical Dr

department: Micro Immuno

institute: Dartmouth College

description: GEX

data_processing:
Real Time Analysis version 2 (RTA2) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Kilobase Million of library size (TPM) were calculated using RSEM.  In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10

source_name: Pmel CD8 T cells

extract_protocol:
Lymph nodes mechanically dissociated and passed through a 40 um filter.  Skin was minced and digested in HBSS containing 3 mg/mL collagenase Type IV and 0.2 mg/mL DNase I at 37 °C for 45 minutes.  Lungs were minced and then digested in serum-free RPMI containing 16.7 mg/mL of Liberase (Roche) and 0.2 mg/mL of DNase I (Sigma-Aldrich), at 37°C for 30 minutes.  Livers were smashed through a mesh filter and then digested in serum-free RPMI containing 0.6 mg/mL Collagenase Type IV (Worthington Biochemical Corporation) and 0.1 mg/mL of DNase I, at 37C for 40 minutes. For both lungs and livers, digests were washed, and buffy coats were isolated by percoll gradient centrifugation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

tag: disease state

value: Melanoma-associated vitiligo

value: LN

value: 16 weeks


title: scSkin_L002

description: GEX

value: Skin


title: scLiver_L004

description: GEX

value: Liver


title: scSkin_L001

description: GEX


title: scLiver_L003

description: GEX


title: scD45LN_L001

description: GEX


title: scD45LN_L002

description: GEX


title: scSkin_L003

description: GEX


title: scLiver_L001

description: GEX


title: scSkin_L004

description: GEX


title: scLung_L002

description: GEX

value: Lung


title: scLung_L001

description: GEX


title: scLung_L004

description: GEX


title: scLung_L003

description: GEX


title: scLiver_L002

description: GEX


title: Skin_TCR_S4_L004

description: GEX

source_name: Skin

extract_protocol:
Lymph nodes mechanically dissociated and passed through a 40 um filter.  Skin was minced and digested in HBSS containing 3 mg/mL collagenase Type IV and 0.2 mg/mL DNase I at 37 °C for 45 minutes.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+CD44+ T cells

tag: strain


title: Skin_TCR_S4_L003

description: GEX

tag: age


title: Skin_TCR_S4_L002

description: GEX


title: Skin_TCR_S4_L001

description: GEX


title: Skin_GEX_S3_L004

description: GEX


title: Skin_GEX_S3_L003

description: GEX


title: Skin_GEX_S3_L002

description: GEX


title: Skin_GEX_S3_L001

description: GEX


title: LN_TCR_S2_L004

description: GEX

source_name: Lymph Node

value: Lymph Node


title: LN_TCR_S2_L003

description: GEX


title: scD45LN_L003

description: GEX


title: LN_TCR_S2_L002

description: GEX


title: LN_TCR_S2_L001

description: GEX


title: LN_GEX_S1_L004

description: GEX


title: LN_GEX_S1_L003

description: GEX


title: LN_GEX_S1_L002

description: GEX


title: Liver_1

description: GEX

data_processing:
Real Time Analysis version 2 (RTA2) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Genome_build: mm10

source_name: Liver

value: Pmel CD8 T cells

value: Melanoma-associated Vitiligo


title: Lung_1

description: GEX

source_name: Lung


title: Skin_1

description: GEX


title: Spleen_1

description: GEX

source_name: Spleen

value: Spleen


title: Mem_LN_1

description: GEX


title: Lung_2

description: GEX


title: Skin_2

description: GEX


title: Skin_3

description: GEX


title: Spleen_2

description: GEX


title: Liver_3

description: GEX


title: Lung_3

description: GEX


title: Spleen_3

description: GEX


title: TIL_1

description: GEX

source_name: Tumor

value: Tumor


title: TIL_3

description: GEX


title: TIL_2

description: GEX


title: Lung_4

description: GEX


title: TIL_4

description: GEX


title: Skin_4

description: GEX


title: Spleen_4

description: GEX


title: Liver_4

description: GEX


title: TDLN_D12_3

description: GEX


title: TDLN_D12_1

description: GEX


title: TDLN_D12_2

description: GEX


title: Mem_LN_4

description: GEX


title: LN_GEX_S1_L001

description: GEX


title: Naive_1

description: GEX


title: Mem_LN_2

description: GEX


title: Liver_2

description: GEX


title: Naive_2

description: GEX


title: Mem_LN_3

description: GEX


title: Naive_4

description: GEX


title: Naive_3

description: GEX


title: FAXINO80WT-2

city: Research Triangle Park

first: Guang

last: Hu

state: NC

address: 111 TW Alexander DR

department: ESCBL

institute: National Institute of Environmental Health Sciences

data_processing:
RNA-seq reads were first trimmed adapter with cutadapt (v1.9), then discard reads with length less than 15 and removed the one with quality less than 20. Filtered reads were aligned to mm9 reference with STAR (v2.5.2b) with parameters of --outFilterMismatchNoverLmax 0.04. For RNA-seq with ERCC spike-in, the ERCC reads were aligned separately to ERCC92 reference.Genomic features at gene level were generated with featureCounts (v1.5.1).
Genome_build: mm9
Supplementary_files_format_and_content: TXT: RPKM were normalized to the ERCC spike-in, loess normalization function from R affy package was used to adjust the values.

source_name: embryonic stem cell line

growth_protocol: For the naïve pluripotent state, mouse ESCs were cultured in 2iL medium containing N2B27 medium supplemented with PD0325901 (1 mM, Selleck), CHIR99021 (3 mM, Selleck) and 1000 units/ml recombinant murine LIF (Millipore) on gelatin-coated plates (2iL). For the primed pluripotent state, mouse ESCs were cultured in  FAX medium containing N2B27 supplemented with FGF-2 (Peprotech, 12 ng/ml), Activin A (Peprotech, 20 ng/mL), and XAV-939 (2 uM Selleck) on human fibronectin-coated plates (Millipore). The N2B27 medium contains (1000 ml): 500 ml DMEM/F12 (Invitrogen; 11320), 500 ml Neurobasal (Invitrogen; 21103), 5 ml N2 supplement (Invitrogen; 17502048), 10 ml B27 supplement (Invitrogen; 17504044) and 0.1% bovine serum albumin fraction V (Thermofisher).

extract_protocol:
For RNA-seq with spike-in controls, 10 ul of 1:100 dilution of the ERCC Spike-In Mix #1 was added to the lysate of 1 million cells before RNA extraction. Total RNA was then extracted as described above. For RNA-seq library preparation, 1 mg total RNA was used to prepare the RNA-seq library with the Truseq RNA Library Prep Kit V2 with Ribo-Zero (Illumina).
Truseq RNA Library Prep Kit V2 with Ribo-Zero (Illumina)

treatment_protocol: For inducible gene deletion, cells were treated with 100 nM 4-OHT for two days, then cultured for another 2 days for experiments.

tag: line

value: INO80 CKO

tag: state

value: Primed


title: FAXINO80WT-1


title: 2iLINO80WT-2

value: Naïve


title: FAXINO80KO-2


title: 2iLINO80WT-1


title: 2iLINO80KO-2


title: FAXINO80KO-1


title: 2iLINO80KO-1


title: 2iLH2azWTFAH3K27me3-1

data_processing:
ChIP-seq reads were aligned to mm9 reference with bowtie (v1.1.2) with parameters -v 2 -m 1 --best --strata -I 15 -X 1000 after filtering adapter with cutadapt (v1.9) and only keep reads with quality greater than 20. PCR duplicates were removed after alignment.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig: bedtools genomeCoverageBed was used for generate bedGraph file, coverage then normalized to reads per 10 million aligned reads, bedGraphToBigWig was used to produce final bigWig

source_name: Mouse embryonic stem cell line

growth_protocol: For routine culture, mouse ESCs were maintained in the ESGRO medium (Millipore) on tissue culture plates pretreated with 0.1% gelatin. For the naïve pluripotent state, mouse ESCs were cultured in 2iL medium containing N2B27 medium supplemented with PD0325901 (1 mM, Selleck), CHIR99021 (3 mM, Selleck) and 1000 units/ml recombinant murine LIF (Millipore) on gelatin-coated plates (2iL). For the primed pluripotent state, mouse ESCs were cultured in FA or FAX medium containing N2B27 supplemented with FGF-2 (Peprotech, 12 ng/ml), Activin A (Peprotech, 20 ng/mL), and XAV-939 (2 uM Selleck) on human fibronectin-coated plates (Millipore). The N2B27 medium contains (1000 ml): 500 ml DMEM/F12 (Invitrogen; 11320), 500 ml Neurobasal (Invitrogen; 21103), 5 ml N2 supplement (Invitrogen; 17502048), 10 ml B27 supplement (Invitrogen; 17504044) and 0.1% bovine serum albumin fraction V (Thermofisher).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Chromatin was fragmented by MNase digestion followed by ChIP. Immunoprecipitated DNA-protein complex was eluted with the elution buffer (50 mM Tris–Cl (pH 7.5), 10 mM EDTA, 1% sodium dodecyl sulphate) at 65°C for 15 min. The elution was collected and reverse-crosslinked at 65 °C overnight, diluted with 1 volume of TE buffer and treated with RNase A at 37 °C for 30 min followed by 0.2 μg/ml Proteinase K at 55 °C for 60 min. The immunoprecipitated DNA was purified from the elution by the Zymo DNA Clean & Concentrator Kit.
ChIP-seq libraries were prepared as instructions of Nextflex Rapid DNA-seq Kit (PerkinEImer). Libraries of H2az1 CKO/H2az2 KO cell lines were prepared as instructions of Nextera DNA Flex prep kit.

tag: cell line

value: H2az1 CKO/H2az2 KO

tag: chip antibody

tag: antibody cat#

value: Activemotif 39155


title: 2iLH2azWTFAInput


title: 2iLH2azWTFAH3K27me3-2


title: 2iLH2azKOFASuz12

value: CellSignaling #3737


title: 2iLH2azKOFAH3K27me3-2


title: TDLN_D12_4

description: GEX

tag: cell type

tag: tissue


title: 2iLH2azKOFAH3K27me3-1


title: 2iLH2azWTFAEzh2

value: CellSignaling #5246


title: 2iLH2azKOFAInput


title: 2iLINO80WTFAH3K27me3Input


title: 2iLINO80WTFAH3K27me3-2


title: 2iLH2azKOFAEzh2


title: 2iLINO80WTFAH3K27me3-1


title: 2iLINO80KOFAH3K27me3Input


title: 2iLINO80KOFAH3K27me3-2


title: 2iLINO80KOFAH3K27me3-1


title: FAXINO80WTH3K27me3-2


title: m10Ezh2KOH2az

value: Ezh2 KO

value: Activemotif 39943


title: 2iLH2azWTFASuz12


title: m10EedKOH2az

value: Eed KO


title: m10WTH2az


title: FAXINO80WTSuz12


title: FAXINO80WTH3K27ac-1

value: Abcam ab4729


title: FAXINO80WTH3K27me3-1


title: FAXINO80WTH3K27ac-2


title: FAXINO80KOH3K27me3-2


title: m10WTInput


title: FAXINO80WT64U

data_processing:
MNase-seq reads were aligned with bowtie (v1.1.2) with parameters -v 2 -m 1 --best --strata -I 15 -X 1000. The distribution of the reads fragment was plotted and reads located at highest peak region around 100 to 200 were selected for later analysis.
Supplementary_files_format_and_content: bigWig: bedtools genomeCoverageBed was used for generate bedGraph file using mid point of each fragment, coverage then normalized to reads per 10 million aligned reads, bedGraphToBigWig was used to produce final bigWig

source_name: mouse embryonic stem cell line

growth_protocol: For the naïve pluripotent state, mouse ESCs were cultured in 2iL medium containing N2B27 medium supplemented with PD0325901 (1 mM, Selleck), CHIR99021 (3 mM, Selleck) and 1000 units/ml recombinant murine LIF (Millipore) on gelatin-coated plates (2iL). For the primed pluripotent state, mouse ESCs were cultured in FA or FAX medium containing N2B27 supplemented with FGF-2 (Peprotech, 12 ng/ml), Activin A (Peprotech, 20 ng/mL), and XAV-939 (2 uM Selleck) on human fibronectin-coated plates (Millipore). The N2B27 medium contains (1000 ml): 500 ml DMEM/F12 (Invitrogen; 11320), 500 ml Neurobasal (Invitrogen; 21103), 5 ml N2 supplement (Invitrogen; 17502048), 10 ml B27 supplement (Invitrogen; 17504044) and 0.1% bovine serum albumin fraction V (Thermofisher).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Chromatin was fragmented by MNase digestion. 4, 16, 64 or 256 U of MNase (NEB) were added to per 2M pre-warmed cells and incubated at 37 °C for 10 min. Digestion was halted by addition of MNase stop buffer (20mM EDTA, 20mM EGTA, 0.4% SDS and 0.5mg/ml Proteinase K). The mixtures were incubated at 65 °C for 60 min to reverse crosslinks. DNA was cleaned up by Gel Purification Column (Qiagen).
100 ng DNA from each digestion were used to prepare DNA libraries as described in the Nextflex Rapid DNA-seq Kit (PerkinEImer).  Size selection was performed after adaptor ligation with Agencourt AMPure XP beads (Beckman Coulter)


title: FAXINO80KOH3K27me3-1


title: FAXINO80KOSuz12


title: FAXINO80KOH3K27ac-1


title: FAXINO80KOH3K27ac-2


title: FAXINO80WT256U


title: FAXINO80WT4U


title: FAXINO80KO256U


title: FAXINO80KO16U


title: FAXINO80WT16U


title: 2iLINO80KOSuz12


title: 2iLINO80WTH3K27ac-1


title: 2iLINO80WTSuz12


title: 2iLINO80WT256U


title: 2iLINO80KOH3K27ac-2


title: 2iLINO80WT16U


title: 2iLINO80KOH3K27me3-1


title: 2iLINO80KOH3K27me3-2


title: 2iLINO80KO4U


title: FAXINO80HAInput


title: MEFINO80WTinput

source_name: Mouse embryonic fibroblasts


title: FAXINO80KO4U


title: MEFINO80WTH2az


title: FAXINO80HA-2

value: HA

value: CellSignaling #3724


title: FAINO80HAInput-1


title: 2iLINO80KO256U


title: 2iLINO80KO16U


title: 2iLINO80WT64U


title: 2iLINO80WTH3K27me3-2


title: MEFINO80KOinput


title: FAINO80HAInput-2


title: 2iLINO80WTH3K27ac-2


title: FAINO80HA-2


title: 2iLINO80WTH3K27me3-1


title: MEFINO80KOH2az


title: 2iLINO80WT4U


title: FAXINO80KO64U


title: FAINO80HA-1


title: FAXINO80WTH2az-2


title: 2iLINO80KOH3K27ac-1


title: 2iLINO80KO64U


title: FAXINO80HA-1


title: 2iLINO80HAInput-2


title: FAXINO80WTH2azInput


title: 2iLINO80HAInput-1


title: FAXINO80WTH2az-1


title: FAXINO80KOH2az-2


title: 2iLINO80HA-2


title: FAXINO80KOH2azInput


title: 2iLINO80WTH2az-1


title: 2iLINO80WTH2az-2


title: FAXINO80KOH2az-1


title: Jowoon 60 DAH embryo rep 1

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

country: South Korea

institute: Seoul National University

data_processing:
Base calling
Quality check
Trimming: Cutadapt
Size selection and Quality filtering: Trimmomatic
Filtering: bowtie1 alignment on rice-specific rRNA/tRNA/snRNA/snoRNA database (RNACentral)
Alignment: bowtie1 alignment on IRGSPv1.0
Annotation: bowtie1 alignment on mature microRNA sequence from miRBase(v22) and PMIRen
Differentially expression gene: edgeR
Genome_build: IRGSPv1.0
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each Sample

organism: Oryza sativa

source_name: Rice seed

growth_protocol: All plant materials were cultivated in the experimental field of Seoul National University, Suwon, South Korea.

extract_protocol:
Total RNA was harvested using Trizol reagent.
Lexogen Small RNA-Seq Library Prep Kit V2 for Illumina platforms (Cat. No. 052.96)  was used with 2 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Untreated

value: Embryo

tag: genotype

value: Wild type

tag: maturation stage

value: 60 days after heading

tag: ecotype

value: Jowoon


title: 2iLINO80KOH2az-2

value: INO80 CKO


title: 2iLATAC-3

data_processing:
Filtered ATAC-seq reads were aligned with bowtie(v1.1.2) with parameters: -v 2 -m 1 –best –strata. The first 9 bp from both end of the aligned fragments were used as open chromatin reads. Reads from chrM were removed. The remained reads then used for building tracks.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig: bedtools genomeCoverageBed was used for generate bedGraph file, coverage then normalized to reads per 10 million aligned reads, bedGraphToBigWig was used to produce final bigWig

extract_protocol:
Extract by Zymo DNA purification column
ATAC-seq protocol as described(Corces et al., 2017)

treatment_protocol: Cell nuclei were tagged by transposase Tn5


title: Jowoon 60 DAH embryo rep 2


title: FAXATAC-2

value: Primed


title: FAXATAC-1


title: 2iLINO80WTH2azInput

value: Naïve


title: 2iLATAC-2


title: Jowoon 45 DAH embryo rep 2

value: 45 days after heading


title: FAXINO80WTH3K4me3-2

value: Activemotif 39159


title: 2iLINO80KOH2az-1


title: 2iLATAC-1


title: 2iLINO80KOH2azInput


title: Jowoon 45 DAH embryo rep 1


title: FAXINO80WTH3K4me3-1


title: Jowoon 30 DAH embryo rep 2

value: 30 days after heading


title: FAXINO80WTEzh2-2

value: CellSignaling #5246


title: FAXINO80WTEzh2-1


title: Tcf4_knock_out_5

city: Erlangen

first: Marie-Theres

last: Wittmann

address: Schwabachanlage 10

department: Institute of Human Genetics

institute: Universitätsklinikum Erlangen

data_processing:
Illumina RTA 1.18.66.3 was used for base calling.
Base calling files were converted to FASTQ files and demultiplexed using Cell Ranger v2.1.0 (10x Genomics) mkfastq with standard parameters.
Cell Ranger v2.1.0 quant was used to map the demultiplexed reads to the mm10 reference genome v2.1.0 (10x Genomics), process cell barcodes, generate expression matrices of UMI (unique molecule identifier) counts and estimate the number of cells using standard parameters.
Seurat v2.3.4 was used under R v3.6.0 to filter cells by the number of genes expressed, the number of unique molecular identifiers and the percentage of mitochondrial genes expressed, cluster and visualize cells by similarity in gene expression and identify cluster markers. Differentially expressed gene analysis was performed using the MAST algorithm as implemented in Seurat. Gene regulatory network analysis was performed using SCENIC v.1.1.2-2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_Seurat_count_matrix.txt: Tab-delimited text files with UMI counts per gene per cell after initial filtering in Seurat (1000-5000 genes per cells, 1800-10000 UMIs and <6% of mitochondrial transcripts).

source_name: Embryonic brain E18.5

growth_protocol: Wildtype and Tcf4 knock out embryos were littermates from breedings of Tcf4 haploinsufficient mice. Female mice were bred in the afternoon and vaginal post-coitum protein plug check was performed the next morning. This time point was defined as E0.5. At E18.5 pregnant dams were sacrificed, neocortices of WT and KO littermate embryos were microdissected and a single cell suspension was prepared.

extract_protocol:
For each sample 10000 cells were loaded onto a Chromium Single Cell A Chip (10x Genomics) to generate single cell bead emulsions of about 5000 cells for reverse transcription and cell bar coding according to the manufacturer's instructions.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and i7 Multiplex kit (10X Genomics) according to the manufacturer's instructions. Libraries were sequenced on an Illumina HiSeq 2500 using the recommended read lengths for Chromium Single Cell 3' v2 chemistry.

value: neocortex

tag: strain/background

tag: genotype/variation

value: Tcf4 knockout

tag: developmental stage


title: 2iLINO80HA-1


title: FAXINO80WTInput


title: Tcf4_knock_out_4


title: FAXINO80KOH3K4me3-2


title: FAXATAC-3


title: Jowoon 30 DAH embryo rep 1


title: Tcf4_knock_out_2


title: Gopum 60 DAH embryo rep 2

value: Gopum


title: FAXINO80KOEzh2-1


title: Tcf4_knock_out_1


title: Gopum 60 DAH embryo rep 1


title: wildtype_5

value: wildtype


title: FAXINO80KOInput


title: 2iLINO80WTEzh2-2


title: Gopum 45 DAH embryo rep 2


title: Gopum 45 DAH embryo rep 1


title: 2iLINO80WTEzh2-1


title: wildtype_3


title: 2iLINO80WTInput


title: 2iLINO80KOH3K4me3-2


title: Gopum 30 DAH embryo rep 2


title: wildtype_2


title: 2iLINO80KOEzh2-2


title: Gopum 30 DAH embryo rep 1


title: 2iLINO80KOH3K4me3-1


title: wildtype_1


title: FAXINO80KOH3K4me3-1


title: 2iLINO80KOEzh2-1


title: 2iLINO80KOInput


title: FAXINO80KOEzh2-2


title: 2iLINO80WTH3K4me3-2


title: 2iLINO80WTH3K4me3-1


title: wildtype_4


title: BL_014

status: Public on Jul 03 2021

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: University of Zurich

description: processed data file: Count_QC-raw-count.txt

data_processing:
Basecalls performed using Illumina's bcl2fastq 2.19.0.
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using 2.5.3a with following parameters:  --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated by Rsubread 1.26.0 with the following parameters: 'Multimapping reads : primary only', 'Multi-overlapping reads : counted', 'Overlapping bases : 10'
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Count_QC-raw-count.txt: Count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: B cell

extract_protocol:
RNeasy Plus Micro Kit (QIAGEN).
TruSeq RNA stranded.

treatment_protocol: Direct isolation of B cells from frozen PBMC.

tag: disease condition

value: healthy

tag: stimulation

value: unstimulated

tag: time point

value: baseline

value: B cells

tag: subject


title: BL_005


title: BL_006


title: 72h_US_055


title: 72h_US_014


title: BL_055


title: 72h_RV_IFN_006

value: rhinovirus + interferon-alpha


title: 72h_RV_IFN_014


title: 72h_US_006


title: 72h_RV_IFN_055


title: 72h_RV_IFN_005


title: 72h_US_005


title: 72h_RV_055

value: rhinovirus


title: 72h_RV_014


title: 28S22: Lung_silicosis_28d_rep2

city: Jinan

first: Gongchang

last: Yu

state: Shandong

address: NO.18877, Jingshi Road

department: Toxicology Department

institute: Shandong Academy of Occupational Health and Occupational Medicine

description: LncRNAs expression after 28d in silica-induced rat lung

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat lncRNA Microarray V3（8*60K）for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 14.8 (Agilent). Probe that at least 1 out of 2 samples flagged as P were maintained.

organism: Rattus norvegicus

source_name: rat lung, silicosis, 28d,  replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA was extracted using AMBION RNA isolation kit (AM1561) and then quantified using the NanoDrop ND-2000 (Thermo Scientific). The RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: The rat lungs were isolated and flash-frozen in liquid nitrogen, and stored at -80 °C for lncRNA microarray expression analysis

value: lung tissue

tag: gender

value: male


title: VitD_119

city: Nagoya

first: Tadashi

last: Iida

state: AICHI

department: Gastroenterology and Hepatology

country: Japan

institute: Nagoya university

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: Primary cultured human PSCs isolated from three patients with PDAC (163, 52, and 119) were administered with DMSO (1 µM), calcipotriol (Cal, 1 µM), and Am80 (1 µM) for 48 h. Total RNA was then extracted by RNA Plus mini kit(Quigane).RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: subject status

value: PDAC patient

tag: subject id

value: cancer-associated fibroblasts (CAF)

tag: treatment

value: calcipotriol (Cal, 1 µM) for 48 h


title: 28S23: Lung_silicosis_28d_rep3

source_name: rat lung, silicosis, 28d,  replicate3


title: 28C17: Lung_saline solution_28d_rep3

description: LncRNAs expression after 28d in saline solution-induced rat lung

source_name: rat lung, saline solution, 28d,  replicate3


title: 28S21: Lung_silicosis_28d_rep1

source_name: rat lung, silicosis, 28d,  replicate1


title: 28C15: Lung_saline solution_28d_rep1

source_name: rat lung, saline solution, 28d,  replicate1


title: Am80_163

value: Am80 (1 µM) for 48 h


title: Am80_119


title: Am80_52


title: DMSO_163

value: DMSO (1 µM) for 48 h


title: DMSO_52


title: VitD_163


title: VitD_52


title: 28C16: Lung_saline solution_28d_rep2

source_name: rat lung, saline solution, 28d,  replicate2


title: DMSO_119


title: Control

city: Hamilton

first: Yonghong

last: Wan

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

description: replicate 1

hyb_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions

scan_protocol: Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays were scanned according to the manufacturer’s instructions

data_processing: The obtained data were processed with VST transformation and quantile normalization (lumi). Only annotated and detected genes were selected

label: biotin

source_name: Mouse tumor

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.

tag: strain

tag: age

value: 6-8 weeks

value: tumor


title: 72h_IFN_055

value: interferon-alpha

tag: cell type


title: 72h_RV_006


title: 72h_IFN_005


title: 72h_RV_005


title: 72h_IFN_006


title: 24h_US_006


title: 24h_US_055


title: ACT+MS-275 d5 rep3

description: replicate 3

label_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays according to the manufacturer’s instructions

tag: tissue


title: ACT+MS-275 d5 rep1

description: replicate 1


title: ACT d5 rep4

description: replicate 4


title: ACT+MS-275 d5 rep4

description: replicate 4


title: 24h_US_005


title: ACT+MS-275 d5 rep2

description: replicate 2


title: 24h_RV_IFN_055


title: 24h_RV_IFN_014


title: 24h_RV_IFN_006


title: 24h_RV_014


title: ACT d5 rep2

description: replicate 2


title: ACT+MS-275 d3 rep4

description: replicate 4


title: 24h_RV_055


title: 24h_RV_IFN_005


title: 24h_RV_006


title: 72h_IFN_014


title: ACT d5 rep3

description: replicate 3


title: 24h_RV_005


title: 24h_IFN_055


title: ACT+MS-275 d3 rep3

description: replicate 3


title: ACT d5 rep1

description: replicate 1


title: 24h_IFN_014


title: ACT+MS-275 d3 rep2

description: replicate 2


title: ACT+MS-275 d3 rep1

description: replicate 1


title: ACT d3 rep1

description: replicate 1


title: 24h_IFN_006


title: 62MN_BL_A

value: asthmatic


title: ACT d3 rep3

description: replicate 3


title: 24h_IFN_005

value: healthy


title: 53KW_d3_A


title: 59HI_d3_A


title: 59HI_BL_A


title: 53KW_BL_A


title: ACT d3 rep2

description: replicate 2


title: 49BV_d7_N


title: 49BV_d3_N


title: 49BV_BL_N


title: ACT+MS-275 d1 rep3

description: replicate 3


title: ACT+MS-275 d1 rep4

description: replicate 4


title: 42GH_d3_N


title: 59HI_d7_A


title: ACT+MS-275 d1 rep2

description: replicate 2


title: ACT+MS-275 d1 rep1

description: replicate 1


title: ACT d1 rep4

description: replicate 4


title: ACT d1 rep1

description: replicate 1


title: WT_MMC9_Cell78_scRNA-seq

city: Ann Arbor

first: Sunil

last: Tomar

address: 109 Zina Pitcher Place

institute: University of Michigan

description: scRNAseq: WT small intestinal MMC9s from WT mice following Ova/alum model of food allergy.

data_processing:
Raw reads were aligned to the reference Mus musculus mm9  (GRCm38) using Hisat-build pipeline. Raw reads were extracted using featureCounts function from the subread-2.0.0 package.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Text file

source_name: Small intestinal WT MMC9

extract_protocol:
Zymogen's QuickRNA kit based isolation of RNA using manufacturer's protocol
Libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: Small intestine

tag: tag

value: WT


title: WT_MMC9_Cell77_scRNA-seq


title: WT_MMC9_Cell74_scRNA-seq


title: WT_MMC9_Cell76_scRNA-seq


title: WT_MMC9_Cell79_scRNA-seq


title: WT_MMC9_Cell81_scRNA-seq


title: WT_MMC9_Cell80_scRNA-seq


title: WT_MMC9_Cell75_scRNA-seq


title: WT_MMC9_Cell73_scRNA-seq


title: 42GH_BL_N

value: baseline

value: B cells


title: ACT d1 rep2

description: replicate 2


title: ACT d1 rep3

description: replicate 3


title: WT_MMC9_Cell72_scRNA-seq


title: 39AG_BL_A

value: rhinovirus


title: WT_MMC9_Cell71_scRNA-seq


title: 38HF_d7_N


title: WT_MMC9_Cell70_scRNA-seq


title: 38HF_d3_N


title: WT_MMC9_Cell69_scRNA-seq


title: 33KT_d3_N


title: WT_MMC9_Cell68_scRNA-seq


title: WT_MMC9_Cell67_scRNA-seq


title: 32LR_d7_N


title: WT_MMC9_Cell66_scRNA-seq


title: 39AG_d3_A


title: 32LR_d3_N


title: WT_MMC9_Cell65_scRNA-seq


title: 32LR_BL_N


title: WT_MMC9_Cell64_scRNA-seq


title: 31HL_d7_N


title: 31HL_d3_N


title: WT_MMC9_Cell63_scRNA-seq


title: WT_MMC9_Cell61_scRNA-seq


title: WT_MMC9_Cell59_scRNA-seq


title: 26EV_d3_A


title: 26EV_d7_A


title: WT_MMC9_Cell62_scRNA-seq


title: 19TK_d7_N


title: WT_MMC9_Cell58_scRNA-seq


title: WT_MMC9_Cell57_scRNA-seq


title: WT_MMC9_Cell60_scRNA-seq


title: WT_MMC9_Cell56_scRNA-seq


title: 26EV_BL_A


title: BbWor1-KO-BTB-rep2

city: Ji nan

first: zhang

middle: tong

last: sheng

address: 3501 Daxue Road, Changqing District,

institute: Qilu University of Technology

data_processing:
Sequencing of RNA samples was performed on the BGISEQ-500 platform at BGI-Shenzhen, China.
Entire clean reads were mapped to the reference genome with HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, and then the gene expression level was evaluated by RSEM (v1.2.12)
Genome_build: GCA_000280675.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Beauveria bassiana ARSEF 2860

source_name: Beauveria bassiana ARSEF 2860

growth_protocol: HTC model:culture on SDAY medium；CTH model: cultured on GB broth；BTB model:inoculated into NLB broth.

extract_protocol:
Total RNA was extracted from fungal cultures of each mode with TRIzol-A+ reagent.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: Disruption Wor1 by homologous recombination

tag: genotype

value: BbWor1 KO

tag: model

value: BTB (blastospore to blastospore)


title: BbWor1-KO-BTB-rep1


title: BbWor1-KO-BTB-rep3


title: 38HF_BL_N


title: BbWor1-KO-HTC-rep3

value: HTC (hyphae to conidia)


title: WT_MMC9_Cell54_scRNA-seq


title: BbWor1-KO-HTC-rep2


title: WT_MMC9_Cell53_scRNA-seq


title: BbWor1-KO-HTC-rep1


title: WT_MMC9_Cell52_scRNA-seq


title: BbWor1-KO-CTH-rep1

value: CTH (conidia to hyphae)


title: BbWor1-KO-CTH-rep2


title: WT_MMC9_Cell51_scRNA-seq


title: WT_MMC9_Cell50_scRNA-seq


title: WT_MMC9_Cell49_scRNA-seq


title: BbWor1-KO-CTH-rep3


title: WT_MMC9_Cell48_scRNA-seq


title: WT-BTB-rep3


title: WT-BTB-rep1


title: WT_MMC9_Cell47_scRNA-seq


title: WT-BTB-rep2


title: WT_MMC9_Cell46_scRNA-seq


title: WT-HTC-rep2


title: WT_MMC9_Cell43_scRNA-seq


title: WT_MMC9_Cell55_scRNA-seq


title: WT-HTC-rep1


title: WT-CTH-rep3


title: WT_MMC9_Cell45_scRNA-seq


title: WT_MMC9_Cell44_scRNA-seq


title: WT_MMC9_Cell42_scRNA-seq


title: WT_MMC9_Cell41_scRNA-seq


title: WT-CTH-rep1


title: WT_MMC9_Cell40_scRNA-seq


title: WT-CTH-rep2


title: WT_MMC9_Cell38_scRNA-seq


title: WT_MMC9_Cell36_scRNA-seq


title: WT_MMC9_Cell35_scRNA-seq


title: WT_MMC9_Cell34_scRNA-seq


title: WT_MMC9_Cell31_scRNA-seq


title: WT_MMC9_Cell32_scRNA-seq


title: WT-HTC-rep3


title: WT_MMC9_Cell29_scRNA-seq


title: WT_MMC9_Cell27_scRNA-seq


title: WT_MMC9_Cell26_scRNA-seq


title: WT_MMC9_Cell25_scRNA-seq


title: WT_MMC9_Cell22_scRNA-seq


title: WT_MMC9_Cell33_scRNA-seq


title: WT_MMC9_Cell21_scRNA-seq


title: WT_MMC9_Cell18_scRNA-seq


title: WT_MMC9_Cell19_scRNA-seq


title: WT_MMC9_Cell17_scRNA-seq


title: WT_MMC9_Cell24_scRNA-seq


title: WT_MMC9_Cell20_scRNA-seq


title: WT_MMC9_Cell23_scRNA-seq


title: WT_MMC9_Cell15_scRNA-seq


title: WT_MMC9_Cell16_scRNA-seq


title: WT_MMC9_Cell39_scRNA-seq


title: WT_MMC9_Cell13_scRNA-seq


title: WT_MMC9_Cell37_scRNA-seq


title: WT_MMC9_Cell14_scRNA-seq


title: H3.9 [A47-49]

city: Los Angeles

first: Juehua

state: CA

address: 615 Charles E. Young South BSRB 457

institute: UCLA

data_processing:
filtered using FastQC
aligned to the GRCh38 human genome assembly using HISAT2
quantified and analyzed using DESeq2 R package
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human plasma exosome

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: plasma

value: S100A16 siRNA transfected


title: H3.10 [A47-50]


title: H3.8 [A47-48]


title: WT_MMC9_Cell12_scRNA-seq


title: WT_MMC9_Cell30_scRNA-seq


title: H3.7 [A47-47]

value: MYEOV siRNA transfected


title: WT_MMC9_Cell28_scRNA-seq


title: H3.4 [A47-44]

value: KCNN4 siRNA transfected


title: H3.6 [A47-46]


title: H3.5 [A47-45]


title: WT_MMC9_Cell11_scRNA-seq


title: WT_MMC9_Cell10_scRNA-seq


title: H3.3 [A47-43]


title: WT_MMC9_Cell9_scRNA-seq


title: WT_MMC9_Cell8_scRNA-seq


title: control7 [A47-27]


title: control9 [A47-29]


title: H3.1 [A47-41]

value: DDX60L siRNA transfected


title: control8 [A47-28]


title: control10 [A47-30]


title: H3.2 [A47-42]


title: control6 [A47-26]


title: WT_MMC9_Cell6_scRNA-seq


title: WT_MMC9_Cell5_scRNA-seq


title: control4 [A47-24]


title: control3 [A47-23]


title: control5 [A47-25]


title: control1 [A47-21]


title: control2 [A47-22]


title: WT_MMC9_Cell4_scRNA-seq


title: H1.9 [A47-09]


title: WT_MMC9_Cell2_scRNA-seq


title: H1.10 [A47-10]


title: WT_MMC9_Cell3_scRNA-seq


title: WT_MMC9_Cell1_scRNA-seq


title: H1.6 [A47-06]


title: H1.7 [A47-07]


title: H1.5 [A47-05]


title: H1.4 [A47-04]


title: Il4_MMC9_bulkRNA-seq

description: Bulk RNAseq: IL4ra-/- MMC9s: Following adoptive transfer model of food allergy, IL4ra-/- small intestinal MMC9s from food allergic mice that that undergone 7 oral Ova challenges were isolated for RNAseq

source_name: Small intestinal IL4ra-/- MMC9

value: IL-4Ra-/- (loss of function mutant)


title: H1.8 [A47-08]


title: WT_MMC9_Cell7_scRNA-seq


title: H1.2 [A47-02]

value: Control siRNA transfected


title: H1.1 [A47-01]


title: H1.3 [A47-03]


title: 12975 MAT 1

first: David

last: Osuna de la Peña

address: 5 University Street

department: Respiratory Medicine

institute: University College London

data_processing:
Base calling done on the NovaSeq 6000 Sequencing System, which runs RTA3.
Filtering of rRNA was performed on the fastq files of tissue samples to reduce GC bias with SortMeRNA 2.1.
Fastq files were pseudoaligned to the GENCODE v30 primary assembly with kallisto v.0.46.0.
Transcript counts were imported into R with tximport and normalised for differential expression analysis at the gene level with DESEq2 3.9.
Genome_build: GENCODE v30 (GRCh38)
Supplementary_files_format_and_content: kallisto_tpm_allsamples.tsv (Kallisto output files (.h5) with transcript abundances in TPM.)
Supplementary_files_format_and_content: DESeqDataSet.tsv (Normalised counts used for differential expression analysis with DESeq2.)

source_name: Pancreatic adenocarcinoma cells

extract_protocol:
Total RNA was extracted from disassociated tissues and cultures using a Qiagen RNeasy Mini kit and quantified on a NanoDrop 2000; RNA quality was measured on an Agilent Tapestation 4200.
Illumina TruSeq (done by Oxford Genomics) with polyA selection of mRNA.

value: Pancreatic adenocarcinoma

tag: material

value: cells

tag: patient

tag: sample type

value: Patient-derived pancreatic cancer organoids cultured in Matrigel for 7 days


title: 12975 2D 2

value: Patient-derived pancreatic cancer cells cultured on 2D polystyrene for 7 days


title: 12975 SPH 1

value: Patient-derived pancreatic cancer cells cultured in suspension for 7 days


title: 12975 2D 1


title: 12560 SPH 2


title: 12975 MAT 2


title: 12560 MAT 2


title: NH7

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to GENCODE GRCh38.p13 genome assembly using STAR
Counts were generated by Rsubread
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Skin biopsy

extract_protocol:
RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) skin biopsies with a Qiagen® RNeasy FFPE Kit.
Library preparation for RNA-seq was performed by using the TruSeq  Stranded RNA library preparation kit including polyA enrichment (Illumina) from total RNA.

tag: condition

value: NH


title: NH1


title: 12560 MAT 1


title: 12560 PA 1

value: Patient-derived pancreatic cancer cells cultured in 3D PA hydrogel for 7 days


title: NH5


title: MPR7

value: MPR


title: 12560 2D 2


title: Il4F709_MMC9_bulkRNA-seq

description: Bulk RNAseq: IL4raY709F MMC9s: Following adoptive transfer model of food allergy, IL4raY709F small intestinal MMC9s from food allergic mice that that undergone 7 oral Ova challenges were isolated for RNAseq

source_name: Small intestinal  IL4raY709F MMC9

value: BALB/c

value: Small intestine

value: IL-4RaY709F (IL-4RA gain of function mutant)


title: 12975 SPH 2


title: 12560 2D 1


title: MPR6


title: WT_MMC9_bulkRNA-seq

description: Bulk RNAseq: WT MMC9s: Following adoptive transfer model fo food allergy, WT small intestinal MMC9s from food allergic mice that that undergone 7 oral Ova challenges were isolated for RNAseq

value: WT


title: 12975 PA 2


title: 12560 PA 2


title: 12556 SPH 2


title: 12975 PA 1


title: M-LMSC

city: suzhou

first: Zhiyuan

last: Zheng

address: 199,Ren ai Road

institute: Soochow University

description:
MMTV-PyMT
4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat(version:2.0.9).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after TopHat alignment, and then normalized by TMM (trimmed mean of M values) method. Finally, the FPKM value of each gene was calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample ...

source_name: lung MSCs

growth_protocol: LMSCs were cultured in DMEM medium supplemented with 10% FBS, 2 mM glutamine, 100 U/ml penicillin, and 100 g/ml streptomycin (all from Invitrogen).

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung derived mesenchymal stromal cells

value: lung

tag: tumor progress

value: M-LMSC

value: 13 week


title: MPR5


title: MPR4


title: NH4


title: A-LMSC

description:
MMTV-PyMT
2

value: A-LMSC

value: 7 week


title: NH3


title: 12560 SPH 1

value: Pancreatic adenocarcinoma

value: cells


title: 12556 MAT 2

value: Patient-derived pancreatic cancer organoids cultured in Matrigel for 7 days


title: 28d_RNA-seq_rep2

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases..
Then sequence quality was verified using fastp. We used HISAT2 to map reads to the genome of Solanum lycopersicum (Version: V3.2) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit by perl scripts in house.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Genome_build: Excel files include FPKM values for each Sample
Supplementary_files_format_and_content: fastq files are the raw date of RNA-seq and m6A MeRIP-seq

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: All plants were grown in greenhouse under a long day condition (16-h-light/8-h-dark) at 26°C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately more than 200 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into ~100-nt-long oligonucleotides using divalent cations under elevated temperature. Then the cleaved RNA fragments were subjected to incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) supplemented with BSA (0.5 μg μl−1). The mixture was then incubated with protein-A beads and eluted with elution buffer (1 × IP buffer and 6.7mM m6A). Eluted RNA was precipitated by 75% ethanol. Eluted m6A-containing fragments (IP) and untreated input control fragments are converted to final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was ~100±50 bp.
And then we performed the paired-end 2×150bp sequencing on an Illumina Novaseq™ 6000 platform at the LC-BIO Bio-tech ltd (Hangzhou, China) following the vendor's recommended protocol.

tag: cultivar

value: Micro-Tom

tag: state

value: 28-day-growth tomato fruit

value: The equatorial plate of tomato fruit

tag: time point


title: 28d_RNA-seq_rep1


title: MPR1

value: MPR


title: 12556 PA 2

value: Patient-derived pancreatic cancer cells cultured in 3D PA hydrogel for 7 days


title: PM-LMSC

description:
MMTV-PyMT
3

value: PM-LMSC


title: COVID4

value: COVID


title: COVID3


title: 12556 PA 1


title: 28d_m6A MeRIP-seq_rep1


title: 20d_RNA-seq_rep2

value: 20-day-growth tomato fruit


title: 20d_RNA-seq_rep1


title: COVID1


title: 20d_m6A MeRIP-seq_rep2


title: 12556 2D 1

value: Patient-derived pancreatic cancer cells cultured on 2D polystyrene for 7 days


title: 12556 2D 2


title: 12975 PRI

source_name: Pancreatic adenocarcinoma

value: tumour piece

value: Primary pancreatic adenocarcinoma tumour


title: 12560 PRI


title: 12d_RNA-seq_rep2

value: 12-day-growth tomato fruit


title: 20d_m6A MeRIP-seq_rep1


title: 12556 SPH 1

value: Patient-derived pancreatic cancer cells cultured in suspension for 7 days


title: MPR2