title: VB264_z1


title: VB241_z2

status: Public on Oct 19 2024

type: SRA

city: Paris

first: Clarice

last: Groeneveld

address: 11 rue de Pierre et Marie Curie

country: France

institute: Institut Curie

library_source: transcriptomic

data_processing:
We applied the CurieCoreTech RNA-seq pipeline v 3.1.8 (https://github.com/bioinfo-pf-curie/RNA-seq) with standard parameters to align and quantify the RNA-seq.
ComBat-seq for batch correction
log2 counts per million normalization
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing log2 counts per million normalized expression
Supplementary files format and content: tab delimited file containing raw counts data

molecule: polyA RNA

organism: Homo sapiens

source_name: urothelial carcinoma

extract_protocol:
Using an annotated hematoxylin-eosin-saffron stained slide for reference, each tumor area was individually macrodissected from the corresponding FFPE tissue block. One to 10 10-µm thick sections were cut from each tumor area using a microtome and then processed using commercially available FFPE kits, Maxwell Rapid Sample Concentrator (RSC) RNA FFPE Kit (Cat. #AS1440) and Maxwell RSC microRNA (miRNA) Tissue Kit (Cat. #AS1460), and a Maxwell RSC device from Promega. RNA isolation was performed according to the manufacturer’s protocol (Total RNA and miRNA purification from FFPE samples using FFPE preprocessing and the Maxwell RSC miRNA Tissue Kit) provided by Promega.
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 30 mRNA-Seq Library PrepKit FWD

tag: tissue

value: urothelial carcinoma

tag: sample type

value: TURBT

tag: treatment

value: neoadjuvant chemotherapy


title: VB247_z1


title: VB262


title: VB264_z2


title: VB231


title: VB223


title: VB241_z1


title: VB186


title: VB182


title: VB215


title: VB157_z2


title: VB157_z1


title: VB155


title: VB152


title: VB135


title: VB096


title: VB136


title: VB510


title: VB055_1_z3


title: VB247_z2


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title: VB519_z2


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title: VB473_z2


title: VB459_A_z3


title: VB447_z1


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title: VB404


title: VB403


title: VB362_z1


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title: VB363


title: VB459_A_z2


title: VB358


title: VB332


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title: VB429


title: VB300


title: VB324


title: VB290_z1


title: VB296


title: VB024


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title: VB102_z3


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title: VB450


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title: VB446_z1


title: VB445


title: VB323_z1


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title: VB411


title: VB412


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title: VB374_B


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title: VB458


title: VB488


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title: VB009_z1


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title: VB213


title: VB285_B


title: VB120


title: VB092


title: VB081


title: VB125


title: VB036


title: VB160_z1


title: VB076


title: VB197


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title: VB023


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title: VB011


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title: VB407_z2


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title: VB423


title: VB380


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title: VB370_E


title: VB378


title: VB370_A1


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title: VB355


title: VB345


title: VB366


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title: VB334_1


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title: VB330


title: VB331


title: VB317_B_z2


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title: VB289


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title: VB313_z2


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title: VB242


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title: VB225_z1


title: VB382_3


title: VB222_A3_z2


title: VB209


title: VB198_1


title: VB134_1


title: VO267_C_z1

value: Cystectomy


title: VO267_C_z2


title: VO207


title: VO267_E


title: VB222_A3_z1


title: VB207_3


title: VB246


title: VB267


title: VB389


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title: VO010_2


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title: VB280


title: VB066


title: VO280


title: VO066_z1


title: VB163


title: VB232


title: VB166_z2


title: VO232


title: VO075_8


title: VB115_B


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title: VO127_D


title: VB166_z1


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title: VB442_z2


title: VO075_1


title: VB102_z2


title: VB062_z2


title: VB062_z1


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title: VB141


title: VO141


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title: VB052


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title: VO056_D


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title: VO057


title: VB118_z1


title: VB107


title: VB057_z1


title: VO010


title: VB057_z2


title: VB005_z1


title: VB010_z2


title: VB010_z1


title: VB002_z1


title: BEAS-2B, ZQ, 2

city: Beijing

first: Lulu

last: Zhang

address: 16 Dongzhimen South St, Dongcheng District, Beijing

country: China

institute: Chinese Academy of Traditional Chinese Medicine

data_processing:
cufflinks v2.1.1
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

growth_protocol: BEAS-2B cell were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with RNase-free DNase I (Takara, Kusatsu, Japan). A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) .

treatment_protocol: BEAS-2B cells in both groups were pretreated with medium and ZQ for 24 hours, respectively, then collected after 2 hours of stimulation with MRSA, following an infection ratio of 1:1.

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

value: WT


title: BEAS-2B, control, 2


title: BEAS-2B, ZQ, 1


title: VB002_z2


title: BEAS-2B, control, 1


title: P4239

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

country: USA

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v2.10)
Trimmed reads aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.8a)
featureCounts (v2.0.2)[3] was used to count the number of mapped reads to each gene.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: Comma delimited file includes CPM values for each sample

source_name: subcutaneous adipose

extract_protocol:
Frozen adipose tissue was disrupted using ceramic beads and grinder system (MP Biomedicals LLC FastPrep-24 5G and Lysing Matrix D tubes with 1.4mm Ceramic beads for the discovery cohort) in Qiazol Lysis Reagent. RNA was purified using the Qiagen RNEasy Plus Mini kit. An on-column DNAse digestion was performed for the discovery and VA cohorts. RNA was frozen at -80 degrees Celsius until sequencing.
The NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) was used.
ssRNA-seq

value: subcutaneous adipose


title: P4226


title: BEAS-2B, control, 3


title: P4234


title: P4221


title: P4222


title: P4238


title: P4219


title: P4217


title: P4215


title: P4152


title: P4216


title: P4195


title: P4201


title: P4208


title: P4199


title: P4194


title: P4189


title: BEAS-2B, ZQ, 3


title: P4188


title: P4172


title: P4177


title: P4162


title: P4171


title: P4161


title: P4151


title: P4154


title: P4116


title: P4109


title: HUES8-cis-deletion_hESC_(Nanopore-seq)

city: Ulm

first: Sarah

last: Merz

address: Albert-Einstein-Allee 23

department: Institute of Molecular Oncology and Stem Cell Biology

country: Germany

institute: Ulm University Hospital

description: clone #75

library_source: genomic

data_processing:
The samples were subjected to analysis using unaligned BAM files. The Epi2Me human variation workflow was executed to generate DNA methylation data, structural variant data, and phased aligned BAM files (based on the GRCh38 reference genome) for the genomic region spanning coordinates chr15.hg38:52707645_53586740. A minimum coverage threshold of 1 was applied. Additionally, the BAM files underwent manual inspection using the Integrative Genomic Viewer.
Assembly: Reference genome (GRCh38) was used for alignment.
Supplementary files format and content: bedmethyl.gz, contains methylation patterns
Supplementary files format and content: sv.vcf.gz, for identifying cis/trans localization of two deletions

molecule: genomic DNA

source_name: hESC HUES8

growth_protocol: Either HUES8 hESC were used or subjected to in vitro pancreatic differentiation according to the protocol published by Merz et al., Theranostics (2023) (doi:10.7150/thno.78323.)

extract_protocol:
Cells were harvested at hESC or pancreatic progenitor (PP) stage. For this purpose, HMW (high molecular weight) DNA was extracted using the Promega Wizard Genomic DNA Purification Kit for cultured cells, according to the manufacturer´s manual. The DNA was dissolved overnight at 4°C and quantified by using the Quant-ITTM dsDNA Assay kit.
Approximately 2.5 - 4.5 µg of the extracted DNA was sheared using g-TUBEs and used as input for nanopore library preparation with the ligation sequencing DNA V14 kit according to the manufacturer´s protocol.
Each library was loaded on a MinION R10.4.1 flow cell and sequenced with a MinION Mk1B device for up to 72 h. Throughout the sequencing process, the flow cells were reloaded 1-2 times after a nuclease flush with the same library according to the manufacturer´s instructions to enhance sequencing yield. For adaptive sampling a more than 800 kb region (chr15.hg19: 52999842_53878937) with the “fast modified basecalling for 5hmC and 5mC in CG context” basecall model of the MinKNOW software and integrated Guppy was set.

value: hESC HUES8

value: heterozygous 108kb deletion of Patitent 1 (Pat1-del) and ONECUT1 heterozgyous knockout on the same allel (cis)


title: P4017


title: HUES8-trans-deletion_hESC_(Nanopore-seq)

description: clone #65

value: heterozygous 108kb deletion of Patitent 1 (Pat1-del) and ONECUT1 heterozgyous knockout on different  allels (trans)


title: HUES8-WT_PP_(Nanopore-seq)

value: wildtype


title: HUES8-WT_hESC_(Nanopore-seq)


title: P4103


title: P4096


title: P4117


title: P4159


title: P4070


title: P4064


title: P4087


title: EXT1-/-  rep2

city: Cambridge

first: Deepsing

last: Syangtan

state: MA

address: 77 Massachusetts Ave.

department: Chemistry

institute: MIT

data_processing:
The trimming software skewer(Jiang et al.2014)was used to preprocess raw fastq files.
Samples were normalized by the method of trimmed mean of M-values (TMM).
Reads were aligned against the selected reference genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013)
Mapped reads for both genes and transcripts (isoforms) are counted in each sample using RSEM (RNASeq by Expectation Maximization), described inLi and Dewey (2011)
Analysis of differentially expressed genes is performed with a glm using the edgeR package(Robinson, McCarthy, and Smyth2010).
Assembly: Human genes (GRCh38.p10)
Supplementary files format and content: Results from contrast at the gene level are written to a MS Excel spreadsheet. Information includes gene/transcript length, FDR, effective length, TPM, and FPKM.

growth_protocol: WT and EXT1-/- hPSCs were maintained in in E8 medium (Gibco) on vitronectin (Gibco)-coated tissue culture plates at 37 °C, 5% CO2. Cells were passaged manually using EDTA (1 mM) every 4-5 days, with the addition of 5 µM Y-27632 dihydrochloride (Tocris) on the first day of passage.

extract_protocol:
Total RNA extraction was performed using TRIzol (Life Technologies) and Direct-zol RNA MiniPrep kit (Zymo Research) as per manufacturer instructions.
Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina).

treatment_protocol: WT and EXT1-/- cells were dissociated with accutase (Stem Cell Technologies) and seeded at a density of 100,000 cells per cm2 on vitronectin-coated plates, using E8 medium supplemented with 5 μM Y-27632 dihydrochloride. The E8 medium was changed every day over the 2 next days. On the third day, differentiation was initiated with RPMI-1640 medium (Gibco) supplemented with 6 μM CHIR-99021 (Tocris). Following 28 hrs differentiation, the cells were collected for analysis.

value: Human embryonic stem cells

value: EXT1 knockout

value: mesendoderm differentiation


title: WT rep2


title: P4165


title: EXT1-/-  rep4


title: P4035


title: WT rep3


title: WT rep1


title: EXT1-/-  rep3


title: P4032


title: WT rep4


title: 4-R3-2_S9

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

data_processing:
The RNA-seq fragments were mapped to TAIR10 reference genome using Hisat2 v2.2.0, with default parameters and trimming 50nt on the 3’ end. After trimming, fragments show a median Phred quality score of at least 30. Trinotate was used to annotate the functions of all the transcripts per gene in the reference genome. Trinotate helped to gather the results of Blastn v2.6.0, Blastp v2.6.0, Hmmer v3.1b2, SignalP v4.1, tmHmm v2.0. Kallisto v0.42.4 was used to map and quantify the RNA-seq fragments, for each library. An average of ~95% mapping for all the libraries was obtained. The quantifications for each library were stored in different tables. Via a custom R script v4.2.0, the Kallisto pseudo-alignments were gathered and quantifications into a counts data frame. Using the counts data frame, the package edgeR R was used. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research was used to perform the differential expression analysis. Each temperature condition (0°C, 4°C, and 10°C) was compared to the control condition, 22°C. Transcripts that showed an adjusted p-value (false discovery rate, FDR) lower than 0.01 were deemed significant in the analysis.
Assembly: TAIR10
Supplementary files format and content: countMat_transcript.tab
Supplementary files format and content: cpmMat_transcript.tab

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: The seeds of Arabidopsis thaliana ecotype Columbia 0 (Col-0) were surface-sterilized by immersing them in a solution of 20% (v/v) household bleach (approximately 2.7% sodium hypochlorite) for 5 min, after which they were rinsed five times with sterile distilled water. The sterilized and stratified seeds were vernalized for two days at 4ºC. Afterward, they were germinated and cultivated in vitro on petri plates containing 0.2x Murashige and Skoog medium (MS) (PhytoTechnology Laboratories®), adjusted pH of 7.0, with 0.5% (w/v) sucrose, and 1% (w/v) agar. This cultivation was carried out in a chamber with controlled temperature conditions (22ºC±1ºC), and a light cycle of 16h of light (13,000 lux) followed by 8h of darkness.

extract_protocol:
Total RNA extraction from plant material subjected to the low-temperature treatments (0ºC, 4ºC, and 10ºC) and as control (22ºC) for 24h was conducted following the ConcertTM Plant RNA Reagent protocol (Invitrogen Life Technologies, Waltham, Massachusetts, USA). The quality of the RNA samples was evaluated using a 1% agarose gel and 0.5X TBE buffer. RNA concentration was determined using a NanoDrop ND-1000 UV–vis spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).
Each set of samples was analyzed in triplicate. Subsequently, the RNA samples were prepared for shipment to the GENEWIZ company (Burlington, MA, USA) for paired-end RNA sequencing, following the RNAstable® protocol for RNA preservation at room temperature. Sequencing was performed with HiSeq 2500 technology (Illumina) in rapid mode with v2 reagents. The readings produced were 250 bp reads per end, according to the manufacturer’s instructions.

treatment_protocol: After growing for two weeks, 14-day-old plantlets were subjected to low temperatures of 0ºC, 4ºC, and 10ºC for 24h. Control plants were maintained in a growth chamber at 22ºC. After the cold treatments, the plants were harvested, rapidly frozen in liquid nitrogen, and stored at -80°C. Each temperature condition had three biological replicates (n=3), with each replicate comprising groups of 10 plantlets per Petri plate.

value: Whole plant

tag: ecotype

value: Columbia 0

value: Temperature 4ªC


title: 4-R2-2_S8


title: P4023


title: 4-R1-2_S7


title: P4021


title: P4016


title: 22-R3-2_S3

value: Temperature 22ªC


title: P4092


title: 22-R2-2_S2


title: EXT1-/-  rep1


title: 22-R1-2_S1


title: 10-R2-2_S11

value: Temperature 10ªC


title: DT40_H2A.Z-1_KO

type: RNA

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

description: Gene expression in H2A.Z-1 KO cells

hyb_protocol: Following fragmentation,10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0).

label: Biotin

organism: Gallus gallus

source_name: DT40 H2A.Z-1 KO cells, replicate1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ug total RNA (GeneChip 3' IVT Express Kit, Affymetrix).

growth_protocol: DT40 cells were cultured at 38 ºC in Dulbecco’s modified medium supplemented with 10% fetal bovine serum, 1% chicken serum, 2-merchaptoethanol, penicillin and streptomycin.

extract_protocol: Total RNAs were extracted with the RNeasy mini kit (QIAGEN) according to the manufacture’s protocol.

treatment_protocol: To suppress expression of the tetracycline repressive H2A.Z.1 transgene, tetracycline was added to the culture medium to a final concentration of 2 µg/ml. Each cell was cultured in the presence of tetracyclin for 72 hours.

tag: cell origin

value: B cell


title: Primary mammary epithelial cells without stimulation, replicate 5

city: Shanghai

first: Rongze

last: Ma

state: Shanghai

address: zhongke road

institute: Shanghaitech University

data_processing:
Raw sequencing data were processed using FastQC for quality control.
Adapters were trimmed and low-quality bases removed using Cutadapt (v1.9.1).
Reads were aligned to the mouse reference genome (GRCm39.107) using HISAT2 (v2.2.1).
Gene expression levels were quantified using HTSeq and normalized to TPM values.
Differential expression analysis was performed using DESeq2.
Assembly: GRCm39.107 (Mus musculus).
Supplementary files format and content: Processed data files are in CSV format and contain TPM values for each gene across all samples.

organism: Mus musculus

source_name: Mammary gland

growth_protocol: Primary mammary epithelial cells were isolated from Mus musculus mammary gland tissues and cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from mammary epithelial cells using TRIzol reagent according to the manufacturer's instructions, followed by DNase I treatment and purification using a RNeasy Mini Kit.
RNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina, following the manufacturer’s protocol, with poly-A selection and fragmentation steps included.

treatment_protocol: BGN protein was added to the culture medium at a concentration of 100 ng/mL for the treatment group. The control group did not receive any BGN protein stimulation.

value: Mammary gland

value: Primary cells

value: Epithelial cell

value: Wild-type

value: Control


title: DT40_H2A.Z-2_KO

description: Gene expression in H2A.Z-2 KO cells

source_name: DT40 H2A.Z-2 KO cells, replicate1


title: Primary mammary epithelial cells without stimulation, replicate 4


title: P4053

value: subcutaneous adipose


title: P4111


title: 0-R3-2_S6

value: Temperature 0ªC


title: 10-R3-2_S12


title: P4196


title: 0-R2-2_S5


title: P4167


title: Primary mammary epithelial cells without stimulation, replicate 3


title: ONECUT1het/Pat1-del-het_trans_PP_rep3 (RNAseq)

description: ATGTGATT (barcode)

data_processing:
Data processing utilized the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables43. Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to GENCODE v38.
Assembly: Reference genome (GRCh38) was used for alignment.
Supplementary files format and content: tab-delimited textfile contains raw counts

growth_protocol: HUES8 hESC were subjected to in vitro pancreatic differentiation according to the protocol published by Merz et al., Theranostics (2023) (doi:10.7150/thno.78323.)

extract_protocol:
Cells were harvested at pancreatic progenitor (PP) stage. Total RNA was isolated using GeneJET RNA purification Kit (Thermo Fisher Scientific) according to the manufacturer's protocol.
Barcoded cDNA of each sample was generated with a Maxima RT polymerase using oligo-dT primers containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5'-ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adapter. NEB Ultra II FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated, and 3’-end-fragments were finally amplified using primers using Illumina P5 and P7 overhangs. Sequencing of the library was performed on a NextSeq 500 (Illumina) with 61 cycles for the cDNA in read1 and 19 cycles for the barcodes and UMIs in read2.

value: hESC HUES8

value: heterozygous 108kb deletion of Patient 1 (Pat1-del) and ONECUT1 heterozgyous knockout on different  allels (trans)


title: ONECUT1het/Pat1-del-het_cis_PP_rep4 (RNAseq)

description: AGAACCAA (barcode)

value: heterozygous 108kb deletion of Patient 1 (Pat1-del) and ONECUT1 heterozgyous knockout on the same allel (cis)


title: P4110


title: Primary mammary epithelial cells without stimulation, replicate 2


title: P4007


title: ONECUT1het/Pat1-del-het_trans_PP_rep1 (RNAseq)

description: ATTCACGG (barcode)


title: ONECUT1het/Pat1-del-het_trans_PP_rep2 (RNAseq)

description: ATGAACTG (barcode)


title: Primary mammary epithelial cells without stimulation, replicate 1


title: ONECUT1het/Pat1-del-het_cis_PP_rep2 (RNAseq)

description: TCTTGGAA (barcode)


title: Primary mammary epithelial cells stimulated with BGN protein, replicate 5

value: BGN stimulation


title: P4098


title: 10-R1-2_S10

value: Whole plant


title: P4181


title: siZFPL1-4

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

institute: China Medical University

data_processing:
After screening for CutAdapt-based 3'end adapter sequences or reads with average quality score lower than Q20, the high-quality sequences were compared with the reference genome (Assembly GRCm38). The processed data were then normalized and derepeated. Finally fold change and p-value for Students’ t-test were calculated for control and siZFPL1 groups.
Assembly: GRCm38
Supplementary files format and content: comma-delimited csv  file includes the FPKM for each sample

source_name: xenograpted from human

growth_protocol: Hepatocellular carcinoma cells were extracted  from the tissue

extract_protocol:
We used Trizol Reagent (Invitrogen Life Technologies) to extract total RNA in control group (n=3) and siZFPL1 group (n=3). The sequencing library was prepared using the TruSeq RNA sample preparation kit (Illumina, USA) and sequenced at the Hiseq platform (Illumina) of Shanghai Personal Biotechnology Co. LTD. (Shanghai, China). After screening for CutAdapt-based 3'end adapter sequences or reads with average quality score lower than Q20, the high-quality sequences were compared with the reference genome (Assembly GRCm38). The processed data were then normalized and derepeated. Finally fold change and p-value for Students’ t-test were calculated for control and siZFPL1 groups.
The sequencing library was prepared using the TruSeq RNA sample preparation kit (Illumina, USA) and sequenced at the Hiseq platform (Illumina) of Shanghai Personal Biotechnology Co. LTD. (Shanghai, China).

treatment_protocol: ZFPL1 was knocked down in HUH-7 cell line and afterwards the cell line was transplanted to mouse

value: hepatocellular carninoma


title: 0-R1-2_S4

value: Columbia 0


title: ONECUT1het/Pat1-del-het_cis_PP_rep1 (RNAseq)

description: ATGGCCAG (barcode)


title: ONECUT1het/Pat1-del-het_cis_PP_rep3 (RNAseq)

description: ATCGCATT (barcode)


title: siZFPL1-3


title: Pat1-del-hom_PP_rep3 (RNAseq)

description: GAACAGAA (barcode)

value: homozygous 108kb deletion of Patient 1 (Pat1-del)


title: Primary mammary epithelial cells stimulated with BGN protein, replicate 3


title: P4108


title: siZFPL1-2


title: P4192


title: Primary mammary epithelial cells stimulated with BGN protein, replicate 2


title: P4013


title: siZFPL1-1


title: Pat1-del-hom_PP_rep2 (RNAseq)

description: TAACCAGA (barcode)


title: Primary mammary epithelial cells stimulated with BGN protein, replicate 1


title: P4076


title: control-3

value: control


title: RNA_seq_Ash2l_gKO_L_Z.rep2

city: shanghai

first: Haorui

last: Luo

address: 320 Yue Yang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Raw RNA-seq reads were subjected to remove adapter contamination and low-qualified sequences using trim_galore (version: 0.6.7) under paired-end mode, trimmed paired-end reads shorter than 20 were discarded. Reads on transcripts of mm10 Refseq annotation were counted using kallisto quant. Differential expressed genes were identified using DEseq2 packages with the RNA-seq mapped reads counts on mm10 Refseq transcripts. Volcano plots of differential gene expression were visualized using the ggplot2 package in R with significant genes (P value < 0.05, |FoldChange| ≥ 1.5). Functional annotation was performed using R packages clusterProfiler, msigdbr. Trimmed RNA-seq data were aligned to the mouse genome build mm10 using STAR (version: 2.7.0a) with ENCODE RNA-seq pipeline, mapped RNA-seq reads in sam files were converted to bam files using ‘samtools sort’. Then annotates mapped reads to transposable elements with TEtranscripts (version:2.2.3).
For ChIP-seq, Low-quality bases and adapter-containing reads were first trimmed from all ChIP-seq raw data using trim-galore package (version: 0.6.7) under default parameters, clean reads shorter than 20 bp were discarded. Trimmed ChIP-seq data were aligned to the reference genome of mouse mm10 assembly using bowtie2 (version: 2.3.1) with default parameters. The resulting SAM files were converted to BAM files using the SAMtools (version:1.9) view command, after which the BAM files were sorted and indexed, and potential PCR duplicates were removed using the picard (version:2.18.7) MarkDuplicates function. DeepTools (v.3.4.3) was used to generate occupancy heatmaps, and the resulting normalized occupancy matrix was used to generate average profile plots. In brief, the BAM files were converted into BigWig files using the bamCoverage function. For comparison, quantitative ChIP–seq data using spike-in normalization were used, normalization to theDrosophila (dm6) spike-in was performed. Before identify peaks with MACS2 (version:2.1.1), we subsample all the bam files.
For NOMe-seq, Firstly, raw sequencing data were trimmed with 9-bp random primer, and adapters and low-quality bases were removed using software trim_galore (version: 0.6.7) with below parameters ‘-quality 20 -stringency 3 -length 50 -clip_R1 9 -clip_R2 9 -paired -trim1 -phred33’. Then, the clean reads were aligned against mouse reference genome (UCSC, mm10) using software Bismark (version: 0.22.1) with a paired-end and non-directional aligned mode. Finally, PCR duplicated reads were removed from aligned BAM files using picard (version:2.18.7) MarkDuplicates. Only the detected cytosine site with the read depth greater than 5 was considered in this study. The methylation level or chromatin accessibility level of each cytosine site was defined as the number of methylated reads ‘C’ divided by the number of all detected reads (methylated and unmethylated reads, ‘C+T’). We used WCG (ACG/TCG) for DNA methylation analysis and GCH (GCA/GCC/GCT) for chromatin accessibility analysis.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: contains RNA-seq, ChIP-seq and NOMe-seq data

source_name: testis

extract_protocol:
RNA samples were extracted with Trizol, chromatin for ChIP was extracted with  lysis buffer (20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS)
RNA libraries were constructed using TrueSeq Stranded Total RNA Library Prep Kit. ChIP-seq libraries were constructed using KAPA DNAHyperPrep kit.

value: testis

value: leptotene/zygotene spermatocytes


title: Pat1-del-hom_PP_rep1 (RNAseq)

description: ATGAAGGA (barcode)


title: control-4


title: RNA_seq_Ash2l_gKO_L_Z.rep1


title: P4314


title: Primary mammary epithelial cells stimulated with BGN protein, replicate 4

value: Mammary gland

value: Primary cells


title: Pat1-del-het_PP_rep3 (RNAseq)

description: GAGTAGCA (barcode)

value: heterozygous 108kb deletion of Patient 1 (Pat1-del)


title: RNA_seq_Ctrl_L_Z.rep2

value: wild-type


title: control-2


title: Pat1-del-het_PP_rep2 (RNAseq)

description: TATCAAGC (barcode)


title: control-1


title: P4299

value: subcutaneous adipose


title: RNA_seq_Ctrl_L_Z.rep1


title: P4041


title: P4296


title: Pat1-del-het_PP_rep1 (RNAseq)

description: ATCACCGT (barcode)


title: Pat1-del-het_PP_rep4 (RNAseq)

description: TAATATAG (barcode)


title: P4107


title: P4003


title: P4004


title: RNA_seq_Ash2l_gKO_A4.rep2

value: A4 spermatogonia


title: ao13

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC, location AMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of raw reads

source_name: aorta

extract_protocol:
Aortas were snap frozen in liquid nitrogen and subsequently lyzed in TRIzol. B1b cells, defined as CD19hiB220loIgMhiCD5lo, were sorted from peritoneal lavage fluid using FACSAria II SORP cell sorter spun down, stored at -80 ˚C and dissolved in TRIzol. Total RNA was isolated from these samples using the Direct-zol RNA Microprep kit.
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

tag: strain

value: ApoE-/-

value: aorta

value: cre


title: RNA_seq_Ash2l_gKO_A4.rep1


title: ONECUT1hom_PP_rep2 (RNAseq)

description: ATTATCGC (barcode)

value: hESC HUES8

value: ONECUT1 homozygous knockout


title: ao9


title: ao10

value: wt


title: RNA_seq_Ctrl_A4.rep2


title: P4293


title: ONECUT1hom_PP_rep1 (RNAseq)

description: AGAAGCTT (barcode)


title: ao8


title: RNA_seq_Ctrl_A4.rep1


title: P4289


title: ONECUT1het_PP_rep4 (RNAseq)

description: TATAGTGT (barcode)

value: ONECUT1 heterozygous knockout


title: P4288


title: ONECUT1het_PP_rep3 (RNAseq)

description: GAGTTCTG (barcode)


title: ao7


title: NOMe_seq_Ash2l_gKO_Z_rep2

data_processing:
Raw RNA-seq reads were subjected to remove adapter contamination and low-qualified sequences using trim_galore (version: 0.6.7) under paired-end mode, trimmed paired-end reads shorter than 20 were discarded. Reads on transcripts of mm10 Refseq annotation were counted using kallisto quant. Differential expressed genes were identified using DEseq2 packages with the RNA-seq mapped reads counts on mm10 Refseq transcripts. Volcano plots of differential gene expression were visualized using the ggplot2 package in R with significant genes (P value < 0.05, |FoldChange| ≥ 1.5). Functional annotation was performed using R packages clusterProfiler, msigdbr. Trimmed RNA-seq data were aligned to the mouse genome build mm10 using STAR (version: 2.7.0a) with ENCODE RNA-seq pipeline, mapped RNA-seq reads in sam files were converted to bam files using ‘samtools sort’. Then annotates mapped reads to transposable elements with TEtranscripts (version:2.2.3).
For ChIP-seq, Low-quality bases and adapter-containing reads were first trimmed from all ChIP-seq raw data using trim-galore package (version: 0.6.7) under default parameters, clean reads shorter than 20 bp were discarded. Trimmed ChIP-seq data were aligned to the reference genome of mouse mm10 assembly using bowtie2 (version: 2.3.1) with default parameters. The resulting SAM files were converted to BAM files using the SAMtools (version:1.9) view command, after which the BAM files were sorted and indexed, and potential PCR duplicates were removed using the picard (version:2.18.7) MarkDuplicates function. DeepTools (v.3.4.3) was used to generate occupancy heatmaps, and the resulting normalized occupancy matrix was used to generate average profile plots. In brief, the BAM files were converted into BigWig files using the bamCoverage function. For comparison, quantitative ChIP–seq data using spike-in normalization were used, normalization to theDrosophila (dm6) spike-in was performed. Before identify peaks with MACS2 (version:2.1.1), we subsample all the bam files.
For NOMe-seq, Firstly, raw sequencing data were trimmed with 9-bp random primer, and adapters and low-quality bases were removed using software trim_galore (version: 0.6.7) with below parameters ‘-quality 20 -stringency 3 -length 50 -clip_R1 9 -clip_R2 9 -paired -trim1 -phred33’. Then, the clean reads were aligned against mouse reference genome (UCSC, mm10) using software Bismark (version: 0.22.1) with a paired-end and non-directional aligned mode. Finally, PCR duplicated reads were removed from aligned BAM files using picard (version:2.18.7) MarkDuplicates. Only the detected cytosine site with the read depth greater than 5 was considered in this study. The methylation level or chromatin accessibility level of each cytosine site was defined as the number of methylated reads ‘C’ divided by the number of all detected reads (methylated and unmethylated reads, ‘C+T’). We used WCG (ACG/TCG) for DNA methylation analysis and GCH (GCA/GCC/GCT) for chromatin accessibility analysis.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: contains RNA-seq, ChIP-seq and NOMe-seq data
Library strategy: NOMe-Seq

value: zygotene spermatocytes


title: P4284


title: NOMe_seq_Ash2l_gKO_Z_rep1


title: ONECUT1hom_PP_rep3 (RNAseq)

description: TACATCCT (barcode)


title: ONECUT1het_PP_rep2 (RNAseq)

description: TCCAACGG (barcode)


title: ao4


title: P4267


title: NOMe_seq_Ctrl_Z_rep2


title: ao5


title: ONECUT1het_PP_rep1 (RNAseq)

description: ATGTTGAG (barcode)


title: ao3


title: P4266


title: NOMe_seq_Ctrl_Z_rep1


title: WT_PP_rep3 (RNAseq)

description: ATGAATAT (barcode)

value: wildtype


title: P4262


title: ao2


title: H3K4me3 ChIP_seq_Ash2l_gKO_L_Z_rep1

value: testis


title: P4261


title: WT_PP_rep2 (RNAseq)

description: ATTGCTGA (barcode)


title: WT_PP_rep1 (RNAseq)

description: TAATAATC (barcode)


title: ao1


title: P4258


title: EC_2

city: Fuzhou

first: Chengyu

last: Lv

address: Xuefu North Road, Minhou County, Fuzhou

institute: Fujian Medical University

data_processing:
Sequencing reads were mapped to hg38-rmalt
Gene expression was counted using featureCounts
DEG were further processed with DEGSeq
Genome_build: hg38

source_name: Endometrial cancer tissues

extract_protocol:
Endometrial cancer tissues and corresponding adjacent noncancerous tissues were collected and subjected to RNA extraction (E.Z.N.A. Total RNA Kit I)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: Endometrial cancer


title: P4257


title: H3K4me3 ChIP_seq_Ctrl_L_Z_rep1

value: leptotene/zygotene spermatocytes


title: B1b6

source_name: peritoneal lavage


title: P4249


title: EC_1


title: H3K4me3 ChIP_seq_Ctrl_L_Z_rep2


title: B1b5


title: H3K4me3 ChIP_seq_Ash2l_gKO_A4_rep2


title: B1b4


title: P4247


title: H3K4me3 ChIP_seq_Ash2l_gKO_L_Z_rep2


title: NC_1

source_name: adjacent noncancerous tissues

value: Adjacent noncancerous tissues

value: Endometrium


title: NC_2


title: P4246


title: B1b3


title: P4245


title: B1b7


title: E9.5_KDR+/PECAM1+_tdTomato+_snRNAseq

city: Oxford

first: Oliver

middle: Andrew

last: Stone

state: Oxfordshire

address: IDRM, Old Road Campus, Roosevelt Drive

department: Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description: FACS sorted CD45-CD41-KDR+PECAM1+ Pax3Cre;tdTomato+ve cells

library_source: transcriptomic single cell

data_processing:
CellRanger-arc v2.00 was used to call cells and map reads to mm10 with tdTomato added
Seurat v5.0.1 and Signac v1.12.0 were used for normalisation and clustering
Weighted nearest neighbour UMAP used for visualisation.
Assembly: mm10
Supplementary files format and content: e9pos_unanalysed_PAPERforUpload.rds is a seurat object containing both RNA and ATAC assays with no cells filtered out (i.e. before analysis)
Supplementary files format and content: e9pos_doubletfilteredPAPERforUpload.rds is a seurat object containing RNA and ATAC assays. It contains all the processing, QC, filtering and analysis steps performed in Lupu, Grainger, Kirschnick et. al.

molecule: nuclear RNA

source_name: Angioblasts and endothelial cells

extract_protocol:
Embryos were dissociated using 2 mg/ml Collagenase IV and 0.2 mg/ml Dnase I in 10% FBS/PBS, stained with surface antibodies against CD41, CD45, KDR and CD31, then FACS sorted.
Using the 10xChromium Next GEM Single Cell Multiome ATAC + Gene Expression kit.
Paired snATAC-seq and scRNA-seq

value: Angioblasts and endothelial cells


title: E9.5_KDR+/PECAM1+_tdTomato+_snATACseq

library_source: genomic single cell


title: B1b2


title: H3K4me3 ChIP_seq_Ctrl_A4_rep2

value: wild-type


title: LSG-SjD, scRNA-seq, GEX

city: Fukuoka

first: Lijing

last: Yan

address: Maidashi 3-1-1, Higashi-ku

institute: Kyushu University

description: 10x Genomics

data_processing:
The 10x Genomics Cell Ranger 6.0 software suite was utilized for reads alignment and the creation of a gene-cell unique molecular identifier (UMI) matrix, employing the GRCh38 reference genome. Cells exhibiting an abnormally high level of mitochondrial gene expression were removed from the analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Sjögren's disease (SjD) biopsy tissue

extract_protocol:
Fresh tissue sample from surgically obtained SjD were preserved in Tissue Storage Solution (130-100-008, Miltenyi Biotec). Tissue sample was transferred into gentleMACS C tubes (130-093-237, Miltenyi Biotec) and cut into small pieces in RPMI-1640 with L-glutamine and phenol red (189-02025, FUJIFILM). Then the tissue was made into a cell suspension using the Multi Tissue Dissociation Kit I (130-110-201, Miltenyi Biotec) and the gentleMACS Octo Dissociator with Heaters (130-096-427, Miltenyi Biotec). The cell suspension was de-aggregated by 100 μm MACS SmartStrainer (130-098-463, Miltenyi Biotec) and transferred into a 5 mL Round Bottom Polystyrene Test Tube with Cell Strainer Snap Cap (352235, Falcon). After washing twice with EasySep buffer (20144, STEMCELL), erythrocytes were removed with Red Blood Cell Lysis Solution (130-094-183, Miltenyi Biotec). Following separation, cells were preserved in CELLBANKER 1 plus (11912, ZENOGEN PHARMA) and stored at -80°C for scRNA-seq. Positive selection of CD45+ cells was performed with the EasySep Human PE Positive Selection Kit II (17664, STEMCELL). Cells labelled with magnetic particles coated with anti-CD45+ antibody were separated using EasySep Magnet (18000, STEMCELL).
The number and viability of separated CD45+ cells were assessed using a LUNA-FX7 automated cell counter (L70001, Logos Biosystems) and the cell concentration was adjusted to 10,000 single cells. These cells were then loaded into a 10x Genomics Chromium device according to the protocol of Chromium Single Cell 5' Reagent Kits (v2) as previously described.

value: Labial salivary gland

value: CD45+ cells

tag: disease state

value: Sjogren's disease


title: proQ-3XFLAG_hcd_rep1

status: Public on Oct 18 2024

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

institute: Friedrich Schiller University

library_source: other

data_processing:
cDNA reads were imported into CLC Genomics Workbench v 22.0.2 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: 3´ trim: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  5' trim: GATCGTCGGACTGTAGAACTCTGAACGTGTAGA; Trim quality scores limit 0.05, Trim ambiguous nucleotides 2
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = forward, Maximum number of hits for a read = 10, expression value: TPM
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NC_002505, NC_002506
Supplementary files format and content: xlsx file including total reads, TPM from each sample and differential gene expression (fold change and FDR values)

molecule: other

organism: Vibrio cholerae C6706

growth_protocol: Vibrio cholerae C6706  WTand proQ::3XFLAG were grown overnight in LB media. The following day bacteria were diluted 1:1000 in fresh media. At OD 0.2 and OD 2.0, cells were collected.

extract_protocol:
Cells equivalent to 50 OD600 units were collected and cells were lysed using glass beads. RNA-Co-immunoprecipitation using anti-FLAG-antibody following protein G sepharose, Solution was washed and RNA fraction was isolated with phenol-chloroform-isoamylalcohol. RNA was treated with TurboDNase to remove DNA contaminations.
cDNA was synthesized by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB)  according to the manufacturer's instructions. cDNA libraries were column-based purified and cleaned left-sided using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

value: CoIP


title: proQ-3XFLAG_hcd_rep2


title: H3K4me3 ChIP_seq_Ctrl_A4_rep1

value: A4 spermatogonia


title: WT_hcd_rep3


title: proQ-3XFLAG_hcd_rep3


title: WT_lcd_rep3


title: proQ-3XFLAG_lcd_rep3


title: WT_hcd_rep2


title: proQ-3XFLAG_lcd_rep2


title: WT_lcd_rep2


title: WT_hcd_rep1


title: WT_lcd_rep1


title: H3K4me3 ChIP_seq_Ash2l_gKO_A4_rep1


title: MIP_SE_SA_TSB_rep1_ribodep

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description:
SE + SA 50:50 mix (100ng each)_BR1_Control cultures_Depletion + No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

data_processing:
quality control with FastQCv0.12.1
adapter removal with Cutadatv4.4 (bulk, SPE) and seqtkv1.2-r122 (MIP)
alignment with BWA-MEMv0.7.12-r1188
read extraction and filtering with bamtoolsv2.5.2 (MAPQ >30, NM<4)
count tables generated with SAMtoolsv0.7.17-r1188
Assembly: GCF_017329165.1 (Sa M2872), GCF_006094375.1 (Se ATCC 14990), GCF_002993865.1 (Sa USA300)
Supplementary files format and content: Supp_Table_06_Bulk_data_expdb.xlsx: table of bulk RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_05_Bulk_data_refdb.xlsx: table of bulk RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_08_MIP_data_expdb.xlsx: table of MIP RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_07_MIP_data_refdb.xlsx: table of MIP RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_10_SPE_data_expdb.xlsx: table of SPE RNA-seq samples mapped to Se Tu3298 and Sa USA300, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.
Supplementary files format and content: Supp_Table_09_SPE_data_refdb.xlsx: table of SPE RNA-seq samples mapped to Se ATCC 14990 and Sa M2872, data sheets include probe and CDS raw counts, CPMs, TPMs, and log transformations.

organism:
Staphylococcus aureus
Staphylococcus epidermidis

source_name: bacterial culture

extract_protocol:
RNA was extracted using RNeasy 96 QIAcube HT kit (Qiagen, Hilden, Germany) according to the manufacturer’s directions. Samples were eluted in nuclease-free water (Qiagen, Hilden, Germany) and frozen at -80°C until sequencing preparation.
The sequencing libraries were prepared with NEBNext rRNA Depletion Kit v2 (New England Biolabs, Ipswich, MA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) following the manufacturer’s directions.

treatment_protocol: S. aureus and S. epidermidis were grown in TSB, TSB pH 4.8 or on reconstructed human epidermidis for bulk and targted RNA-seq with and without ribo-depletion and/or SPIA.

value: bacterial culture

tag: strain se

tag: seqeuncing appraoch

value: Molecular Loop (MIP)

tag: experimental batch

value: batch 2

tag: treatment rrna

value: ribo-depletion

tag: treatment spia

value: no SPIA

tag: treatment media

value: TSB


title: P4244

tag: tissue

value: subcutaneous adipose


title: MIP_SE_SA_TSB_rep2_ribodep

description:
SE + SA 50:50 mix (100ng each)_BR2_Control cultures_Depletion + No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep3

description:
SE + SA 50:50 mix (50ng total)_BR3_Acidic stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: no ribo-depletion

value: Acid


title: MIP_SE_SA_acid_rep1

description:
SE + SA 50:50 mix (78ng total)_BR1_Acidic stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep2

description:
SE + SA 50:50 mix (73ng total)_BR2_Acidic stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep3

description:
SE + SA 50:50 mix (98ng total)_BR3_Urea stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: Urea


title: MIP_SE_SA_TSB_rep3

description:
SE + SA 50:50 mix (116ng total)_BR3_Control cultures_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep1

description:
SE + SA 50:50 mix (90ng total)_BR1_Urea stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0

description:
SE + SA 50:50 mix (10ng each)_original Apr cultures_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: batch 1


title: MIP_SE_SA_urea_rep2

description:
SE + SA 50:50 mix (94ng total)_BR2_Urea stress culture_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0_ribodep_spia

description:
SE + SA 50:50 mix (100ng each)_original Apr cultures_Depletion + SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: SPIA


title: MIP_SE_SA_TSB_rep2

description:
SE + SA 50:50 mix (113ng total)_BR2_Control cultures_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep1

description:
SE + SA 50:50 mix (190ng total)_BR1_Control cultures_No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: proQ-3XFLAG_lcd_rep1


title: MIP_RHE_SE_SA_mix6_spia

description:
RHE_SA+SE mix (wells: C01+G07) (10ng each)_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

source_name: skin + bacterial culture

value: skin + bacterial culture


title: MIP_SE_SA_TSB_rep2_ribodep_spia

description:
SE + SA 50:50 mix (100ng each)_BR2_Control cultures_Depletion + SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0_ribodep

description:
SE + SA 50:50 mix (100ng each)_original Apr cultures_Depletion + No SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0_spia

description:
SE + SA 50:50 mix (10ng each)_original Apr cultures_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix1_spia

description:
RHE_SA+SE mix (wells: H02+B03) (10ng each)_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep3_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Acidic stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix2_spia

description:
RHE_SA+SE mix (wells: A01+C03) (10ng each)_ SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep2_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Acidic stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep3_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Urea stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep2_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Urea stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep1_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Acidic stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep1_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Urea stress culture_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep3_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Control cultures_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep2_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Control cultures_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep1_half_spia_ribodep

description:
SE + SA 50:50 mix (100ng each)_BR1_Control cultures_Depletion + 1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: half SPIA


title: MIP_SE_SA_TSB_rep1_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Control cultures_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix6_half_spia

description:
RHE_SA+SE mix (wells: C01+G07) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix4_spia

description:
RHE_SA+SE mix (wells: E03+C07) (10ng each)_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix3_half_spia

description:
RHE_SA+SE mix (wells: D02+F04) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep2_half_spia_ribodep

description:
SE + SA 50:50 mix (100ng each)_BR2_Control cultures_Depletion + 1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix1_half_spia

description:
RHE_SA+SE mix (wells: H02+B03) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix4_half_spia

description:
RHE_SA+SE mix (wells: E03+C07) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix3_spia

description:
RHE_SA+SE mix (wells: D02+F04) (10ng each)_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix5_half_spia

description:
RHE_SA+SE mix (wells: B01+D07) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep3_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Acidic stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep1_ribodep_spia

description:
SE + SA 50:50 mix (100ng each)_BR1_Control cultures_Depletion + SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep3_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Urea stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep1_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Acidic stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0_half_spia

description:
SE + SA 50:50 mix (10ng each)_original Apr cultures_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_mix2_half_spia

description:
RHE_SA+SE mix (wells: A01+C03) (10ng each)_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep2_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Urea stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep1_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Control cultures_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep2_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Control cultures_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep3_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR3_Control cultures_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_ICHT_DNA

description:
ICHT_24_3_Human Source_well H4
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_urea_rep1_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR1_Urea stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_DNA_50ng_95_5

description:
50ng of 5:95 mix (SA:SE)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_DNA_10ng_95_5

description:
10ng of 5:95 mix (SA:SE)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_TSB_rep0_half_spia_ribodep

description:
SE + SA 50:50 mix (100ng each)_original Apr cultures_Depletion + 1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_DNA_50ng_5_95

description:
50ng of 95:5 mix (SA:SE)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_acid_rep2_half_spia

description:
SE + SA 50:50 mix (10ng each)_BR2_Acidic stress culture_1/2 SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_50ng

description:
SE + SA 50:50 mix (50ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SA_SA_DNA_1ng

description:
SE + SA 50:50 mix (1ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_cocul_50ng

description:
SE + SA 50:50 co-culture (50ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

source_name: RHE + bacterial culture

value: RHE + bacterial culture


title: MIP_SA_SA_DNA_10ng

description:
SE + SA 50:50 mix (10ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_RHE_SE_SA_10ng

description:
RHE_SE+SA mix (G04+E04) (10ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_DNA_10ng_5_95

description:
10ng of 95:5 mix (SA:SE)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_100pg

description:
SE + SA 50:50 mix (100pg each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_10ng_rep2

description:
*SE + SA 50:50 mix (10ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: MIP_SE_SA_1ng

description:
SE + SA 50:50 mix  (1ng each)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: SPE_SE_SA_DNA_10ng_5_95

description:
10ng of 95:5 mix (SA:SE)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: Allegro (SPE)


title: SPE_SE_SA_DNA_10ng_95_5

description:
10ng of 5:95 mix (SA:SE)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_DNA_1ng

description:
SE + SA 50:50 mix (1ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_DNA_50ng_5_95

description:
50ng of 95:5 mix (SA:SE)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_DNA_50ng_95_5

description:
50ng of 5:95 mix (SA:SE)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_cocul_50ng

description:
SE + SA 50:50 co-culture (50ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_RHE_SE_SA

description:
RHE_SE+SA mix (G04+E04) (10ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: MIP_SE_SA_cocul_10ng

description:
SE + SA 50:50 co-culture (10ng)
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx


title: SPE_SE_SA_spia_100pg

description:
SE + SA 50:50 mix (100pg each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_DNA_10ng

description:
SE + SA 50:50 mix (10ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_spia_1ng

description:
SE + SA 50:50 mix  (1ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_SE_SA_spia_rep2

description:
*SE + SA 50:50 mix (10ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: SPE_RHE_SE_SA_spia


title: SPE_SE_SA_spia_rep1


title: MIP_SE_SA_10ng_rep1


title: RNAseq_SE_SA_cocul_10ng

description:
SE + SA 50:50 co-culture (10ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: bulk RNA-Seq


title: RNAseq_SE_SA_1ng

description:
SE + SA 50:50 mix (1ng each)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx

value: bacterial culture


title: RNAseq_SE_SA_100ng

description:
SE + SA 50:50 mix (100ng each)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx


title: RNAseq_SE_SA_cocul_100ng

description:
SE + SA 50:50 co-culture (100ng)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx


title: RNAseq_SE_SA_10ng

description:
SE + SA 50:50 mix (10ng each)
Supp_Table_06_Bulk_data_expdb.xlsx
Supp_Table_05_Bulk_data_refdb.xlsx


title: Alveolar macrophages,inoculated with primary 4T1 tumour for 2 weeks,rep2

first: wang

last: jiaqi

address: 320 Yueyang Road

institute: The Shanghai Institute of Nutrition and Health (SINH) of the Chinese Academy of Sciences (CAS)

data_processing:
Sequence reads were mapped to the mouse reference genome using HiSat2 (version 2.0.5). Normalization and identification of differentially expressed genes were performed using DESeq2. The resulting P values were adjusted using the and Hochberg approach for controlling the false discovery rate.
Assembly: mm 10
Supplementary files format and content: Microsoft Excel  includes gene counts for each sample

source_name: Lung

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen)
Sequencing libraries were generated using the NEBNext Ultra RNA library prep kit for Illumina (NEB), following the manufacturer’s instructions

value: Lung

tag: Sex

value: Female

value: macrophage

value: WT


title: Alveolar macrophages, without 4T1 tumor inoculation ,rep2


title: Alveolar macrophages,inoculated with primary 4T1 tumour for 2 weeks ,rep1


title: SPE_SE_SA_cocul_spia

description:
SE + SA 50:50 co-culture (10ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: TSB


title: Alveolar macrophages,without 4T1 tumor inoculation ,rep1


title: CD45+, old, 3dpi

city: Lisboa

first: Pedro

last: Sousa-Victor

address: Avenida Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular (iMM)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: mm10
Supplementary files format and content: TSV files containing detected cellular barcodes (barcodes.tsv) and corresponding features (features.tsv) as returned by Cell Ranger. MTX sparse matrix containing counts as returned by Cell Ranger.
Supplementary files format and content: Tab-delimited text files containing processed count matrices in log2(counts+1).

source_name: Skeletal muscle

extract_protocol:
CD45pos cells were isolated by FACS, from n.i. and injured SkM at 1, 3 and 5 dpi from yg (3 months) and old (25 months) female mice. Cells were isolated in two sessions using yg and old mice: n.i. and injured SkMs at 3 dpi in the first session, injured SkMs at 1 dpi and 5 dpi in the second session. For each condition, isolated CD45pos cells from two independent animals were pooled as one sample. After FACS, cell concentration and viability (80-90%) of each cell suspension were determined using 0.4% trypan blue (Gibco™: 15250061). Cells were washed and resuspended in 1x PBS (calcium and magnesium free) containing 0.04% BSA, to a final concentration of 1000 cells/µl. In brief, 20,000 CD45pos cells per condition were loaded onto a 10X Genomics Chromium platform
Library was performed according to the manufacter’s instructions (single cell 3’ kit v3.1 protocol, 10X Genomics).

value: Skeletal muscle

tag: sequencing lane

tag: sorting day

tag: treatment

value: Old


title: CD45+, old, 1dpi

tag: cell type

tag: genotype


title: CD45+, old, 5dpi


title: SPE_SE_SA_50ng

description:
SE + SA 50:50 mix (50ng each)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: no ribo-depletion

value: no SPIA


title: CD45+, young, 0dpi

value: Young


title: Liver_vehicle_3

city: Chuncheon-si

first: Yong-Hyun

last: Han

state: Kangwondo

address: 307-ho, College of Pharmacy, 1, Kangwondaehak-gil

department: College of Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Liver

growth_protocol: FPC diet-fed mice were administered with vehicle- or APB-R3 during 8 weeks three times a week.

extract_protocol:
Liver tissue was homogenized using easy-BLUE™ (iNtRON, Seongnam, Korea) and TissueLyser II (Qiagen, Hilden, Germany). Total RNA was isolated using the RNeasy mini kit (Qiagen) following the manufacturer's protocol.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: Vehicle or 8mg/kg of APB-R3 was administered intraperitoneally.

value: Liver

value: Wild-type, male

value: Vehicle


title: Liver_R3_1


title: Liver_vehicle_2


title: KO_Ang2

city: Wenzhou

first: Guang

last: Liang

address: Chashan University Town Ouhai District, Wenzhou City Zhejiang Province, PRC

institute: Wenzhou medical university

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

value: JOSD2 KO

value: Ang II


title: Liver_vehicle_4


title: Liver_R3_2


title: CD45+, old, 0dpi


title: CD45+, young, 3dpi


title: KO_Ang1


title: KO_Ang3


title: Liver_R3_4


title: MIP_RHE_SE_SA_mix5_spia

description:
RHE_SA+SE mix (wells: B01+D07) (10ng each)_SPIA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

value: skin + bacterial culture

value: Molecular Loop (MIP)

value: batch 2

value: SPIA


title: Liver_R3_3


title: Ang3

value: WT


title: CD45+, young, 5dpi


title: Liver_vehicle_1


title: MIP_SE_DNA_10ng_mouse_stool_100ng

description:
10ng SE + 100ng Mouse stool gDNA
Supp_Table_08_MIP_data_expdb.xlsx
Supp_Table_07_MIP_data_refdb.xlsx

source_name: stool + bacterial culture

value: stool + bacterial culture

value: batch 1


title: SPE_mouse_stool_DNA_10ng

description:
Mouse Stool Microbiome (10 ng)
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

source_name: stool

value: stool

value: Allegro (SPE)


title: Ang1


title: CD45+, young, 1dpi

value: Skeletal muscle


title: SPE_SE_SA_DNA_1ng_mouse_stool

description:
1ng of SE+SA 50:50mix + 10ng Mouse stool Microbiome gDNA
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx

value: no ribo-depletion

value: no SPIA


title: SPE_SE_SA_DNA_10ng_mouse_stool

description:
10ng of SE+SA 50:50mix + 100ng Mouse stool Microbiome gDNA*
Supp_Table_10_SPE_data_expdb.xlsx
Supp_Table_09_SPE_data_refdb.xlsx


title: WT, noBL, T4, batch2, rep2

city: Freiburg

first: Choongman

last: Lee

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
SnakePipes 2.8.1 was used to generate the count matrix, with options –trim, --fastqc and using reference MM10 – gencodeM19
Assembly: GRCm38
Supplementary files format and content: counts_WT_LiTEC.tsv, tsv file, read counts generated by featureCounts
Supplementary files format and content: genes.t2g,tsv file containing the accession to symbol mapping for the gencode M19 reference used to align and count.

source_name: mESCs

growth_protocol: mouse embryonic stem cells (mESCs) were cultured in 37C 5% CO2 incubator with serum-free 2i media (1:1 of DMEM/F-12 and Neurobasal media supplemented with 1x N-2 supplement, 1x B-27 supplement, 100 U/ml PenStrep, 3 μg/ml AlbuMAXTM II, 1x MEM NEAA, 1mM sodium pyruvate, 1mM L-glutamine, 0.1 μM 2-mercaptoethanol, 1mM MEK inhibitor, 3mM GSK3β inhibitor, and 100 U/ml recombinant mouse LIF)

extract_protocol:
TRIzol Reagent (Invitrogen, 15596026) was used to extract RNA
TruSeq Stranded mRNA protocol

treatment_protocol: Doxycycline (2 ug/ml) were incubated for 2 days beforehand. For blue light exposure, cells in 6-well were put on top of blue LED panel (~3.24 mW/cm^2 on average) for 30 min, then, after 0 hour, 1 hour and 4 hour, RNA was extracted.

value: mESCs

value: untreated, T4


title: WT, noBL, T4, batch2, rep3


title: WT, noBL, T4, batch1, rep1


title: WT, noBL, T1, batch2, rep2

value: untreated, T1


title: WT, noBL, T1, batch1, rep1


title: WT, noBL, T1, batch2, rep3


title: Ang2

value: aorta


title: WT, noBL, T0, batch2, rep3

value: untreated, T0


title: WT, noBL, T0, batch1, rep1


title: LiTEC, noBL, T4, batch2, rep3

value: LiTEC transfected


title: WT, BL, T4, batch1, rep1

value: Blue light, T4


title: LiTEC, noBL, T4, batch1, rep1


title: WT, noBL, T0, batch2, rep2


title: WT, BL, T4, batch2, rep3


title: WT, BL, T1, batch2, rep2

value: Blue light, T1


title: WT, BL, T0, batch2, rep3

value: Blue light, T0


title: WT, BL, T4, batch2, rep2

value: WT


title: LiTEC, noBL, T1, batch1, rep1


title: LiTEC, noBL, T0, batch2, rep3


title: WT, BL, T0, batch2, rep2


title: WT, BL, T0, batch1, rep1


title: LiTEC, noBL, T1, batch2, rep3


title: LiTEC, noBL, T0, batch2, rep2


title: LiTEC, noBL, T1, batch2, rep2


title: LiTEC, noBL, T4, batch2, rep2


title: LiTEC, BL, T1, batch2, rep3


title: LiTEC, noBL, T0, batch1, rep1


title: LiTEC, BL, T1, batch1, rep1


title: LiTEC, BL, T1, batch2, rep2


title: LiTEC, BL, T4, batch1, rep1


title: LiTEC, BL, T0, batch2, rep3


title: LiTEC, BL, T0, batch2, rep2


title: LiTEC, BL, T0, batch1, rep1


title: LiTEC, BL, T4, batch2, rep2


title: WT, BL, T1, batch1, rep1


title: WT, BL, T1, batch2, rep3


title: CD25KO

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

data_processing:
Cell Ranger
Assembly: mm10
Supplementary files format and content: tab-seprated values files and matrix files

source_name: spleen

extract_protocol:
FACS purified, live Treg cells were washed in cold PBS with 0.04% BSA twice and resuspended for sequencing.
Cells were encapsulated in a 10X Chromium Single Cell Controller and libraries were constructed using the 10X Single Cell 3' Reagent Kit.

value: spleen

tag: cell line

value: CD25KO Tregs

value: 2mg/kg tamoxifen IP 5 days


title: LiTEC, BL, T4, batch2, rep3


title: KO_eTreg_3

data_processing:
Cell Ranger
HISAT2 (ver.2.2.1) for alignment
Raw counts were generated with UCSC annotations
Assembly: mm10
Supplementary files format and content: tab-deliminated text files with the raw counts for each Sample

source_name: Spleen and lymph nodes

extract_protocol:
RNA was extracted using Qiagen Rneasy kit
Library preparation was completed with the KAPA RNA Hyperprep kit with RiboErase (HMR)

value: Spleen and lymph nodes

value: CD25KO effector Tregs


title: KO_eTreg_2


title: CD25WT

value: CD25WT Tregs


title: KO_cTreg_3

value: CD25KO central Tregs


title: KO_cTreg_2


title: KO_eTreg_1


title: WT_eTreg_3

value: CD25WT effector Tregs


title: KO_cTreg_1


title: WT_cTreg_1

value: CD25WT central Tregs


title: cont9_P

city: Cambridge

first: Simon

last: Mages

address: 415 Main St.

institute: Broad Institute

description: XXX_R1.fastq.gz contains the transcript sequence and XXX_R2.fastq.gz contains bead barcode (14bp) followed by bead UMI sequence (8bp).

data_processing:
Base-calling from images was performed by a custom MATLAB package ArrayCaller (https://github.com/MacoskoLab/ArrayCaller/).
The sequenced reads were processed by Slide-seq tools pipeline (https://github.com/MacoskoLab/slideseq-tools) to generate the gene count matrix and match bead barcode between array and sequenced reads.
Assembly: GRCm38.81
Supplementary files format and content: Puck_XXX.digital_expression.txt.gz is the gene count matrix where the rows are genes and columns are beads.
Supplementary files format and content: Puck_XXX_matched_bead_locations.txt.gz is the bead spatial location file where the rows are in the order as Puck_XXX.digital_expression.txt.gz.
Supplementary files format and content: Puck_rawimage_XXX.tar.gz contains the raw image from puck sequencing, which is used to obtain the spatial location of the bead barcodes.
Library strategy: Slide-seq

source_name: normal colon

extract_protocol:
10 mm sections were cut and the Slide-seq V2 protocol was used as previously described15. For mouse experiments, four and six arrays were collected from normal colons and premalignant lesions respectively. The muscularis was fit onto the array of both healthy and dysplastic lesions to allow appropriate orientation.
Nextera XT

treatment_protocol: Mice were injected to the submucosal layer of the colon with 4-hydroxytamoxifen (EMD Millipore # 579002) dissolved in ethanol at a concentration of 100 mM.  Tumors and matching colon tisuuea were resected at  3 weeks after 4-hydroxytamoxifen injection.

value: normal colon

value: Tissue

value: No treatment


title: AV10b_P

source_name: Colorectal pre-malignant lesion

value: Colorectal pre-malignant lesion

value: Apcfl/flVillincreERT2  mice

value: injection with 4-hydroxytamoxifen to the submucosal layer of the colon, monitoring for 3 weeks


title: WT_eTreg_1


title: cont10_P


title: AV13_P


title: AV11a_P


title: cont8_P


title: AV10a_P


title: STZ, replicate 2, scRNAseq

first: Robin

last: Choudhury

address: L6 West Wing, John Radcliffe Hospital, Headley Way

department: Cardiovascular Medicine, Radcliffe Department of Medicine

description: 10X Genomics

data_processing:
Samples were demultiplexed and reads from Unique Molecular Identifiers were aligned and counted per gene with 10X Genomics Cell Ranger 5.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files; one file per animal multiplexed from cells of heart, kidney, liver and spleen.

source_name: multiplexed sample: Heart, kidney, liver, spleen

extract_protocol:
Heart (ventricle), liver and kidneys were dissected and finely minced on ice using scissors. Cells were enzymatically dissociated in collagenase II (500U/ml; Thermo Fisher 17101015) in 10 ml HBSS, with agitation at 37°C for 1 hour. Dissociated heart, liver and kidney cells were passed through a 70 µm cell strainer and rinsed with 3 ml ice-cold HBSS. Spleens were passed through a 70 µm cell strainer into 1X Red Cell Lysis Buffer (1.5 mM ammonium chloride, 100 µM sodium bicarbonate, 11 µM EDTA disodium) and incubated for 10 minutes at room temperature. All cells were centrifuged for 5 min at 400 g at 4°C, then resuspended in 10% v/v DMSO in foetal bovine serum (FBS), aliquoted and frozen at -80ºC before sequencing. Cells were revived by thawing at 37 °C for 1 min in a water bath and slowly transferred into 10 ml tubes filled with 9 ml pre-warmed RPMI containing 10% FBS and centrifuged at 500 g for 5 min. Next, cells were resuspended in 500 µl RPMI containing 10% FBS and labelled with commercially available DNA-labelled antibodies (TotalSeq-A, Biolegend) at 4 °C for 30 min. Following incubation, cell suspensions were washed three times with PBS containing 2 % BSA. After the final wash, cell suspensions were resuspended in PBS containing 2 % BSA and a viability dye (Zombie Red, Biolegend) for discrimination between live and dead cells. Next, 10,000 viable cells were sort-purified from the four organs of each individual mouse using a SH800 cell sorter (Sony). The four cell fractions were pooled for processing as a single sample according to the manufacturer’s protocol, while the antibody-linked barcodes enabled sample-specific demultiplexing of the sequencing data.
scRNA-seq libraries were generated using the Chromium Controller and the Next GEM Single Cell 3’ Reagent Kit (v3, 10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina NovaSeq 6000 platform.

value: multiplexed sample:Heart, kidney, liver, spleen

tag: strain

value: Male

tag: disease

value: Diabetic


title: STZ, replicate 3, scRNAseq

description: 10X Genomics


title: WT_eTreg_2


title: cont7_P

value: WT


title: AV11b_P


title: STZ, replicate 4, scRNAseq

description: 10X Genomics


title: STZ, replicate 1, scRNAseq

description: 10X Genomics


title: Control, replicate 3, scRNAseq

description: 10X Genomics

value: Control


title: Control, replicate 1, scRNAseq

description: 10X Genomics


title: WT_cTreg_2

value: Spleen and lymph nodes

value: 2mg/kg tamoxifen IP 5 days


title: AV12_P


title: Control, replicate 2, scRNAseq

description: 10X Genomics


title: FZD5/8 antagonist, scRNAseq

city: Leiden

first: Vincent

last: van Unen

state: ZH

address: Albinusdreef 2

department: Immunology

institute: Leiden University

data_processing:
Sequences from scRNA-seq were processed with Cell Ranger software (10X Genomics) with UMI (unique molecular identifier) collapsing and alignment to the GRCm38 mouse transcriptome. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38-mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: jejunum

extract_protocol:
Lgr5+ Intestinal stem cells were isolated by flow cytometry from the jejunum of Lgr5-eGFP-IRES-CreER mice (n=3 mice per condition).
RNA isolation used the PicoPure RNA Isolation Kit (Applied Biosystems, Cat: KIT0204), followed by 10x Genomics Chromium 3’ library preparation and NGS sequencing.

value: Lgr5+ Intestinal stem cells

value: jejunum

tag: culture

value: GFP+ cells

value: female

tag: age

value: 10-12 weeks

tag: type of_prep

value: V3.1 NextGEM


title: Fc control, scRNAseq


title: WT_cTreg_3

value: CD25WT central Tregs


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 36

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

data_processing:
Base calling: Base calling was done by Illumina Real Time Analysis (v3.4.4)
Demultiplex: output was demultiplexed and converted to FastQ format with Bcl2fastq (v2.20.0, Illumina).
Indexing: The fathead minnow reference genome (assembly GCA_016745375.1; Martinson et al., 2022) was indexed with STAR (v2.7.10a, except for the estrone exposure, which used v2.7.9a) and concurrently had in-house gene annotations loaded. The following sample specific parameters were used to generate the genome index: --genomeSAindexNbases 13 --sjdbOverhang 149.
Quality control and trimming: After performing quality control on the raw FastQ data using FastQC and MultiQC (v1.12), raw reads were trimmed using Trim Galore! (v0.6.6) to remove sequencing adapters and low-quality bases and filter out trimmed reads shorter than 20 bp. Trim Galore! is a wrapper script that makes use of the publicly available adapter trimming tool Cutadapt (v4.0).
Mapping: Trimmed reads were then mapped to the indexed genome with STAR version 2.7 using the default parameters except for the use of: --outSAMattributes NH HI AS NM XS.  Samtools (v1.15.1) was used to sort and index the alignment files.
Assign counts: HTSeq (v2.0.1) was used to assign counts to each gene with the following parameters: -f bam -r pos -s no. FastQC and MultiQC (v1.12) were used to assess quality control metrics of the processed reads.  Counts to each gene were parsed, and count data for each exposure condition written to a single tab-delimited matrix file with samples arranged as columns and genes arranged in rows.
Filter counts: Raw counts were first screened to see if any exhibited total counts <2M, and a boxplot of log10 raw counts (+1) for each sample was generated to look for samples with unusual counts distribution. Lowly expressed genes were removed from the raw count matrices using edgeR’s (Robinson et al., 2010) built-in filtering function, filterByExpr(), in version 3.40.2; namely, genes with < 15 reads across all samples and < 10 reads in the smallest group (treatment or control) sample size were filtered out.
Count normalization and filtering: Normalization factors for the filtered count matrices were calculated using the trimmed mean of M-values method via the edgeR function calcNormFactors(). Filtered counts were then normalized by applying a log2 transformation to the counts per million (CPM) read with a pseudo-count of 1 added (to prevent occurrence of any negative count values for downstream analyses, i.e., log2(CPM+1)). Any sample with a filtered, normalized count distribution (assessed via boxplot) that markedly deviated from the rest of the samples within an individual chemical dataset was removed. Multidimensional scaling (MDS) plots were generated to look for possible outliers. Individual samples separated from all remaining replicate samples within the same treatment group on either the first or second principal component by >2x the span of all other samples on the corresponding PC axis were considered strong outliers and removed. If multiple potential outlier samples were present on the same PCA, they were only removed if each outlier sample corresponded to a different treatment group, as such samples were unlikely to represent any reproducible dose-dependent effect.
Assembly: assembly GCA_016745375.1
Supplementary files format and content: *.txt file raw count matrix
Supplementary files format and content: *.txt file count matrix with all filtering, normalization and quality control filters applied. Header rows provide unique sample ID and expsoure concentrations. Starting at row 5, rows are genes and columns are normalized counts with a psuedo-count of 1 added, log2 transformed, and filtered.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Total RNA was isolated from each homogenate using MagMAX-96 Total RNA Isolation kits (AM1830, Thermo Fisher Scientific, MA, USA) following the manufacturer’s instructions.  All isolated RNA was quantified with spectrophotometry (Synergy HTX plate reader and a Take3 microvolume plate, BioTek, VT, USA) and 16 randomly chosen RNA samples per 96-well plate were analyzed with electrophoresis (4200 Tapestation, Agilent, CA, USA) to confirm quality of the RNA isolation procedure (RINe > 9).
Each cDNA library was prepared from 250 ng of total RNA using commercially available kits that select for mRNA (SENSE mRNA-Seq Library Prep kit, Lexogen, NH, USA) following the manufacturer’s instructions.  The quality and size distribution of libraries was determined using a 4200 TapeStation, and concentrations were measured with a fluorescence-based assay (Quant-iT PicoGreen dsDNA Assay, Thermo Fisher Scientific, MA, USA).

value: GLTED-Duluth-wt

value: 5-6 dpf

tag: dev stage

value: larvae

value: whole body

value: not determined

tag: store cond

value: -80 deg C

tag: collection date

tag: geo loc_name

value: USA:Minnesota, Duluth

tag: biomaterial provider

value: US EPA Great Lakes Toxicology & Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804

tag: birth location

tag: breeding method

value: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  All embryos were fertilized within a two-hour window.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use. All  procedures involving larval fathead minnows were approved by an animal care and use committee in accordance with the Guide for the Care and Use of Laboratory Animals (National Research Council, 2011; US EPA Animal Care and Use Plan # Eco24-09-001).

tag: collected by

tag: exposure duration

tag: measured conc

tag: measured conc_units

value: mg/L

tag: nominal conc

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units

value: parathion (DTXSID7021100)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 37

tag: strain

tag: age

tag: tissue

tag: Sex

value: Great Lakes Toxicology & Ecology Division

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 30

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 38

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 40

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 42

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 43

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 33

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 34

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 28

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 26

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 39

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 27

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 25

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 45

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 29

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 31

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 22

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 23

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 19

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 20

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 35

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 47

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 21

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 32

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 46

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 44

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 18

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 17

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 15

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 12

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 9

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 14

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 13

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 8

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 41

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 2

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 36

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name

value: methidathion (DTXSID5020819)


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 7

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 10

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 6

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 11

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 35

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 4

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 3

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 32

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 31

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 33

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 16

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 28

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 30

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 29

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 26

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 27

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 22

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 5

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 24

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 23

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 25

tag: biomaterial provider

tag: birth location

tag: breeding method

tag: collected by


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 18

tag: exposure duration

tag: measured conc

tag: measured conc_units

tag: nominal conc


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 17

tag: strain

tag: nominal conc_units

tag: extrapolated conc

tag: extrapolated conc_units


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to parathion, sample 1

tag: age

tag: tissue

tag: Sex

tag: treatment


title: RNA-Seq of larval fathead minnow whole body after 24 h exposure to methidathion, sample 34

tag: dev stage

tag: store cond

tag: collection date

tag: geo loc_name