title: K1 - NutlinGSK - rep1 [RNA-seq]

city: Aurora

first: Joaquin

middle: M

last: Espinosa

state: CO

department: Pharmacology, Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 4000 RTA software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
FASTQC (v0.11.5) was used to assess sequence data quality.
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf(v1.04) tool from EAutils.
FastQ Screen (v0.9.1) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) and Bowtie2 (v2.2.3.0) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v1.3.1)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6.4)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene_id --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

growth_protocol: TPC1 and K1 cells were cultivated in RPMI (TPC1) or DMEM (K1) media (Gibco, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Peak Serum) and 1% antibiotic-antimycotic mixture (Gibco). Cells were plated a day before the treatment and maintained in a humidified atmosphere with 5% of CO2 at 37°C.

extract_protocol:
TRI Reagent (Millipore Sigma)
Strand-specific poly(A)+-enriched mRNA (Illumina TruSEQ mRNA)

treatment_protocol: Cells were treated treated with vehicle (0.2% DMSO), 10 microM Nutlin-3a, 25 microM GSK2830371, and drug combinations for 24 hours.

value: papillary thyroid carcinoma

value: NutlinGSK


title: K1 - GSK - rep2 [RNA-seq]

status: Public on Nov 01 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment

value: GSK


title: B6 Liver Control Replicate 1

city: Salt Lake City

first: Clement

last: Chow

state: UT

address: EIHG 5200 15 North 2030 East

institute: University of Utah

data_processing:
Fastq files were trimmed by using seqtk v1.2 software.
Parental RNA-seq reads were aligned to strain specific reference genomes using Bowtie2 v2.2.9
F1 reads were aligned to masked genomes using STAR v2.6 software.
Alignment files were sorted and converted using samtools v1.12
The Deseq2 default normalization method (median of ratios) was used to normalize counts using Deseq2 v1.28.1
Genome_build: GRCmm39, CAST_EiJ_v1
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Tissues were removed and placed on dry ice and stored at -80°C. RNA was harvested using Trizol reagent and Direct-zol RNA MiniPrep Kit Rna column extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold.

treatment_protocol: Control treatment mice were injected with DMSO using IP injection. TM treatment mice were injected with TM dissolved in DMSO using IP injection (final concentration of 1mg TM per 1kg mouse weight). Mice were euthanized 24 hours later.

tag: strain

tag: age

value: 15-23 weeks

tag: Sex

value: Male

value: DMSO

tag: replicate

value: Replicate 1


title: K1 - GSK - rep1 [RNA-seq]


title: LamCiR_1wk_4 (RNA-seq)

city: La Jolla

first: Adam

middle: Jeffrey

last: Engler

state: CA

address: 9500 Gilman Drive, MC 0412

department: Bioengineering

institute: UC San Diego

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
L1d

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt
Quality scores were assessed using FastQC2. Reads were aligned to the Drosophila melanogaster genome build dm6 using STAR
Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library
Genome_build: dm6
Supplementary_files_format_and_content: text files with Relative Log Expression (RLE) values for each sample

organism: Drosophila melanogaster

source_name: Heart

extract_protocol:
Hearts were exposed and removed, put in Quizol reagent before flash freezing and storing at -80. Subsequently RNA was harvested using Qiagen miRNeasy extraction kit. TruSeq Stranded mRNA Library Prep Kit High Throughput was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Heart

value: 1 week

value: attp2, LamC iR


title: liver, NC3

city: Shanghai

first: Liqun

last: Yang

address: No 160, Pujian road

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Qubit3.0/ Nanodrop used for basecalling.
RNA sequencing libraries were prepared with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). Paired-end sequencing was completed using a Novaseq 6000 by Jiangxi HaploX Biotechnology Co., Ltd (China). Low-quality sequences and adapters were filtered by Fastp software and the clean reads mapped to the reference genome of the Mus musculus (mmu10) using HISAT2 v2.1.0.
HISAT2 uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a wholegenome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two conditions/groups (no replicats) was performed using the EdgeR R package (1.20.0).
Genome_build: mmu10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Liver samples were obtained after 48 hours of hepatectomy.Total RNA was extracted from mouse liver tissue (n=3) using Trizol Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and RNA integrity (RIN>=6.5 & 28s/18s>=1.0) verified using an Agilent Bioanalyzer 4200 (Agilent technologies, Santa Clara, CA, US).
RNA sequencing libraries were prepared with the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611). Paired-end sequencing was completed using a Novaseq 6000 by Jiangxi HaploX Biotechnology Co., Ltd (China). Low-quality sequences and adapters were filtered by Fastp software and the clean reads mapped to the reference genome of the Mus musculus (house mouse) using HISAT2 v2.1.0.

treatment_protocol: Dexmedetomidine 25 μg.kg-1 was injected intraperitoneally 30 minutes before a 70% hepatectomy performed in mice.

value: liver

value: 8 weeks

value: control


title: MM6_NS_rep2

city: Guangzhou

first: Hengyou

last: Weng

state: Guangdong

address: Room 304, Building D, 190 Kaiyuan Ave,

institute: Guangzhou Laboratory

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shNS_rep2

data_processing:
The raw RNA-seq reads were quality checked by FastQC (version 0.11.5) and then adaptors trimmed by Cutadapt (version 3.4). The processed reads were mapped to human transcriptome built with gene annotations (hg38, GENCODE v37) by STAR (version 2.7.2b) with parameters recommended by ENCODE project.
The aligned results were then passed to RSEM (version 1.2.31) to estimate the read count of genes.
Finally, the estimated read counts of genes were analyzed by DESeq2 (version 1.32.0) to identify differentially expressed genes with following parameters: sfType=poscounts, test=Wald and lfcShrink(type=none).
Assembly: hg38
Supplementary files format and content: Raw read gount of genes and processed results from DESeq2

source_name: Human AML cell MonoMac6

extract_protocol:
Total RNA from MonoMac6 cells with or without IGF2BP2 knockdown was isolated using the TRIzol reagent (Thermo fisher Scientific).
Library construction of 1 µg RNA per sample was made using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: shNS

value: Human acute myeloid leukemia (AML) cells


title: LamCiR_1wk_3 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
L1c


title: LamCiR_1wk_5 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
L1e


title: ICO1, 6 hrs reoxygenation after hypoxia

city: Rotterdam

first: Henk

middle: P.

last: Roest

state: Choose State

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: Erasmus MC

data_processing:
.fastq files were uploaded to the Galaxy public server (usegalaxy.org) and quality checked using FASTQC
Sequenced readswere filtered by removing reads containing adapters, reads containing more then 10% undetermined bases, and with a Qscore<=5
Quality filtered and trimmed sequences were mapped against the human genome using HISAT2 (v2.2.1)
Mapped reads were converted to counts using FeatureCounts (v2.0.1)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Matrix table (tab-delimited .txt format) with raw gene counts for every gene and every sample. Annotations include ENTREZID, SYMBOLS, GENE NAMES, and transcript lengths

source_name: 3D-organoids cultured in BME

growth_protocol: Intrahepatic cholangiocyte organoids (ICOs) were initiated and cultured using an established protocol. In brief, donor liver tissue (0.5~1 cm3) was minced, rinsed twice with Earle's balanced salt solution (EBSS, Thermo-Fisher, Waltham, USA), and digested in collagenase solution (2.5 mg/ml collagenase Type A, Sigma-Aldrich, St. Louis, USA) in Advanced DMEM/F-12 medium (Invitrogen, Carlsbad, USA) for 15 minutes at 37 °C. Cold Advanced DMEM/F-12 was added to stop the digestion. The single-cell suspension was filtered using a 70 µm Nylon cell strainer and centrifuged at 1500 rpm, 5 minutes, at 4°C. After that, the cell pellets were collected at the bottom and subsequently mixed with BME (Basement Membrane Extract, Type 2, R&D Systems, Minneapolis, USA). Cell droplets were then seeded in multi-well plates. Initiating medium was added after the solidification of BME and the cells were cultured at 37 °C in a humidified atmosphere with 5% CO2. After three days of culture in initial medium, the cells were refreshed with expansion medium in which noggin, Wnt, Y27632, and hES cell cloning recovery supplement were deprived.

extract_protocol:
Total RNA was isolated using the miRNEAsy kit (Qiagen) according to the manufacturer's protocol and eluted in RNAse-free water. Samples were mRNA enriched using oligodT
Library construction was performed at the Novogene sequencing facilities, Cambridge, UK.  In short, purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR. The single strand circle DNA (ssCir DNA) was formatted as the final library.

treatment_protocol:
After culturing over three passages, the ICOs were transferred to a hypoxia workstation (Invivo2, Baker Ruskinn, Maine, USA) to mimic the ischemia-reperfusion injury in vitro. ICOs were cultured in expansion medium and exposed to hypoxia (~1% O2, 5% CO2). The duration of hypoxia was tested ranging from 6 to 120 hours (data not shown). The optimal duration of hypoxia was set at 72 hours based on the response of ICOs transduced with HIF1-a reporter. ICOs were refreshed with expansion medium and switched to normoxic condition (reoxygenation phase, 21% O2, 5% CO2) and cultured for 6 and 24 hours. The bight-field images of ICOs were captured using the EVOS cell imaging system (Thermo-Fisher, Waltham, USA). The average diameter of stimulated organoids was determined in bight-filed images (at least 25 organoids per subgroup) in triplicate using Image J software (NIH) as previously described before.
Hypoxic Growth conditions (specific for this Sample):  Culturing in expansion medium under normal atmospheric gas conditions with 5% CO2

value: Liver

tag: gender

value: M

value: Cholangicoyte organoids

value: Reoxygenation (6 hours)

tag: sample id in manuscript


title: MM6_shRNA-1_rep1

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shRNA-1_rep1


title: K1 - Nutlin - rep2 [RNA-seq]

value: papillary thyroid carcinoma

value: Nutlin


title: B6 Liver TM Replicate 1

value: 15-23 weeks

value: Male

value: TM


title: LAD2 mast cells, IL-33 treatment, replicate 7 [R1974]

city: Southampton

first: Anna

last: Willis

address: Southampton General Hospital, Tremona Road

country: United Kingdom

institute: University of Southampton

data_processing:
Alignment of RNA-seq data was performed using HISAT2
Counts data was extracted from HISAT2 output using SAMtools
Assembly: hg38
Supplementary files format and content: .csv file, raw counts

source_name: LAD2 Mast Cell

extract_protocol:
RNA was extracted using a Monarch total RNA miniprep kit
RNA libraries for RNA-seq were prepared using Novogenes's library construction protocol

value: LAD2 Mast Cell

value: Mast cell


title: neoAC CellC #2

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Illumina bcl2fastq v2.20 software was used for basecalling
RNA-seq reads were mapped to mouse genome (GRCm38/p5) with STAR (version 2.7.3a) using the following parameters:  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Reads were assigned to genes with featureCounts (-t exon -g gene_id, version 2.0.1) using Gencode GRCm38/vM12 gene annotation
Genome_build: GRCm38/p5
Supplementary_files_format_and_content: Tab delimited text file with raw read counts per gene for each sample

source_name: cultured neonatal astrocytes

growth_protocol: Astrocytes generated from embryonic stem cells (AGES) were differentiated from neural stem cells (NSCs) using BMP4. Adult and neonatal astrocytes were isolated from mouse brains using magnetic activated cell sorting (ABDK Kit, Miltenyi).

extract_protocol:
Total RNA from frozen cell pellets or astrocytic cultures was isolated using the NucleoSpin miRNA kit (Macherey Nagel, 740971-250)
RNA sequencing libraries were prepared using the TruSeq™ Stranded mRNA Library Prep kit (20020594, Illumina) starting from 100 ng of total RNA (RIN ≥7) on an epMotion® 5075 TMX workstation (Eppendorf)


title: Patient Derived Xenograft model BCM-3104

city: Houston

first: Michael

middle: T

last: Lewis

state: TX

address: 1 Baylor Plaza N1210

department: Breast Center

institute: Baylor College of Medicine

description: RNAseq of human HER2+ tumor tissue graft on mouse mammary fat pad

data_processing:
Raw reads were split into human/epithelial (graft) and murine/stromal (host) reads using Xenome v1.0.1
Human and Mouse reads were aligned to hg38 and mm10 reference genomes respectively using RSEM/STAR v2.5.3a_modified
The above STAR run was run internally by rsem-calculate-expression (RSEM v1.2.31), which then quantified transcripts and genes, producing isoform and gene level results.
Genome_build: hg38/mm10
Supplementary_files_format_and_content: A matrix file was generated using expected counts values from RSEM results. Each row represents a gene and each column represents a xenograft model

organism:
Homo sapiens
Mus musculus

source_name: Patient-Derived Xenograft

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Rubicon ThruPlex DNA-Seq (protocol: QAM-108-002, kit p/n R400428) library preparation protocolss

treatment_protocol: Not applicable

value: Human breast tumor tissue graft on mouse mammary fat pad

tag: tumor subtype

value: human HER2+ tumor

value: SCID/Bg mouse host

value: untreated


title: LAD2 mast cells, IL-33 control, replicate 7 [R1971]

value: Control


title: MM6_NS_rep1

description: rna-seq_raw_gene_read_count.xlsx: MM6_IGF2BP2_shNS_rep1

value: shNS

value: Human acute myeloid leukemia (AML) cells


title: K1 - Nutlin - rep1 [RNA-seq]


title: K1 - NutlinGSK - rep2 [RNA-seq]

value: NutlinGSK


title: liver, NC2

value: liver

value: 8 weeks

value: control


title: ICO5, 6 hrs reoxygenation after hypoxia

value: Liver

value: F

value: Cholangicoyte organoids

value: Reoxygenation (6 hours)


title: liver, DEX3

value: dexmedetomidine


title: TPC1 - NutlinGSK - rep2 [RNA-seq]

value: papillary thyroid carcinoma


title: K1 - DMSO - rep1 [RNA-seq]

value: DMSO


title: liver, DEX2


title: ICO1, No treatment

treatment_protocol:
After culturing over three passages, the ICOs were transferred to a hypoxia workstation (Invivo2, Baker Ruskinn, Maine, USA) to mimic the ischemia-reperfusion injury in vitro. ICOs were cultured in expansion medium and exposed to hypoxia (~1% O2, 5% CO2). The duration of hypoxia was tested ranging from 6 to 120 hours (data not shown). The optimal duration of hypoxia was set at 72 hours based on the response of ICOs transduced with HIF1-a reporter. ICOs were refreshed with expansion medium and switched to normoxic condition (reoxygenation phase, 21% O2, 5% CO2) and cultured for 6 and 24 hours. The bight-field images of ICOs were captured using the EVOS cell imaging system (Thermo-Fisher, Waltham, USA). The average diameter of stimulated organoids was determined in bight-filed images (at least 25 organoids per subgroup) in triplicate using Image J software (NIH) as previously described before.
Hypoxic Growth conditions (specific for this Sample):  After culturing under hypoxic conditions, ICOs were refreshed with expansion medium and switched to normoxia condition (reoxygenation phase, 21% O2, 5% CO2) and cultured for 6 hours

value: M

value: Normoxia


title: K1 - DMSO - rep2 [RNA-seq]


title: LamCiR_1wk_2 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
L1b

value: Heart

value: 1 week

value: attp2, LamC iR


title: TPC1 - NutlinGSK - rep1 [RNA-seq]


title: Patient Derived Xenograft model BCM-2277

description: RNAseq of human TNBC tumor tissue graft on mouse mammary fat pad

value: Human breast tumor tissue graft on mouse mammary fat pad

value: human TNBC tumor

value: SCID/Bg mouse host

value: untreated


title: liver, NC1

value: liver

value: 8 weeks

value: control


title: liver, DEX1


title: ICO1, Hypoxia treated

treatment_protocol:
After culturing over three passages, the ICOs were transferred to a hypoxia workstation (Invivo2, Baker Ruskinn, Maine, USA) to mimic the ischemia-reperfusion injury in vitro. ICOs were cultured in expansion medium and exposed to hypoxia (~1% O2, 5% CO2). The duration of hypoxia was tested ranging from 6 to 120 hours (data not shown). The optimal duration of hypoxia was set at 72 hours based on the response of ICOs transduced with HIF1-a reporter. ICOs were refreshed with expansion medium and switched to normoxic condition (reoxygenation phase, 21% O2, 5% CO2) and cultured for 6 and 24 hours. The bight-field images of ICOs were captured using the EVOS cell imaging system (Thermo-Fisher, Waltham, USA). The average diameter of stimulated organoids was determined in bight-filed images (at least 25 organoids per subgroup) in triplicate using Image J software (NIH) as previously described before.
Hypoxic Growth conditions (specific for this Sample):  After culturing over three passages, the ICOs were transferred to a hypoxia workstation (Invivo2, Baker Ruskinn, Maine, USA) for 72 hours to mimic the ischemia-reperfusion injury in vitro. ICOs were cultured in expansion medium and exposed to hypoxia (~1% O2, 5% CO2).

value: Liver

value: Cholangicoyte organoids

value: Hypoxia (72 hours)


title: LamCiR_1wk_1 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
L1a


title: attp2_5wk_2 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C5b

value: 5 weeks


title: TPC1 - Nutlin - rep2 [RNA-seq]

value: papillary thyroid carcinoma

value: Nutlin


title: attp2_5wk_5 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C5f


title: ICO5, Hypoxia treated

value: F


title: 15405X11 T+C2 3 (4-OHT+Cer)

first: Ying

last: Li

address: 15 North 2030 East, Eccles Institute of Human Genetics

department: NUIP

description: 15405X11_181015_A00421_0021_BHG3THDMXX_S129_L002

data_processing:
The mouse GRCm38 genome and gene feature files were downloaded from Ensembl release 94
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCount output files combined into a tab-delmited raw count matrix

source_name: Intestinal Organoids

growth_protocol: Intestinal organoids were cultured in IntestiCult™ Organoid Growth Medium (Stemcell Technologies)

extract_protocol:
Total RNA was extracted with RNeasy Pure mRNA Bead Kit (Qiagen, Cat. 180244)
RNA libraries were constructed using Illumina TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold (Human, Mouse, Rat)

treatment_protocol: Matured organoids were treated with vehicle, 4-OHT or 4-OHT plus C2-ceramide (4-OHT+Cer) for 48 hours

tag: tissue/cell type

value: Intestinal Organoids

value: 4-OHT plus C2-ceramide


title: ICO5, No treatment

value: Normoxia


title: attp2_1wk_4 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1e

value: Heart

value: 1 week


title: attp2_5wk_4 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C5e


title: ICO2, 6 hrs reoxygenation after hypoxia

value: M

value: Reoxygenation (6 hours)


title: TPC1 - DMSO - rep1 [RNA-seq]

value: DMSO


title: ICO2, Hypoxia treated


title: TPC1 - GSK - rep2 [RNA-seq]

value: GSK


title: 15405X9 T+C2 1 (4-OHT+Cer)

description: 15405X9_181015_A00421_0021_BHG3THDMXX_S127_L002


title: attp2_5wk_3 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C5d


title: attp2_1wk_2 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1c


title: 18761X2 Sptlc2δIEC

description: 18761X2_210224_A00421_0290_BHVNH3DSXY_S8

data_processing:
Samples were demultiplexed with 10x cellranger mkfastq version 5.0.0 to create fastq files with the R1 cell barcode+UMI and R2 sequence.
Reads were aligned to the mouse genome (refdata-gex-mm10-2020-A from 10X Genomics ) using cellranger count with expected-cells set to 10000 per library
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: Crypts from mouse small intestine

extract_protocol:
The small intestine of Sptlc2fl/fl, Sptlc2δIEC mice was isolated and opened longitudinally, followed by rinsing in cold PBS. The tissue was then sliced into small fragments roughly about 2 mm long. The tissue was incubated in 20mM EDTA-PBS on ice for 60 min, while shaking every 15 min. The tissue was then shaken vigorously and the supernatant was collected as fraction 1 in a new conical tube. The tissue was incubated in fresh 20mM EDTA-PBS and a new fraction was collected every 15 min. Fractions were collected until the supernatant consistent almost entirely with crypts. The final fraction (enriched for crypts) was passed through a 70μm filter and washed twice in PBS. The cell pellets were dissociated with 15ml of TrypLE Express (Invitrogen) for 45 min at 37°C, while shaking every 5 min. The single cell suspension was then passed through a 40μm filter and counted by Countess 3 automated cell counter (ThermoFisher).
Single cells were processed using the 10X genomics Chromium Single Cell 3’ Gene Expression Library protocol v3.1 with UDI. The resulting cDNA barcoded library was sequenced using the NovaSeq 6000 instrument and reagent kit v1.5 with 150x150 bp sequencing at a depth of 200 million read-pairs.

treatment_protocol: Mice were treated with tamoxifen (1 mg per mouse) for two days before crypts isolation

tag: strain background

tag: genetic information

value: Crypts from small intestine


title: TPC1 - GSK - rep1 [RNA-seq]


title: ICO3, 6 hrs reoxygenation after hypoxia

value: Liver


title: 18761X1 Sptlcfl/fl

description: 18761X1_210224_A00421_0290_BHVNH3DSXY_S7

value: Sptlcfl/fl


title: attp2_5wk_1 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C5a


title: 15405X7 Tamoxifen 3 (4-OHT)

description: 15405X7_181015_A00421_0021_BHG3THDMXX_S125_L002


title: 15405X12 T+C2 4 (4-OHT+Cer)

description: 15405X12_181015_A00421_0021_BHG3THDMXX_S130_L002


title: TPC1 - Nutlin - rep1 [RNA-seq]


title: w1118_5wk_4 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK08_w1118_5wk


title: ICO3, Hypoxia treated

value: Cholangicoyte organoids

value: Hypoxia (72 hours)


title: attp2_1wk_5 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1g


title: TPC1 - DMSO - rep2 [RNA-seq]

value: papillary thyroid carcinoma


title: ICO2, No treatment


title: Dual-specificity Aptamer Wnt+ Rep3

city: Baltimore

first: Yi

last: Zhu

address: 511 WBSB, 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins University, School of Medicine

data_processing:
Analysis of the RNA-Seq data was performed on the Galaxy online platform, following the protocols by (Doyle et al., 2021). Sequencing adaptors were trimmed from the raw reads using Trim Galore. Trimmed reads were mapped to the human reference genome (GRCh38.p13) using HISAT2. Mapped reads were counted to each genes by featureCounts. Differential expression of genes was analyzed with DESeq2.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: A csv file generated by DESeq2 that contains the results of differential analysis on every gene, comparing Dual-specificity Aptamer vs. Individual Aptamers in Wnt - samples

source_name: Cultured Cells

growth_protocol: Cells were cultured in DMEM with 1 g/L glucose, pyruvate and GlutaMAX (Gibco), supplemented with 10% heat-inactivated Fetal bovine serum, 200 U/mL penicillin and 200 µg/mL streptomycin.

extract_protocol:
At 24 hr post-transfection, medium was discarded, and cells were lysed using 1 mL of TRIzol Reagent per culture dish. Lysates were mixed by pipetting, transferred into a Phasemaker tube (Invitrogen A33248) and incubated at room temperature for 5 min. The aqueous phase was separated by adding 200 μL chloroform, thoroughly vertexing and spinning at 12,000 rcf for 15 min at 4 °C. The upper aqueous layer was carefully collected without toughing the other layers. RNA was precipitated with isopropanol, washed with 70% ethanol, dissolved in nuclease-free water, and submitted to GENEWIZ (South Plainfield, NJ, USA) for sequencing.
Library construction was performed by GENEWIZ.

treatment_protocol: 2E6 HEK293T cells were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+). Ac5S, the OGT inbititor, was added into culture media at 50 μM at 4 hr post-transrection and present in all fresh media since then.

value: Cells were treated with 50 μM Ac5S for 20 hr.


title: attp2_1wk_3 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1d


title: w1118_5wk_3 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK07_w1118_5wk

value: 5 weeks


title: HDAC1 over-expressed in SH-SY5Y cells rep2

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

description: HDAC1 over-expressed

data_processing:
Raw data were cleaned with Trimmomatic
Cleaned reads were mapped to hg38 genome using bowtie2
The sam files were transformed into count matrix using the featureCounts function of the Rsubread package
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

growth_protocol: SH-SY-5Y cells were cultured under standard conditions (37 °C, 5% CO2, 95% air) in Advanced MEM/F12 supplemented with 10% (vol/vol) FBS, 25 mM Hepes, glutamax, primocin (100 μg/mL), and geneticin (250 μg/mL). SH-SY-5Y stably transfected with lentivirus overexpressing HDAC1(LV-HDAC1) and the control lentivirus (LV-con).The lentivirus were purchased from Shanghai Genchem.

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

treatment_protocol: One replicate of these cells was treated for 48 hours.

tag: genotype

value: HDAC1 Over-expression


title: ICO3, No treatment


title: HDAC1 over-expressed in SH-SY5Y cells rep1

description: HDAC1 over-expressed


title: 15405X8 Tamoxifen 4 (4-OHT)

description: 15405X8_181015_A00421_0021_BHG3THDMXX_S126_L002

value: Intestinal Organoids


title: Dual-specificity Aptamer Wnt+ Rep2


title: 15405X4 Control 4 Vehicle

description: 15405X4_181015_A00421_0021_BHG3THDMXX_S122_L002

value: vehicle


title: w1118_5wk_1 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK05_w1118_5wk

value: Heart


title: attp2_1wk_1 (RNA-seq)

description:
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1b

value: 1 week


title: Control samples rep2

description: control

value: Control


title: 15405X10 T+C2 2 (4-OHT+Cer)

description: 15405X10_181015_A00421_0021_BHG3THDMXX_S128_L002

value: 4-OHT plus C2-ceramide


title: Dual-specificity Aptamer Wnt+ Rep1


title: Control samples rep1

description: control


title: 15405X6 Tamoxifen 2 (4-OHT)

description: 15405X6_181015_A00421_0021_BHG3THDMXX_S124_L002


title: Individual Aptamers Wnt+ Rep2


title: Individual Aptamers Wnt+ Rep3


title: 15405X2 Control 2 Vehicle

description: 15405X2_181015_A00421_0021_BHG3THDMXX_S120_L002


title: Individual Aptamers Wnt+ Rep1


title: P1_R

city: Tianjin

first: 傅

last: 雪航

state: Tianjin

address: heping

institute: CAMS & PUMC

data_processing:
Raw data (raw reads) of fastq format were firstly processed through CASAVA. In this step, clean data (clean reads) were obtained by removing reads adapter related, reads containing N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using HISAT2 and paired-end clean reads were aligned to the reference genome using HISAT2
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include  FPKM values for each Sample

source_name: bone marrow mononuclear cells

extract_protocol:
Mononucleated cells from bone marrow samples was isolated using Ficoll ,total RNA was isolated from bone marrow samples using TRIzol reagent according to the manufaturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow mononuclear cells

tag: time

value: after BiTE therapy


title: Dual-specificity Aptamer Wnt- Rep2


title: Dual-specificity Aptamer Wnt- Rep1


title: 15405X1 Control 1 Vehicle

description: 15405X1_181015_A00421_0021_BHG3THDMXX_S119_L002


title: 15405X3 Control 3 Vehicle

description: 15405X3_181015_A00421_0021_BHG3THDMXX_S121_L002


title: P1_Pre

value: before BiTE therapy


title: Dual-specificity Aptamer Wnt- Rep3


title: 20660_APPHKO_F

city: MINNEAPOLIS

first: Ling

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

data_processing:
Base calling was done with RTA3 software in the NovaSeq 6000 system.
3' trimming for Illumina adapters was performed using trimmomatic v0.33, and quality control of reads were performed using FastQC v0.11.7
Sequence reads were aligned to Mus musculus genome (mm10) using HISAT2 v2.1.0.
Cleaned and name-sorted alignments were processed with the featureCounts tool.
Genome_build: mm9
Supplementary_files_format_and_content: A matrix table with raw gene counts of every gene (in ensembl ID and gene symbols) for all 12 samples in CSV format

source_name: cortex

extract_protocol:
Total RNA was extracted from the frontal cortex using AurumTM Total RNA Fatty and Fibrous Tissue Kit (732-6830; Bio-Rad) following the manufacturer’s instructions. RNA quantity was measured using Quant-iT RiboGreen Assay Kit (Thermofisher), and the quality was determined by the Agilent Bioanalyzer system.
mRNA libraries were prepared following Illumina TruSeq Stranded mRNA library prep workflow

value: F

tag: rin


title: w1118_1wk_4 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK04_w1118_1wk


title: Patient Derived Xenograft model BCM-7821

description: RNAseq of human TNBC tumor tissue graft on mouse mammary fat pad

value: Human breast tumor tissue graft on mouse mammary fat pad

value: human TNBC tumor

value: SCID/Bg mouse host

value: untreated


title: 15405X5 Tamoxifen 1 (4-OHT)

description: 15405X5_181015_A00421_0021_BHG3THDMXX_S123_L002


title: Patient Derived Xenograft model BCM-15006


title: w1118_1wk_3 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK03_w1118_1wk


title: Individual Aptamers Wnt- Rep2

value: Cells were treated with 50 μM Ac5S for 20 hr.


title: Patient Derived Xenograft model BCM-15003


title: w1118_5wk_2 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK06_w1118_5wk

value: 5 weeks


title: 20570_APPHKO_F


title: Patient Derived Xenograft model BCM-7482


title: 20793_APPHKO_M

value: M


title: Individual Aptamers Wnt- Rep3


title: w1118_1wk_2 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK02_w1118_1wk


title: Dual-specificity Aptamer_Wnt+_Rep3

data_processing:
Analysis of the RNA-Seq data was performed on the Galaxy online platform, following the protocols by (Doyle et al., 2021). Sequencing adaptors were trimmed from the raw reads using Trim Galore. Trimmed reads were mapped to the human reference genome (GRCh38.p13) using HISAT2. Mapped reads were counted to each genes by featureCounts. Differential expression of genes was analyzed with DESeq2.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: A csv file generated by DESeq2 that contains the results of differential analysis on every gene, comparing Individual Aptamers vs. Dual-specificity Aptamers in Wnt - samples
Supplementary_files_format_and_content: A csv file generated by DESeq2 that contains the results of differential analysis on every gene, comparing Individual Aptamers vs. Dual-specificity Aptamers in Wnt + samples

treatment_protocol: 2E6 HEK293T cells were seeded per 10cm dish and transfection was performed after 24 hr (at 40% - 60% confluency). 1.5 μg of plasmids encoding Individual or Dual-speficity aptamers were dissolved in 100 μL Opti-MEM medium. 6 μg of TransIT-X2 Transfection Reagent (Mirus Bio) was added to the mixture, incubated at room temperature for 20 min and distributed evenly into the cell culture. Media were changed to fresh DMEM at 6 hr post-transfection. At 20 hr post-transfection, culture media were changed to fresh DMEM (Wnt-) or 50% (v/v) Wnt3A-conditioned DMEM (Wnt+).

tag: cell line


title: NSG ID8, ABX, Cisplatin, Replicate 4

city: Cleveland

first: Peter

last: Bazeley

state: OH

address: 9500 Euclid Avenue

department: Lerner Research Institute

institute: Cleveland Clinic

data_processing:
Adapter removal and quality trimming was performed with Trimgalore (version 0.5.0).
Adapter removed, trimmed reads were aligned to the Mus musculus genome assembly (GRCm38 version 99, ftp://ftp.ensembl.org/pub/release99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz) using STAR (version 2.6.1d).
Aligned reads were counted at the exon level and summarized at the gene level with the featureCounts tool from the Subread package (version 1.6.4), using annotations for build GRCm38 (version99,ftp://ftp.ensembl.org/pub/release99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz)
Assembly: GRCm38
Supplementary files format and content: featureCounts - paired-end, reversely stranded, exons summarized to genes - Ensembl Gene ID, Gene Length, Read Count

molecule: polyA RNA

source_name: ovarian surface epithelium cell line

extract_protocol:
Tumors were collected at endpoint from NSG ID8 mice and snap frozen in liquid nitrogen. Prior to RNA extraction (Takara Nucleospin), tumors were crushed using ice-cold mortar and pestle under sterile conditions.
Following RNA isolation, cDNA libraries were prepared by the LRI Genomics Core facility and sent to Macrogen Inc. for RNA sequencing.

value: ovarian surface epithelium cell line

tag: cell type

value: epithelium

tag: antibiotics

value: ABX

tag: chemotherapy

value: Cisplatin


title: 20659_APPHKO_F


title: Dual-specificity Aptamer_Wnt+_Rep2


title: Individual Aptamers Wnt- Rep1

tag: strain

tag: treatment


title: NSG ID8, H2O, Placebo, Replicate 3

value: Placebo


title: NSG ID8, ABX, Cisplatin, Replicate 3


title: Patient Derived Xenograft model BCM-0104


title: Patient Derived Xenograft model BCM-0132


title: w1118_1wk_1 (RNA-seq)

description:
w1118 1 and 5 week _normalizedCounts
NK01_w1118_1wk

value: Heart

tag: age

value: 1 week


title: 20670_APPHKO_M

tag: Sex


title: NSG ID8, H2O, Placebo, Replicate 2

tag: tissue


title: Patient Derived Xenograft model BCM-0113

extract_protocol:
PDX tumor were harvested from mice and trimmed of excess fat pad tissue. Representative tumor fragments were snap frozen in liquid nitrogen. Tumor was homogenized and RNA extracted using the RNeasy Mini Kit from Qiagen.
NuGEN Ovation RNA-Seq v2 Kit (protocol p/n 7102, kit p/n 7102-08) along with ThermoFisher’s ERCC RNA Spike-In Control Mixes Protocol (publication number 4455352, rev. D) and the Rubicon ThruPlex DNA-Seq (protocol: QAM-108-002, kit p/n R400428) library preparation protocols


title: Patient Derived Xenograft model BCM-7649


title: NSG ID8, ABX, Cisplatin, Replicate 2


title: NSG ID8, H2O, Cisplatin, Replicate 4


title: Patient Derived Xenograft model BCM-0046


title: NSG ID8, H2O, Cisplatin, Replicate 3


title: 20598_APP_F


title: Individual Aptamers_Wnt+_Rep3


title: Dual-specificity Aptamer_Wnt+_Rep1


title: Individual Aptamers_Wnt+_Rep1


title: NSG ID8, ABX, Placebo, Replicate 2


title: Individual Aptamers_Wnt+_Rep2


title: 20464_APP_F


title: Dual-specificity Aptamer_Wnt-_Rep3


title: 20459_APP_M


title: 20676_APP_F


title: 20458_APP_M


title: NSG ID8, H2O, Placebo, Replicate 1


title: Sema4D rep3

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

country: Japan

institute: Osaka University

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were mapped to mm10 using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
FPKMs was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: articular chondrocytes

extract_protocol:
Total RNA was isolated using  Nucleospin RNA Plus kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary articular chondrocytes were stimulated with or without semaphorin 4D.

value: ICR

value: Primary articular chondrocytes

value: cartilage

value: postnatal 4 days

value: semaphorin 4D


title: Individual Aptamers_Wnt-_Rep3


title: 20563_APPHKO_M


title: NSG ID8, H2O, Cisplatin, Replicate 2


title: Sema4D rep2


title: Dual-specificity Aptamer_Wnt-_Rep2


title: Individual Aptamers_Wnt-_Rep2


title: NSG ID8, ABX, Placebo, Replicate 1


title: Sema4D rep1


title: Individual Aptamers_Wnt-_Rep1


title: rat colon, fresh frozen, rep D, experiment 1

city: Cambridge

last: Lyubetskaya

address: 100 Binney St

institute: Bristol-Myers Squibb

description:
Illumina NextSeq 550
Visium ST library

data_processing:
All sequencing outputs were processed using SpaceRanger-1.2.1 (10x Genomics) with rat (Rnor6.0ERCC-ensembl98), mouse (mm10-2020-A), and human (GRCh38-2020-A) references.
Assembly: Rnor6.0ERCC-ensembl98, mm10-2020-A, GRCh38-2020-A
Supplementary files format and content: 10x Genomics SpaceRanger output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5, scalefactors_json.json, tissue_hires_image.png, tissue_positions_list.csv
Supplementary files format and content: Full scale TIFF images
Library strategy: ST RNAseq (Visium and Visium for FFPE)

organism: Rattus norvegicus

source_name: Colon

growth_protocol: B16F10 and MC38 mouse tumor samples were grown by subcutaneous implantation of 1e6 or 1.5e6 B16F10 or MC38 cells, respectively, into the flank of female C57BL/6 mice. Tumors were harvested 10 days (d10) or 16 days (d16) post-implantation.

extract_protocol:
Rat colons were collected from 6-8 week-old Sprague-Dawley rats and were rinsed with ice-cold PBS before O.C.T. or FFPE embedding. Mouse syngeneic tumors were collected in ice-cold PBS before O.C.T. embedding. O.C.T. embedding was accomplished by placing tissue in a cryomold with ice-cold TissueTek O.C.T. Compound on an aluminum block pre-cooled in a dry ice ethanol bath. FFPE tissues were first placed in 10% neutral buffered formalin for 24-hour fixation, after which tissue was processed for embedding in a Sakura VIP automated system with vacuum/pressue cycles, dehydrating in graded alcohols to xylene and then paraffin, and embedded into blocks for sectioning.  All tumor resection smples were obtained with informed concesnt from BioIVT and Discovery Life Sciences. The Donor-A tumor (BioIVT) was divided prior to fixation, one half was O.C.T. embedded, the other half was FFPE embedded.
All mouse B16F10 and MC38 samples, and fresh-frozen (FF) rat colon and Donor-A PDAC samples were processed with the Visium Spatial Gene Expression kit (10X Genomics, PN-1000184) according to manufacturer protocol (10X Genomics, CG000160 Rev A and CG000238 Rev D for sectioning/staining and library preparation, respecitvely). Rat colon FF samples with a coverslip (wCS) were coverslipped during imaging, according to manufacturer protocol (10X Genomics, CG000160 RevA). Rat colon and Donor-A FFPE polyA-capture (FFPE-pA) samples were processed as described in Villacampa, et al., Cell Genomics 2021, using reagents from the Visium Spatial gene Expression kit (10X Genomics, PN-1000184), with a modified permeabilization, using 2X permeabilization enzyme for 60 minutes (permebailization enzyme was dissovled at 4 mg/ml (4X) in 0.1 N HCl and diluted to 2X in 0.1 N HCl). Donor A-C FFPE probe samples (FFPE-probes) were processed according to the Visium FFPE Regeant kit with Human Transcriptome Probe kit (10X Genomics, PN-100362 and PN-1000364) according to manufacturer protocol (10X Genomics, CG000409 Rev A and CG000407 Rev A for sectioning/staining and library preparation, respectively).

value: Colon


title: NSG ID8, ABX, Cisplatin, Replicate 1


title: 20770_APP_M


title: JY_20_IM_Control_WGP_2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
The annotation file was parsed to exclude mitochondria and ribosomal protein genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 21,965 gene locations.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: IM Control WGP

growth_protocol: 6-8 weeks old C57Bl/6 mice maintained under Specific Pathogen Free (SPF) conditions with 12 hrs light/dark cycle and 55% humidity.

extract_protocol:
PBS vs WGP-trained mice were euthanized on Day 7 following treatment to harvest the lungs. Lungs were digested and processed to obtain single cell suspensions. The Lung single cell suspensions were stained with fluorochrome-labelled antibodies to obtain the Lung Interstitial macrophages. Cells were then washed with Ice-cold PBS, stored in TRIzol followed by RNA extraction (QIAGEN RNAeasy Kit), quantification IQubit fluorometric assay) and sequencing.
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN Cat# 0520-24) and PolyA selection.

treatment_protocol: 6-8 weeks old C57Bl/6 mice maintained under Specific Pathogen Free (SPF) conditions were injected intra-peritoneally with 1mg of WGP or PBS for 6 days.

value: Interstitial macrophage

value: B-Glucan (WGP)


title: Dual-specificity Aptamer_Wnt-_Rep1


title: 1-chloro-3-(4-chlorophenoxy) benzene_3

type: RNA

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

description: Gene expression after 24hr exposure of 1-chloro-3-(4-chlorophenoxy) benzene (30 µM)

hyb_protocol: The labeled samples were hybridized to the SurePrint G3 GE 8×60K Ver 2.0 Microarray (Agilent Technologies, Palo Alto, CA, USA) with rotation at 10 rpm for 17 h at 65°C.

scan_protocol: After hybridization, the microarray chips were washed with the Gene Expression Wash Pack (Agilent Technologies, Palo Alto, CA, USA) and scanned with a DNA microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing: All microarray data were processed using Genespring GX 14.5 (Agilent Technologies, Palo Alto, CA, USA). These data were normalized and modified using quality control flags.

source_name: hepatocytes, 24h, 1-chloro-3-(4-chlorophenoxy) benzene, 30 µM

label_protocol: RNA was converted to cDNA and then the labeled cRNA were produced from the cDNA using the Low Input Quick Amp Labeling kit (Agilent Technologies, Palo Alto, CA, USA).

growth_protocol: Cryopreserved male Sprague Dawley rat primary hepatocytes (KaLy-Cell, Plobsheim, France) were used for in vitro assay. The cells were cultured at 37°C with 5% CO2 in the supplied medium (Kurabo, Osaka, Japan).

extract_protocol: After the 24 hours exposure with each chemical, total RNAs were extracted from rat primary hepatocytes using the miRNeasy kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. For elucidating the gene expression profile, 100 ng of RNA in total were used for microarray analysis.

treatment_protocol: After 24 h pre-culture, the cells were exposed to each chemical at 30 µM for 24 h.

value: primary hepatocytes

tag: treatment/time point

value: Sprague Dawley

tag: gender

value: Male


title: Diclosan_2

description: Gene expression after 24hr exposure of Diclosan (30 µM)

source_name: hepatocytes, 24h, Diclosan, 30 µM

value: after 24hr exposure of Diclosan (30 µM)


title: Triclosan_2

description: Gene expression after 24hr exposure of Triclosan (30 µM)

source_name: hepatocytes, 24h, Triclosan, 30 µM


title: 1-chloro-3-(4-chlorophenoxy) benzene_2

value: after 24hr exposure of 1-chloro-3-(4-chlorophenoxy) benzene (30 µM)


title: NSG ID8, H2O, Cisplatin, Replicate 1

value: ovarian surface epithelium cell line

value: epithelium

value: Cisplatin


title: Diclosan_3


title: JY_19_IM_Control_WGP_1


title: Control rep1

value: control


title: rat colon, fresh frozen, rep B, experiment 1

description:
Illumina NextSeq 550
Visium ST library


title: Diclosan_1


title: JY_14_IM_Control_PBS_2

source_name: IM Control PBS

value: PBS


title: JY_21_IM_Control_WGP_3


title: 30_WT (F480Low CD11b High Macrophages)

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Demultiplex with Casava
Alignment with Hisat2
Genome_build: Mm10

source_name: Kidney

growth_protocol: Cell suspensions were prepaired fresh from murine kidneys

extract_protocol:
Samples were homoginised in RLT+ (Qiagen) and RNA extracted with Rneasy plus micro kit (Qiagen)
Libraries were constructed with Takara pico input stranded

treatment_protocol: Cells were stimulated with 100 ng/ml LPS in complete RPMI for 2hrs at 37C with 5% CO2 after which cells were sorted as F4/80 low CD11b high

value: WT


title: Control rep2

value: ICR

value: Primary articular chondrocytes

value: cartilage


title: 29_WT (F480Low CD11b High Macrophages)


title: rat colon, fresh frozen, rep A, experiment 1

description:
Illumina NextSeq 550
Visium ST library

value: Colon


title: JY_15_IM_Control_PBS_3

value: Interstitial macrophage


title: Control rep3

value: postnatal 4 days


title: rat colon, fresh frozen, rep D, experiment 2

description:
Illumina NextSeq 550
Visium ST library


title: cre1-91 deletion mutant [C. cinerea AmutBmut], replica 2

city: Szeged

first: Botond

last: Hegedüs

state: Csongrád-Csanád

address: Temesvári krt. 62

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Center

description:
Cre1_91_2
QuantSeq 3′ mRNA-Seq library

data_processing:
Adapter sequences, polyA reads, and low-quality tails were removed using bbduk version 38.92.
Trimmed reads were mapped to the reference genome using STAR version 2.6.1a_08-27.
Only CDS gene annotations were considered in the read to gene assignment step with a 400 bp overhang added at the 3' ends of each gene. For the assignment, the featureCounts version Rsubread_2.6.4 function of the Rsubread package was used.
For differential gene expression analysis, library read count normalization, the edgeR version 3.34.0 and limma version 3.48.3 packages were used.
Assembly: JGI: Coprinopsis cinerea Amut1Bmut1 pab1-1 v1.0
Supplementary files format and content: tab-delimited text files include raw count values for each Sample [CopciAB_QuantSeq_rawcounts_allsamples.tsv]
Supplementary files format and content: tab-delimited text files include normalized data (CPM values) for each Sample [CopciAB_QuantSeq_CPM_allsamples.tsv]

organism: Coprinopsis cinerea AmutBmut pab1-1

source_name: Vegetative mycelium

growth_protocol: All colonies were grown on YMG medium (0.2% glucose) overlaid with cellophane for 84 hrs in the dark at 28°C. Mycelia were collected and homogenised in liquid nitrogen using a mortar and pestle.

extract_protocol:
Total RNA was isolated using the Quick RNA mini kit (Zymo Research, USA)
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3 mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Vegetative mycelium

value: cre1-91 deletion mutant


title: JY_13_IM_Control_PBS_1


title: Triclosan_3

value: primary hepatocytes

value: after 24hr exposure of Triclosan (30 µM)

value: Sprague Dawley

value: Male


title: 1-chloro-3-(4-chlorophenoxy) benzene_1

value: after 24hr exposure of 1-chloro-3-(4-chlorophenoxy) benzene (30 µM)


title: rat colon, fresh frozen, rep C, experiment 1

description:
Illumina NextSeq 550
Visium ST library


title: cre1-91 deletion mutant [C. cinerea AmutBmut], replica 1

description:
Cre1_91_1
QuantSeq 3′ mRNA-Seq library


title: Triclosan_1


title: rat colon, fresh frozen, rep C, experiment 2

description:
Illumina NextSeq 550
Visium ST library


title: VC_DMSO_2

description: Gene expression after 24hr exposure of control (DMSO)

source_name: hepatocytes, 24h, DMSO

value: after 24hr exposure of control (DMSO)


title: VC_DMSO_3


title: 26_KI (F480Low CD11b High Macrophages)

value: KI


title: cre1-43 deletion mutant [C. cinerea AmutBmut], replica 2

description:
Cre1_43_2
QuantSeq 3′ mRNA-Seq library

value: cre1-43 deletion mutant


title: VC_DMSO_1


title: LSCs, cxcl12_WT4_1

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The quality of the samples was verified using FASTQC software. FASTQ files were mapped to mouse genome assembly version GRCm38, UCSC version M25, using Salmon version 1.3 using default parameters.
Gene expression quantification were then imported to R using tximport package
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file including Matrix table with raw count values for each gene

source_name: Bone marrow

extract_protocol:
Bone marrow cells were harvested from  bones and LSCs were sorted by Fluorescence-activated cell sorting according to the manuscript methods description. Low input 3´end RNA-Seq was performed following Massively Parallel RNA sequencing (MARS-Seq) protocol adapted for bulk RNA-Seq and sequenced using Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Leukemia stem cells (LSCs)

value: Prx1-Cxcl12-wild type


title: LSCs, cxcl12_WT4_2


title: rat colon, fresh frozen, rep B, experiment 2

description:
Illumina NextSeq 550
Visium ST library


title: 25_KI (F480Low CD11b High Macrophages)


title: cre1-43 deletion mutant [C. cinerea AmutBmut], replica 1

description:
Cre1_43_1
QuantSeq 3′ mRNA-Seq library


title: rat colon, fresh frozen, rep A, experiment 2

description:
Illumina NextSeq 550
Visium ST library


title: 21_WT (F480Low CD11b High Macrophages)

value: WT


title: LSCs, cxcl12_WT3_1


title: control strain [C. cinerea AmutBmut], replica 3

description:
Wild_type_3
QuantSeq 3′ mRNA-Seq library

value: control strain


title: LSCs, cxcl12_WT3_2


title: rat colon, FFPE, rep D, experiment 3

description:
Illumina NextSeq 550
Visium ST library, modified for FFPE polyA-capture

value: Colon


title: 24_KI (F480Low CD11b High Macrophages)


title: 27_KI (F480Low CD11b High Macrophages)


title: 20_KO (F480low CD11b High Macrophages )

value: KO


title: control strain [C. cinerea AmutBmut], replica 1

description:
Wild_type_1
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: rat colon, FFPE, rep C, experiment 3


title: LSCs, cxcl12_WT2_2


title: rat colon, FFPE, rep A, experiment 3


title: LSCs, cxcl12_WT2_1


title: 19_KO (F480low CD11b High Macrophages )


title: 18_KO (F480low CD11b High Macrophages )


title: LSCs, cxcl12_WT1_2


title: rat colon, fresh frozen, rep C, experiment 4

description:
Illumina NextSeq 500 and NextSeq 550 (merged)
Visium ST library


title: 16_KO (F480low CD11b High Macrophages )


title: 14_WT (F480low CD11b High Macrophages )


title: LSCs, cxcl12_MUT8_2


title: rat colon, fresh frozen, rep D, experiment 4


title: rat colon, fresh frozen, with coverslip, rep B, experiment 4


title: control strain [C. cinerea AmutBmut], replica 2

description:
Wild_type_2
QuantSeq 3′ mRNA-Seq library


title: rat colon, fresh frozen, with coverslip, rep A, experiment 4


title: root nodules, MG136 Infected, rep 6

city: Barcelona

first: Lucas

middle: Esteban

last: Wange

address: Dr. Aiguader 88

department: Institut de Biologia Evolutiva

institute: Universitat Pompeu Fabra

description:
ACCCGG
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

data_processing:
demultiplexing, deML
adapter trimming, cutadapt, version 3.4
mapping and counting, zUMIs, version 2.5.4
normalisation and differential expression analysis, DESeq2
Assembly: L. japonicus Gifu v1.2
Supplementary files format and content: raw count matrix as generated by zUMIs
Supplementary files format and content: normalized count matrix as generated by DESeq2

organism: Lotus japonicus

source_name: root nodules

growth_protocol: Lotus japonicus seeds were surface sterilized with 1.2% NaClO, soaked with sterile water for 2 h, and germinated in 0.8% agar plates with ½ Gamborg B5 medium. Seeds were kept at 24 °C for 3 days in darkness, followed by 3 days under a long day photoperiod (16h:8h, light:dark).

extract_protocol:
Six biological replicates were collected for each accession (Infected: MG-70, MG-79, MG-136; Non-infected: MG-9, MG-112, MG-115). Each biological replicate comprised 20 nodules from at least 5 different plants. Nodules were harvested 5 wpi. Total RNA was extracted using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions and treated with DNAse I (Ambion)
prime-seq RNA-sequencing
poly A enrichment, three prime counting

treatment_protocol: For phenotypic screening, 30 seedlings of each L. japonicus accession were transplanted into sterile Tulip-shaped Weck jars (WECK). Each jar contained 10 seedlings grown on 300 ml of a sand:vermiculite mixture (1:2) supplemented with 40 ml of FAB medium. Two days after transferring, seedlings were inoculated with 1 ml of a R. leguminosarum Norway-GFP suspension (OD600 = 0.005) previously washed with sterile water. Plants were grown under a long day photoperiod at 24 °C. Five weeks post inoculation (wpi) plants were harvested and phenotyped.

tag: accession

value: root nodules

tag: phenotype

value: Infected

tag: infection

value: sub-compatible Rhizobium strain


title: 13_WT (F480low CD11b High Macrophages )

tag: genotype


title: LSCs, cxcl12_MUT8_1


title: 12_WT (F480low CD11b High Macrophages )


title: Young_Phf6-WT_4

city: New York

first: Stuart

middle: Aidan

last: Quinn

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Raw reads were demultiplexed and FASTQ files generated using Bcl2fastq v2.20.0.422 (Illumina)
Reads were aligned to the mouse genome (GRCm38) with STAR v2.3.5.3a using the Gencode mouse gene annotation for initial junction estimation in 2-pass, paired-end mode with otherwise default alignment parameters.
Gene level read counts were generated using the R function featureCounts (Rsubread v1.6.0).
Read count normalization and differential gene expression testing was performed using DESeq2 v1.20
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene level summarized read counts are provided prior to library size normalization for direct input to DESeq2

source_name: LT-HSC

extract_protocol:
Fresh LT-HSCs (Lin- Sca-1+ CD117+ CD135- CD150+ CD48-) were FACS-sorted from lineage depleted (mouse lineage depletion kit; Miltenyi Biotec) bone marrow harvested from Phf6-WT and Phf6-KO mice at 16-weeks and 24-months of age. Cells were sorted directly into RLT buffer and total RNA was extracted using the RNAeasy mini kit (Qiagen).
Total RNA concentration was determined using the Qubit RNA HS assay and the RNA Integrity Number (RIN) was measured using the Bioanalyzer system (Agilent) for each total RNA isolate. Only samples with a RIN greater than 8 were used to construct RNA-seq libraries.  RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories; cat. #634888) and sequencing-ready libraries were generated using the Low Input Library Prep Kit v2 (Clontech Laboratories; cat. #634899). Library concentrations were determined using the Qubit dsDNA HS Assay Kit (Invitrogen; cat. #Q32854)

value: bone marrow

value: LT-HSC

tag: developmental stage

value: Young


title: LSCs, cxcl12_MUT7_2


title: root nodules, MG70 Infected, rep 3

description:
ACGCGC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: root nodules, MG115 Non-Infected, rep 4

description:
CTCTCC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Non-Infected


title: root nodules, MG112 Non-Infected, rep 6

description:
CCACGC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: root nodules, MG115 Non-Infected, rep 3

description:
CAGCGC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: Young_Phf6-WT_3


title: LSCs, cxcl12_MUT7_1


title: 20_WT (F480Hi CD11blo Macrophages)

treatment_protocol: Cells were stimulated with 100 ng/ml LPS in complete RPMI for 2hrs at 37C with 5% CO2 after which cells were sorted as F4/80 high CD11b low


title: root nodules, MG70 Infected, rep 4

description:
TTGTCC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: Young_Phf6-WT_2


title: root nodules, MG79 Infected, rep 5

description:
GTCAAG
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: LSCs, cxcl12_MUT6_2


title: 19_WT (F480Hi CD11blo Macrophages)


title: Young_Phf6-WT_1


title: LSCs, cxcl12_WT1_1


title: LSCs, cxcl12_MUT6_1


title: 17_KI (F480Hi CD11blo Macrophages)

value: KI


title: root nodules, MG112 Non-Infected, rep 1

description:
CGACTT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: LSCs, cxcl12_MUT12_2


title: 16_KI (F480Hi CD11blo Macrophages)


title: root nodules, MG112 Non-Infected, rep 5

description:
GGACAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: root nodules, MG70 Infected, rep 5

description:
ATCGAG
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: Young_Phf6-KO_3


title: 15_KI (F480Hi CD11blo Macrophages)


title: Young_Phf6-KO_4


title: LSCs, cxcl12_MUT10_2


title: root nodules, MG79 Infected, rep 3

description:
TTGGAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: 14_KI (F480Hi CD11blo Macrophages)


title: LSCs, cxcl12_MUT12_1


title: 13_WT (F480Hi CD11blo Macrophages)


title: Young_Phf6-KO_1


title: LSCs, cxcl12_MUT10_1


title: 12_WT (F480Hi CD11blo Macrophages)


title: root nodules, MG9 Non-Infected, rep 1

description:
TTATCA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: T8M

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to Ensembl mouse genome GRCm38 using STAR aligner 2.4.2a modified with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --chimSegmentMin 20 --twopassMode None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
Raw counts calculated by STAR aligner with parameter --quantamode were merged to create count matrix. Counts on the second column of each file were used. Downstream paired differential expression analyses (between tumour and normal stroma, developmental and normal stroma) were performed in in R with Bioconductor edgeR Package version 3.28.0 Differentially expressed genes were defined as FDR < 0.1, and absolute value of logFC > 1
Genome_build: GRCm38
Supplementary_files_format_and_content: csv

source_name: AOM/DSS colonic tumour

extract_protocol:
Collected cells were spun at 800 g for 5 minutes.Cells were lysed with 1 ml of trizol, and RNA was isolated using PicoPure™ RNA Isolation Kit (KIT0204, Life Technologies) according to the manufacture’s protocol. DNase treatment were performed with RNase-Free DNase Set (79254, Qiagen) on PicoPure spin columns.
PolyA+ stranded RNA-seq libraries were prepared using the KAPA RNA Hyper Prep kit (Roche). The multiplexed libraries were sequenced on an Illumina NextSeq 500 to obtain a single-end 75 bp read.

treatment_protocol: Four 8-week-old adult mice (2 males and 2 females), four postnatal day 14 mice (2 males and 2 females), and four AOM/DSS-treated mice (2 males and 2 females) were used to isolate colonic cells. Colons were washed three times in Hank’s Balanced Salt Solution (H9394, Sigma) and cut into 0.5 mm pieces with a pair of scissors. Colonic tissue pieces were spun at 450 g for 4 minutes. After discarding the supernatant, the colonic tissues were enzymatically digested with 35.5 mg of type IV collagenase (17104019, Life Technologies) and 1 mg of dispase (17105041, Life Technoogies) in 10 ml of HBSS, at 37 °C for 45 minutes. The digested colonic cells were then filtered through a 40-µm-nylon strainer to remove cell clumps. Cells were stained with the following antibodies: anti-EPCAM-Alexa Fluor 488 (118210, Biolegend), anti-CD31-Alexa Fluor 594 (102520, Biolegend), anti-CD45-APC (103112, Biolegend), and anti-TER119-APC (116212, Biolegend). Dead cells were excluded based on their positive staining for DAPI. FACS-sorting of CD45+ immune cells ,EPCAM+ epithelial cells, CD31+ endothelial cells, and EPCAM-CD31-CD45-TER119- stromal cells was performed using FACSAria Fusion (BD Bioscience). Data analysis was performed using FlowJo version 10.5.3 (LLC, USA).

value: trileanage depleted stroma cells

tag: mouse strain

value: 14 weeks

value: AOM/DSS colonic tumour


title: 9_muMT (F480Hi CD11blo Macrophages)


title: BoHV-1 infected Bos taurus peripheral tonsils 3 hours post DEX treatment, 2

city: Stillwater

first: Clinton

middle: R.

last: Jones

state: Oklahoma

address: 250 McElroy Hall

department: Veterinary Pathobiology

institute: Oklahoma State University

data_processing:
Illumina RTA version 2.11.3, BCL2FASTQ
Mapping reads to Bos taurus genome using bowtie2/2.3.4.1, fastqc/0.11.7, samtools/1.10, trimmomatic/0.38, cufflinks/2.2.1, tophat/2.1.1
Quality control and visualization of differential expression using R 4.2.0 package of cummerBund version 2.38.0
Gene enrichment analyses by submission of official gene names without DE/enrichment values (DAVID) or with DE/enrichment values (STRING, geneontology.org/Panther).
Visualization with R version 4.2.0, Rstudio 2022.07.2+576
Assembly: Bos_taurus.ARS-UCD1.2.101
Supplementary files format and content: PT-gene_exp.diff: contains 1:1 gene exxpression comaprisons between all timepoints which include: the test_id, gene_id, gene, locus, sample_1, sample_2, status value_1, value_2 log2(fold_change), test_stat, p_value, q_value, significant
Supplementary files format and content: PT-genes.fpkm_tracking:  contains gene expression set quality metrics for all timepoints which include: tracking_id, m_count, m_count_variance, m_count_uncertainty_var, m_count_dispersion_var, m_status, t0_count, t0_count_variance, t0_count_uncertainty_var, t0_count_dispersion_var, t0_status t1_count, t1_count_variance, t1_count_uncertainty_var, t1_count_dispersion_var, t1_status, t2_count t2_count_variance, t2_count_uncertainty_var, t2_count_dispersion_var, t2_status, t3_count, t3_count_variance, t3_count_uncertainty_var, t3_count_dispersion_var, t3_status
Supplementary files format and content: PT-genes.read_group_tracking: Contains number of mapped reads for all genes and groups used for normalization in PT-genes.fpkm_tracking. Includes  columns of: tracking_id condition, replicate, raw_frags, internal_scaled_frags, external_scaled_frags, FPKM effective_length, status
Supplementary files format and content: PT-genes.count_tracking: Provides statistics on average read mapping, uncertainty and dispersion variance detection for all differentially expressed genes at each timepoint. Columns include: tracking_id, m_count, m_count_variance, m_count_uncertainty_var, m_count_dispersion_var, m_status t0_count, t0_count_variance, t0_count_uncertainty_var, t0_count_dispersion_var, t0_status, t1_count t1_count_variance, t1_count_uncertainty_var, t1_count_dispersion_var, t1_status, t2_count, t2_count_variance, t2_count_uncertainty_var, t2_count_dispersion_var, t2_status, t3_count, t3_count_variance, t3_count_uncertainty_var, t3_count_dispersion_var, t3_status

organism: Bos taurus

source_name: male Holstein calves

extract_protocol:
Qiagen Total RNA
TruSeq RNA kit

value: peripheral tonsils

tag: breed

value: Holstein

value: male

value: infected

value: Acclimation, BoHV-1 (Cooper) infection, 3 hour Dexamethasone


title: T6M

tag: cell type


title: BoHV-1 infected Bos taurus peripheral tonsils 3 hours post DEX treatment,3

value: WT


title: root nodules, MG79 Infected, rep 4

description:
TTAACT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: root nodules


title: BoHV-1 infected Bos taurus peripheral tonsils 3 hours post DEX treatment, 1


title: T2M

value: 13 weeks


title: 7_muMT (F480Hi CD11blo Macrophages)

value: KO


title: BoHV-1 infected Bos taurus peripheral tonsils 1.5 hours post DEX treatment, 3

value: Acclimation, BoHV-1 (Cooper) infection, 1.5 hour Dexaamethasone


title: T1M

value: 12 weeks


title: root nodules, MG136 Infected, rep 3

description:
TGTATT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Infected

value: sub-compatible Rhizobium strain


title: root nodules, MG70 Infected, rep 1

description:
TATCAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: 4_WT (F480Hi CD11blo Macrophages)


title: root nodules, MG115 Non-Infected, rep 1

description:
TTCATA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Non-Infected


title: root nodules, MG9 Non-Infected, rep 5

description:
TTTATG
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: Young_Phf6-KO_2

value: bone marrow

value: LT-HSC

value: Young


title: 5_WT (F480Hi CD11blo Macrophages)


title: P3M

source_name: Developmental colon

value: trileanage depleted stroma cells

value: 2 weeks

value: Developmental colon


title: P2M


title: BoHV-1 infected Bos taurus peripheral tonsils 1.5 hours post DEX treatment, 2

value: peripheral tonsils

value: Holstein

value: male

value: infected


title: BoHV-1 infected Bos taurus peripheral tonsils 0.5hours post DEX treatment, 3

value: WT

value: Acclimation, BoHV-1 (Cooper) infection, 0.5 hour Dexamethasone


title: 10_muMT (F480Hi CD11blo Macrophages)

value: KO


title: root nodules, MG136 Infected, rep 1

description:
TAGAAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: root nodules


title: 3_WT (F480Hi CD11blo Macrophages)


title: BoHV-1 infected Bos taurus peripheral tonsils 0.5hours post DEX treatment, 2


title: P1M


title: 25_KI

growth_protocol: Mice were housed under SPF conditions]

extract_protocol:
Samples were stored in RNAlater until processing. Samples were homoginised in lysis buffer (Ambion) and RNA extracted with Purelink RNA mini kit (Ambion)
Libraries were constructed with Illumina TruSeq total Stranded RNA library prep kit

treatment_protocol: Mice were infected with UPEC trans urethrealy twice 1 hour apart and culled 12 hours later.

value: KI


title: root nodules, MG112 Non-Infected, rep 2

description:
TAATAG
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: sub-compatible Rhizobium strain


title: root nodules, MG79 Infected, rep 6

description:
TAACAA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Infected


title: BoHV-1 infected Bos taurus peripheral tonsils without DEX treatment control, 3

value: Acclimation, BoHV-1 (Cooper) infection


title: BoHV-1 infected Bos taurus peripheral tonsils 0.5hours post DEX treatment, 1


title: 23_KI


title: root nodules, MG70 Infected, rep 2

description:
TAAAAC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: N6M

source_name: Normal colon

value: 8 weeks

value: Normal colon


title: 22_KI


title: N5M

value: trileanage depleted stroma cells


title: BoHV-1 infected Bos taurus peripheral tonsils 1.5 hours post DEX treatment, 1

value: Acclimation, BoHV-1 (Cooper) infection, 1.5 hour Dexaamethasone


title: P4M

value: 2 weeks

value: Developmental colon


title: N3M


title: root nodules, MG70 Infected, rep 6

description:
GTTAAA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: BoHV-1 infected Bos taurus peripheral tonsils without DEX treatment control, 2

value: peripheral tonsils

value: Holstein


title: BoHV-1 infected Bos taurus peripheral tonsils without DEX treatment control,1

value: male

value: infected


title: 13_WT

value: WT


title: Type I PRMT inhibitor treatment rep2

first: Weiyi

last: Peng

state: Texas

address: 3517 Cullen Blvd, Room 3025

institute: University of Houston

description: PRMT1i 2

library_source: genomic

data_processing:
The reads were mapped to mouse mm10 using HiSAT2/2.1.0 with parameters "--no-spliced-alignment --no-discordant --no-mixed --dta -X 1000" .
picard-tools-1.113 was used to removed duplicated alignments
MACS2/2.1.1.20160309 were used to call peaks.
DiffBind/2.8.0 (DESeq2 method) was used to do differential peak analysis
Supplementary_files_format_and_content: Annotated DiffBind results in Excel format.

molecule: genomic DNA

source_name: MC38/gp100 murine cancer cell line

extract_protocol:
Cells are lysed with a nonionic detergent to yield pure nuclei.
Chromatin was tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: MC38/gp100 cellls were treated with DMSO or 1uM GSK3368712 for 5 days. 100,000 cells were harvested from each group for ATAC-Seq.

tag: cell line

value: treated with 1uM GSK3368712 for 5 days


title: 12_muMT

treatment_protocol: Mice were infected with UPEC trans urethrealy twice 1 hour apart and culled 6 hours later.

value: KO

tag: kidney pair

value: D


title: 16_WT


title: N2M


title: root nodules, MG115 Non-Infected, rep 2

description:
CTTAAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: root nodules

value: Non-Infected

value: sub-compatible Rhizobium strain


title: Type I PRMT inhibitor treatment rep1

description: PRMT1i 1


title: 11_muMT


title: root nodules, MG112 Non-Infected, rep 3

description:
ATTGTT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: scRNA-Seq of lung: adult male cynomolgus monkey M11

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: macFas6
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx.

organism: Macaca fascicularis

source_name: lung

extract_protocol:
Lung tissues were obtained from the control and asthma groups.The tissues were dissociated into single cells in dissociation solution.Single cell suspensions were loaded to 10× Chromium (10× Genomics, USA) to capture more than 3,000 single cells for the Single-cell 3′ Library using Gel Bead Kit V3 (1000075, 10× Genomics, USA) according to the manufacturer’s instructions. The following cDNA amplification and library construction steps were performed according to the manufacturer’s recommendation. Sequencing was performed on the NovaSeq6000 sequencer (Illumina, USA) with a minimum depth of 60,000~90,000 reads per cell and 150 bp (PE150) paired-end reads performed by LC-Bio Technology Co., Ltd (China).
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR.

value: lung

tag: disease

value: asthma

value: 3-5 years old


title: root nodules, MG79 Infected, rep 1

description:
CTAAAA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Infected


title: root nodules, MG9 Non-Infected, rep 4

description:
ATTATC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: 8_muMT

value: C


title: DMSO treatment rep2

description: Control 2

tag: treatment

value: treated with DMSO for 5 days


title: DMSO treatment rep1

description: Control 1


title: 7_muMT


title: scRNA-Seq of lung: adult male cynomolgus monkey C3

value: normal

tag: age


title: root nodules, MG115 Non-Infected, rep 6

description:
ATCTAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: root nodules, MG9 Non-Infected, rep 6

description:
ATAAGT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: KO 2

city: Daegu

first: Hoyul

last: Lee

address: 807, Hoguk-ro, Buk-gu

department: Bio-medical Research Institute

country: South Korea

institute: Kyungpook Nationatl University Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Spleen and lymph nodes

growth_protocol: naïve CD4+ T cells sorted by MACS cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: stimulated for 48 hours in vitro with CD3, CD28 and IL-2.

value: CD4+ T cells

tag: strain

value: PDK4 KO


title: 6_WT

value: B


title: scRNA-Seq of lung: adult male cynomolgus monkey M8

tag: tissue

tag: Sex

value: male


title: root nodules, MG136 Infected, rep 5

description:
AGTATA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: scRNA-Seq of lung: adult male cynomolgus monkey M10


title: 5_WT

value: WT


title: scRNA-Seq of lung: adult male cynomolgus monkey C1


title: smallRNA_prp40ab_rep3

city: Poznan

first: Jakub

middle: Jacek

last: Dolata

address: Uniwersytetu Poznanskiego 6

department: Department of Gene Expression

country: Poland

institute: Adam Mickiewicz University

data_processing:
For small RNA studies reads coresponding to miRNAs were selected using 'mirnasoft' package and counted, analysis was performed using 'DESeq2'
For ChIPseq studes, reads were mapped to the tair10 genome (Bowtie), PCR duplicates were removed (samtools), bam files were used to draw metaplots (ngs.plot), bed files were generated (bedtools) to count reads for particular genomic regions.
Genome_build: tair10
Supplementary_files_format_and_content: small RNA processed data files (txt) contains counted reads coresponding to miRNAs

organism: Arabidopsis thaliana

source_name: aerial part, prp40ab, 21 days

growth_protocol: temp 22°C, long day, 14 days old seedlings were grown on 1/2 MS plates, 21 days old plants were grown on soil

extract_protocol:
according to manufacturers instructions
ChIPseq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode), smallRNA libraries were prepared using TruSeq SmallRNA Library Preparation Kit (Illumina)

value: aerial part

value: 21 days


title: root nodules, MG9 Non-Infected, rep 3

description:
ACTAAA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: root nodules


title: 2_WT

value: A


title: KO 1


title: root nodules, MG112 Non-Infected, rep 4

description:
AATTTC
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

value: Non-Infected

value: sub-compatible Rhizobium strain


title: WT 1


title: WT 2


title: 1_WT


title: smallRNA_WT_rep3

source_name: aerial part, WT, 21 days


title: smallRNA_prp40ab_rep1


title: root nodules, MG9 Non-Infected, rep 2

description:
AAGTTA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds


title: smallRNA_prp40ab_rep2


title: C3KOI

city: Beijing

first: Yifan

last: Zhou

address: No. 30 Shuangqing Road

institute: Tsinghua University

data_processing:
FastQ preparation: mkfastq (cellranger) https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count matrix generation: count (cellranger) https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Aggregation of samples: aggr (cellranger) https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/aggregate
Visualization and comparisons: Adapted Seurat Pipeline  Aggregate All.R
Data Normalization: scTransform (Satija) https://satijalab.org/seurat/v3.1/sctransform_vignette.html
Genome_build: mm10-3.0.0 (mouse)
Supplementary_files_format_and_content: Zipped Matrices - Single Cell Gene Counts

source_name: CD45+ colonic lamina propria immune cells

extract_protocol:
Following dissection, colon tissue was placed in ice-cold PBS immediately and maintained on ice for further processing. Mesenteric material, fat, and Peyer’s patches were removed. Colon sections were cut open, feces removed, and colon tissue was cut into 1-2 cm pieces. Colon tissue pieces were placed in 8 mL ice-cold PBS and shaken vigorously by hand at room temperature for 2 min. Tissue pieces were transferred to 20 mL PBS containing 1 mM DTT (Sigma), 30 mM EDTA (Sigma), and 10 mM HEPES (Sigma) at room temperature. The samples were placed in a bacterial shaker incubator horizontally, rotated at 37 ℃ for 10 min at 200 rpm, and then shaken by hand at room temperature for 1 min40. Tissue pieces were transferred to new tubes containing a fresh solution of 20 mL PBS, 30 mM EDTA, and 10 mM HEPES, and were shaken for a second 10 minutes as indicated. The tissue pieces were rinsed gently with RPMI medium containing 2% heat-inactivated FBS (RPMI/2% FBS) at room temperature. Tissues pieces were transferred to tubes containing 5 mL of RPMI medium, 10% FBS, 200 U/ml collagenase VIII (Sigma), and 150 μg/ml DNase I (Sigma). Tissues were digested by shaking in a bacterial shaker incubator at 100 rpm at 37 ℃ for 1 h, and then shaken by hand at room temperature for 1 min. The digested tissues were placed on a 100 μm cell strainer; single cells in the flow-through were collected. Cells were centrifuged at 600 g for 5 min at 4℃ and resuspended in 4 mL 40% Percoll (Sigma) in RPMI/2% FBS. The Percoll-cell solution was layered on top of 4 mL 80% Percoll in RPMI/2% FBS, and centrifuged at 1300 g at room temperature for 20 min; spins were concluded without using the centrifuge brake. The cells at the interface of the 40% and 80% Percoll solutions were collected; cells were washed once with ice-cold PBS/2%FBS prior to antibody incubations.Colonic LP immune cells were isolated and sorted for live CD45+ cells by fluorescence-activated cell sorting (FACS).
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

value: IgG

value: Colonic lamina propria

tag: i7 index id


title: root nodules, MG79 Infected, rep 2

description:
AATGTA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

tag: accession

value: Infected


title: root nodules, MG115 Non-Infected, rep 5

description:
AAATCA
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

tag: phenotype


title: scRNA-Seq of lung: adult male cynomolgus monkey C2

value: lung

value: 3-5 years old


title: smallRNA_WT_rep2


title: WTC


title: smallRNA_WT_rep1


title: root nodules, MG136 Infected, rep 2

description:
AAACAT
Lj_infection_raw_counts.rds
Lj_infection_filtered_normalised_counts.rds

tag: infection


title: WTI

tag: genotype


title: C3KOC


title: K19006259

status: Public on Oct 31 2022

city: Urakawa

first: Harutaka

last: Murase

state: Hokkaido

address: 535-13, Nishicha

institute: Japan Racing Association

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.8
Trim Galore 0.4.3 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.7.2a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM.fpkm_tracking) were used to determine the expression level of genes
Based on fragments per kilobase of exon (FPKM.fpkm_tracking), all 37 samples were divided into four groups using k-means clustering (R Ver 3.1)
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEGs) between samples from the each clusters and control groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.fpkm_tracking.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total RNA was isolated from tissue samples using RNeasy Mini Kit (#74104: Qiagen). RNA concentrations and quantities were confirmed using the Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, MA, USA). Then, RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) >7.0.
A total of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Chorioallantois

tag: group

value: Cluster 4


title: K19007432


title: K19005695


title: K19006752


title: SCL-II cells overexpressing pcDNA3.1

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

description: Gene expression data from SCL-II over expressing pcDNA3.1

hyb_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

data_processing: RMA (PARTEK)

label: biotin

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

growth_protocol: not relevant

extract_protocol: Skin biopsies were snap-frozen and stored in liquid nitrogen. Before thawing, epidermal layers were separated from adipose tissues using scalpel. Total RNA from fresh frozen tissues was extracted using the Qiagen RNeasy mini kit (Cat. # 74104). Quantity and quality were evaluated using Nanodrop ND-2000 (Thermo Scientific),

treatment_protocol: not relevant

tag: disease state

value: cutaneous squamous cell carcinoma (CSCC)

value: tumor cell line SCL-II

tag: cell line source

value: SCL-II cells were derived from primary an undifferentiated SCC lesion from the face (Cancer Res. 1983 Dec;43(12 Pt 1):5995-6011.)

value: control


title: K19002985


title: K19005031

value: Cluster 3


title: K19007062

value: Cluster 2


title: K19006741


title: K19007006


title: K19003753


title: K19005015


title: MET1 cells overexpressing miR-199a

description: Gene expression data from MET1 overexpressing miR-199a-3p

scan_protocol: Affymetrix 3' IVT labeling protocol  https://www.affymetrix.com/support/downloads/manuals/3_ivt_express_kit_manual.pdf

value: tumor cell line MET1

value: MET1 were established from forehead skin a primary SCC lesion (British Journal of Cancer (2006) 94, 1446–1451. doi:10.1038/sj.bjc.6603135)

value: overexpressing miR-199a-3p


title: K19004099


title: K19004204


title: K19005862


title: K19006627


title: K19004120


title: K19005032


title: K19006739


title: K19003760


title: K19002827


title: K19004627


title: K19004551


title: K19002362


title: K19003968


title: MET1 cells overexpressing pcDNA3.1

description: Gene expression data from MET1 over expressing pcDNA3.1


title: K19006424

value: Cluster 1


title: K19002159


title: K19006416


title: K19005511


title: K19003720


title: K19005765

value: Control


title: K19002609


title: K19002844


title: K19004008


title: K19005691


title: K19003967


title: K19002804


title: K19004844


title: SYY141-1-cl5-EV

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Paired-end reads were aligned using the RNA-seq aligner STAR (version 2.7.9a) with flags "--alignSJoverhangMin 8" and "--quantMode GeneCounts". For the geome reference and the subsequent gene quantification the gencode gene annotation for hg38 (version GRCh38.p13) was provided to STAR.
Assembly: hg38
Supplementary files format and content: SYY53_54_123_141_raw_counts.csv holds raw gene counts in csv format
Supplementary files format and content: Tonsil_raw_counts.csv holds raw gene counts in csv format
Supplementary files format and content: REH_controls_raw_counts.csv holds raw gene counts

source_name: REH

extract_protocol:
RNA was isolated using RNeasy Kit (Micro or Mini, Qiagen) or TRIzol and 1-bromo-3-chloropropane methods.
Library was constructed using NEBNext Ultra II RNA Library Prep Kit with Poly(A) selection.

value: REH

tag: cell type

value: B-cell acute lymphoblastic leukemia

value: pan-FBXW7 knockout + empty retroviral vector


title: SYY141-4-cl5-b

tag: cell line

value: pan-FBXW7 knockout + FBXW7 beta reconstitution


title: SYY141-2-cl5-a

value: pan-FBXW7 knockout + FBXW7 alpha reconstitution


title: SYY123-3-cl5-g

value: pan-FBXW7 knockout + FBXW7 gamma reconstitution


title: SYY123-1-cl5-EV


title: SYY141-3-cl5-g


title: SYY123-2-cl5-a


title: SYY54-2-MO-a

value: FBXW7 alpha knockdown


title: SYY54-1-MO-ctrl

value: WT


title: SYY54-3-MO-g

value: FBXW7 gamma knockdown


title: SYY53-3-MO-g


title: SYY53-1-MO-ctrl


title: SYY53-4-MO-b

value: FBXW7 beta knockdown


title: ligamentum flavum , ossified IP,rep 2

city: Jinan

first: Dachuan

last: Wang

state: Shandong

address: Jingwu Weiqi Road NO.324

institute: Shandong provincial hospital

description:
treat 2
B02

data_processing:
Paired reads were harvested from Illumina HiSeq 4000 sequencer with quality controlled by Q30. After 3’ adaptor-trimming and the removal of low quality reads by Cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (UCSC HG19) by Hisat2 software (v2.0.4). ExomePeak software was used for identifying RNA m6A-modified regions (m6A peaks) with FDR (false discovery rate) < 0.05. As previously reported, the common methylated RNAs (CMRs) were defined as RNAs containing at least one m6A peak in all samples, while the specific methylated RNAs (SMRs) were the RNAs with m6A modification only in one sample, and m6A peaks of SMRs were defined as specific m6A peaks. Biological process, molecular function and cellular component analysis were performed for the enrichment of differentially methylated genes, CMRs and SMRs.
Assembly: hg19  Supplementary files format and content: Number of raw junction read  Library strategy: m6A-Seq

source_name: ligamentum flavum

extract_protocol:
Trizol reagent (Invitrogen) was applied to extract total RNA.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure with proper adjustments. Briefly, the fragmented RNA was incubated with m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer at 4°C for 2 hours. Then the mixture was immune-precipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) following the manufacturer's instruction. Purified RNA was used for RNA-seq library generation with NEBNext® UltraTM RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer. In addition, the q-PCR was performed to detect the level of m6A using purified RNA fragments

value: ligamentum flavum

tag: antibody


title: SCL-II cells overexpressing miR199a

description: Gene expression data from SCL-II over expressing miR-199a-3p

value: cutaneous squamous cell carcinoma (CSCC)

value: tumor cell line SCL-II

value: SCL-II cells were derived from primary an undifferentiated SCC lesion from the face (Cancer Res. 1983 Dec;43(12 Pt 1):5995-6011.)


title: SYY53-2-MO-a


title: ligamentum flavum , ossified IP,rep 1

description:
treat 1
B01


title: ligamentum flavum ,non ossified IP,rep 3

description:
control 3
A03


title: ligamentum flavum ,non ossified IP,rep 2

description:
control 2
A02


title: ligamentum flavum ,non ossified IP,rep 1

description:
control 1
A01


title: REH-ctrl-S29-L005


title: SYY123-4-cl5-b


title: REH-ctrl-S28-L005


title: LN6ADpos-S5

source_name: normal tonsil cell subset

value: normal tonsil cell subset

value: IgM+IgD+CD19+ normal tonsil B cells


title: LN5ADpos-S2


title: REH-ctrl-S27-L005


title: LN2A-S9

value: IgM+CD19+ normal tonsil B cells


title: SYY54-4-MO-b

value: REH