title: DSP-F8, ribbon, Layer 5

description: Library name: DSP-F8

value: Frontal Cortex Brain Tissue

value: ribbon


title: E. coli K12 BW113, untreated, BT2..

status: Public on Aug 13 2025

type: SRA

city: Calgary

first: Daniel Armando

last: Salazar-Alemán

state: Alberta

address: 2500 University Drive NW

department: Department of Biological Sciences

country: Canada

institute: University of Calgary

description:
Library name: Control 2
AgUnch2

library_source: transcriptomic

data_processing:
Initial FASTQ files were assessed and trimmed with the Bioconductor package rfastp (version 1.10).
Gene expression counts were obtained by aligning to the Escherichia coli K12 BW25113 RefSeq assembly annotation file GCF_000750555.1 using the Bioconductor package Rsubread (version 2.14.2), with counts assigned to the CDS meta-feature.
A counts matrix for the 4,378 identified features was imported into the Bioconductor package DESeq2 (version 1.40.2) for differentially expressed genes determination. The adjusted p-value (p-adj) for multiple test adjustment (Benjamini-Hochberg correction, FDR < 0.05) was set to 0.05.
Differentially expressed genes were defined as those with a p-adj value < 0.05 and whose expression had an absolute fold-change (FC) of at least 2 (|log2 FC| > 1) when contrasting the silver nitrate treatment versus the unchallenged control; those with a negative FC were deemed as down-regulated genes in the silver nitrate treatment, while a positive FC indicated up-regulation.
Assembly: Escherichia coli K12 BW25113 from NCBI RefSeq (GCF_000750555.1)
Supplementary files format and content: Tab-delimited text file specifies gene name (or its "BW25113_[…]" gene ID, if the gene name was not found), along with their respective raw counts for each sample.
Supplementary files format and content: Comma-delimited file with DESeq2 outputs including log2-fold change and p-values. Each gene is identified by its gene name, gene_id and uniprot entry ID.

molecule: total RNA

organism: Escherichia coli

source_name: Bacterial cell

growth_protocol: Escherichia coli K12 BW25113 was cultured in 15mL of M9-glucose minimal media and incubated at 37 ºC 150 rpm for 10 hours in a shaker incubator.

extract_protocol:
2 mL of samples were centrifuged at 14,000 X g for 2 minutes to pellet the cells. Zirconia beads were used for cell lysis for 10 minutes using a bead beater instrument. Total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit AM1925 (Invitrogen, USA) according to the manufacturer's recommendations, including DNase treatment.
Ribosomal RNA depletion was performed using the NEB rRNA Depletion Bacterial Module (New England Biolabs, USA). The cDNA library preparation for Illumina sequencing was executed using the NEBNext Ultra II Directional RNA Library Prep Kit and NEB Indexing Kit (New England Biolabs, USA). After adaptor ligation and amplification, the average library fragment size was 373 bp.

treatment_protocol: Control treatments were grown for 10 hours in M9-glucose minimal media. Experimental treatments were grown for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of silver nitrate (39 µM, 6.22 µg/mL) prior to inoculation.

tag: strain

tag: cell type

value: Bacterial cell

tag: genotype

value: Wild type

tag: treatment

value: Control - no metal challenge


title: early 2-cell, CTR, rep3

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Library name: BAP1_CTR_E2C_RNA_rep3

data_processing:
Raw RNA-seq read pairs were trimmed by Trimgalore (v0.6.6)(https://github.com/FelixKrueger/TrimGalore) with the option “--paired --clip_R2 5”, and aligned to mm10 by STAR (v2.7.9) with the options “--outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAMattributes NH HI NM MD XS AS --alignIntronMax 1000000 --alignMatesGapMax 1000000 --limitBAMsortRAM 30000000000 --outFilterType BySJout”.
Uniquely aligned read pairs were  identified by sambamba (v0.6.8) with the option “-F “mapping_quality >=255”. StringTie (v2.1.7) to generate FPKM values for each gene.
Assembly: mm10
Supplementary files format and content: csv

organism: Mus musculus

source_name: early 2-cell

growth_protocol: Embryos were cultured in KSOM (Millipore) at 37 °C under 5% CO2 with air

extract_protocol:
For RNA-seq, oocytes and embryos were suspended in 7 μl RRI water (199 μl ultrapure H2O with 1 μl RNase inhibitor). Then, 6 μl shearing master mix (1 μl 10X lysis mix, 1 μl Smart scN6, 4 μl scRT Buffer) was added and incubated at 85°C for 6 min and immediately put on ice for 2 min.
The total RNA‐seq libraries were generated using the SMART‐Seq Stranded Kit (Takara) following the manufacturer's protocol.

treatment_protocol: Conditional KO in oocytes was achieved using Gdf9-iCre mediated recombination of Bap1 flox/flox allele

tag: tissue

value: early 2-cell

value: Bap1flox/flox x B6


title: Black_C12_Z21

city: Bethesda

first: Christian

last: Wake

state: MD

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Samples whose sex could not be determined by phenotype (Sex = 'UNK') were left out of this analysis.
Clipping - trimmomaticv 0.39 was used for adapter clipping and quality trimming. It was used in paired-end mode, converting to Phred quality 33, speicifying a minimum trailing and leading base quality of 3, sliding window of size 4 and required quiality of 20, and minimum read length of 50 (-phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50)
Alignment - star v 2.7.9 was used for alignment to genome, specifying maximum multimap per read of 20, max fraction of read length to mismatch as 0.04, and maximum number of junction to be inserted to the genome on the fly at the mapping stage as 1,200,000 (--outFilterMultimapNmax 20 --outFilterMismatchNoverReadLmax 0.04 --limitSjdbInsertNsj 1200000)
Counting - featureCounts from the Subreads package was used for quantification of read abundances per gene/sample. Only primary alignment were counted (--primary) and when relevant assigning a read to the feature with the largest overlap (--largestOverlap).
Genes filtering - genes were then removed if they were present in fewer than 30% of samples, had variance across samples below 100, or were ribosomal genes.
Downsampling - Three samples were above a read depth threshold chosen as 2.75 standard deviations from the mean, and so were randomly down-sampled to have depth just under the threshold while maintaining the same sample order. One sample (Z22) was removed for falling below the equivalent lower threshold.
Normalization - Counts were then normalized with the median of ratios method from DESeq2 v. 1.30.1 (Love, Huber & Anders 2014) implemented in R v 4.0.2
Sample filtering - Principle Component Analysis was conducted on normalized counts with the stats R package, from which 4 samples were flagged as outliers (more than 2.75 standard deviations from the mean of PC1, PC2 or PC3) and removed from the analysis.
Differential expression - comparisons were conducted with DESeq2, using sex, age of euthanasia and library plate as covariates in the statistical models.
Gene Set Enrichment Analysis - GSEA was conducted with R package fgsea and gene sets from canonical pathways (C2CP) in the Molecular Signature Database, MSigDB
Assembly: Taeniopygia guttata genome v1.p.111 from Ensembl, bTaeGut1_v1.p
Supplementary files format and content: Comma-delimited text file with normalized counts per gene (rows) and sample (columns).Row names match ensembl ID format and column names match the Sample "Description" field.

organism: Taeniopygia guttata

source_name: Bone marrow

extract_protocol:
Bulk bone marrow RNA was isolated using cold RNAzol RT (Molecular Research Center). mRNA was purified with Dynabeads Olgio(dt)25 (Invitrogen).
Libraries were constructed with NEBNext Ultra II RNA Prep reagents following manufacturer's protocols (New England Biolabs).

value: Bone marrow

value: C

tag: Sex

value: UNK

tag: euth age

tag: cohort

tag: plate

tag: rna extraction_batch

tag: rin score

tag: library preparation_method

value: Adapted NEBNext Ultra II RNA library prep


title: DSP-F7, ribbon, Layer 3

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Rd

department: Center for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: DSP-F7

data_processing:
GeoMxNGS Pipeline 3.1.1.6 was used to convert fastq files to DCC files. FastQ files were aligned to hg38 genome build.
DCC files were uploaded to GeoMx DSP Control Center 3.1.0.222 for further analysis.
Probe filtration, and normalization steps were conducted using default settings on GeoMx DSP Control Center.
Assembly: GRCh38
Supplementary files format and content: DSP.dcc: gene expression count data for each well
Supplementary files format and content: DSP.stats: quality metrics data for each fastq
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: Frontal Cortex Brain Tissue

extract_protocol:
Samples were processed with xylenes and ethanol washes and embedded in paraffin blocks.
Sequencing libraries of spatial transcriptome data were prepared using the GeoMx Manual Slide Preparation User Manual (Bruker Spatial Biology; MAN-10150-04) with adjustments in antigen retrieval steps.

treatment_protocol: Human postmortem brain tissues were obtained from the National Disease Research Interchange (NDRI). Tissues were fixed and stored at room temperature (RT) in 10% formalin from time of acquisition until dissection for the GeoMx protocol. Brodmann Area 9 (BA9) frontal cortex was dissected from n = 7 samples

tag: segment type

tag: layer

value: Layer 3


title: early 2-cell, CTR, rep1

description: Library name: BAP1_CTR_E2C_RNA_rep1


title: DSP-F6, ribbon, Layer 3

description: Library name: DSP-F6


title: Purple_Hg7_Z20

value: Hg

value: M


title: E. coli K12 BW113, tetrachloroauric acid 10 µM, BT3

description:
Library name: Gold 3
Gold3

data_processing:
Initial FASTQ files were assessed and trimmed with the Bioconductor package rfastp (version 1.10).
Gene expression counts were obtained by aligning to the Escherichia coli K12 BW25113 RefSeq assembly annotation file GCF_000750555.1 using the Bioconductor package Rsubread (version 2.14.2), with counts assigned to the CDS meta-feature.
A counts matrix for the 4,378 identified features was imported into the Bioconductor package DESeq2 (version 1.40.2) for differentially expressed genes determination. The adjusted p-value (p-adj) for multiple test adjustment (Benjamini-Hochberg correction, FDR < 0.05) was set to 0.05.
Differentially expressed genes were defined as those with a p-adj value < 0.05 and whose expression had an absolute fold-change (FC) of at least 2 (|log2 FC| > 1) when contrasting the tetrachloroauric acid treatment versus the unchallenged control; those with a negative FC were deemed as down-regulated genes in the tetrachloroauric acid treatment, while a positive FC indicated up-regulation.
Assembly: Escherichia coli K12 BW25113 from NCBI RefSeq (GCF_000750555.1)
Supplementary files format and content: Tab-delimited text file specifies gene name (or its "BW25113_[…]" gene ID, if the gene name was not found), along with their respective raw counts for each sample.
Supplementary files format and content: Comma-delimited file with DESeq2 outputs including log2-fold change and p-values. Each gene is identified by its gene name, gene_id and uniprot entry ID.

extract_protocol:
2 mL of samples were centrifuged at 14,000 X g for 2 minutes to pellet the cells. Zirconia beads were used for cell lysis for 10 minutes using a bead beater instrument. Total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit AM1925 (Invitrogen, USA) according to the manufacturer's recommendations, including DNase treatment.
Ribosomal RNA depletion was performed using the NEB rRNA Depletion Bacterial Module (New England Biolabs, USA). The cDNA library preparation for Illumina sequencing was executed using the NEBNext Ultra II Directional RNA Library Prep Kit and NEB Indexing Kit (New England Biolabs, USA). After adaptor ligation and amplification, the average library fragment size was 362 bp.

treatment_protocol: Control treatments were grown for 10 hours in M9-glucose minimal media. Experimental treatments were grown for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of tetrachloroauric acid (10 µM, 3.39 µg/mL) prior to inoculation.

value: Tetrachloroauric acid 10 µM sublethal concentration


title: DSP-F5, ribbon, Layer 3

description: Library name: DSP-F5


title: early 2-cell, CTR, rep2

description: Library name: BAP1_CTR_E2C_RNA_rep2


title: Blue_C8_Z19

value: F


title: early 2-cell, matKO, rep3

description: Library name: BAP1_mKO_E2C_RNA_rep3

value: Gdf9-iCre, Bap1flox/flox x B6


title: DSP-F4, ribbon, Layer 3

description: Library name: DSP-F4

value: Frontal Cortex Brain Tissue


title: E. coli K12 BW113, untreated, BT3.

description:
Library name: Control 3
AuUnch3


title: Blue_Hg5_Z18


title: Green_C9_Z15

value: B


title: DSP-F3, ribbon, Layer 3

description: Library name: DSP-F3

value: ribbon


title: E. coli K12 BW113, tetrachloroauric acid 10 µM, BT1

description:
Library name: Gold 1
Gold1

value: Bacterial cell

value: Wild type


title: early 2-cell, matKO, rep2

description: Library name: BAP1_mKO_E2C_RNA_rep2

value: early 2-cell


title: E. coli K12 BW113, untreated, BT2.

description:
Library name: Control 2
AuUnch2

value: Control - no metal challenge


title: Green_Hg2_Z12

value: Bone marrow


title: E. coli K12 BW113, untreated, BT1..

description:
Library name: Control 1
AgUnch1


title: DSP-F1, ribbon, Layer 3

description: Library name: DSP-F1


title: DSP-F2, ribbon, Layer 3

description: Library name: DSP-F2


title: early 2-cell, matKO, rep1

description: Library name: BAP1_mKO_E2C_RNA_rep1


title: MII, CTR, rep1

description: Library name: BAP1_CTR_MII_RNA_rep1

source_name: MII eggs

value: MII eggs


title: FGO, CKO, H2AK119ub1, rep1

description: Library name: BAP1_CKO_GV_H2AK119ub_rep1

library_source: genomic

data_processing:
Raw paired-end reads from CUT&RUN experiments were trimmed using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore) with the --paired option. For FGOs, trimmed reads were aligned to the mm10 mouse reference genome using Bowtie2 (v2.4.2)(Langmead and Salzberg, 2012) with the parameters:
--no-unal --no-mixed --no-discordant -I 0 -X 1000. Uniquely mapped reads were filtered using Sambamba (v0.6.8) (Tarasov et al., 2015) with the criteria: -F "mapping_quality >= 30 and not (unmapped or mate_is_unmapped)". PCR duplicates were removed using Picard (v2.18.22) (http://broadinstitute.github.io/picard/). BigWig coverage files were generated using deepTools (v2.0.0)(Ramirez et al., 2016) with the options:
--binSize 25 --normalizeUsing RPKM --scaleFactor 1.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Fully grown oocyte

extract_protocol:
For CUT&RUN, oocytes and embryos were directly added to the binding buffer containing conA beads.
The CUT&RUN libraries were prepared as previously described (PMID: 40418442)

value: Fully grown oocyte

value: Gdf9-iCre, Bap1flox/flox


title: E. coli K12 BW113, untreated, BT1.

description:
Library name: Control 1
AuUnch1


title: E. coli K12 BW113, tetrachloroauric acid 10 µM, BT2

description:
Library name: Gold 2
Gold2


title: Green_2_C10_Z17

value: C

value: Adapted NEBNext Ultra II RNA library prep


title: FGO, CTR, rep2

description: Library name: BAP1_CTR_GV_RNA_rep2


title: Orange_Hg13_Z8

value: Hg


title: DSP-E11, segmented , Layer 3

description: Library name: DSP-E11

value: segmented

value: Layer 3


title: E. coli K12 BW113, copper sulfate 39 µM, BT3

description:
Library name: Copper 3
Copper3

data_processing:
Initial FASTQ files were assessed and trimmed with the Bioconductor package rfastp (version 1.10).
Gene expression counts were obtained by aligning to the Escherichia coli K12 BW25113 RefSeq assembly annotation file GCF_000750555.1 using the Bioconductor package Rsubread (version 2.14.2), with counts assigned to the CDS meta-feature.
A counts matrix for the 4,378 identified features was imported into the Bioconductor package DESeq2 (version 1.40.2) for differentially expressed genes determination. The adjusted p-value (p-adj) for multiple test adjustment (Benjamini-Hochberg correction, FDR < 0.05) was set to 0.05.
Differentially expressed genes were defined as those with a p-adj value < 0.05 and whose expression had an absolute fold-change (FC) of at least 2 (|log2 FC| > 1) when contrasting the copper sulfate treatment versus the unchallenged control; those with a negative FC were deemed as down-regulated genes in the copper sulfate treatment, while a positive FC indicated up-regulation.
Assembly: Escherichia coli K12 BW25113 from NCBI RefSeq (GCF_000750555.1)
Supplementary files format and content: Tab-delimited text file specifies gene name (or its "BW25113_[…]" gene ID, if the gene name was not found), along with their respective raw counts for each sample.
Supplementary files format and content: Comma-delimited file with DESeq2 outputs including log2-fold change and p-values. Each gene is identified by its gene name, gene_id and uniprot entry ID.

extract_protocol:
2 mL of samples were centrifuged at 14,000 X g for 2 minutes to pellet the cells. Zirconia beads were used for cell lysis for 10 minutes using a bead beater instrument. Total RNA was then extracted with a RiboPure Bacteria RNA Isolation Kit AM1925 (Invitrogen, USA) according to the manufacturer's recommendations, including DNase treatment.
Ribosomal RNA depletion was performed using the NEB rRNA Depletion Bacterial Module (New England Biolabs, USA). The cDNA library preparation for Illumina sequencing was executed using the NEBNext Ultra II Directional RNA Library Prep Kit and NEB Indexing Kit (New England Biolabs, USA). After adaptor ligation and amplification, the average library fragment size was 370 bp.

treatment_protocol: Control treatments were grown for 10 hours in M9-glucose minimal media. Experimental treatments were grown for 10 hours in M9-glucose minimal media spiked with a sublethal concentration of copper sulfate (39 µM, 6.22 µg/mL) prior to inoculation.

value: Copper sulfate 39 µM sublethal concentration


title: E. coli K12 BW113, copper sulfate 39 µM, BT2

description:
Library name: Copper 2
Copper2


title: DSP-E10, segmented , Layer 5

description: Library name: DSP-E10

value: Frontal Cortex Brain Tissue

value: Layer 5


title: FGO, CTR, rep1

description: Library name: BAP1_CTR_GV_RNA_rep1


title: E. coli K12 BW113, copper sulfate 39 µM, BT1

description:
Library name: Copper 1
Copper1


title: MII, CTR, rep2

description: Library name: BAP1_CTR_MII_RNA_rep2


title: Yellow_Hg13_Z40

value: F

value: B


title: Orange_C2_Z39

value: M


title: DSP-E5, segmented, Layer 3

description: Library name: DSP-E5


title: DSP-E6, segemnted, Layer 3

description: Library name: DSP-E6


title: E. coli K12 BW113, untreated, BT2

description:
Library name: Control 2
CuUnch2

value: Bacterial cell

value: Wild type


title: MII, CKO, rep1

description: Library name: BAP1_CKO_MII_RNA_rep1


title: DSP-E3, segmented, Layer 3

description: Library name: DSP-E3


title: FGO, CKO, rep3

description: Library name: BAP1_CKO_GV_RNA_rep3


title: E. coli K12 BW113, untreated, BT3

description:
Library name: Control 3
CuUnch3

value: Control - no metal challenge


title: MII, CKO, rep3

description: Library name: BAP1_CKO_MII_RNA_rep3

value: MII eggs


title: Green_C4_Z31

value: Bone marrow


title: Purple_2_Hg1_Z38


title: SCE50

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

library_source: other

data_processing:
16S-Seq sequencing reads were assembled and denoised using the DADA2 plugin of QIIME2 (version 2023.9). Operational taxonomic unit counts were generated using the DADA2 plugin of QIIME2 (version 2023.9). Taxonomic analysis was performed using the Silva database (release 138).
Assembly: Silva (release 138)
Supplementary files format and content: dna-sequences.fasta contains the Operational Taxonomic Unit sequences in FASTA format.
Supplementary files format and content: feature_table.tsv is text file containing the abundances of OTUs in each sample.
Supplementary files format and content: taxonomy.tsv is text file containing the complete taxonomic classification of the reference sequence.

molecule: other

source_name: stool

extract_protocol:
Total DNA from mouse stool pellets was extracted using a modified Qiagen QIAamp 96 DNA QIAcube HT protocol.
The 16S rRNA gene V1-V3 region was amplified using Accuprime Taq High Fidelity Enzyme from ThermoFisher Scientific. Amplicons were pooled for sequencing using Illumina 2x300 bp V3 reagents on a MiSeq instrument.

value: stool

tag: oral anaphylaxis

value: Resistant


title: DSP-E1, segmented, Layer 3

description: Library name: DSP-E1


title: Yellow_Hg15_Z30

value: Adapted NEBNext Ultra II RNA library prep


title: FGO, CKO, rep2

description: Library name: BAP1_CKO_GV_RNA_rep2

value: Fully grown oocyte

value: Gdf9-iCre, Bap1flox/flox


title: MII, CKO, rep2

description: Library name: BAP1_CKO_MII_RNA_rep2


title: Patient6P, Spatial Transcriptomics, Paracancerous

city: Suzhou

first: YingXi

last: Guo

address: No. 199, Renai Road, Industrial Park

department: IBMS

country: China

institute: Soochow University

description:
Library name: Patient6N_N_20200904NB
10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics “spaceranger mkfastq” to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Rangers default settings
Gene expression level of Refseq coding genes were quantifed using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: features.tsv.gz:list of gene IDs
Library strategy: Spatial Transcriptomics

source_name: Colon cancer paracancerous tissue

extract_protocol:
Fresh frozen tissue were OCT embedded,
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene expression Slides & Reagent kit according to manufacturer's construction

value: Colon cancer paracancerous tissue


title: Orange_C10_Z37

value: C


title: SCE49


title: DSP-E2, segmented, Layer 3

description: Library name: DSP-E2

value: Frontal Cortex Brain Tissue

value: segmented

value: Layer 3


title: SCE48

value: Susceptible


title: Blue_C2_Z29

value: M

value: B


title: Patient6T, Spatial Transcriptomics, Tumor

description:
Library name: Patient6T_T_20200904NB
10x Genomics

source_name: Colon cancer tissue

value: Colon cancer tissue


title: late 2-cell, matKO, rep3

description: Library name: BAP1_mKO_L2C_RNA_rep3

source_name: late 2-cell

value: late 2-cell

value: Gdf9-iCre, Bap1flox/flox x B6


title: Red_C9_Z33

value: Bone marrow

value: F


title: late 2-cell, matKO, rep2

description: Library name: BAP1_mKO_L2C_RNA_rep2


title: E. coli K12 BW113, untreated, BT1

description:
Library name: Control 1
CuUnch1

value: Bacterial cell

value: Wild type

value: Control - no metal challenge


title: Purple_Hg19_Z28

value: Hg

value: Adapted NEBNext Ultra II RNA library prep


title: SCE46

value: stool


title: SCE47

value: Resistant


title: Yellow_2_C16_Z27

value: C


title: Patient4P, Spatial Transcriptomics, Paracancerous

description:
Library name: N_20201016NC
10x Genomics

value: Colon cancer paracancerous tissue


title: Patient4T, Spatial Transcriptomics, Tumor

description:
Library name: T_20201016NC
10x Genomics


title: Purple_C11_Z25


title: SCE44


title: Patient2P, Spatial Transcriptomics, Paracancerous

description:
Library name: N_20200922N
10x Genomics


title: late 1-cell, matKO, rep2

description: Library name: BAP1_mKO_L1C_RNA_rep2

source_name: late 1-cell

value: late 1-cell


title: Vector-3

city: Shenzhen

first: zhou

last: hongzhong

state: Guangdong

address: No. 3002, Shangang West Road, Futian District, Shenzhen, Guangdong Province

department: Shenzhen Institute of Translational Medicine

institute: The Second People's Hospital of Shenzhen (The First Affiliated Hospital of Shenzhen University)

description:
Library name: Vector3
FPKM.Vector3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome of homo_sapiens TFPI2. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens TFPI2
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Tumor tissue

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Tumor tissue

value: tumor pericytes

value: control


title: Red_Hg13_Z26

value: B


title: Green_C17_Z7

value: A


title: late 1-cell, matKO, rep3

description: Library name: BAP1_mKO_L1C_RNA_rep3

value: Gdf9-iCre, Bap1flox/flox x B6


title: late 2-cell, CTR, rep2

description: Library name: BAP1_CTR_L2C_RNA_rep2

value: late 2-cell

value: Bap1flox/flox x B6


title: Blue_2_C19_Z9

value: Bone marrow

value: F


title: SCE41


title: late 2-cell, matKO, rep1

description: Library name: BAP1_mKO_L2C_RNA_rep1


title: TFPI2 overexpressing-3

description:
Library name: TF3
FPKM.TF3

value: TFPI2 overexpressing


title: FGO, CKO, rep1

description: Library name: BAP1_CKO_GV_RNA_rep1

value: Fully grown oocyte

value: Gdf9-iCre, Bap1flox/flox


title: SCE43

value: stool

value: Susceptible


title: late 1-cell, matKO,rep1

description: Library name: BAP1_mKO_L1C_RNA_rep1


title: Vector-2

description:
Library name: Vector2
FPKM.Vector2


title: SCE42


title: Blue_Hg11_Z6

value: Hg

value: M

value: Adapted NEBNext Ultra II RNA library prep


title: TFPI2 overexpressing-2

description:
Library name: TF2
FPKM.TF2

value: Tumor tissue

value: tumor pericytes


title: Vector-1

description:
Library name: Vector1
FPKM.Vector1

value: control


title: SCE38


title: late 2-cell, CTR, rep1

description: Library name: BAP1_CTR_L2C_RNA_rep1


title: Black_C20_Z5

value: C

value: A


title: SCE40

value: Resistant


title: SCE37


title: SCE45


title: SCE39


title: Green_2_Hg13_Z4


title: late 1-cell, CTR, rep2

description: Library name: BAP1_CTR_L1C_RNA_rep2

value: late 1-cell

value: Bap1flox/flox x B6


title: Patient2T, Spatial Transcriptomics, Tumor

description:
Library name: CA_20201020NC
10x Genomics

value: Colon cancer tissue


title: Sample 9, soleus muscle, space

city: Stockholm

first: Alen

last: Lovric

address: Nobels väg 5

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 19
S1019

data_processing:
Raw sequencing reads were submitted to MultiQC (v1.15) for quality control. Alignment to reference genome (GRCm39) was performed using subread sequence aligner and gene counts were summarised using featureCount (v1.5.1). After trimmed mean M normalization, expression values were converted to log2CPM values using edgeR.
Assembly: GRCm39, GENCODE M33
Supplementary files format and content: Text file with raw counts for all samples

source_name: Soleus muscle

extract_protocol:
Bead beater device (BioSpec) was used to homogenate the soleus muscle in TriZol (Invitrogen), followed by chloroform gradient separation and ethanol dilution.  Direct-zol RNA Miniprep Kit (Zymo) was used to purify the RNA.
rRNA-depleted libraries were prepared from 90 ng of total RNA using Ribozero kit (Illumina), and sequenced in pair-end sequenced mode on the NovaSeqXPlus platform (Illumina).

value: Soleus muscle

value: Hind-limb unloading

value: Ionizing radiation

value: Stress hormone


title: Sample 8, soleus muscle, space

description:
Library name: Sample 18
S1018


title: Purple_C9_Z1

value: Bone marrow


title: late 1-cell, CTR, rep1

description: Library name: BAP1_CTR_L1C_RNA_rep1


title: TFPI2 overexpressing-1

description:
Library name: TF1
FPKM.TF1

value: TFPI2 overexpressing


title: Purple_C19_Z3

value: UNK


title: TDP-43 p.G348C, rep2, miRNA-seq

city: Montreal

first: Tomas

last: Durcan

state: QC

address: 3801 University Street

institute: McGill University

data_processing:
Sequencing datasets were analyzed with a modified version of the workflow proposed by Potla et al. 2021 (doi:10.1016/j.ocarto.2020.100131). We adapted this workflow to analyze reads without UMI’s, single end and paired end readsets, and multiple readsets per sample (this workflow is available at https://github.com/neurobioinfo/miRNA_workflow).
After quality control with FastQC, we used cutadapt to remove reads shorter than 15 nt and larger than 32 nt.
We used Bowtie v1.3 to align readsets to the miRBase database v22 and to the human reference genome v104. In order to maximize the number of alignments and to detect rare miRNAs, we used a seed length 20 (Bowtie option -l 20) and allowed 3 mismatches within the seed (Bowtie option -n 3).
MiRNAs aligned to miRBase were counted with Samtools idxstats.
MiRNAs aligned to the reference genome were filtered with TAGBAM from BEDTools and counted with a locally developed script that optimizes counting time (https://github.com/neurobioinfo/miRNA_workflow).
Finally, the local workflow adds miRNAs aligned to miRBase to those aligned to the reference genome for each sample, and generates a miRNA counts matrix with all samples counts.
Before differential expression analyses with the R package DESeq2156, the count matrix was pre-filtered to keep miRNAs having at least 10 counts.
Assembly: v104
Supplementary files format and content: csv file includes raw counts for all samples

source_name: Cultured cells

growth_protocol: iPSCs were differentiated into motor neurons as previously described (Lépine et al. 2023 doi:10.1016/j.isci.2024.109166; Deneault et al. 2021 doi:10.1016/j.ymeth.2021.09.002). Motor neurons were harvested after four weeks post-plating of motor neuron progenitor cells.

extract_protocol:
Total RNA was extracted from MN cultures using the miRNeasy micro kit (Qiagen; Cat#217004) with DNase treatment (Qiagen; Cat#79256) following the manufacturer’s instructions. Samples with RNA integrity numbers above 6.5 determined by a Bioanalyzer (Agilent) were used for library preparation.
RNA libraries were prepared using the NEB small RNA library preparation kit following the manufacturer’s instructions.

value: Cultured cells

tag: cell line

value: TARDBP G348C/AIW002-02

value: Motor neuron

tag: library preparation

value: NEB small RNA


title: SCE34

value: stool


title: Sample 6, soleus muscle, space

description:
Library name: Sample 16
S1016

tag: strain


title: Purple_Hg17_Z2

value: Hg

value: M

value: A

value: Adapted NEBNext Ultra II RNA library prep


title: Sample 10, soleus muscle, space

description:
Library name: Sample 20
S1020


title: SCE33

value: Susceptible


title: TDP-43 p.G348C, rep5, miRNA-seq

tag: cell type


title: TDP-43 p.G348C, rep4, miRNA-seq


title: SCE36

value: Resistant


title: Sample 5, soleus muscle, space

description:
Library name: Sample 15
S1015

value: Soleus muscle

value: Hind-limb unloading


title: Sample 7, soleus muscle, space

description:
Library name: Sample 17
S1017

value: Ionizing radiation

value: Stress hormone


title: SCE35


title: TDP-43 p.G348C, rep3, miRNA-seq


title: injury2

city: Shanghai

first: Minwen

last: Zou

address: 800 Dongchuan Road, Shanghai

institute: Shanghai Jiao Tong University

description: Library name: Sample4

data_processing:
Transcript expression analysis of the RNA sequencing was performed by TopHat and Cufflinks. Significance analysis was performed by P value and false discovery rate (FDR) analyses. Differentially expressed genes were analyzed with the DESeq algorithm with the following criteria: fold change >2 or FDR <0.05.
Assembly: GRCr8
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: left carotid arteries

extract_protocol: Briefly, total RNA was extracted from carotid arteries with TRIzol reagent.

value: left carotid arteries


title: injury1

description: Library name: Sample3


title: Sample 2, soleus muscle, space

description:
Library name: Sample 12
S1012


title: stomach sample from not fin clipped control fish, biological rep4

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Data was processed within OmicsBox v3.3.2
Quality control was performed on raw reads using Trimmomatic v0.39
Quality reads were aligned to the channel catfish Coco_2.0 genome using the STAR aligner v2.7.8a (parameters – 2-pass mapping=true; overhang=149; feature=exon)
Read counts were extracted from BAM files using HTseq v2.0.5 ‘count’ feature (parameters – Quantification Level=exon; Group by=parent; Overlap Mode=union; stranded=strand specific reverse)
Assembly: Coco_2.0 (GCF_001660625.3)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Ictalurus punctatus

source_name: stomach

extract_protocol:
Total RNA was extracted from tissues using the Rneasy Plus Mini Kit (Qiagen) per the manufacturer’s protocol. 250 ng of total RNA from each sample was used for library construction.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Ligation Kit per the manufacturer’s protocol.

value: stomach

tag: disease state

value: mock

tag: time

value: 0 h

tag: feeding state

value: fed

value: not fin clipped


title: TDP-43 p.A382T, rep2, miRNA-seq

tag: tissue

value: Cultured cells

value: TARDBP A382T/AIW002-02

value: Motor neuron

value: NEB small RNA


title: control2

description: Library name: Sample2

source_name: right carotid arteries

value: right carotid arteries


title: control1

description: Library name: Sample1


title: TDP-43 p.G348C, rep1, miRNA-seq

value: TARDBP G348C/AIW002-02


title: TDP-43 p.A382T, rep5, miRNA-seq


title: Sample 10, soleus muscle, control

description:
Library name: Sample 10
S1010

tag: treatment

value: sham-irradiation


title: stomach sample from not fin clipped control fish, biological rep6


title: Sample 1, soleus muscle, space

description:
Library name: Sample 11
S1011

value: Soleus muscle


title: Sample 4, soleus muscle, space

description:
Library name: Sample 14
S1014

value: Hind-limb unloading


title: TDP-43 p.A382T, rep4, miRNA-seq


title: stomach sample from not fin clipped control fish, biological rep2


title: D3-WT-ATAC

city: Beijing

first: Ye-Guang

state: China

address: Haidian  District

institute: Tsinghua University

description: WT

data_processing:
ChIP-seq reads were aligned to the GCRm38/mm10 genome using Bowtie 2 (v2.2.5) and sorted with samtools (v1.5).
Samtools rmdup was used to remove duplicates from ChIP-seq data. *.bw files was processed with bamCoverage.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: colonic crypt

extract_protocol:
the CUT&tTag , ChIP-seq and ATAC-seq were all performed as previously described.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: To study how HBO1 regulates ISC and fetal genes expression, the control and HBO1 KO colonic crypts were subject to CUT&Tag and ChIP-seq with HBO1, H3K14ac and H3K14cr antibodies.Otherwise, the control and HBO1 KO mice were treated with 3% DSS, and the crypts were isolated at day 3 for ATAC-seq.

value: colonic crypt

value: Epithelial cells

tag: genotype

value: WT


title: Sample 3, soleus muscle, space

description:
Library name: Sample 13
S1013

value: Ionizing radiation

value: Stress hormone


title: Isogenic control, rep4, miRNA-seq


title: stomach sample from not fin clipped control fish, biological rep5

value: stomach

value: mock

value: 0 h


title: TDP-43 p.A382T, rep3, miRNA-seq

value: Cultured cells


title: KO2-LI-K14cr

description: HBO1 KO

value: HBO1 KO

value: ChIP antibody


title: KO1-LI-K14cr

description: HBO1 KO


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep6

value: infected

value: 8 h

value: not fed

value: not fin clipped


title: stomach sample from not fin clipped control fish, biological rep3

value: fed


title: TDP-43 p.A382T, rep1, miRNA-seq

value: TARDBP A382T/AIW002-02

value: Motor neuron

value: NEB small RNA


title: Isogenic control, rep3, miRNA-seq


title: Isogenic control, rep5, miRNA-seq


title: WT2-LI-K14cr

description: WT

value: colonic crypt

value: Epithelial cells

value: WT


title: Isogenic control, rep2, miRNA-seq


title: WT1-LI-K14cr

description: WT


title: D3-KO-ATAC

description: HBO1 KO


title: Sample 9, soleus muscle, control

description:
Library name: Sample 9
S1009

value: Soleus muscle

value: sham-irradiation


title: Sample 6, soleus muscle, control

description:
Library name: Sample 6
S1006


title: stomach sample from not fin clipped control fish, biological rep1

value: stomach

value: mock

value: 0 h


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep3


title: Sample 8, soleus muscle, control

description:
Library name: Sample 8
S1008


title: 126-LI-K14ac

description: HBO1 KO

value: HBO1 KO

value: ChIP antibody


title: Sample 7, soleus muscle, control

description:
Library name: Sample 7
S1007


title: 127-LI-K14ac

description: WT


title: 129-LI-K14ac

description: WT


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep5

value: infected

value: 8 h


title: DSP-E12, segmented , Layer 5

description: Library name: DSP-E12

value: Frontal Cortex Brain Tissue

value: segmented

value: Layer 5


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep4

value: not fed

value: not fin clipped


title: Sample 5, soleus muscle, control

description:
Library name: Sample 5
S1005


title: Sample 4, soleus muscle, control

description:
Library name: Sample 4
S1004


title: 126-LI-input

description: HBO1 KO

value: colonic crypt


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep2


title: TDP-43 p.G348C, rep4

data_processing:
Sequencing files were analyzed using the GenePipes RNA-seq pipeline 3.6.0.
Raw reads were clipped for adapter sequence, trimmed for minimum quality (Q30) in 3' and filtered for minimum length of 32 bp using Trimmomatic.
Surviving read pairs were aligned to the human genome assembly hg38 by the ultrafast universal RNA-seq aligner STAR using the recommended two passes approach.
Aligned RNA-seq reads were assembled into transcripts and their relative abundance was estimated using Cufflinks.
Assembly: hg38
Supplementary files format and content: .csv file includes raw counts for all samples

growth_protocol: iPSCs were differentiated into motor neurons as previously described (Lépine et al. 2023 doi: 10.1016/j.isci.2024.109166; Deneault et al. 2021 doi:10.1016/j.ymeth.2021.09.002). Motor neurons were harvested after four weeks post-plating of motor neuron progenitor cells.

extract_protocol:
Total RNA was extracted from MN cultures using the miRNeasy micro kit (Qiagen; Cat#217004) with DNase treatment (Qiagen; Cat#79256) following the manufacturer’s instructions. Samples with RNA integrity numbers above 6.5 determined by a Bioanalyzer (Agilent) were used for library preparation.
RNA libraries were prepared using the NEB mRNA stranded library preparation kit  following the manufacturer’s instructions.

value: Cultured cells

value: TARDBP G348C/AIW002-02

value: Motor neuron

value: NEB mRNA stranded


title: 125-LI-K14ac

description: HBO1 KO

value: Epithelial cells


title: stomach sample from not fed nor fin clipped fish 8 h post infection, biological rep1

value: stomach


title: Sample 3, soleus muscle, control

description:
Library name: Sample 3
S1003

value: Soleus muscle

value: sham-irradiation


title: TDP-43 p.G348C, rep3


title: 125-LI-input

description: HBO1 KO

value: HBO1 KO


title: 129-lLI-input

description: WT

value: WT


title: Isogenic control, rep1, miRNA-seq

value: NEB small RNA


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep6

value: infected

value: 4 h


title: 127-LI-input

description: WT


title: TDP-43 p.G348C, rep2


title: Sample 2, soleus muscle, control

description:
Library name: Sample 2
S1002


title: Sample 1, soleus muscle, control

description:
Library name: Sample 1
S1001


title: HBO1

description: WT

value: ChIP antibody


title: TDP-43 p.A382T, rep5

value: TARDBP A382T/AIW002-02


title: IgG

description: WT


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep3

value: not fed

value: not fin clipped


title: TTFs,  pMXs-Gata4, pMXs-Mef2c, pMXs-TBX5 (GMT) Day 7 iCLM reprogramming, replicate 3

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

description:
Bulk
GMT_3

data_processing:
Briefly, reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID. Differential gene expression analysis was done using the R package DEseq (version 1.38). Cutoff values of fold change>2 and FDR<0.05 were used to select for differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: primary

growth_protocol: Briefly, retroviral constructs were transfected into Platinum E cells using FuGENE 6 transfection reagent. Twenty-four hours after transfection, wild-type fibroblasts were seeded into culture dishes or plates that were precoated with SureCoat (Cellutron) or Matrigel (Corning). Forty-eight hours after transfection, the viral medium was filtered through a 0.45-μm filter and polybrene was added at a concentration of 8 μg/mL. Then, fibroblasts were infected by replacing growth medium with the above viral mixture. The viral infection was serially repeated twice and twenty-four hours after the second infection, the viral medium was replaced with induction medium composed of DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin–selenium–transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). Induction medium was replaced every two to three days until experiments were performed.

extract_protocol:
Total RNA was extracted from TTFs seven days after retroviral transduction, using TRIzol (Invitrogen) according to the vender’s protocol. Illumina RNA-seq was performed by the University of Texas Southwestern Microarray Core Facility.
Library construction was performed per manufacturer protocol for mRNA library construction. Illumina RNA-seq was performed by the University of Texas Southwestern Next Generation Sequencing Core Facility.

value: primary

value: tailtip fibroblast


title: C3H_NAIVE_4

first: Aditi

last: Verma

state: IL

address: 300 East Superior Street Tarry 15-735

department: Department of Medicine

description:
Library name: RK9_S46
Column name in williams.genecounts_bulkrnaseq.tsv:RK9_S46_genecounts

data_processing:
Sequenced reads were aligned to the mouse genome (Ensembl GRCm39 version 110) using the STAR aligner (version 2.7.9a) and counted using HTSeq (version 2.0.2).
Assembly: GRCm39 version 110
Supplementary files format and content: tab delimited tsv file includes raw gene counts for all samples
Supplementary files format and content: processed data in the form of counts matrix in williams.genecounts_bulkrnaseq.tsv

source_name: jejunum

extract_protocol:
RNA was then extracted using the Qiagen miRNeasy Mini Kit (catalog number 217004)
The Illumina Stranded mRNA Prep Kit was used to prepare sequencing libraries from 200 ng of high-quality RNA samples (RIN>7). The Kit procedure was performed without modifications.

treatment_protocol: 6-8 week old naive C57BL/6 and C3H/HeJ mice were co-housed for at least 8 weeks before being euthanized for tissue harvest.

value: jejunum

value: naïve

tag: batch


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep2


title: TTFs,  pMXs-Gata4, pMXs-Mef2c, pMXs-TBX5 (GMT) Day 7 iCLM reprogramming, replicate 2

description:
Bulk
GMT_2

treatment_protocol: Briefly, retroviral constructs were transfected into Platinum E cells using FuGENE 6 transfection reagent. Twenty-four hours after transfection, wild-type fibroblasts were seeded into culture dishes or plates that were precoated with SureCoat (Cellutron) or Matrigel (Corning). Forty-eight hours after transfection, the viral medium was filtered through a 0.45-μm filter and polybrene was added at a concentration of 8 μg/mL. Then, fibroblasts were infected by replacing growth medium with the above viral mixture. The viral infection was serially repeated twice and twenty-four hours after the second infection, the viral medium was replaced with induction medium composed of DMEM/199 (4:1), 10% FBS, 5% horse serum, 1% penicillin/streptomycin, 1% nonessential amino acids, 1% essential amino acids, 1% B-27, 1% insulin–selenium–transferrin, 1% vitamin mixture, and 1% sodium pyruvate (Invitrogen). Induction medium was replaced every two to three days until experiments were performed.


title: TDP-43 p.A382T, rep3

value: Cultured cells

value: Motor neuron

value: NEB mRNA stranded


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep1

value: stomach


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep6

value: 2 h


title: B6_NAIVE_4

description:
Library name: RK4_S42
Column name in williams.genecounts_bulkrnaseq.tsv:RK4_S42_genecounts


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep5


title: TDP-43 p.G348C, rep1

value: TARDBP G348C/AIW002-02


title: TTFs,  pMXs-PHF7, pMXs-Mef2c, pMXs-TBX5 (PMT) Day 7 iCLM reprogramming, replicate 2

description:
Bulk
PMT_2

value: WT


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep4

value: infected


title: stomach sample from not fed nor fin clipped fish 4 h post infection, biological rep4

value: 4 h


title: TDP-43 p.A382T, rep2


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep5


title: Isogenic control, rep5


title: C3H_NAIVE_5

description:
Library name: RK10_S47
Column name in williams.genecounts_bulkrnaseq.tsv:RK10_S47_genecounts


title: TDP-43 p.A382T, rep1


title: Isogenic control, rep4


title: C3H_NAIVE_3

description:
Library name: RK8_S45
Column name in williams.genecounts_bulkrnaseq.tsv:RK8_S45_genecounts


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep3


title: TTFs, pMXs-Mef2c, pMXs-TBX5 (MT) Day 7 iCLM reprogramming, replicate 3

description:
Bulk
MT_3


title: Isogenic control, rep3


title: C3H_NAIVE_1

description:
Library name: RK5_S43
Column name in williams.genecounts_bulkrnaseq.tsv:RK5_S43_genecounts


title: TDP-43 p.A382T, rep4


title: TDP-43 p.G348C, rep5


title: B6_NAIVE_2

description:
Library name: RK2_S40
Column name in williams.genecounts_bulkrnaseq.tsv:RK2_S40_genecounts


title: B6_NAIVE_3

description:
Library name: RK3_S41
Column name in williams.genecounts_bulkrnaseq.tsv:RK3_S41_genecounts


title: TTFs, pMXs-Gata4, pMXs-Mef2c, pMXs-TBX5 (GMT) Day 7 iCLM reprogramming, replicate 1

description:
Bulk
GMT_1


title: TTFs, pMXs-Mef2c, pMXs-TBX5 (MT) Day 7 iCLM reprogramming, replicate 2

description:
Bulk
MT_2


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep2


title: stomach sample from not fed nor fin clipped fish 2 h post infection, biological rep1


title: B6_NAIVE_5

description:
Library name: RK6_S44
Column name in williams.genecounts_bulkrnaseq.tsv:RK6_S44_genecounts


title: TTFs,  pMXs-PHF7, pMXs-Mef2c, pMXs-TBX5 (PMT) Day 7 iCLM reprogramming, replicate 3

description:
Bulk
PMT_3


title: Isogenic control, rep2


title: Isogenic control, rep1


title: TTFs, pMXs-Mef2c, pMXs-TBX5 (MT) Day 7 iCLM reprogramming, replicate 1

description:
Bulk
MT_1


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep6

value: 8 h

value: fed


title: TTFs, pMXs-PHF7, pMXs-TBX5 (PT) Day 7 iCLM reprogramming, replicate 3

description:
Bulk
PT_3


title: Engineered midbrain organoids, Fentanyl treated

city: Bloomington

first: Feng

state: Indiana

address: 107 S Indiana Ave

institute: Indiana University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data of individual samples from 10x scRNA-seq was preprocessed with Cell Range software on 10x cloud (v6.1.2, 10X Genomics). The reads were aligned and quantified according to the hg38 human reference genome (refdata-gex-GRCh38-2020-A, 10x Genomics). The generated data matrix was further analyzed using the Seurat v4 package and R v4.1.0.
Quality control was performed by removing cells with less than 200 genes, more than 25,000 gene-UMIs, more than 10% mitochondrial gene-UMIs, and genes detected in less than 5 cells. The filtered data matrix was further processed following the standard Seurat flow.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Neural organoids

extract_protocol:
The organoids were dissociated into single-cell solutions using a commercially available papain-based dissociation (Neural tissue dissociation kit-P, Miltenyi Biotec) following the manufacturer’s protocol with slight modification. The organoids were washed 3 times with HBSS (without Ca2+ and Mg2+, −/−) and cut into hemispheres with scissors. The cut hemispheres were then incubated in enzyme mix 1 (enzyme P) with 90 RPM orbital shaking for 15 minutes, followed by adding enzyme mix 2 (enzyme A) and incubation for another 30 minutes with orbital shaking. During the incubation, the organoid samples were triturated with a wide bore 1ml tip every 10 to 15 minutes. Then, the samples were filtered through a 30 μm strainer (Miltenyi Biotec) to remove the large aggregates and keep single cells. The single-cell solutions were centrifuged at 300 x g for 8 minutes at 4 oC, and resuspended to the desired concentration (1 million/ml) in the organoid medium without any growth factors, followed by 10X scRNA-seq.
Library construction was performed using Next-GEM Chromium Single Cell 3’ Library & Gel Bead Kit v3.1following the manufacturer's protocol.

value: Neural organoids

value: H9 (WiCell, #hPSCreg WAe009-A)

value: hPSCs

value: Wild type

value: Engineered purfsable scaffold and 2-day 50nM fentanyl treatment


title: Conventional midbrain organoids

description: 10x Genomics


title: TTFs, pMXs-PHF7, pMXs-TBX5 (PT) Day 7 iCLM reprogramming, replicate 2

description:
Bulk
PT_2

value: primary

value: tailtip fibroblast


title: Engineered midbrain organoids

description: 10x Genomics

value: Engineered purfsable scaffold


title: TTFs, pMXs-PHF7, pMXs-Mef2c, pMXs-TBX5 (PMT) Day 7 iCLM reprogramming, replicate 1

description:
Bulk
PMT_1


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep4

value: not fin clipped


title: ChIPaKmg_aly_rep2_INPUT

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description: Library name: ChIPaKmg_aly_rep2_INPUT

data_processing:
Adapters and low-quality bases were trimmed using trimGalore (0.6.6), reads were mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using bwa aln (0.7.18) (Li and Durbin 2009)
DeepTools (3.1.0) was used to generate normalized coverage files (BibWig)
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: BigWig

organism: Drosophila melanogaster

source_name: Testes

extract_protocol:
ChIP-seq was performed using the Low Cell ChIP Kit from Active Motif (#53086). Please see publication for details.
Libraries were made using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® NEB (#E7645L).

value: Testes

tag: chip antibody


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep5

value: stomach


title: ChIPaKmg_aly_rep2

description: Library name: ChIPaKmg_aly_rep2

value: anti-Kmg (Kim et al. 2017)


title: TTFs, pBx-TBX5, Day 7 iCLM reprogramming, replicate 3

description:
Bulk
TBX5_3

value: WT

value: pBx-TBX5, Day 7 iCLM reprogramming


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep2

value: infected


title: Primary breast tumor, RNAseq, B41_493_C40_T_S82

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Align the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
QC methods used samtools sort 1.10, Picard 2.22.4, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: Salmon gene expression file (tab-delimited)

source_name: Primary breast tumor

extract_protocol:
RNA was extracted from paraffin-embedded baseline tumor samples
ribo-zero RNAseq libraries were made using an Illumina TruSeq Stranded Total RNA kit

value: Primary breast tumor

tag: race

value: White

tag: tx arm

tag: Stage

value: III

tag: hr status

value: HR-positive

tag: meno status

value: Pre-menopausal

tag: pcr breast

value: RD

tag: efs time

tag: efs stat

tag: body site

value: Breast

tag: analyte type

value: RNA

tag: is tumor

value: Y

tag: collection age

tag: primary metastatic_tumor

value: Primary

tag: primary tumor_location

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: TTFs, pBx-TBX5, Day 7 iCLM reprogramming, replicate 2

description:
Bulk
TBX5_2

tag: cell line

value: primary

tag: cell type

value: tailtip fibroblast

tag: genotype

tag: strain

tag: treatment


title: ChIPaKmg_aly_rep1_INPUT

description: Library name: ChIPaKmg_aly_rep1_INPUT

tag: tissue

value: Testes

tag: chip antibody


title: Primary breast tumor, RNAseq, B41_416_3_T_S76

tag: race

value: Black

tag: tx arm

value: Trastuzumab

tag: Stage

tag: hr status

tag: meno status

value: Post-menopausal

tag: pcr breast

tag: efs time


title: Primary breast tumor, RNAseq, B41_506_B2_T_S84

value: Primary breast tumor

value: Other

value: II

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

tag: collection age

tag: primary metastatic_tumor

tag: primary tumor_location


title: TTFs, pBx-TBX5, Day 7 iCLM reprogramming, replicate 1

description:
Bulk
TBX5_1

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: strain

tag: treatment

value: pBx-TBX5, Day 7 iCLM reprogramming


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep3

tag: tissue

value: stomach

tag: disease state

value: infected

tag: time

value: 8 h

tag: feeding state

value: fed

value: not fin clipped


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep6

value: 4 h


title: Primary breast tumor, RNAseq, B41_401_B8_T_S75

tag: race

value: White

tag: tx arm

value: Lapatinib

tag: Stage

tag: hr status

value: HR-positive

tag: meno status

value: Pre-menopausal

tag: pcr breast

value: RD

tag: efs time

value: Breast

value: RNA

value: Y

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: ChIPaKmg_aly_rep1

description: Library name: ChIPaKmg_aly_rep1

value: Testes

tag: chip antibody

value: anti-Kmg (Kim et al. 2017)


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep5

value: stomach

value: infected


title: TTFs, pMXs-PHF7, Day 7 iCLM reprogramming, replicate 3

description:
Bulk
PHF7_3

tag: cell line

value: primary

tag: cell type

value: tailtip fibroblast

tag: genotype

value: WT

value: pMXs-PHF7, Day 7 iCLM reprogramming


title: Primary breast tumor, RNAseq, B41_363_1H_T_S47

tag: tissue

value: Primary breast tumor

value: White

value: Lapatinib

value: III

value: HR-negative

value: Post-menopausal

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

tag: collection age

tag: primary metastatic_tumor

tag: primary tumor_location

value: Basal-like


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep4

tag: disease state

tag: time

value: 4 h

tag: feeding state

value: fed

tag: treatment

value: not fin clipped


title: TTFs, pMXs-PHF7, Day 7 iCLM reprogramming, replicate 2

description:
Bulk
PHF7_2

tag: strain


title: TTFs, pMXs-PHF7, pMXs-TBX5 (PT) Day 7 iCLM reprogramming, replicate 1

description:
Bulk
PT_1


title: Primary breast tumor, RNAseq, B41_512_A4_T_S85

tag: race

tag: tx arm

value: Trastuzumab

tag: Stage

tag: hr status

tag: meno status

tag: pcr breast

value: RD

tag: efs time

value: Breast

value: RNA

value: Y

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep3

tag: tissue

value: stomach

value: infected


title: TTFs, pMXs-PHF7, Day 7 iCLM reprogramming, replicate 1

description:
Bulk
PHF7_1

tag: cell line

value: primary

tag: cell type

value: tailtip fibroblast

tag: genotype

value: WT

value: pMXs-PHF7, Day 7 iCLM reprogramming


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate2

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: Ccnd1KO_2

data_processing:
Trim adapters and low‑quality bases with Trim Galore 0.6.7.
Align reads to the mouse mm10 genome with HISAT2 2.2.1.
Count reads per gene using featureCounts 2.0.3.
Generate QC reports (FastQC 0.74, then summarize with MultiQC) and perform PCA for sample relationships.
Perform differential expression analysis and generate Normalized counts with DESeq2 2.11.40.8.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Normalized_counts_file_on_data_155_data_154_and_others_Ccnd1KO_3weeks.csv

source_name: Liver

growth_protocol: C57BL/6J mice rested ≥2 weeks upon receipt; maintained on normal chow, 12 h light/12 h dark, ad libitum

extract_protocol:
Flash‑frozen liver piece (m‑lobe) homogenized in TRIzol; total RNA isolated using Zymo Direct‑zol RNA Kit per manufacturer’s instructions
PolyA capture

treatment_protocol: At 17 months, mice received retro‑orbital injection of AAV8‑TBG‑saCas9 carrying either Ccnd1‑targeting sgRNA or Rosa26 control (3×10¹¹ vg/mouse); m‑lobe harvested 3 weeks later, flash‑frozen.

value: Liver


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate4

description: Library name: Ccnd1KO_4


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate5

description: Library name: Ccnd1KO_5


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate3

description: Library name: Ccnd1KO_3


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgCcnd1 replicate1

description: Library name: Ccnd1KO_1


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate4

description: Library name: Rosa26KO_4


title: TTFs, pMXs-Empty, Day 7 iCLM reprogramming, replicate 2

description:
Bulk
Empty_2

value: pMXs-Empty, Day 7 iCLM reprogramming


title: stomach sample from fed but not fin clipped fish 8 h post infection, biological rep1

tag: disease state

tag: time

value: 8 h

value: fed


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep2

value: 4 h

tag: feeding state

tag: treatment

value: not fin clipped


title: Primary breast tumor, RNAseq, B41_321_1D_T_S40

value: Primary breast tumor

tag: race

value: White

value: III

value: HR-positive

value: Pre-menopausal

value: RD

tag: efs stat

tag: body site

value: Breast

tag: analyte type

tag: is tumor

tag: collection age

tag: primary metastatic_tumor

tag: primary tumor_location


title: stomach sample from fed but not fin clipped fish 4 h post infection, biological rep1

value: stomach

value: infected


title: Primary breast tumor, RNAseq, B41_313_C13_T_S32

value: Asian

tag: tx arm

value: Lapatinib

tag: Stage

value: II

tag: hr status

tag: meno status

value: Post-menopausal

tag: pcr breast

tag: efs time

value: RNA

value: Y

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate3

description: Library name: Rosa26KO_3

tag: tissue

value: Liver

tag: strain

tag: genotype

value: WT

tag: treatment


title: TTFs, pMXs-Empty, Day 7 iCLM reprogramming, replicate 1

description:
Bulk
Empty_1

tag: cell line

value: primary

tag: cell type

value: tailtip fibroblast

value: pMXs-Empty, Day 7 iCLM reprogramming


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate2

description: Library name: Rosa26KO_2


title: Primary breast tumor, RNAseq, B41_305_1A_T_S27

value: Primary breast tumor

tag: race

value: Black

value: Trastuzumab

value: HR-negative

value: RD

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

tag: collection age


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep5

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: fed

value: not fin clipped


title: Primary breast tumor, RNAseq, B41_312_A5_T_S30

value: White

tag: tx arm

value: Lapatinib

tag: Stage

value: II

tag: hr status

value: HR-positive

tag: meno status

value: Pre-menopausal

tag: pcr breast

tag: efs time

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

tag: primary tumor_location

tag: tumor treatment


title: 17mo mouse treated with AAV-TBG-saCAS9-u6-sgRosa26 Replicate1

description: Library name: Rosa26KO_1

tag: tissue

value: Liver

tag: strain

tag: genotype

value: WT

tag: treatment


title: Primary breast tumor, RNAseq, B41_346_A5_T_S48

value: Primary breast tumor

tag: race

value: Trastuzumab

value: HR-negative

value: RD

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

tag: collection age

value: Treated

tag: rnaseq subtype


title: DIO-zeta_4-1

city: Seoul

first: UnHo

last: Kang

address: 15F, 241, Gangnam-daero, Seocho-gu

country: South Korea

institute: Arontier

data_processing:
sequence files were checked for quality with FastQC
adapters were trimemd by Trimmomatic
trimmed sequences were mapped by HISAT2
mapped files were assembled by StringTie
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts, FPKM, TPM for each sample

source_name: small intestine

extract_protocol:
Total RNA was harvested using Rneasy mini kit (Qiagen).
Total RNA sequencing libraries were generated using Illumina TruSeq Stranded Total RNA Sample prep kit with Ribo-zero Human/Mouse/Rat.

value: small intestine

value: PKCzeta overexpression


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep4

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: fed

value: not fin clipped


title: Primary breast tumor, RNAseq, B41_329_A14_T_S35

value: White

tag: tx arm

value: Lapatinib

tag: Stage

value: III

tag: hr status

value: HR-positive

tag: meno status

value: Post-menopausal

tag: pcr breast

tag: efs time

value: Breast

value: RNA

tag: primary metastatic_tumor


title: DIO-zeta_2-1

tag: tissue

tag: treatment


title: TTFs, pMXs-Empty, Day 7 iCLM reprogramming, replicate 3

description:
Bulk
Empty_3

tag: cell line

value: primary

tag: cell type

value: tailtip fibroblast

tag: genotype

value: WT

tag: strain

value: pMXs-Empty, Day 7 iCLM reprogramming


title: Primary breast tumor, RNAseq, B41_288_D5_T_S25

value: Primary breast tumor

tag: race

value: Trastuzumab

value: II

value: Pre-menopausal

value: RD

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

value: Y

tag: collection age

value: Primary

tag: primary tumor_location

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep3

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: fed

value: not fin clipped


title: HiC_JE2_delta_5parS

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: Library name: HiC_JE2_delta_5parS

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Staphylococcus aureus Hi-C, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For WGS, we mapped reads in each FASTQ file back to the genome of Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Staphylococcus aureus JE2  genome was divided into DpnII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Staphylococcus aureus JE2 was then divided into bins 5 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Staphylococcus aureus JE2 (NCBI Reference Sequence GCF_002085525.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of WGS results.

organism: Staphylococcus aureus

source_name: Bacterial cell

extract_protocol:
Wild type and mutant cells of Staphylococcus aureus JE2 growing in TSB were crosslinked using 7 % formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: Bacterial cell

value: JE2, delta_5parS

tag: treatment

value: Cells were grown in TSB at 37°C with agitation until early-exponential phase (OD600 0.3-0.4)


title: Primary breast tumor, RNAseq, B41_236_A4_T_S90

tag: tissue

value: White

tag: tx arm

value: Lapatinib

tag: Stage

tag: hr status

value: HR-positive

tag: meno status

value: Post-menopausal

tag: pcr breast

tag: efs time

value: Breast

value: RNA

tag: primary metastatic_tumor


title: WGS_JE2_FROS_Ter_delta_spoIIIE

description: Library name: WGS_JE2_FROS_Ter_delta_spoIIIE

tag: strain

tag: cell type

tag: genotype

value: JE2 spoIIIE::delta_spoIIIE Spa::TetR-mNG Terminus-tetO array

value: Cells were grown in TSB at 37°C with agitation until the mid-exponential phase (OD600 0.6-0.8)


title: DIO-GFP_3-1

value: small intestine

value: control


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep2

value: stomach

value: infected


title: Primary breast tumor, RNAseq, B41_226_B9_T_S34

value: Primary breast tumor

tag: race

value: Trastuzumab

value: II

value: Pre-menopausal

value: RD

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor

value: Y

tag: collection age

value: Primary

tag: primary tumor_location

tag: tumor treatment

value: Treated


title: DIO-GFP_1-4

tag: tissue

tag: treatment


title: WGS_JE2_FROS_Ori_delta_spoIIIE

description: Library name: WGS_JE2_FROS_Ori_delta_spoIIIE

value: Bacterial cell

value: JE2 spoIIIE::delta_spoIIIE Spa::TetR-mNG Ori-tetO array


title: DIO-GFP_1-1


title: WGS_JE2_FROS_Ori_delta_xerC

description: Library name: WGS_JE2_FROS_Ori_delta_xerC

value: JE2 xerC::delta_xerC Spa::TetR-mNG Ori-tetO array


title: PBMCs treated with K21 and labelled with 4sU

city: Rīga

first: Bhupesh

last: Prusty

address: Rātsupītes iela 5

country: Latvia

institute: Rīga Stradiņš University

description:
Library name: PBMC3
SCC101_5_Bhupesh_Sample_GEX_H6

data_processing:
The sequencing data was processed using the CellRanger (v8.0.0 ) GEX+ADT pipeline, which conducts QC, cell filtration, read alignment, and generation of feature-barcode matrices. SLAM analysis was carried out using GRAND-SLAM v3. The reads were aligned to the human (GRCh38) reference genome. To obtain higher numbers of usable cells, we set the parameter ‘--expect-cells=10000’ within CellRanger. Seurat (v4.1, https://satijalab.org/seurat/) R packages were used to calculate QC matrices and to filter cells and features. For filtering of cells (https://github.com/satijalab/seurat/issues/3396), we first removed empty droplets. Subsequently, we removed low-quality cells with unique feature counts greater than 8000 or less than 200. Furthermore, low-quality or dying cells that exhibited extensive mitochondrial contamination were removed. Genes with expression for at least three cells are retained for filtering. (Hao Y ,  Hao S ,  Andersen-Nissen E , et al. Integrated analysis of multimodal single-cell data[J].  2021). Quality control (QC) was based on (1) nFeature_RNA: number of unique genes detected in each cell; (2) nCount_RNA: total number of molecules detected within a cell; (3) percent.mt: percentage of reads that map to the mitochondrial genome. Mitochondrial QC metrics were generated, calculating the percentage of counts originating from a set of features (the set of all genes starting with “MT-” mitochondrial genes).
Assembly: GRCh38
Supplementary files format and content: Separate folders for each individual sample

source_name: PBMCs from the same one individual

growth_protocol: Freshly isolated PBMCs were grown for 2 hrs in the presence (0.2 mM K21) or absence of K21. 200 mM 4sU was also added to the cell culture media at the time of K21 addition, which allowed 2 h of 4sU incorporation into the cells. PBMCs were washed and fixed in methanol.

extract_protocol:
The methanol fixation was allowed to proceed for 30 minutes at -20 °C. Then, 10 mM iodoacetamide (IAA) was added to each of the methanol-fixed cells, and the mixture was left at 4 °C overnight with gentle agitation. The next day, cells were centrifuged down, resuspended in quenching buffer containing DTT (DBPS, 0.1% BSA, 1 U/μl RNaseOUT, 100 mM DTT) for 5 min at room temperature. Cells were then centrifuged down, resuspended in resuspension buffer (DBPS, 0.01% BSA, 0,5 U/μl RNaseOUT, 1mM DTT). Cells were then passed through a 0,4m filter, counted, and proceeded for the 10X Genomics microfluidics run.
PBMCs with and without K21 were loaded separately into a lane on the same chip, targeting 5000 cells per lane. The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ v3.1 Reagent Kit according to the manufacturer‘s guidelines (10× Genomics). cDNA libraries were uniquely sample-indexed and pooled for sequencing. A Illumina sequencing run was used to sample balance on a NextSeq 500 flowcell (Illumina) targeting > 50,000 reads/cell.

value: PBMCs from the same one individual

value: Immune cells

value: WT


title: DIO-zeta_4-2

value: small intestine

value: PKCzeta overexpression


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep6

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: fed

value: not fin clipped


title: stomach sample from fed but not fin clipped fish 2 h post infection, biological rep1


title: WGS_JE2_FROS_Ter_delta_xerC

description: Library name: WGS_JE2_FROS_Ter_delta_xerC

value: JE2 xerC::delta_xerC Spa::TetR-mNG Terminus-tetO array

value: Cells were grown in TSB at 37°C with agitation until the mid-exponential phase (OD600 0.6-0.8)


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep6

value: 8 h

value: not fed

value: fin clipped


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep5


title: Primary breast tumor, RNAseq, B41_214_C5_T_S32

value: Primary breast tumor

value: White

tag: tx arm

tag: Stage

value: III

tag: hr status

value: HR-negative

tag: meno status

value: Pre-menopausal

tag: pcr breast

value: RD

tag: efs time

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

value: Treated

tag: rnaseq subtype

value: Basal-like


title: Primary breast tumor, RNAseq, B41_178_J15_T_S8

tag: race

value: II

value: HR-positive

tag: efs stat

tag: body site

tag: analyte type

tag: is tumor


title: WGS_JE2_FROS_Ter

description: Library name: WGS_JE2_FROS_Ter

tag: strain

tag: cell type

value: Bacterial cell

tag: genotype

value: JE2 Spa::TetR-mNG Terminus-tetO array

tag: treatment

value: Cells were grown in TSB at 37°C with agitation until the mid-exponential phase (OD600 0.6-0.8)


title: PBMCs treated with IL-2 and PHA and labelled with 4sU

description:
Library name: PBMC2
SCC101_5_Bhupesh_Sample_GEX_H5

tag: tissue

value: PBMCs from the same one individual

value: Immune cells

value: WT

value: IL-2 and PHA treated


title: Primary breast tumor, RNAseq, B41_177_A1_T_S6

value: Primary breast tumor

value: White

tag: tx arm

value: Lapatinib

tag: Stage

value: III

value: HR-negative

value: Post-menopausal

tag: collection age

tag: primary tumor_location

tag: tumor treatment


title: WGS_JE2_FROS_Ori

description: Library name: WGS_JE2_FROS_Ori

value: JE2 Spa::TetR-mNG Ori-tetO array


title: Primary breast tumor, RNAseq, B41_164_2_T_S96

tag: hr status

tag: meno status

tag: pcr breast

value: RD

tag: efs time

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

value: Treated

value: Basal-like


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep3

value: stomach

tag: disease state

value: infected

tag: time

value: 8 h

tag: feeding state

value: not fed

value: fin clipped


title: Case #10, ARMS FFPE tissue, Female, 10 years old [RNA-seq]

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: Library name: Case #10

data_processing:
Pseudo-alignment and transcript quantification with Salmon
Importing gene counts in R using tximeta
Normalization with variance stabilizing transformation
Assembly: hg38
Supplementary files format and content: vst-normalized counts for each sample

source_name: Head/Neck Alveolar Rhabdomyosarcoma

extract_protocol:
We extracted RNA following ReliaPrep™ FFPE Total RNA kit (Promega)
We used the SureSelect XT HS RNA according to manufacturer recommendations (Agilent Technologies)

value: Head/Neck Alveolar Rhabdomyosarcoma

tag: group

value: B

tag: Sex

value: Female

tag: age

value: 10 years old


title: PBMCs, treated with vehicle control and labelled with 4sU

description:
Library name: PBMC1
SCC101_5_Bhupesh_Sample_GEX_H4

source_name: PBMCs from one individual

tag: tissue

value: PBMCs from one individual

tag: cell type

value: Immune cells

tag: genotype

value: WT

tag: treatment

value: No


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep4


title: Primary breast tumor, RNAseq, B41_147_2H_T_S43

value: Primary breast tumor

tag: race

value: White

tag: tx arm

value: Trastuzumab

tag: Stage

value: II

value: HR-positive

value: Pre-menopausal

value: RD

tag: efs stat

tag: body site

value: Breast

tag: analyte type

value: RNA

tag: is tumor

value: Y

tag: collection age

tag: primary tumor_location

tag: rnaseq subtype


title: Case #9, ARMS FFPE tissue, Male, 17 years old [RNA-seq]

description: Library name: Case #9

value: Head/Neck Alveolar Rhabdomyosarcoma

tag: group

value: B

value: Male

value: 17 years old


title: Primary breast tumor, RNAseq, B41_130_M_T_S75

value: Lapatinib

value: III

tag: hr status

tag: meno status

tag: pcr breast

tag: efs time

tag: primary metastatic_tumor

value: Primary

tag: tumor treatment

value: Treated


title: Case #8, ARMS FFPE tissue, Male, 15 years old [RNA-seq]

description: Library name: Case #8

tag: tissue

tag: genotype

tag: Sex

tag: age

value: 15 years old


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep1

value: stomach

tag: disease state

value: infected

tag: time

value: 8 h

tag: feeding state

value: not fed

tag: treatment

value: fin clipped


title: Primary breast tumor, RNAseq, B41_105_1A_T_S87

value: Primary breast tumor

tag: race

value: White

tag: tx arm

tag: Stage

value: II

value: HR-negative

value: Pre-menopausal

value: RD

tag: efs stat

tag: body site

value: Breast

tag: analyte type

tag: is tumor

tag: collection age

tag: primary tumor_location

value: Basal-like


title: WGS_JE2

description: Library name: WGS_JE2

tag: strain

tag: cell type

value: Bacterial cell

value: JE2 delta_spa

value: Cells were grown in TSB at 37°C with agitation until the mid-exponential phase (OD600 0.6-0.8)


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep6

tag: tissue

value: 4 h


title: stomach sample from fin clipped but not fed fish 8 h post infection, biological rep2

value: stomach


title: BS_DKO_Rep2

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: Bisulfite sequencing of hippocampal genomic DNA from Mutyh-/-XOgg1-/- mouse

data_processing:
Reads were trimmed and quality was assessed using FastQC.
Reads were aligned to the mouse reference genome GRCm38, followed by a separate extraction of genome-wide 5mC in the context of CG, CHG and CHH by using Bismark (v.0.22.3)
The 5mC count data was cleaned by filtering out low reads of coverage <4 in each cytosine.
The differentially methylated regions (DMRs) were identified by HMST-Seq-Analyzer which extrcats methylated regions from predefined genomic areas (e.g. TSS, TES, and gene body) and DMRs were predicted by robust statistical tests (Wilcoxon rank-sum test) between samples.
The common DMRs among 4 pair-wise comparisons (KO1-WT1, KO2-WT1, KO1-WT2, KO2, WT2) were defined as the true DMRs.
Assembly: GRCm38
Supplementary files format and content: .xlsx files containing HMST-Analyzer output for CG, CHG and CHH across both replicates with rratios

source_name: Hippocampus

growth_protocol: C57BL/6N background mice in standard home-cage housing (12h light/dark, ad libitum food and water, 19-22°C, 50-50% air humidity).

extract_protocol:
DNA was extracted using the AllPrep DNA/RNA/Protein mini kit (Qiagen, 80004), according to manufacturer’s protocol.
Total hippocampal DNA was fragmented by sonication using a Bioruptor (Diagenode) to a mean size of approximately 250 bp, followed by blunt-ending and dA addition to 3'-end.
Adaptor ligation with methylated adaptors was performed according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (Zymo research, D5005). After treatment with sodium bisulfite, unmethylated cytosine residues were converted to uracil whereas 5-methylcytosine (5mC) remains unaffected. Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen, 28704) and amplified by PCR. After PCR amplification, uracil residues were converted to thymine.

treatment_protocol: Animals were sacrificed by cervical dislocation at 6 months of age and hippocampi were dissected, isolated, snap-frozen in liquid nitrogen and stored at −80°C until further use.

value: Hippocampus

tag: genotype

tag: conversion treatment

value: Sodium bisulfite - EZ DNA Methylation-Gold kit (Zymo, D5005)


title: Case #6, ARMS FFPE tissue, Male, 15 years old [RNA-seq]

description: Library name: Case #6

value: Head/Neck Alveolar Rhabdomyosarcoma

tag: group

value: B

tag: Sex

value: Male

tag: age

value: 15 years old


title: BS_Ogg1_Rep2

description: Bisulfite sequencing of hippocampal genomic DNA from Ogg1-/- mouse


title: Case #7, ARMS FFPE tissue, Male, 14 years old [RNA-seq]

description: Library name: Case #7

value: 14 years old


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep5

tag: disease state

value: infected

tag: time

tag: feeding state

value: not fed

tag: treatment

value: fin clipped


title: Primary breast tumor, RNAseq, B41_84_A4_T_S63

value: Primary breast tumor

tag: race

value: White

tag: tx arm

tag: Stage

value: II

tag: hr status

value: HR-positive

tag: meno status

value: Pre-menopausal

tag: pcr breast

value: RD

tag: efs time

tag: efs stat

tag: body site

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype

value: Normal-like


title: BS_DKO_Rep1

tag: cell type

value: Hippocampus

tag: genotype

tag: conversion treatment

value: Sodium bisulfite - EZ DNA Methylation-Gold kit (Zymo, D5005)


title: Case #3, ARMS FFPE tissue, Female, 0.5 years old [RNA-seq]

description: Library name: Case #3

tag: tissue

value: Head/Neck Alveolar Rhabdomyosarcoma

tag: group

value: A

tag: Sex

value: Female

tag: age

value: 0.5 years old


title: Primary breast tumor, RNAseq, B41_79_A3_T_S41

value: Primary breast tumor

tag: race

value: White

tag: tx arm

value: Trastuzumab

tag: Stage

value: Post-menopausal

tag: analyte type

tag: is tumor

tag: collection age

tag: primary tumor_location


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep4

value: stomach

tag: disease state

value: infected

tag: time

value: 4 h

tag: feeding state

value: not fed

tag: treatment

value: fin clipped


title: BS_Mutyh_Rep1

description: Bisulfite sequencing of hippocampal genomic DNA from Mutyh-/- mouse

tag: cell type

tag: genotype

value: Mutyh-/-


title: Case #4, ARMS FFPE tissue, Female, 0.92 years old [RNA-seq]

description: Library name: Case #4

tag: tissue

value: 0.92 years old


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep2


title: Case #2, ARMS FFPE tissue, Male, 0.83 years old [RNA-seq]

description: Library name: Case #2

tag: group

value: Male

value: 0.83 years old


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep3


title: BS_Ogg1_Rep1

value: Hippocampus

tag: conversion treatment

value: Sodium bisulfite - EZ DNA Methylation-Gold kit (Zymo, D5005)


title: BS_Mutyh_Rep2


title: stomach sample from fin clipped but not fed fish 4 h post infection, biological rep1


title: BS_WT_Rep2

description: Bisulfite sequencing of hippocampal genomic DNA from WT mouse

value: WT


title: Primary breast tumor, RNAseq, B41_24_3B_T_S51

value: Lapatinib

value: II

tag: hr status

value: HR-positive

tag: meno status

tag: pcr breast

value: RD

tag: efs time

tag: efs stat

tag: body site

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: BS_WT_Rep1


title: Primary breast tumor, RNAseq, B41_23_E9_T_S96

value: Primary breast tumor

tag: race

value: White

tag: tx arm

tag: Stage

value: HR-negative

value: Post-menopausal

tag: analyte type

tag: is tumor

tag: collection age

tag: primary tumor_location


title: Case #1, ARMS FFPE tissue, Male, 0.67 years old [RNA-seq]

description: Library name: Case #1

tag: tissue

value: Head/Neck Alveolar Rhabdomyosarcoma

tag: group

value: A

tag: genotype

tag: Sex

value: Male

tag: age

value: 0.67 years old


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep5

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: not fed

tag: treatment

value: fin clipped


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep6


title: GCB_Ezh2_RNAseq_repl3

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

description:
Library name: Sample_38_GCB_Ezh2_RNAseq_repl3
DAPI-,B220+Fas+CD38dim at 7 months post bone marrow transplant

data_processing:
RNA sequencing results were aligned to mm10 using STAR (STAR_2.6.1a) and annotated to RefSeq using the Rsubread package (Rsubread_1.28.1)
Assembly: mm10
Supplementary files format and content: TPM

source_name: Germinal center B cells

extract_protocol:
Included as additional column of SAMPLES section
RNA was purified with AllPrep DNA/RNA Kit (Qiagen, 80204) and sent to Medgenome for library preparation and sequencing

tag: cell type

value: Germinal center B cells


title: SW480_hypoxia-2_DNMT3A_ip

city: Taipei

first: Che-Kun James

last: Shen

address: No. 128號, Section 2, Academia Rd, Nangang District

country: Taiwan

institute: Institute of Molecular Biology, Academia Sinica

data_processing:
we initially utilized BWA MEM (version 0.7.17) (Li and Durbin 2010) for read mapping to the human genome (GRCh38).
Subsequently, we filtered out read alignments with multiple hits or mapping quality less than 30 or without paired alignment.
Then we utilized MACS2 (Zhang, Liu et al. 2008) to perform peak calling. MACS2 takes the alignment file (in BAM format) of ChIP-seq reads as input and a control file helps in accounting for background noise and biases.
MACS2 is run with parameter "--nomodel --extsize 147 --keep-dup all -q 0.05" to identify narrow peaks. We retained only those peaks with a q-value cutoff of 0.05.
We used DeepTools (version 3.5.4) to perform read depth normalization and signal subtraction. The bamCoverage module within DeepTools was utilized to generate coverage tracks after normalizing to a depth of 1× (reads per genome coverage).
To obtain the ChIP-seq signal, the 'bigwigCompare' function of the DeepTools software was employed, with the input signal subtracted from the ChIP-seq signal.
Assembly: GRCh38
Supplementary files format and content: bigWig file for each sample
Supplementary files format and content: narrowPeak file for each IP and input pair

source_name: Large intestine; Colon

growth_protocol: The colon cancer cell line SW480 was cultured under 5% CO2 at 37 °C in DMEM (Invitrogen) supplemented with 10% FBS (v/v) (Biological Industries) and 1% (v/v) penicillin-streptomycin (Invitrogen)

extract_protocol:
Cell were fixed with 1% Formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).
The DNA libraries were prepared using KAPA HyperPrep library preparation kit (Roche) following standard protocols.

treatment_protocol: To induce hypoxia, the cells were transferred from a normoxic incubator (5% CO2 and 20% O2) to a hypoxic incubator (5% CO2 and 1% O2) for 24 hr. Increased levels of HIF-1α, as assayed by Western blotting, were used to assess induction of hypoxia.

value: Large intestine; Colon

tag: cell line

value: Colorectal carcinoma

value: Wild type

tag: rep

value: Hypoxia


title: hASCs cells, Passed_3

city: London

first: Arghya

last: Paul

state: Ontario

address: Thompson Engineering Building

department: Chemical Engineering

institute: The University of Western Ontario

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl. Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

source_name: hASCs

growth_protocol: hASCs were cultured under media conditions consisting of α-minimal essential media (alpha-MEM, Thermo Fisher Scientific) with 10% fetal bovine serum (Thermo Fisher Scientific) supplemented with 1 % penicillin/streptomycin. After every 2-3 days, culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of 70% to 80%. All experiments were completed with cell populations under P2-5.

extract_protocol:
After the neutralization and removal of trypsin, the cell pellet was resuspended in 𝛼-MEM and subdivided into aliquots containing 0.5 × 106 cells. Cells were passed through the microfluidic chip and collected at the outlet. After squeezing, hASCs were left for 5 min at room temperature. Then, RNA was extracted from the cells using an RNeasy Mini Kit (Qiagen) and quantified using a NanoDrop spectrophotometer. Next, the mRNA samples were converted to cDNA using the High-Capacity cDNA Conversion Kit (Applied Biosystems,USA).
RNA libraries for Rna-seq were prepared using SMARTER RNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: hASCs pellets resuspended in α-MEM was used as the control, whereas hASCs resuspended in α-MEM and passed through the microfluidic chip was used as the experimentalgroup.

value: hASCs

value: Not passed through


title: SW480_hypoxia-1_input


title: Primary breast tumor, RNAseq, B41_30_15_T_S52

value: Primary breast tumor

tag: race

value: Black

tag: tx arm

value: Lapatinib

tag: Stage

value: III

tag: hr status

value: HR-positive

tag: meno status

value: Post-menopausal

tag: pcr breast

value: RD

tag: efs time

tag: efs stat

tag: body site

value: Breast

value: RNA

value: Y

tag: primary metastatic_tumor

value: Primary

tag: tumor treatment

value: Treated

tag: rnaseq subtype


title: SW480_hypoxia-2_input

tag: tissue

value: Large intestine; Colon

value: Colorectal carcinoma

tag: genotype


title: GCB_Ezh2_RNAseq_repl2

description:
Library name: Sample_37_GCB_Ezh2_RNAseq_repl2
DAPI-,B220+Fas+CD38dim at 7 months post bone marrow transplant

tag: cell type

value: Germinal center B cells


title: GCB_Ezh2_RNAseq_repl4

description:
Library name: Sample_39_GCB_Ezh2_RNAseq_repl4
DAPI-,B220+Fas+CD38dim at 7 months post bone marrow transplant


title: hASCs cells, Passed_2

tag: cell line

value: hASCs

tag: treatment


title: stomach sample from fin clipped but not fed fish 2 h post infection, biological rep3

data_processing:
Data was processed within OmicsBox v3.3.2
Quality control was performed on raw reads using Trimmomatic v0.39
Quality reads were aligned to the channel catfish Coco_2.0 genome using the STAR aligner v2.7.8a (parameters – 2-pass mapping=true; overhang=149; feature=exon)
Read counts were extracted from BAM files using HTseq v2.0.5 ‘count’ feature (parameters – Quantification Level=exon; Group by=parent; Overlap Mode=union; stranded=strand specific reverse)
Assembly: Coco_2.0 (GCF_001660625.3)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: stomach

extract_protocol:
Total RNA was extracted from tissues using the Rneasy Plus Mini Kit (Qiagen) per the manufacturer’s protocol. 250 ng of total RNA from each sample was used for library construction.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Ligation Kit per the manufacturer’s protocol.

value: stomach

tag: disease state

value: infected

tag: time

value: 2 h

tag: feeding state

value: not fed

value: fin clipped


title: GCB_Ezh2_RNAseq_repl1

description:
Library name: Sample_36_GCB_Ezh2_RNAseq_repl1
DAPI-,B220+Fas+CD38dim at 7 months post bone marrow transplant


title: hASCs cells, Passed_1

value: Not passed through


title: hASCs cells, Not Passed_3, control

value: Passed through


title: SW480_hypoxia-1_DNMT3A_ip

value: Wild type

tag: rep

value: Hypoxia