title: Glyceoll II 24 hour-set 3

value: WT

value: Glyceoll II 24 hour


title: GFP Low, clone B

status: Public on Sep 30 2024

type: SRA

city: Santa Cruz

first: Susan

last: Carpenter

state: CA

address: Red Hill Rd, Biomedical Sciences

department: MCD

country: USA

institute: UC Santa Cruz

description:
GFPlo_B
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

library_source: other

data_processing:
for i in *fastq.gz; do name=$(basename $i); cutadapt -j 24 -a GTTTAAGAGCTAAGCTGGAAACAGCATAGCA -o "${name%%_S*}"_trimmed.fastq.gz  "$i" ;done
mageck count -l lib7_Mageck_format.txt -n LPS_HiLo --sample-label hi_A,hi_B,hi_C,lo_A,lo_B,lo_C,LPS_A,LPS_B,LPS_C --fastq GFPhi_A_trimmed.fastq.gz GFPhi_B_trimmed.fastq.gz GFPhi_C_trimmed.fastq.gz GFPlo_A_trimmed.fastq.gz GFPlo_B_trimmed.fastq.gz GFPlo_C_trimmed.fastq.gz yesLPS_A_trimmed.fastq.gz yesLPS_B_trimmed.fastq.gz yesLPS_C_trimmed.fastq.gz
Bin <- c('lo','hi') binStartQ <- c(0.001, 0.799); binEndQ <- c(0.20, 0.999);  binStats <- data.frame(Bin,binStartQ,binEndQ); binStats$fraction = binStats$binEndQ - binStats$binStartQ; binStats$binStartZ = qnorm(binStats$binStartQ); binStats$binEndZ = qnorm(binStats$binEndQ)
guideLevelStats = findGuideHitsAllScreens(experiments = unique(binReadMat["expt"]),                                             countDataFrame = binReadMat, binStats = binStats,                                             sortBins = c("lo", "hi"), unsortedBin = "LPS",                                            negativeControl = "isNontargeting")
PMA analysis: DESeq2 log2fold change was determined for each guide between noPMA and PMA_day_11. PMA_day_11 was removed from analysis due to low coverage. Sets of guides that target a specific gene were compared via Mann Whitney U with log2fold change as the input.
Assembly: Hg19
Supplementary files format and content: lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.
Supplementary files format and content: LPS_HiLo.count.txt; raw counts of guide RNAs from mageck count function for LPS Screen.
Supplementary files format and content: PMA.count.tsv
Supplementary files format and content: All_genes_UnsortedBackground.tsv; MAUDE significance testing output by sample from LPS experiment.
Supplementary files format and content: 5kb_hicFindTADs_domains.bed; TAD calls from HiCExplorer hicFindTads function against Hg38.
Supplementary files format and content: chr_THP1.Ctrl_5kb.cool; Cool file for canonical chromosomes generated with cooler cload pairs function against Hg38.

molecule: other

organism: Homo sapiens

growth_protocol: All THP1 cell lines were cultured in RPMI 1640 supplemented with 10% low-endotoxin fetal bovine serum (ThermoFisher), 1X penicillin/streptomycin, and incubated at 37°C in 5% CO2.

extract_protocol:
Flow cytometry and PCR amplification of genomic sgRNA sequences were conducted as previously described in detail in https://doi.org/10.1016/j.celrep.2020.108541.
10 sgRNAs were designed for each TSS of hg19 annotated lncRNAs expressed in THP1s at baseline and upon stimulation. The sgRNA library also included 700 non-targeting control sgRNAs, and sgRNAs targeting 50 protein coding genes as positive controls. The sgRNA library was designed and cloned as previously described in DOI: 10.1126/science.aah7111
Guide-Seq

treatment_protocol: Library infected and selected THP1-NFkB-EGFP-CRISPRi-sgRNA cells were expanded to 2000X coverage. Cells were stimulated with LPS (200 ng/mL) for 24 h to induce expression of NFkB-EGFP.

tag: cell line

tag: cell type

value: human leukemia monocytic cells

tag: clonal line

value: clone B

tag: treatment

value: 24h LPS

tag: sorted population

value: GFP Low


title: Clinical isolate 60

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

library_source: transcriptomic

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 20 –max-intronlen 3000 --rna-strandness RF
Properly oridented reads and mapped to maximum three locations were extracted using samtools (version: 1.11)
Transcriptome assembly on these aligned reads were performed using StringTie version 2.1.4 with parameters --fr -m 150 -j 3 -g 20.  Each assembled transcripts were quantified by same version of Stringtie with e options.
Assembly: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary files format and content: Comma-delimited text file includes TPM values assembled transcripts for each samples

molecule: total RNA

organism: Plasmodium falciparum

source_name: packed red blood cells

growth_protocol: Material has been obtained from in vivo clinical samples.

extract_protocol:
8 volumes of TRIzol reagent (Invitrogen) (v/v) were added to 0.5 ml infected packed red blood cells. Samples were vortexed at 7000 RPM for 1 min. Chlorophorm was added in 1:5 volumetric ratio, vortexed and samples were centrifuged for 15 min to separate phases as previously described (2,3). Supernatant was aspirated and transferred to the new tubes. Equal volume of 100% ethanol was added to the supernatant and RNA was extracted using ZYMO DirectZol-96 RNA kit (ZYMO) following manufacturer instructions. RNA was eluted in 17 ul of RNAse/DNAse free water, and its purity was assessed by spectrometry on Nanodrop (Thermo Scientific). RNA concentration was estimated using RNA-specific Qubit fluorometric assay (Invitrogen). RNA integrity was assessed on Bioanalyzer RNA Nano Chip (Agilent).
RNA sequencing libraries have been prepared from 100 ng of purified total RNA using ZYMO-Seq RiboFree Total RNA Library Kit (ZYMO) following manufacturer’s instructions with some modifications to the protocol described below. This protocol allows for generation of stranded, rRNA and human globin depleted libraries. Whole protocol has been scaled down to use half of the recommended volume of each reagent. Depletion step of rRNA (both human and the parasite) and globin has been adjusted to 4 hours at 68oC. 14 cycles of PCR have been used for final index incorporation. Resulted libraries have been eluted in 15ul of the elution buffer and verified by real-time PCR, fluorometric DNA concentration assay (Invitrogen) and Bioanalyzer DNA High-Sensitivity chip (Agilent Technologies) by Novogene Singapore. 96 libraries (total RNA) have been equimolarly pooled and sequenced per one lane of Novaseq S4 sequencing technology (Illumina) generating approximately 750GB data per lane (Novogene, Singapore). Technical replicates of 3D7 lab strain gDNA/RNA were also included on each sequencing lane to control for library preparation and sequencing efficiency.

treatment_protocol: Patients were randomly assigned (1:1) to one of two treatments using block randomisation, depending on their location: in Thailand, Cambodia, Vietnam, and Myanmar patients were assigned to either dihydroartemisinin-piperaquine or dihydroartemisinin-piperaquine plus mefloquine; at three sites in Cambodia they were assigned to either artesunate-mefloquine or dihydroartemisinin-piperaquine plus mefloquine; and in Laos, Myanmar, Bangladesh, India, and the Democratic Republic of the Congo they were assigned to either artemether-lumefantrine or artemether-lumefantrine plus amodiaquine. All drugs were administered orally and doses varied by drug combination and site.

tag: time point

value: packed red blood cells

value: Prior to ACT/TACT treatment


title: 18hr_rpt2 miRNA

city: Ultimo

first: Dayna

last: Sais

state: New South Wales

address: 15 Broadway

country: Australia

institute: University of Technology Sydney

description:
fhe_miRNA_rawcount_matrix.txt
mmu_miRNA_rawcount_matrix.txt

data_processing:
Single end reads were sequenced, each samples was run in two lanes resulting in two Fastq files (L001 and L002), which were merged before processing. The quality of the miRNA seq and total RNA seq raw Fastq files was assessed using FastQC v0.11.9, and adapters were removed using Cutadapt v1.12. For miRSeq fastq files, reads with lengths <18bp and >26bp were discarded also using Cutadapt. The mature miRNA sequences of Mus musculus were retrieved from miRbase (Release 22.2) and were used to build the index for alignment using Bowtie2 and miRSeq reads were aligned to the mature M. musculus miRNAs. MiRNA seq reads that did not align against the M. musculus miRNAs were then aligned against all published miRNA sequences for F. hepatica derived from miRBase version 21 repositorry [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021 using Bowtie version 1.3.0. Counts for M. musculus and F. hepatica miRNAs were extracted from the resultant Sam files using SamTools. For Total RNA sequencing the Mus musculus genome sequences (GRCm39.genome.ensembl release 108) were retrieved from Gencode (Release M31) and was used to build the index for alignment using Bowtie2. Counts for Mus musculus mRNA and lncRNAs were extracted using Gencode (Release M31) annotation files and HT-Seq count.
Assembly: mm10
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu miRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu mRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for mmu lncRNAs for each sample
Supplementary files format and content: tab-deliminated text files include the raw counts for fhe miRNAs for each sample

organism: Mus musculus

source_name: peritoneal macrophage

extract_protocol:
Total RNA was harvested from five replicates for each timepoint using RNAzol (Molecular Research Centre) according to manufactureres instructions. For construction of sequencing libraries, 2ug of totoal RNA was use for miRNA-seq and 1.5ug total RNA for RNA seq.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA prep with RiboZero Plus kit (35M reads/sample) and for miRSeq using Qiaseq miRNA prep kit (75M reads/sample)  following manufacturers insctructions.

value: peritoneal macrophage


title: 18hr_rpt1 miRNA


title: NSIP-B1 | 003 | Full ROI

city: London

first: Marco

last: Mura

state: Ontario

address: 800 Commissioners Road E

department: Medicine, Respirology

country: Canada

institute: Western University

data_processing:
Probe count and sample metadata files were obtained from GeoMx DSP control center/v3.0.0.113. standR package was used to perform data exploration and normalization (Liu et al 2023 NAR).
Raw or log2 normalized count output from 'assay' function of standR package
Assembly: hg38
Supplementary files format and content: DCC: output from GeoMX NGS pipeline (Nanostring)

source_name: Lung

growth_protocol: not applicable

extract_protocol:
FFPE sections underwent immunofluorescence with morphology markers (DNA SYTO 13, pan-cytokeratin Alexa Fluor 532, alpha-smooth muscle actin PE-Cy5, and CD45 Alexa Fluor 593) to locate lung microenvironments of interest
in situ RNA probes conjugated to barcodes by a photocleavable linker were hybridized to the sections
Regions of interest were exposed to UV light to decouple the barcoding oligo from RNA probes. Decoupled oligos were collected, indexed by ROI location, and sequenced on Nextseq 1000/2000. GeoMx NGS pipeline (Illumina) was used to produce DCC files from FASTQ files on the GeoMX DSP software.

treatment_protocol: not applicable

tag: tissue

value: Lung

tag: patient id

tag: annotation

value: peripheral

tag: condition

value: NSIP

tag: roi replicate

tag: anno

tag: patid

tag: disease

value: Y

tag: batch

value: first

tag: type

tag: anno type

tag: outcome

value: Bad


title: Glyceoll II 24 hour-set 2

city: New Orleans

first: Elizabeth

middle: Carol

last: Martin

state: LA

address: 1430 Tulane Avenue

department: Medicine

institute: Tulane University

data_processing:
The sequencing reads which contained low-quality, adaptor-polluted and high content of unknown base (N) reads, were removed prior to further downstream  analyses
After reads filtering,  clean reads were mapped to reference human genome using HISAT. On average 88.91% reads are mapped, and the uniformity of the mapping result for each sample suggests that the samples are comparable.
Assembly: not provided
Supplementary files format and content: Data files represent differentially expressed genes as detected by RSEM, gene expression values are identiifed by TPM. Gene change is Log2 fold change with phytocompound as numerator and vehicle control as denominator

molecule: polyA RNA

source_name: cell line

extract_protocol:
Extracted RNA was quantified and assessed for integrity using a Bioanalyzer (Agilent Technologies, Santa Clara, CA). The total RNA was extracted using a Direct-zol RNA purification kit (Zymo research, Irvine, CA).
The mRNA was then purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces. The fragmented mRNA was synthesized into first-strand cDNA using random primers. The second strand of cDNA was synthesized with dUTP instead of dTTP. The cDNA thus synthesized was subjected to end-repair and 3′ adenylation. Subsequently, adaptors were ligated to the ends of this 3 ′ adenylated cDNA fragments. U-labeled second-strand template was digested with Uracil-DNA-Glycosylase (UDG) and PCR amplification was performed and sequencing on the DNBSEQ (DNBSEQ Technology) platform was performed

value: cell line

tag: cell line

tag: cell type

value: Breast cancer

tag: genotype


title: NSIP-B1 | 002 | Full ROI


title: 6hr_rpt5 miRNA

tag: treatment


title: GFP High, clone C

description:
GFPhi_C
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

tag: clonal line

value: clone C

tag: sorted population

value: GFP High


title: Glyceoll II 24 hour-set 1

tag: tissue

value: WT

value: Glyceoll II 24 hour


title: NSIP-B1 | 001 | Full ROI

tag: patient id

tag: annotation


title: 6hr_rpt4 miRNA


title: 18hr_rpt4 miRNA


title: Glyceoll I 24 hour-set 3

value: Glyceoll I 24 hour


title: GFP High, clone A

description:
GFPhi_A
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: human leukemia monocytic cells

value: clone A

value: 24h LPS


title: miRNA_keloid3

city: Shanghai

first: Jiayi

last: Mao

address: Zhi Zao Ju road

country: China

institute: shanghai ninth people's hospital

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low-quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. T
The reads without 3’adapter and insert tag, the reads shorter than 15 nt and longer than 41nt from the raw data were filtered, and the clean reads were obtained.
Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs).
These RNAs were aligned and then subjected to the BLAST [ 1 ] search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam) [2] and GenBank databases (http://www.ncbi.nlm.nih.gov/genbank/).
The known miRNAs were identified by aligning against miRBase v.21 database (http://www.mirbase.org/)
Assembly: Differentially expressed miRNAs were identified with the threshold of p value < 0.05. While the p value was calculated with DEG algorithm [5] in the R package for experiment with biological replicates, and with Audic Claverie statistic [6] for experiment without biological replicates.
Supplementary files format and content: The targets of differentially expressed miRNAs were predicted by using software miranda [7] in animal, with the parameter as follows: S ≥ 150 ΔG ≤ −30 kcal/mol and demand strict 5' seed pairing
Supplementary files format and content: targetfinder[8] was used for miRNA target prediction

source_name: skin

extract_protocol:
a. Add 5 μl total RNA (1 μg) and 1 μl RNA 3’Adapter to a new nuclease-free PCR tube on ice. Gently pipette the entire volume up and down 6 times to mix thoroughly. b. Incubate the tube at 70°C for 2 mins and then immediately place the tube on ice. c. Prepare the following mix in a new, nuclease-free PCR tube on ice. (Ligation Buffer 2, RNase Inhibitor 1, T4 RNA Ligase 2, Deletion Mutant 1, Total Volume 4).  d.Add 1 μl Stop Solution (STP) and gently pipette the entire volume up and down to mix thoroughly. Continue to incubate the reaction tube on the thermal cycler at 28°C for 15 mins and then immediately place the tube on ice. e. Add 1 μl of RNA 5’ Adapter to a new, nuclease-free 0.2 ml PCR tube. Incubate the tube at 70°C for 2 mins and then immediately place the tube on ice. f. Prepare the following mix in a tube on ice. g. Add 3 μl of the mix to the reaction from step d. Gently pipette the entire volume up and down to mix thoroughly. Incubate the tube at 28°C for 1 hour and then immediately place the tube on ice.
Load 1 μl sample on an Agilent Technologies 2100 Bioanalyze.

value: skin

tag: disease state

value: keloid


title: CHP-A3 | 012 | Full ROI

value: Lung

value: neutral

tag: condition

value: CHP

tag: roi replicate

tag: anno

value: Good


title: 6hr_rpt3 miRNA

value: peritoneal macrophage


title: GFP Low, clone A

description:
GFPlo_A
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: GFP Low


title: Glyceoll I 24 hour-set 2

value: cell line

value: Breast cancer


title: miRNA_keloid2


title: CHP-A3 | 011 | Full ROI

tag: patid

tag: disease

value: Y

tag: batch

value: first


title: 6hr_rpt1 miRNA


title: 6hr_rpt2 miRNA


title: Glyceoll I 24 hour-set 1

value: WT


title: CHP-A3 | 010 | Full ROI

tag: type

tag: anno type

tag: outcome


title: miRNA_Ctrl2

value: healthy

tag: genotype


title: CHP-A3 | 008 | Full ROI

value: fibrosis


title: GLY 24 hour-set 3

tag: cell line

tag: cell type

tag: treatment

value: GLY 24 hour


title: miRNA_keloid1

tag: tissue


title: GLY 24 hour-set 2


title: CHP-A3 | 009 | Full ROI

tag: patient id


title: miRNA_Ctrl3


title: D0_rpt5 miRNA

value: Uninfected


title: GFP High, clone B

description:
GFPhi_B
LPS_HiLo.count.txt
All_genes_UnsortedBackground.tsv
lib7_Mageck_format.txt; Library of guides and target genes in Mageck compatible format.

value: human leukemia monocytic cells

tag: clonal line

value: clone B

value: 24h LPS

tag: sorted population

value: GFP High


title: D0_rpt4 miRNA


title: CHP-A3 | 006 | Full ROI

value: Lung

tag: annotation

value: inflammatory

tag: condition

value: CHP


title: CHP-A3 | 005 | Full ROI

tag: roi replicate

tag: anno

value: Good


title: Daidzein 24 hour_set 2

value: cell line

value: Daidzein 24 hour


title: D0_rpt1 miRNA

value: peritoneal macrophage


title: CHP-A3 | 007 | Full ROI

tag: patid

tag: disease

value: Y

value: first


title: D0_rpt3 miRNA


title: Daidzein 24 hour_set 1

value: Breast cancer

value: WT


title: miRNA_Ctrl1

value: skin

tag: disease state

value: healthy


title: Daidzein 24 hour_set 3


title: CD11c_CGRP_3 [Jointmac13797728]

city: Cambridge

first: Tetsuo

last: Hasegawa

address: Francis Crick Ave

country: United Kingdom

institute: University of Cambridge

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797728

data_processing:
Fastq files from sequencing libraries were trimmed of the first 3 nucleotides of the R1 strand. Contaminating adaptor sequences and poor-quality bases were removed using Trim Galore (Babraham bioinformatics). Libraries were only trimmed for quality.
Quality of resulting files were assessed by FastQC and aligned to the mm10 genome using HISAT2, followed by gene-level quantification using the Featurecount function from the Rsubread package in R.
Assembly: mm10
Supplementary files format and content: Raw counts matrix (txt) - individual libraries
Supplementary files format and content: Raw counts matrix (txt) - combined

source_name: Synovium

extract_protocol:
RNA extraction was performed using RNeasy plus mico kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA contamination was removed using Optimal DNA depletion columns (Qiagen).
Libraries were prepared using the SMARTer stranded total RNAseq mammalian pico input kit (Takara) according to the manufacturer’s instructions. 5 ng of total RNA was used for production of libraries.
Total RNA-seq, 2 x 150bp paired-end sequencing performed on Novaseq6000 (Illumina)

value: Synovium

value: Macrophages

value: CGRP


title: D0_rpt2 miRNA

value: Uninfected


title: CD11c_CGRP_2 [Jointmac13797727]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797727


title: GLY 24 hour-set 1

value: GLY 24 hour


title: ST-00020824-M

city: Portland

first: Rosalie

last: Sears

state: OR

address: 2730 SW Moody Ave, CL4RS

department: Molecular and Medical Genetics

institute: Oregon Health & Science University

description: Metastisis to the Liver

data_processing:
Paired-end fastq sequences were trimmed using trim-galore (ver 0.6.3) and default parameters.
Pseudoalignment was performed with kallisto (ver 0.44.0) using genome assembly GRCh38.p5 and gencode (ver 24) annotation using default parameters.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create gene level counts and abundances (TPMs).
Quality checks were assessed with FastQC (ver 0.11.8) and MultiQC (ver 1.7).
Assembly: GRCh38.p5
Supplementary files format and content: Gene level count estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Gene level TPM estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Per sample h5 file output from the kallisto pipeline is provided.
Supplementary files format and content: Gene level TMM normalized (edgeR method) estimates are provided as a matrix in tab delimited text format. Feature annotations are provided in the first few columns as well as a column with expression level filtering status. The TMM gene level estimates provided are not log scaled and are generated from the h5 files using general recommendations for importing from the kallisto method as given here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto & https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR

source_name: Liver

extract_protocol:
Starting with sectioned FFPE PDAC specimen blocks, Clinical pathologists marked regions of high tumor content (>20% ratio of tumor to normal nuclei) on H&E stained slides for RNA extraction. Solid tumor total nucleic acid was extracted from these tumor regions on adjacent FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
100ng of RNA for each tumor sample was heat fragmented in the presence of magnesium to an average size of 200 bp. Library preps were hybridized to the xGENExome Research Panel v1.0 (Integrated DNA Technologies) and target recovery was performed using Streptavidin-coated beads, followed by amplification with the KAPA HiFi Library Amplification Kit.

tag: tumor type

value: Met

value: Liver

value: scraped tumor


title: HeLa cells, siVIM-270_3G>FA

city: Bunkyo-ku

first: Seongjin

last: An

state: Tokyo

department: Graduate School of Frontier Science

country: Japan

institute: The University of Tokyo

description: Gene Expression

data_processing:
RNA-Seq data was mapped using Hisat2 (v2.2.1)
Gene expression levels were quantified as transcripts per million (TPM) using featureCounts (v2.0.1) with default settings.
Assembly: The RNA-Seq data was mapped against the human genome sequence using the GRCh38 assembly, release 105, from Ensembl.
Supplementary files format and content: The processed data files are provided in Excel (.xlsx) format. The content includes gene expression levels quantified as transcripts per million (TPM).
The file contains the following columns: Gene name, TPM values

source_name: cervical cancer

growth_protocol: A HeLa cell suspension (0.5 x 10^5 cells/mL) was inoculated into a well of 24-well culture plate 1 day before transfection.

extract_protocol:
Total RNA was purified using FastGene RNA Premium Kit (NIPPON Genetics) and the quality of the total RNA was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and a Bioanalyzer (Agilent Technologies).
Total RNAs were extracted from HeLa cells for RNA-seq analysis. The RNA libraries for RNA-seq were prepared using the DNBSEQ-G400 Platform (BGI)

treatment_protocol: Cells were transfected with 50 nM of each siRNA using 2 µL of Lipofectamine 2000 (Thermo Fisher Scientific). At 24 h post-transfection, cells were harvested from two wells per one sample.

value: cervical cancer

value: HeLa

value: cervical cancer cells


title: CHP-A3 | 002 | Full ROI

value: Lung

value: granuloma

value: CHP

value: Y

tag: batch

tag: type

tag: anno type

tag: outcome

value: Good


title: HeLa cells, siVIM-270

description: Gene Expression

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment


title: IAIE_CGRP_3 [Jointmac13797725]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797725

tag: tissue

value: Synovium


title: CD11c_CGRP_1 [Jointmac13797726]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797726

value: Macrophages


title: ST-00020944-M

description: Metastisis to the Liver


title: HeLa cells, Mock

description: Gene Expression

value: Mock


title: Unclassifiable-A5 | 013 | Full ROI

tag: patient id

tag: annotation

value: neutral

value: UNC

value: first


title: ST-00020630-T

description: Primary pancreas tumor

source_name: Pancreas

value: Primary

value: Pancreas


title: CHP-A3 | 004 | Full ROI

value: inflammatory

tag: condition

tag: roi replicate


title: ST-00021060-F

description: Primary pancreas tumor

value: scraped tumor


title: Unclassifiable-A5 | 011 | Full ROI

tag: anno

tag: patid


title: CHP-A3 | 003 | Full ROI

tag: disease


title: HeLa cells, siVIM-270_8C>FA

description: Gene Expression

value: cervical cancer

value: HeLa

value: cervical cancer cells


title: IAIE_CGRP_1 [Jointmac13797723]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797723

value: CGRP


title: ST-00020482-T

description: Primary pancreas tumor

tag: tumor type


title: Unclassifiable-A5 | 010 | Full ROI

value: Lung

value: fibrosis

value: Y

tag: batch


title: SH-SY5Y cells, Control RA

city: Bangkok

first: Anchalee

last: Prasansuklab

address: Sabbasastravicaya Building (11th floor), Soi Chulalongkorn 62, Phyathai Road, Pathumwan

country: Thailand

institute: College of Public Health Sciences, Chulalongkorn University

data_processing:
Sequencing data is called raw reads or raw data, and quality control (QC) is then performed on the raw reads to determine whether the sequencing data is suitable for subsequent analysis. After quality control, the filtered clean reads were aligned to the reference sequence. The software SOAPnuke developed by BGI was used for sequencing data filtering. After the alignment, the statistics of the mapping rate and the distribution of reads on the reference sequence are used to determine whether the alignment result passes the second QC of alignment. Then, gene quantification analysis and other analysis based on gene expression were performed.
Assembly: GRCh38.p13 (GCF_000001405.39)
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: Human neuroblastoma SH-SY5Y cells were maintained in DMEM containing 10% FBS and antibiotics (100 U/mL penicillin and 100 µg/mL streptomycin) and grown at 37˚C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was harvested using GENEzol reagent (Geneaid) and was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by the following steps: 1) used oligo dT beads to enrich and purify mRNA with poly A tail; 2) fragmented the RNA and generated the first-strand cDNA using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP; 3) subjected the synthesized cDNA to end-repair and 3' adenylated addition, then adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) selectively degraded the dUTP-marked strand by Uracil-DNA-Glycosylase(UDG), then amplified the remaining strand to generate a cDNA library suitable for sequencing; 5) denatured the PCR product by heat and the single strand DNA was cyclized by splint oligo and DNA ligase; 6) synthesized DNA nanoball; 7) performed sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Neuronal differentiation was induced by the treatment of 10 µM retinoic acid in DMEM containing 1% FBS for 24 h. After that differentiated cells were treated with 1 µM B[a]P alone ot in combination with 25 µg/mL ACEE for an additional 48 h.

value: neuroblastoma cells

value: retinoic acid


title: CD11c_Healthy_3 [Jointmac13797719]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797719

value: Synovium

value: Macrophages

value: Control


title: CHP-A3 | 001 | Full ROI

value: granuloma

value: CHP

value: first

tag: type

value: Good


title: IAIE_CGRP_2 [Jointmac13797724]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797724


title: Unclassifiable-A5 | 009 | Full ROI

value: UNC

tag: anno type


title: SH-SY5Y cells, RA_PAH_ACEE

value: retinoic acid and B[a]P and ACEE


title: ST-00020385-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: ST-00020904-T

description: Primary pancreas tumor


title: ST-00020341-T

description: Primary pancreas tumor


title: Unclassifiable-A5 | 007 | Full ROI

value: Lung

value: lymphoid

tag: outcome


title: SH-SY5Y cells, RA_PAH

tag: cell line

value: retinoic acid and B[a]P


title: ST-00021340-F

description: Primary pancreas tumor

tag: cell type


title: ST-00020926-F

description: Primary pancreas tumor


title: ST-00019945-T

description: Primary pancreas tumor


title: ST-00019682-T

description: Primary pancreas tumor


title: CD11c_Healthy_2 [Jointmac13797718]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797718

tag: genotype


title: CD11c_Healthy_1 [Jointmac13797717]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797717

tag: treatment


title: IAIE_Healthy_3 [Jointmac13797716]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797716

tag: tissue


title: SKNBE2_METTL3KD_plusRA_rep1

city: Göteborg

first: Tanmoy

last: Mondal

address: Bruna stråket 16

department: Department of Laboratory Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Single-end m6A-RIP sequencing data obtained from SMARTer-Stranded Total RNA-Seq Kit v2 was processed using FastQC v0.11.9  and Trim Galore v0.6.6 for quality control. Trimmed reads were mapped to the GRCh38 reference genome using HISAT2 v2.2.1 preserving strand information (parameters -U –rna-strandness F). Uniquely mapping reads were filtered after duplicate removal and filtering using markDuplicates from PIcard v2.23.5 and Sambamba v0.7.1, respectively.
Assembly: GRCh38
Supplementary files format and content: featureCounts matrix for RNA-seq counts
Supplementary files format and content: bigwig files for m6A-RIP, ChIP-seq coverage
Supplementary files format and content: narrowPeak files for m6A-RIP, ChIP-seq peak-calling

growth_protocol: h9 hESC (human embryonic stem cells) were cultured on Matrigel coated plates with iPS-Brew XF (StemMACS; Miltenyi, 130104368) media. To differentiate hESC to trunk neural crest cells (tNCC), hESC were dissociated using Accutase and seeded (day 0) on Matrigel coated plates to induce differentiation to neuromesodermal progenitor cells (NMP, day 3) which were then driven to tNCC (days 7-9), sympathoadrenal precursors (SAP, day 12), and further towards sympathetic neurons (SN, day 19) as previously described (Frith, T.J.R. and Tsakiridis, A. Curr Protoc Stem Cell Biol, 49, e81, 2019). For neural crest stem cellc (NCSC) induction, hESCs were dissociated using Accutase and seeded (day 0) on Matrigel coated plates at a density of 2x104 cells/cm2 in iPS-Brew XF media with ROCK inhibitor (Y-27632 10 μM). Following induction day 1, media was replaced to NCSC differentiation medium without ROCK inhibitor as previously described (Menendez, Kulik et al., Nat Protoc. 2013). NCSC differentiation medium was replaced every 2 days and cells were passaged on Matrigel coated plates after 3-4 days of reaching 90% confluency. SHEP cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin. SK-N-BE(2) cells were cultured in DMEM/F-12 media supplemented with 10% FBS, 1x GlutaMAX, and penicillin/streptomycin. All the cells were confirmed to be mycoplasma-negative using the MycoAlert Mycoplasma detection assay (Lonza, LT07218) and maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
RNA for RNA-seq and m6A RIP-seq was extracted from cells using using TRIZOL reagent (ThermoFisher Scientific, 15596026) and Direct-zol RNA Miniprep (ZYMO research, R2050). For ChIP-seq cells were fixed with formaldehyde (1% final concentration) for 15 min at RT. Fixed cells were washed with cold PBS, lysed and the chromatin was sheared using a Bioruptor (Diagenode) until an average fragment size range of 200-500 bp was achieved. Immunoprecipitation of solubilized chromatin was carried out with 3 µg of METTL3 MYCN / H3K27ac antibody overnight at 4°C. The immunoprecipitated complex was captured using a mix of Protein A and G Dynabeads (Invitrogen), washed and RNase A treated before eluting the DNA. The ChIP DNA was directly used to make libraries.
m6A-RIP-seq: RNA was isolated using TRIZOL reagent (Invitrogen). RNA fragmentation followed by m6A-RIP was performed with 15ug of RNA spiked-in with 9 ng of Bacterial RNA. Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian) from Takara and single-end sequenced (1X 88 bp) on Illumina NextSeq 2000 platform. RNA-seq: Short-insert libraries were prepared at BGI Tech Solutions (Hong Kong) for strand specific mRNA sequencing on a DNBSEQ platform with a PE100 sequencing read length. ChIP-seq: ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, E7645L following manfactures protocol.

treatment_protocol: MYCN induction in SHEP cells was carried out by addition of 200 ng/ml of Doxycycline for 24h

tag: antibody


title: SKNBE2_Controlsh_plusRA_rep2


title: IAIE_Healthy_2 [Jointmac13797715]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797715


title: ST-00020285-T

description: Primary pancreas tumor


title: ST-00019590-T

description: Primary pancreas tumor


title: SKNBE2_Controlsh_plusRA_rep1


title: Unclassifiable-A5 | 008 | Full ROI

tag: patient id

tag: annotation

value: fibrosis

value: Y


title: IAIE_Healthy_1 [Jointmac13797714]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13797714

value: Synovium


title: Lyve1_IC_3 [Jointmac13451011]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451011

value: Macrophages

value: IC


title: Unclassifiable-A5 | 004 | Full ROI

tag: condition

tag: roi replicate

value: fibroblast


title: SKNBE2_METTL3KD_rep2


title: SKNBE2_METTL3KD_plusRA_rep2


title: Unclassifiable-A5 | 003 | Full ROI

tag: anno

tag: patid


title: SKNBE2_METTL3KD_rep1


title: IAIE_IC_3 [Jointmac13451009]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451009


title: ST-00020291-T

description: Primary pancreas tumor

tag: tumor type


title: ST-00019601-T

description: Primary pancreas tumor


title: Unclassifiable-A5 | 001 | Full ROI

tag: disease

tag: batch


title: ST-00019601-M

description: Metastisis to the Duodenum

source_name: Duodenum

value: Met

value: Duodenum


title: Unclassifiable-A5 | 006 | Full ROI

value: first

tag: type

tag: anno type

value: Good


title: tNCC_METTL3KD_rep2

source_name: tNCC

value: tNCC


title: ST-00019429-M

description: Metastisis to the Duodenum


title: CD11c_IC_2 [Jointmac13451007]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451007


title: SKNBE2_Controlsh_rep1


title: UIP-A10 | 012 | Full ROI

value: neutral

value: IPF

tag: outcome


title: Unclassifiable-A5 | 005 | Full ROI

value: UNC


title: UIP-A10 | 011 | Full ROI

value: Lung


title: IAIE_IC_2 [Jointmac13451006]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451006

tag: cell type


title: ST-00019429-T

description: Primary pancreas tumor

value: Primary

value: Pancreas

value: scraped tumor


title: UIP-A10 | 010 | Full ROI

value: Y


title: tNCC_Controlsh_rep2


title: ST-00019458-T

description: Primary pancreas tumor


title: tNCC_METTL3KD_rep1


title: Lyve1_IC_1 [Jointmac13451005]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451005

value: Synovium

tag: genotype


title: UIP-A10 | 009 | Full ROI

value: lymphoid


title: CD11c_IC_1 [Jointmac13451004]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451004

value: Macrophages

tag: treatment

value: IC


title: ST-00018525-T

description: Primary pancreas tumor

tag: tissue


title: tNCC_Controlsh_rep1

tag: antibody


title: UIP-A10 | 008 | Full ROI

tag: patient id


title: IAIE_IC_1 [Jointmac13451003]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451003


title: SKNBE2_Controlsh_rep2


title: ST-00019466-T

description: Primary pancreas tumor


title: Lyve1_IC_2 [Jointmac13451008]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451008


title: ST-00020281-M

description: Metastisis to the Liver

value: Met

value: Liver


title: UIP-A10 | 007 | Full ROI

tag: annotation

value: first


title: ES_stable_METTL3KD_812sh_NCSC_day7_rep1

source_name: NCSC

value: NCSC


title: UIP-A10 | 006 | Full ROI

value: fibrosis

tag: condition

value: Good


title: ST-00020323-M

description: Metastisis to the Omentum

source_name: Omentum

value: Omentum


title: IAIE_Healthy_3 [Jointmac13451000]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451000

value: Control


title: ES_stable_Controlsh_NCSC_day7_rep2


title: CD11c_Healthy_3 [Jointmac13451001]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451001


title: UIP-A10 | 005 | Full ROI

value: Lung

value: IPF

tag: roi replicate


title: ES_stable_Controlsh_NCSC_day7_rep1


title: ST-00020251-M

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Peritoneum


title: UIP-A10 | 004 | Full ROI

tag: anno


title: Lyve1_Healthy_2 [Jointmac13450999]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450999


title: Non-native rep_2

city: Srinagar

first: Mudasir

last: Zahoor

state: Jammu and Kashmir

address: Hazratbal, Srinagar

department: CIRI

country: India

institute: University of Kashmir

description: 2x100bp reads

library_source: genomic

data_processing:
Illumina HISeq platform was used to yield 2x100bp reads
Bisulfite DNA was denatured, annealed with random primers to get ssDNA. The ssDNA with terminal tagging oligo at 3'-end was used to synthesise double stranded DNA followed by PCR amplification of adapter tagged libraries.
Reads obtained were mapped using BatMeth2 with the reference genome.
Ratio of methylated reads to the total reads gave the estimation of methylation level of a specific cytosine.
Assembly: Reference based alignment
Supplementary files format and content: A wig. tiled data file (TDF) file for both native and non-native samples.

molecule: genomic DNA

organism: Erigeron canadensis

source_name: leaf tissue at flowering stage

extract_protocol:
Fresh leaf samples were collected from both native and non-native sites of Conyza canadensis. The young leaves collected were immediately frozen using liguid nitrogen and stored in -80 degrees till DNA extraction. Total DNA was extracted from both native and non-native leaf samples using plant DNA extraction kit (QIAGEN) and 10μg of DNA from all the four samples was send for whole genome bisulfite sequencing.
BS-Seq library construction and sequencing was performed on both native and non-native samples following manufacturers protocol.

value: leaf tissue at flowering stage

value: Plant cells

value: Wild type

value: Sodium busulfite


title: ST-00019171-M

description: Metastisis to the Duodenum

value: Duodenum

value: scraped tumor


title: ST-00019194-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: UIP-A10 | 003 | Full ROI

value: fibroblast

tag: patid

value: Y

value: first


title: Non-native rep_1

description: 2x100bp reads


title: UIP-A10 | 002 | Full ROI

value: Good


title: IAIE_Healthy_2 [Jointmac13450997]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450997

value: Synovium

value: Macrophages


title: Native rep_2

description: 2x100bp reads


title: UIP-A10 | 001 | Full ROI

value: Lung


title: ES_stable_METTL3KD_812sh_NCSC_day7_rep2

value: NCSC


title: Lyve1_Healthy_3 [Jointmac13451002]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13451002

value: Control


title: ST-00020218-T

description: Primary pancreas tumor

tag: tumor type


title: ST-00020232-M

description: Metastisis to the Retroperitoneum

source_name: Retroperitoneum

value: Met

value: Retroperitoneum


title: Lyve1_Healthy_1 [Jointmac13450996]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450996


title: Native rep_1

description: 2x100bp reads

value: leaf tissue at flowering stage

value: Plant cells

value: Wild type


title: C8_SN_MYCN_plusDOX_DMSO_rep1

data_processing:
Single-end m6A-RIP sequencing data obtained from SMARTer-Stranded Total RNA-Seq Kit v2 was processed using FastQC v0.11.9 and Trim Galore v0.6.6 for quality control. Trimmed reads were mapped to the GRCh38 reference genome using HISAT2 v2.2.1 preserving strand information (parameters -U –rna-strandness F). Uniquely mapping reads were filtered after duplicate removal and filtering using markDuplicates from PIcard v2.23.5 and Sambamba v0.7.1, respectively.
Assembly: GRCh38
Supplementary files format and content: featureCounts matrix for RNA-seq counts
Supplementary files format and content: bigwig files for m6A-RIP, ChIP-seq coverage
Supplementary files format and content: narrowPeak files for m6A-RIP, ChIP-seq peak-calling

source_name: C8 SN

value: C8 SN

tag: assay type


title: CD11c_Healthy_1 [Jointmac13450995]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450995


title: C8_SN_MYCN_plusDOX_DMSO_rep2


title: ST-00019056-T

description: Primary pancreas tumor

value: Primary

value: scraped tumor


title: ST-00020236-T

description: Primary pancreas tumor

value: Pancreas


title: IAIE_Healthy_1 [Jointmac13450994]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450994


title: hESC_h9_Input_ChIPseq_rep1

source_name: h9 hESC

value: h9 hESC


title: ST-00020217-T

description: Primary pancreas tumor


title: CD11c_IC_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070220

value: IC


title: ST-00021351-T

description: Primary pancreas tumor


title: tNCC_METTL3_ChIPseq_rep1

value: tNCC

value: METTL3 (Abcam, ab195352)


title: tNCC_K27ac_ChIPseq_rep1

value: H3K27ac (Abcam, ab4729)


title: CD11c_Healthy_2 [Jointmac13450998]

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13450998

value: Synovium

value: Macrophages


title: SHEP_plusDOX_METTL3_ChIPseq_rep1

source_name: SHEP

value: SHEP


title: tNCC_MYCN_ChIPseq_rep1

value: MYCN (Abcam, ab16898)


title: Lyve1_IC_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070218


title: CD11c_IC_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070217


title: SHEP_plusDOX_MYCN_ChIPseq_rep1


title: ST-00019043-M

description: Metastisis to the LymphNode

source_name: LymphNode

value: Met

value: LymphNode


title: IAIE_IC_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070216


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep6

type: RNA

city: Zurich

first: Darren

last: Gilmour

address: Winterthurerstrasse 190

department: Department of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R6

hyb_protocol: Following fragmentation and labeling as described in WT Terminal Labeling and Controls Kit of Affymetrix #901524, cDNA was hybridized on GeneChip Affymetrix Zebrafish Gene 1.0 ST Arrays for 16 hours at 45°C.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Affymetrix Power Tools (APT) was used to pre-process the microarray samples and the expression values for 'meta' probe sets were calculated using the Robust Microarray Analysis (RMA) normalization procedure. The probe sets were filtered using the detected above background (DABG) method available from Affymetrix Power Tools. The 'meta' probe sets with median DABG P value of <0.05 were retained if present in at least half of the replicate samples.

label: biotin

organism: Danio rerio

label_protocol: The standard protocol of Ambion WT Expression Kit (#4491974) was used for the synthesis of Biotinylated cDNA from 500ng of total RNA.

growth_protocol: Zebrafish (Danio rerio) strains were maintained using standard procedures (Westerfield, M. The Zebrafish Book 5th edn). Zebrafish embryos were raised at 26–30°C in E3 buffer. All zebrafish experiments were carried out on embryos younger than 3 day post-fertilization, following the principles and guidelines of the European Molecular Biology Laboratory and the European Commission, Directive 2010/63/EU.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Three experimental groups were treated as follows: 1) Wild type group (LLP_WT) from cldnb:lynGFP, cxcr4b:nls-tdTomato transgenics was treated with 10 μM RU486 and 0.1% DMSO. 2) FGF inhibition group (LLP_SU5402-FGFR1inh) derived from cldnb:lynGFP, cxcr4b:nls-tdTomato transgenics was treated with 1 μM SU5402, 0.1% DMSO and 10 μM RU486. 3) FGF induction group (LLP_FGFoverexp) as derived from cldnb:lynGFP, cxcr4b:nls-tdTomato, cxcr4b:LexPR, lexOP:Fgf3-GFP transgenics was treated with 10 μM RU486 and 0.1% DMSO.

value: Lateral line primordium cells

value: FGF ligand overexpression


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep3

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R3


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep4

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R4


title: Lyve1_IC_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070221


title: ST-00019006-T

description: Primary pancreas tumor


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep6

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R6

value: SU5402 (FGFR1 inhibitor)


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep2

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R2


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep1

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R1


title: ST-00018988-T

description: Primary pancreas tumor

value: Primary


title: Lyve1_IC_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070215


title: hESC_h9_K27ac_ChIPseq_rep1


title: IAIE_IC_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070219


title: ST-00003662-T

description: Primary pancreas tumor

value: scraped tumor


title: CD11c_IC_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070214


title: Zebrafish Lateral Line Primordium with FGF overexpression biological rep5

description:
Gene expression data for FGF overexpressed lateral line primordium cells from Zebrafish
LLP_FGFoverexp_R5


title: IAIE_IC_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070213


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep5

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R5


title: ST-00018955-T

description: Primary pancreas tumor

value: Pancreas


title: ST-00020225-T

description: Primary pancreas tumor


title: SHEP_minusDOX_METTL3_ChIPseq_rep1


title: hESC_h9_METTL3_ChIPseq_rep1

value: h9 hESC


title: ST-00018963-T

description: Primary pancreas tumor


title: SHEP_minusDOX_MYCN_ChIPseq_rep1


title: ST-00020223-T

description: Primary pancreas tumor


title: hESC_h9_MYCN_ChIPseq_rep1


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep4

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R4


title: Lyve1_Healthy_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070212

value: Control


title: ST-00020215-F

description: Primary pancreas tumor


title: CD11c_Healthy_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070211


title: ST-00020308-M

description: Metastisis to the Peritoneum

value: Peritoneum


title: tNCC_Input_b2_rep1

value: tNCC


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep2

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R2


title: SHEP_plusDOX_Input_rep1


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep1

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R1


title: Zebrafish Lateral Line Primordium untreated control biological rep6

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R6

value: none; untreated


title: ST-00020209-T

description: Primary pancreas tumor


title: Lyve1_Healthy_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070209

value: Synovium


title: Zebrafish Lateral Line Primordiumtreated with Fgfr1-inhibitor, SU5402 biological rep3

description:
Gene expression data for SU5402 treated lateral line primordium cells from Zebrafish
LLP_SU5402-FGFR1inh_R3


title: SHEP_minusDOX_Input_rep1


title: tNCC_m6A_rep1

value: m6A (Synaptic Systems, Cat# 202003)


title: CD11c_Healthy_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070208

value: Macrophages


title: IAIE_Healthy_2

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070207


title: IAIE_Healthy_3

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070210


title: ST-00018809-T

description: Primary pancreas tumor


title: ST-00019598-T2

description: Primary pancreas tumor


title: Zebrafish Lateral Line Primordium untreated control biological rep4

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R4


title: ST-00019598-T

description: Primary pancreas tumor


title: Zebrafish Lateral Line Primordium untreated control biological rep3

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R3


title: tNCC_Input_rep1


title: Zebrafish Lateral Line Primordium untreated control biological rep2

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R2


title: C8_SN_MYCN_plusDOX_STM_rep2

value: C8 SN


title: Zebrafish Lateral Line Primordium untreated control biological rep5

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R5


title: CD11c_Healthy_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070205


title: ST-00020205-T

description: Primary pancreas tumor


title: IAIE_Healthy_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070204


title: E18NNEW_pUCSSMmu_lib_KL965

city: Rochester

first: Fergus

last: Couch

address: 200 1st St SW

institute: MAYO CLINIC ROCHESTER

description: targeted DNA

data_processing:
FASTQ files of sequenced samples from Illumina MiSeq or NextSeq were trimmed for adapter sequences using cutadapt (v3.5).
SeqPrep (v1.2) converted the paired-end reads into single reads.
The single reads were aligned to the human reference genome (GRCh38) utilizing bwa-mem (v0.7.17).
Following alignment, a custom-developed tool `CountReads` was used for the analysis of DNA sequencing data, with a particular focus on mutation identification and characterization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited files for each variant from the library, day 5 and d14 for each replicate
Library strategy: amplicon based sequencing (AMPLN)

source_name: HAP1 cell

growth_protocol: HAP1 cell (Horizon discovery) were maintained in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Harvested cell pellets were thawed and genomic DNA were extracted by using Monarch Genomic DNA purification kit (NEB). Target region specific primer were used for PCR using Q5 High-Fidelity 2X Master Mix (NEB). Addaptor and index were added for each target region PCR product and samples were purified using AMPure XP beads and sent for sequencing.
Homologous arms (HA) that are 600-1000bp upstream and downstream flanking each target region were amplied from HAP1 cells and cloned into TOPO vector; site-directed mutagenesis PCR were performed in the HA arm vector to introduce target region saturation mutations with the PAM or sgRNA recognition site -destroying to avoind re-cutting by Cas9. Pooled mutagenesis PCR product was phosphorylated and transformed into MaxEfficient DH5a competent cells, grow overnight at 37 degree and library plasmids were extracted by ZymoPUREII MaxiPrep kit.

treatment_protocol: day -1: 2 million HAP1 cells seeded; day 0: transfection with library and sgRNA/Cas9 counstruct; day 1: 1ug/ml puromycin treatment; day 4: change back to regular medium; day 5: half of the cells were harvested for genomic DNA extraction, remaining cells continue culturing and passaged at 3-day interval; day 14: 5 million cells were harvested.

tag: cell line

value: HAP1 cell

tag: gene

tag: exon

tag: flowcellid

tag: grch38 fixd_mut_position

tag: grch38 fixd_mut

value: G>C

tag: fixd mut_aa_pos


title: E18NNEW_D5_KL965

description: targeted DNA


title: Lyve1_Healthy_1

description:
Takara SMARTer stranded total RNAseq mammalian pico input kit
Jointmac13070206

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: C8_SN_MYCN_plusDOX_rep2

tag: antibody


title: ST-00020221-T

description: Primary pancreas tumor


title: E18NNEW_D14_KL965

description: targeted DNA


title: Notch1f/f 3

city: Chicago

first: Kostandin

middle: V

last: Pajcini

state: IL

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Alignment to mm10 performed using STAR v2.7
Counts processed using FeatureCounts with Ensembl GTF build 110
Assembly: mm10

source_name: Adult (6 week old) mouse lung endothelial cells

extract_protocol:
Mouse lung endothelial cells from WT, DNMAML, Notch1f/f (n=3 for each condition) were sorted into RNA lysis buffer (Qiagen) and stored at -80ºC until RNA extraction. Total RNA was extracted using RNeasy Plus Kit (Qiagen) with inclusion of DNAse treatment step.
RNA sequencing libraries for Illumina sequencing were prepared in one batch using strand-specific using CORALL Total RNA-seq Library Prep Kit with Unique Dual Indices with RiboCop HMRv2 rRNA Depletion (Lexogen).

tag: strain

tag: sorting markers


title: ST-00020206-F

description: Primary pancreas tumor


title: ST-00019367-T

description: Primary pancreas tumor


title: C8_SN_MYCN_plusDOX_rep1


title: Notch1f/f 2


title: C8_SN_MYCN_minusDOX_rep2


title: Zebrafish Lateral Line Primordium untreated control biological rep1

description:
Gene expression data for Untreated lateral line primordium cells from Zebrafish
LLP_WT_R1

value: Lateral line primordium cells


title: C8_SN_MYCN_plusDOX_STM_rep1


title: E17NEW_pUCSSMmu_lib_KH8HJ

description: targeted DNA


title: ST-00020208-F

description: Primary pancreas tumor


title: E17NEW_D14_KH8HJ

description: targeted DNA


title: SKNBE2_m6A_rep1


title: Notch1f/f 1


title: C8_SN_MYCN_minusDOX_rep1


title: E19NEW_pUCSSMmu_lib_KH85K

description: targeted DNA


title: E17NEW_D5_KH8HJ

description: targeted DNA


title: SKNBE2_Input_rep1


title: DNMAML 3

value: DNMAML


title: ST-00020195-T

description: Primary pancreas tumor


title: ST-00020207-T

description: Primary pancreas tumor


title: ST-00020203-M

description: Metastisis to the Liver

value: Met

value: Liver


title: ST-00021359-M

description: Metastisis to the Perigastric Nodule

source_name: Perigastric Nodule

value: Perigastric Nodule

value: scraped tumor


title: NB_tumor_2_Input_rep1

source_name: NB tumor

value: NB tumor


title: WT 3

value: WT


title: E19NEW_D14_KH85K

description: targeted DNA


title: DNMAML 2


title: WT 2


title: NB_tumor_1_Input_rep1


title: WT 1


title: ST-00019607-M

description: Metastisis to the Peritoneum

value: Peritoneum


title: e14.5 liver, HTO-derived cDNA

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads sample_metadata.txt contains HTO barcodes for each sample.

data_processing:
Sequencing data were aligned to mm10 mouse reference using the Cell Ranger 3.0.2 pipeline (10x Genomics). Counting cell hashing tag were performed using CITE-seq Count version 1.3.4..
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files
Supplementary files format and content: Sample meta information

source_name: e14.5 liver

extract_protocol:
We used e14.5 male mouse liver (n=3 per group) to study transcriptional alteration at single-cell resolution. The e14.5 mouse liver samples were dissociated on 70 µm filters, then each sample was stained with unique cell hashing antibodies (BioLegend). The cell-hashing antibody information can be in sample_metadata.txt.
3,000-4,000 cells per sample were targeted on the 10x Genomics Chromium platform. Single-cell mRNA libraries were built using the Chromium Next GEM Single Cell 3’ Library Construction V3 Kit.

treatment_protocol: We performed dietary manipulations on C57BL/6J female mice. Five weeks old female mice (F0) were fed vitamin D deficient (0.0 IU/g vitamin D, VDdef) or sufficient (1.0 IU/g vitamin D, VDsuf) diets for five weeks before mating to the control diet-fed male mice and throughout the subsequent pregnancy. VDdef-fed females were supplemented with 1.5% calcium gluconate. After delivery, all F0 mice were fed VDsuf diets. The offspring were fed a VDsuf diet after weaning and maintained the diet until the sampling.

value: e14.5 liver


title: E17NEW_D5_KH5D6

description: targeted DNA


title: E19NEW_D5_KH85K

description: targeted DNA


title: ST-00004898-M

description: Metastisis to the Lung

source_name: Lung

value: Lung


title: DNMAML 1


title: E17NEW_pUCSSMmu_lib_KH5D6

description: targeted DNA


title: NB_tumor_2_m6A_rep1


title: NB_tumor_1_m6A_rep1


title: ST-00021339-F

description: Primary pancreas tumor

source_name: Pancreas

value: Primary

value: Pancreas


title: h9_NCSC_day7_m6A_rep1

source_name: h9 NCSC day7

value: h9 NCSC day7

value: m6A (Synaptic Systems, Cat# 202003)


title: e14.5 liver, mRNA-derived cDNA

description: Six samples were processed for scRNA-seq analysis on hashed-tagged single channel of 10x genomics. 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell


title: E17NEW_D14_KH5D6

description: targeted DNA

value: HAP1 cell


title: ST-00004898-T

description: Primary pancreas tumor


title: E15NEW_pUCSSMmu_lib_KFY75

description: targeted DNA

value: G>A


title: PD1 liver VDS6

data_processing:
After checking the quality of the sequencing files using FastQC and trimming low-quality reads and adapter sequences using Cutadapt, the obtained sequences were aligned to the mouse mm10 reference genome with the gencode M15 gene annotation using STAR aligner.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated with AllPrep DNA/RNA micro kit (QIAGEN).
After we depleted ribosomal RNAs from total RNA, we generated the RNA-seq libraries using KAPA RNA HyperPrep with RiboErase kit (Roche).

tag: Sex

value: male

value: VDS


title: ST-00018616-T

description: Primary pancreas tumor

tag: tumor type


title: h9_NCSC_day7_Input_rep1


title: PD1 liver VDS5


title: ST-00018628-T

description: Primary pancreas tumor


title: E15NEW_D14_KFY75

description: targeted DNA


title: PD1 liver VDS4


title: h9_NCSC_day14_m6A_rep1

source_name: h9 NCSC day14

value: h9 NCSC day14


title: h9_NCSC_day14_Input_rep2


title: PD1 liver VDS3

value: Liver


title: E15NEW_D5_KBC3T

description: targeted DNA


title: E15NEW_pUCSSMmu_lib_KBC3T

description: targeted DNA


title: h9_NCSC_day14_Input_rep1


title: ST-00020185-M

description: Metastisis to the Omentum

source_name: Omentum

value: Met

value: Omentum


title: ST-00019368-T

description: Primary pancreas tumor

value: scraped tumor


title: ST-00018584-T

description: Primary pancreas tumor


title: E17NEW_pUCSSMmu_lib_K3FWT

description: targeted DNA

value: G>C


title: PD1 liver VDS2


title: h9_hESC_m6A_rep1

value: h9 hESC


title: E15NEW_D14_KBC3T

description: targeted DNA


title: ST-00016623-T

description: Primary pancreas tumor


title: E17NEW_D5_K3FWT

description: targeted DNA


title: ST-00020190-M

description: Metastisis to the Liver


title: h9_hESC_Input_rep2


title: PD1 liver VDD6

value: VDD


title: h9_NCSC_day7_Input_rep2


title: E15NEW_D5_KFY75

description: targeted DNA


title: PD1 liver VDD5


title: h9_hESC_Input_rep1


title: PD1 liver VDS1


title: ST-00018426-T

description: Primary pancreas tumor


title: E17NEW_D14_K3FWT

description: targeted DNA


title: PD1 liver VDD4


title: MPP-AML RNAP II

city: Boston

first: Grant

last: Rowe

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
FastQC
CUT&RUNTools
CUT&RUN.  Raw data were processed using FastQC and CUT&RUNTools and mapped to hg19.  Parameters of individual software called by CUT&RUNTools, including Bowtie2, Trimmomatic, Picard (http://broadinstitute.github.io/picard/), Samtools were left unchanged. E. coli spike-in DNA was used for normalization.  We mapped the sequencing reads to E. coli genome using Bowtie2 (–end-to-end –very-sensitive –no-overlap –nodovetail–no-mixed –no-discordant) and calculated the "spike_in_ratio" in each sample as ‘‘Ecoli_reads/Total_reads’’. The bigwig tracks were generated using bamCoverage from deeptools package with "scale_factor" calculated as 1/(spike_in_ratio * cell_number_factor), where "cell_number_factor" to balance signal based on cell input and pooled from the triplicate samples.
RNA-seq.  For the trimming and quality improvement of RNA-seq reads, we utilized Trimmomatic (version 0.39). Paired reads were processed with the following parameters: adapter removal (TruSeq3-PE.fa), trimming of low-quality bases at the beginning and end (minimum score of 3), application of a 4-base sliding window to maintain an average quality above 15, and exclusion of reads shorter than 36 bases. The reads were processed generating files of both paired and unpaired processed reads. For mapping the processed RNA-seq reads, we employed the STAR software (version 2.7.10b). The paired reads, after trimming, were aligned to the reference genome (Homo_sapiens. GRCh38.86). To ensure the quality of mapping, the basic two-pass mode was activated, allowing only unique alignments. For the quantification of gene expression from the RNA-seq alignments, we used RSEM (version 1.3.1).
Assembly: hg19
Supplementary files format and content: CUT&RUN .bw
Supplementary files format and content: RNA-seq raw counts
Library strategy: CUT&RUN

source_name: AML cells

growth_protocol: IMDM/20% FCS, 100 ng/ml hSCF, 50 ng/ml hTPO, 10 ng/ml hFLT3L, 10 ng/ml hIL-3, 10 ng/ml hIL-6

extract_protocol:
RNA: RNAeasy; CUT&RUN: Epizyme
NEB

value: AML cells

tag: cell subset

value: MPP-AML

value: RNAP II


title: ubr-5(-) pabp-2 (RNAi) Biol Rep3

city: Dallas

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

description:
BPW181_pabp-2_3
igenomes.genes_B-VS-D.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to C elegans genome using STAR (v2.7.10a)
Duplicate alignments were removed using picard-tools(v2.10)
Read counted using featureCounts and normalized using trimmed mean of M values (TMM) methods
Normalized read counts generated using edgeR (version 3.12)
Assembly: ce10
Supplementary files format and content: glmLRT.txt: Files with Diﬀerential expressed gene list (as indicated in the corresponding sample description field)
Supplementary files format and content: igenomes.genes_normalized.counts.CPM.tab, normalized counts

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: wild type and BPW181 strains were maintained on OP50 without stress prior to experiment

extract_protocol:
Trizol extraction method
Illumina NextSeq 500 Kit

treatment_protocol: Bleached and synchronous L1 were fed mock or pabp-2 RNAi and collected at L4 stage

value: whole organism

value: ubr-5(-) pabp-2 (RNAi)

value: pabp-2 RNAi in HT115


title: Progenitor-AML RNAP II

value: Progenitor-AML


title: ST-00020186-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: PD1 liver VDD3

value: male


title: HSC-AML RNAP II

value: HSC-AML


title: ST-00018360-T

description: Primary pancreas tumor


title: Progenitor-AML MLL-N

value: MLL-N


title: ST-00018386-T

description: Primary pancreas tumor


title: PD1 liver VDD1

value: Liver


title: Progenitor-AML MLL-C

value: MLL-C


title: Progenitor-AML H3K27me3


title: ubr-5(-) Biol Rep3

description:
BPW181_mock_3
igenomes.genes_A-VS-C.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt

value: ubr-5(-) RNAi in HT115


title: ST-00020181-T

description: Primary pancreas tumor

value: scraped tumor


title: ubr-5(-) Biol Rep2

description:
BPW181_mock_2
igenomes.genes_A-VS-C.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt


title: MPP4 VDS2

source_name: multipoint progenitor 4 cells (MPP4)

value: multipoint progenitor 4 cells (MPP4)

value: VDS


title: MPP4 VDS3


title: ST-00020178-T

description: Primary pancreas tumor


title: ubr-5(-) Biol Rep1

description:
BPW181_mock_1
igenomes.genes_A-VS-C.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt


title: Progenitor-AML H3K27Ac

value: AML cells


title: ST-00020175-T

description: Primary pancreas tumor


title: Progenitor-AML H3K4me3


title: ST-00020213-M

description: Metastisis to the Liver

value: Met


title: pabp-2 (RNAi) Biol Rep3

description:
N2_pabp-2_3
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_B-VS-D.glmLRT.txt

value: whole organism

value: pabp-2 (RNAi)


title: MPP4 VDD3

value: VDD


title: ST-00018260-T

description: Primary pancreas tumor


title: ubr-5(-) pabp-2 (RNAi) Biol Rep2

description:
BPW181_pabp-2_2
igenomes.genes_B-VS-D.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt

value: ubr-5(-) pabp-2 (RNAi)

value: pabp-2 RNAi in HT115


title: MPP-AML MLL-N

value: MPP-AML


title: MPP4 VDD2

value: male


title: pabp-2 (RNAi) Biol Rep2

description:
N2_pabp-2_2
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_B-VS-D.glmLRT.txt


title: ubr-5(-) pabp-2 (RNAi) Biol Rep1

description:
BPW181_pabp-2_1
igenomes.genes_B-VS-D.glmLRT.txt
igenomes.genes_C-VS-D.glmLRT.txt


title: PD1 liver VDD2


title: MPP-AML MLL-C


title: pabp-2 (RNAi) Biol Rep1

description:
N2_pabp-2_1
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_B-VS-D.glmLRT.txt


title: MPP4 VDD1


title: MPP-AML H3K27me3


title: ST-00018268-T

description: Primary pancreas tumor

value: Primary

value: Pancreas


title: wild type Biol Rep3

description:
N2_mock_3
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_A-VS-C.glmLRT.txt

value: wild type

value: mock RNAi in HT115


title: ST-00018269-T

description: Primary pancreas tumor


title: wild type Biol Rep2

description:
N2_mock_2
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_A-VS-C.glmLRT.txt


title: MPP-AML H3K27Ac


title: wild type Biol Rep1

description:
N2_mock_1
igenomes.genes_A-VS-B.glmLRT.txt
igenomes.genes_A-VS-C.glmLRT.txt


title: Paired_tag_islet_H3K27ac_16week_B15_sub_library_rep1_RNA#01

city: SCOTTSDALE

first: Zong

last: Wei

state: Arizona

address: 13400 E Shea Blvd

institute: Mayo Clinic

data_processing:
Preprocessing of Paired-tag were carried out with the scripts available from GitHub (https://github.com/cxzhu/Paired-Tag).Cellular barcodes were extracted from Read2 and assigned to each sample barcodes (12 initial tubes for tagmentation and reverse transcription) and combination of ligated barcodes. The first base of BC#1, BC#2 and BC#3 should locate within 84-87th, 47-50th and 10-13th base of Read2. We identify the positions of barcodes by matching the linker sequences adjacent to the cellular barcodes.Cleaned reads were first mapped to a mouse GRCm38 genome reference genome with STAR (version: 2.7.3a) for RNA or bowtie2 for DNA. Duplicates were removed based on the mapped position, cellular barcode, PCR index and UMI.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include cell embeddings for each cell.

molecule: nuclear RNA

source_name: Pancreatic Islet

extract_protocol:
Single-cell suspension were prepared from the pancreatic islet, Spin-down cells at 300 g for 5 mins, resuspended the cells in 1 mL 0.2% NIB-RPI(1 mL 0.2% NIB, 20 µL Protease Inhibitor (50X), 25 µL SUPERase IN and 12.5 µL RNaseOUT). Sit on ice for 5 min.Count the nuclei using cell counter.
Libraries were constructed by Paired-tag workflow, briefly: First, permeabilized nuclei were incubated with antibodies (H3K27ac, Cell Signaling #8173S, H3K4me1, Cell Signaling #5326S) targeting chromatin regions of interest to trigger the targeted binding of protein A-fused Tn5. Tagmentation reaction and reverse transcription (RT) were then sequentially performed: reactions were carried out in 12 different wells, with the same set of barcodes in transposase adaptors and RT primers, to label different samples or replicates (1st round of barcodes). Next, a ligation-based combinatorial barcoding strategy was used to introduce the 2nd and 3rd rounds of barcodes to nuclei, by sequential attaching well-specific DNA barcodes from 96-well plates to the 5’-end of both DNA fragments and cDNA from RT. Lastly, barcoded nuclei were divided into sub-libraries and lysed, the DNA/cDNA was purified to give rise DNA and RNA libraries for sequencing

treatment_protocol: Mice were maintained on chow or high fat diets for 8 or 16 weeks

value: Pancreatic Islet

value: high-fat diet (HFD), 16week


title: MPP-AML H3K4me3


title: MPP4 VDS1

value: multipoint progenitor 4 cells (MPP4)


title: Paired_tag_islet_H3K27ac_16week_B15_sub_library_rep1_RNA#02


title: ST-00018179-T

description: Primary pancreas tumor

value: scraped tumor


title: Xrn2-444-555Δ ChIP, DMSO, replicate2

city: OXFORD

first: Krzysztof

last: Kus

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

description: Xrn2 ChIP with V5 antibody (Xrn2 with region between 444-555 replaced by linker)

data_processing:
Reads trimmed and quality controlled with fastp (0.20.0)
Reads were aligned to concatenated genome of S.pombe and S. cerevisiae using STAR (2.7.3a)
Reads were split to each of the organisms keeping all alignments with samtools and bash command line
Reads which had too distant pairs were further filtered using a custom script
Aligned, filtered files were sorted and indexed using samtools
BigWig files were prepared using bamCoverage, normalised to sequencing depth while ignoring duplicates.
Input signal was subtracted from the ChIP signal. For DMSO-treated samples, a common input was used for background removal.
Reversal of the normalisation and application of spike-in normalisation factors were performed for comparisons of DMSO samples, while sequencing depth factors were used for comparisons between auxin- and DMSO-treated samples.
Negative values were filtered out.
Assembly: ASM294v2 from pombase.org
Supplementary files format and content: bigwig with normalised occupancy (input subtracted and without negative values). For comparisons between auxin and DMSO: sequencing depth normalisation was used (“normed” in filename). Comparing DMSO conditions spike-in was utilised (“spike” in filename). Additionally, mean bigwig file is provided.

organism: Schizosaccharomyces pombe

source_name: yeast

growth_protocol: Strains were grown in YES media.

extract_protocol:
Cells were disrupted using bead beating, and chromatin was isolated and sheared with a Bioruptor Pico. Immunoprecipitation (IP) was performed using beads coated with antibodies against Rpb1 (8WG16) or Xrn2 (anti-V5)
The library was prepared following the ChIP-Seq protocol. Briefly, IP DNA or input DNA was treated with pronase. The samples were then subjected to decrosslinking at 65°C, followed by RNA degradation using an RNase A/T1 mix and purification with the ChIP DNA Clean & Concentrator kit. Purified IP DNA or input DNA was used for library preparation according to the manufacturer's recommendations for the NEBNext Ultra II DNA Library Prep kit with Sample Purification Beads for Illumina.

treatment_protocol: The cells were treated with either 1 mM auxin or DMSO for 2 hours at 25°C. Spike-in cells (S. cerevisiae SCC-6xV5) were added, and the cultures were crosslinked with formaldehyde, washed, and frozen.

value: yeast

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6 Xrn2-444-555{delta}-2xV5-hphMX

value: DMSO treated


title: Paired_tag_islet_H3K27ac_16week_B15_sub_library_rep1_DNA#02


title: HSC-AML MLL-C

value: AML cells

value: HSC-AML

value: MLL-C


title: ST-00020164-M

description: Metastisis to the Liver

value: Met

value: Liver


title: Paired_tag_islet_H3K27ac_16week_B15_sub_library_rep1_DNA#01


title: HSC-AML MLL-N

value: MLL-N


title: ST-00018301-T

description: Primary pancreas tumor

value: Primary


title: Xrn2-444-555Δ ChIP, DMSO, replicate1


title: Paired_tag_islet_H3K4me1_16week_B14_sub_library_rep1_RNA#01


title: ST-00018232-M

description: Metastisis to the Lung

value: Lung


title: Xrn2 ChIP, DMSO, replicate2

description: Xrn2 ChIP with V5 antibody (Xrn2 wild-type)

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6 Xrn2-2xV5-hphMX


title: ST-00018257-T

description: Primary pancreas tumor

value: Pancreas


title: HSC-AML H3K27me3


title: HSC-AML H3K27Ac


title: HSC-AML H3K4me3


title: Paired_tag_islet_H3K4me1_16week_B14_sub_library_rep1_DNA#01

value: Pancreatic Islet


title: cotyledon seed, replicate 1, scATAC-Seq

city: Davis

first: John

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California

data_processing:
Base calls were processed into fastq files using Illumina bcl2fastq v2.20.0.422.
Raw files were analyzed by 10X Genomics Cell Ranger ARC v1.0, using a custom soybean reference ( built using genome version Wm82.a2.v1).
Single-cell feature counts were generated using the "count" function.
Ambient RNA contamination was removed using the R package SoupX v1.6.1 with default parameters and the resulting snRNA count matrix was imported in Seurat v4.1.1 for downstream analyses.
Assembly: Wm82.a2.v1
Supplementary files format and content: SoupX_filtered_matrix.mtx contains detected, cell-associated barcodes in Matrix Market Exchange (MEX) format.  The matrix elements are the number of UMIs associated with a feature (row) and a barcode (column), after ambient RNA contamination was removed using SoupX. The TSV files correspond to the gene IDs and cellular barcodes.
Supplementary files format and content: filtered_feature_bc_matrix.h5 contains the features detected (genes and peaks) in rows, while the columns consist of all cell-associated barcodes.  The format is the Hierachical Data Format (H5).
Supplementary files format and content: atac_fragments.tsv.gz and atac_peaks.bed are fragments created by two separate transposition events and the genomic intervals having local enrichment of transposase cut-sites, respectively, in BED format.

organism: Glycine max

source_name: cotyledon stage seed cells

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Fresh cotyledon stage seeds were hand chopped in lysis buffer (15mM Tris pH7.5, 20mM NaCl, 80mM KCl, 0.5mM Spermine, 5mM 2-ME, 0.05% Triton X-100, 80U/ml RNase inhibitor (Roche, 3335399001)), then filtered through 40um and 20um nylon mesh.  Nuclei were diluted with 3 volumes cold wash buffer (20mM MES pH5.4, 0.4M Mannitol, 20mM KCl, 0.1% BSA, 80U/ml RNase inhibitor), and resuspended in 1ml cold wash buffer. DAPI-stained nuclei were counted on a hemocytometer, spun again and resuspended to achieve a target concentration of 3500 nuclei/ul.
Library was constructed using 10,000 nuclei, following 10X Genomics protocol for Chromium Next GEM Single Cell Multiome ATAC+Gene expression v1 assay.

value: cotyledon stage seed cells

value: Williams 82


title: ST-00018236-T

description: Primary pancreas tumor

value: scraped tumor


title: Paired_tag_islet_H3K4me1_8week_B12_sub_library_rep1_RNA#02

value: high-fat diet (HFD), 8week


title: Xrn2 ChIP, DMSO, replicate1

value: yeast


title: ST-00018136-T

description: Primary pancreas tumor


title: ST-00018932-T

description: Primary pancreas tumor


title: Xrn2 ChIP, auxin, replicate2

value: auxin treated


title: Xrn2 ChIP, auxin, replicate1


title: PolII ChIP, DMSO, Xrn2-444-555Δ, replicate1

description: Pol II ChIP with 8WG16 antibody

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6 Xrn2-444-555{delta}-2xV5-hphMX

value: DMSO treated


title: ST-00017985-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K4me1_8week_B11_sub_library_rep1_RNA#01


title: Paired_tag_islet_H3K4me1_8week_B12_sub_library_rep1_DNA#02


title: Paired_tag_islet_H3K4me1_8week_B12_sub_library_rep1_RNA#01


title: glmS ribozyme variant library, cleaved, 60 s

city: Baltimore

first: Sarah

middle: A

last: Woodson

state: MD

address: 3400 N. Charles St.

department: Biophysics

institute: Johns Hopkins University

data_processing:
Sequences at 12 different self-cleavage stages were demultiplexed using indexes at two ends of the reads by the software of HiSeq 3000 (PE150) at the sequencing service (Novogene).
Reads with average quality score > 21.5 were retained and a matched segment was identified in each set of paired-end reads for combining them into a longer read covering 152 mutation sites. The reads were trimmed from two ends until 7-bp outside the mutation zone. Discard the paired-end reads with any unmatched bases (to the reference sequence) in the 7-bp extensions.
The trimmed reads were aligned to the reference glmS ribozyme sequence (see suppliementary file: gS_mut_zone_ref.txt) using Needleman–Wunsch algorithm (sigma score matix: 1 for match, -5 for mismatch; gap = 300).
The counts of single mutants at each timepoint were used for calculating the fraction of self-cleavage.
Assembly: Bacillus subtilis, UD1022, locus CP011534 (nucleotide 501 to 670)
Supplementary files format and content: tab-deliminated text file includes raw counts of single mutants for each library
Supplementary files format and content: tab-deliminated text file includes self-cleavage parameters of single mutants
Library strategy: DNA HiSeq

organism: Bacillus subtilis

extract_protocol:
Plasmid encoding the parental B. subtilis glmS ribozyme was isolated from DH5-alpha cells using Monarch Plasmid Miniprep Kit (NEB).
The methylated plasmid was used to construct a plasmid variant library using nicking mutagenesis (Wrenbeck et al., 2016). The library was in vitro transcribed, allowed to self-cleave at 6 timepoints, purified by PAGE, and reverse transcribed into 12 barcoded (cleaved and uncleaved products for each of the 6 timepoints) output cDNA sub-libraries. The sub-libraries were pooled and sequenced in parallel.

value: locus CP011534 (nucleotide 501 to 670)

tag: genetic modification

value: Mutagenesis

value: Cleaved fraction of ribozyme self-cleavage

tag: time

tag: library i7_index_sequence

tag: library i5_index_sequence


title: ST-00018724-T

description: Primary pancreas tumor

data_processing:
Paired-end fastq sequences were trimmed using trim-galore (ver 0.6.3) and default parameters.
Pseudoalignment was performed with kallisto (ver 0.44.0) using genome assembly GRCh38.p5 and gencode (ver 24) annotation using default parameters.
Bioconda package bioconductor-tximport (ver 1.12.1) was used to create gene level counts and abundances (TPMs).
Quality checks were assessed with FastQC (ver 0.11.8) and MultiQC (ver 1.7).
Assembly: GRCh38.p5
Supplementary files format and content: Gene level count estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Gene level TPM estimates are provided as a matrix in tab delimited text format.  Feature annotations are provided in the first few columns.
Supplementary files format and content: Per sample h5 file output from the kallisto pipeline is provided.
Supplementary files format and content: Gene level TMM normalized (edgeR method) estimates are provided as a matrix in tab delimited text format. Feature annotations are provided in the first few columns as well as a column with expression level filtering status. The TMM gene level estimates provided are not log scaled and are generated from the h5 files using general recommendations for importing from the kallisto method as given here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto & https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR


title: Paired_tag_islet_H3K4me1_8week_B11_sub_library_rep1_DNA#02


title: Paired_tag_islet_H3K4me1_8week_B12_sub_library_rep1_DNA#01


title: cotyledon seed, replicate 1, scRNA-Seq


title: PolII ChIP, DMSO, Xrn2-444-555Δ, replicate2

description: Pol II ChIP with 8WG16 antibody


title: glmS ribozyme variant library, cleaved, 30 s


title: PolII ChIP, DMSO, replicate2

description: Pol II ChIP with 8WG16 antibody


title: glmS ribozyme variant library, cleaved, 180 s


title: Paired_tag_islet_H3K4me1_8week_B11_sub_library_rep1_RNA#02


title: ST-00020165-T

description: Primary pancreas tumor


title: ST-00017915-M

description: Metastisis to the Lung

value: Met


title: PolII ChIP, DMSO, replicate1

description: Pol II ChIP with 8WG16 antibody


title: Paired_tag_islet_H3K4me1_8week_B11_sub_library_rep1_DNA#01


title: glmS ribozyme variant library, cleaved, 10 s


title: ST-00020168-M2

description: Metastisis to the Liver

value: Liver


title: Paired_tag_islet_H3K27ac_8week_B10_sub_library_rep1_RNA#02


title: ST-00018002-T

description: Primary pancreas tumor

value: Primary


title: glmS ribozyme variant library, un-cleaved, 180 s

value: Un-cleaved fraction of ribozyme self-cleavage


title: PolII ChIP, auxin, replicate1

description: Pol II ChIP with 8WG16 antibody

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6 Xrn2-2xV5-hphMX


title: glmS ribozyme variant library, cleaved, 0 s

value: 0 s


title: ST-00017966-T

description: Primary pancreas tumor

value: Pancreas


title: ST-00018938-T

description: Primary pancreas tumor


title: Input, DMSO, replicate2

description: input sequencing


title: ST-00017975-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K27ac_8week_B10_sub_library_rep1_RNA#01

value: Pancreatic Islet


title: Input, DMSO, replicate1

description: input sequencing


title: PolII ChIP, auxin, replicate2

description: Pol II ChIP with 8WG16 antibody


title: Input, auxin, replicate1

description: input sequencing


title: glmS ribozyme variant library, un-cleaved, 60 s


title: ST-00018893-T

description: Primary pancreas tumor

value: scraped tumor


title: glmS ribozyme variant library, un-cleaved, 30 s


title: Paired_tag_islet_H3K27ac_8week_B10_sub_library_rep1_DNA#01

value: high-fat diet (HFD), 8week


title: Input, auxin, replicate2

description: input sequencing

value: yeast


title: Paired_tag_islet_H3K27ac_8week_B9_sub_library_rep1_RNA#01


title: glmS ribozyme variant library, un-cleaved, 10 s


title: ST-00017945-T

description: Primary pancreas tumor


title: ST-00017945-T2

description: Primary pancreas tumor


title: XRN2 DEGRON, MUT XRN2 (D235A) RESCUE, AUXIN, REP1

data_processing:
Reads trimmed and quality controlled with fastp (0.20.0)
Reads were aligned to concatenated genome of S.pombe and S. cerevisiae using STAR (2.7.3a)
Reads were split to each of the organisms keeping all alignments with samtools and bash command line
Reads which had too distant pairs were further filtered using a custom script
Aligned, filtered files were sorted and indexed using samtools
Bigwig files were prepared and separated by strand with bedtools genomecov (including -bg -strand -du -split -scale options). As scaling factor spike-in value was used. Bedgraphs were sorted and transformed to bigwigs using bedGraphToBigWig.
Assembly: ASM294v2 from pombase.org
Supplementary files format and content: bigwig with normalized coverage using spiked-in reads for plus strand
Supplementary files format and content: bigwig with normalized coverage using spiked-in reads for minus strand
Library strategy: TT-seq

growth_protocol: Strains were grown in YES media (with reduced uracil to 10mg/L) to OD600=~0.5

extract_protocol:
Total RNAs were extracted by a standard hot phenol method from 4-thiouracil labelled cells (S.pombe mixed with S.cerevisiae as a spike-in).
Library was prepared following TT-seq (chem) protocol. Briefly, RNA was treated with DNAse, subjected to NaOH fragmentation, followed by RNA biotinylation and purification on streptavidin beads. Purified RNA (50ng) was used in library preparation following manufacture recommendations for NEBNext ultra II directional RNA library prep kit for Illumina.

treatment_protocol: Auxin (1 mM final) or DMSO treatment for 2 hours at 25°C. Thiouracil labelling (5 mM final) for 6 minutes. Cells harvested and snap-frozen in liquid nitrogen

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Xrn2-3xmAID-5xFLAG-kanMX6 ura4::Xrn2-D235A-2xV5-hphMX

value: auxin treated


title: glmS ribozyme variant library, un-cleaved, 5 s

value: 5 s


title: XRN2 DEGRON, MUT XRN2 (D235A) RESCUE, AUXIN, REP2


title: Paired_tag_islet_H3K27ac_8week_B9_sub_library_rep1_DNA#02


title: glmS ribozyme variant library, cleaved, 5 s

value: locus CP011534 (nucleotide 501 to 670)


title: Paired_tag_islet_H3K27ac_8week_B10_sub_library_rep1_DNA#02


title: XRN2 DEGRON, WT XRN2 RESCUE, AUXIN, REP2

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Xrn2-3xmAID-5xFLAG-kanMX6 ura4::Xrn2-2xV5-hphMX


title: ST-00020154-M

description: Metastisis to the Liver

extract_protocol:
Starting with sectioned FFPE PDAC specimen blocks, Clinical pathologists marked regions of high tumor content (>20% ratio of tumor to normal nuclei) on H&E stained slides for RNA extraction. Solid tumor total nucleic acid was extracted from these tumor regions on adjacent FFPE tissue sections using Chemagic 360 sample-specific extraction kits (Perkin Elmer) and digested by proteinase K. RNA was purified from the total nucleic acid by DNase-I digestion.
100ng of RNA for each tumor sample was heat fragmented in the presence of magnesium to an average size of 200 bp. Library preps were hybridized to the xGENExome Research Panel v1.0 (Integrated DNA Technologies) and target recovery was performed using Streptavidin-coated beads, followed by amplification with the KAPA HiFi Library Amplification Kit.


title: glmS ribozyme variant library, un-cleaved, 0 s

value: Mutagenesis


title: Paired_tag_islet_H3K27ac_8week_B9_sub_library_rep1_DNA#01


title: ST-00018362-T

description: Primary pancreas tumor


title: XRN2 DEGRON, WT XRN2 RESCUE, AUXIN, REP1


title: Paired_tag_islet_H3K27ac_0week_B8_sub_library_rep1_RNA#01

value: normal chow (NC)


title: ST-00020196-M

description: Metastisis to the Falciform Ligament

source_name: Falciform Ligament

value: Met

value: Falciform Ligament


title: XRN2 DEGRON, NO RESCUE, DMSO, REP2

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Xrn2-3xmAID-5xFLAG-kanMX6

value: DMSO treated


title: Paired_tag_islet_H3K27ac_0week_B8_sub_library_rep1_DNA#01


title: ST-00018888-T

description: Primary pancreas tumor

value: Primary


title: Paired_tag_islet_H3K27ac_8week_B9_sub_library_rep1_RNA#02


title: ST-00017838-M

description: Metastisis to the Liver

value: Liver


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep2_RNA#04

value: Pancreatic Islet


title: XRN2 DEGRON, NO RESCUE, DMSO, REP1


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_RNA#04


title: XRN2 DEGRON, NO RESCUE, AUXIN, REP1


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep2_RNA#03


title: SPT5 DEGRON, DMSO, REP2

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6


title: ST-00017762-T

description: Primary pancreas tumor

value: Pancreas

value: scraped tumor


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_RNA#03


title: ST-00020148-T

description: Primary pancreas tumor


title: RANKL scRNAseq

city: Marseille

first: Magali

last: Irla

address: 163 Av. de Luminy

country: France

institute: Centre d’Immunologie de Marseille-Luminy (CIML)

description: 10x Genomics

data_processing:
Raw fastq files were processed using the Cell Ranger software (v6.0.1) from 10x Genomics. Alignment was done on the GRCm38 reference genome. All clustering analyses were performed using the Seurat v4.3.0 package in R v4.2.2.
Assembly: GRCm38
Supplementary files format and content: Gzipped tab separated value and matrix files containing the cellular barcodes (barcodes.tsv.gz), the list of features (features.tsv.gz) and the UMI matrix count (matrix.mtx.gz).

source_name: Thymus

extract_protocol:
Thymic single cell suspensions were obtained by mechanical digestion in the presence of DNase I (100 µg/ml) and Liberase TM (50 µg/ml) for 40 min and washed PBS 5%BSA 1mM EDTA. Samples were enriched for CD45- cells using the autoMACS® Pro Separator with the Depletes program (Miltenyi). Viable CD31+ EC and EpCAM+ TEC were sorted using a BD FACSAriaIII cell sorter. Sorted EC and TEC from each sample were pooled and loaded in a single capture well for subsequent 10x Genomics Single Cell 5’ v32 workflow, targeting a capture of 10,000 cells.
Libraries were performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).  The resulting libraries containing distinct i5 and i7 indexes were pooled and sequenced together on an Illumina NextSeq2000 platform using a P2 flow cell (100 cycles).

treatment_protocol: Aged mice were treated for 3 consecutive days with GST (control) or RANKL proteins and thymi were withdrawn 21 days after the first injection.

value: Thymus

value: EpCAM+ thymic epithelial cells (TECs) and CD31+ endothelial cells (Ecs)

value: C57BL/6 mice

value: RANKL

tag: age

value: 10-12 months old


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_RNA#02


title: ST-00017549-T

description: Primary pancreas tumor


title: SPT5 DEGRON, AUXIN, REP1

value: yeast

value: auxin treated


title: SPT5 DEGRON, AUXIN, REP2


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep2_DNA#04

value: normal chow (NC)


title: XRN2 DEGRON, NO RESCUE, AUXIN, REP2


title: ST-00020144-M

description: Metastisis to the Lung

value: Met

value: Lung


title: ST-00017838-T

description: Primary pancreas tumor


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_DNA#04


title: ST-00017440-T

description: Primary pancreas tumor


title: 3T3-L1 treated with Tsuru_rep3

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

institute: UNIVERSITY OF TSUKUBA

description: Gene expression data from 3T3-L1 treated with Tsuru for 9 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S Array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

source_name: 3T3-L1 cells were treated with Tsuru for 9 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: Mouse 3T3-L1 cells (Riken, Tsukuba, Japan) were cultured in DMEM (Sigma, Tokyo, Japan) supplemented with fetal bovine serum (FBS) (Gibco™) and 1% Penicillin-Streptomycin (Sigma-Aldrich, USA) at 37oC in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: The 3T3-L1 was seeded at 3.0x104 cells/cm2 in preadipocytes medium (DMEM containing 10% FBS). After post confluence (DO), the medium was replaced with induction medium containing 1% of 1000x cell-based assay IBMX solution, 1000x insulin solution and 1000x adipogenesis assay dexamethasone solution with Tsuru treatment at 1/1000 and 1/100 of dilution of 100mg/ml Tsuru and without treatment (control) . At Day 3 (D3), the induction medium was replaced with insulin medium that is preadipocytes medium with 1% of 1000x Insulin Solution. The differentiation continued for 9 days (D9) and the differentiation medium was replaced every two days until D9.

value: Mouse fibroblast-like cell line

tag: cell line

value: Tsuru


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep2_DNA#03


title: ST-00020149-M

city: Portland

first: Rosalie

last: Sears

institute: Oregon Health & Science University

description: Metastisis to the Peritoneum

source_name: Peritoneum

value: Peritoneum


title: 3T3-L1 maintained in Medium_rep2

description: Gene expression data without Tsuru treatment for 9 days

source_name: 3T3-L1  cells without treatment for 9 days

value: control


title: SPT5 DEGRON, DMSO, REP1

value: h- ura4-D18 ade6::ade6+ -Padh15 -skp1-OsTIR1-natMX6-P-adh15-skp1-AtTIR1-2NLS Spt5-3xmAID-5xFLAG-kanMX6

value: DMSO treated


title: 3T3-L1 treated with Tsuru_rep2


title: Paired_tag_islet_H3K27ac_0week_B7_sub_library_rep1_RNA#01

value: Pancreatic Islet