title: T-Cell, Ctrl, Intestine

description: Library name: 91


title: P1_HC_sc_library

status: Public on Apr 29 2025

type: SRA

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

department: Pediatrics

country: Canada

institute: The University of British Columbia

library_source: transcriptomic single cell

data_processing:
RNA was sequenced on the Illumina NextSeq 2000 with Paired-end (2 x 115bp)
R1 and R2 reads were filtered based on read length, quality, and highest single nucleotide frequency. R1 reads are annotated to identify cell labels, unique molecular identifiers, and filtered for >6 Poly(T) tail. Bowtie2 version 2.2.9 was used to map the R2 reads to the reference sequences
R1 and R2 with the same cell labels, UMI sequences, and genes were collapsed into a single molecule
Putative cells were determined by considering all reads associated with Distribution-based error correction (DBEC)-adjusted molecules. The minimum second derivative along the cumulative reads curve is identified as the inflexion point, after which the cells are labelled as noise. Filtered putative reads that align to a sample tag sequence were used to identify sample labels for a cell
Labelled DBEC-adjusted molecule counts are present in a tab-delimited .txt format. Each file has a label for sample-specific cell labeling
Assembly: Homo Sapiens (GRCh38)
Supplementary files format and content: Raw counts are presented as .csv files

molecule: total RNA

organism: Homo sapiens

source_name: Regulatory T cells (Tregs) and conventional T cells (Tconvs)

extract_protocol:
Human peripheral blood from the patient (P1) or two age-matched and sex-matched controls were collected in sodium heparin tubes and peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation. CD3+ T cells were enriched from PBMC using an EasySep Human T cell isolation kit (#1791, Stemcell Technologies) and sorted for CD4+CD25+CD127lo regulatory T cells (Tregs) or CD4+CD25-CD127+ conventional T cells (Tconvs). Tregs and Tconvs were either left untreated or stimulated with PMA+ionomycin for 4 hours before RNA extraction.
The samples underwent reverse transcription, Exonuclease I treatment, and cDNA amplification. mRNA PCR products were separated from sample tag products with double-sided size selection using AMPure beads. Separated products were further amplified using PCR and then purified. PCR products were then PCR amplified using the Illumina i7 index primer. Libraries were diluted to 650pM and multiplexed for paired-end (2 x 115bp) sequencing on a NextSeq2000 Sequencing System (Illumina) at 200 cycles P3 for 1.1 billion reads.

tag: cell type

tag: genotype

value: HC and patient

tag: treatment

value: Unstimulated and stimulated for 4h with PMA+ionomycin


title: Met_ethyl4hydroxybenzoate_111988_5_11uM_TC00003602_C12

city: RTP

first: Monique

last: Hazemi

state: NC

address: 109 T.W. Alexander Dr

country: USA

institute: US EPA

description:
Library name: TC00003602_C12
TC00003602_C12

library_source: transcriptomic

data_processing:
Read alignment: Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts: Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: aime_prepilot_count_data.csv.gz: A table of probe counts in CSV format, with rows corresponding to TempO-seq probe IDs (see httr_aime_prepilot-probe_manifest.csv file for probe ID mapping information) and columns corresponding to sample IDs.
Supplementary files format and content: httr_aime_prepilot-probe_manifest.csv: For each probe ID listed in the table of probe counts (aime_prepilot_count_data.csv.gz), a corresponding mapping of probe sequence, Entrez ID, and gene symbol are listed.

growth_protocol: Experiments were peformed in VM7Luc4E2 cells, a sub-clone of MCF-7 breast adenocarcinoma cells that stably expresses and estrogen receptor trans-activation reporter construct. Prior to experimentation, VM7Luc4E2 cultures were maintained in growth medium (Minimum Essential Medium alpha (MEMa) supplemented with 10% fetal bovine serum (FBS) and 1X Gibco Anti-Anti antibiotics). Four days prior to seeding in assay plates, cultures were switched to estrogen-stripping medium (Dulbecco’s Modified Eagle Medium (DMEM) (low glucose, with pyruvate, no phenol red) supplemented with 5% charcoal/dextran-treated FBS and 4 mM L-Glutamine). Estrogen stripping was performed by refreshing the estrogen-stripping media daily for four days. For chemical testing experiments, VM7Luc4E2 cells were passaged, resuspended in assay medium (DMEM (low glucose, with pyruvate, no phenol red) supplemented with 1% charcoal/dextran-treated FBS, 4 mM L-Glutamine and 10 mM HEPES), and plated in 384-well plates in a volume of 30 µL per well and an initial seeding density of 7,500 cells / well. Cells were allowed a 24 hour recovery period prior to treatment with AIME conditioned medium.  Cells were lysed for TempO-Seq analysis 24 hours after treatment with AIME conditioned medium.

extract_protocol:
At 24 hours after treatment with condition media, assay plates were removed from the incubator, assay wells were washed twice with 1X phosphate-buffered saline and the final PBS wash was aspirated from each well leaving a residual volume of 10 µL.  Cells were subsequently lysed by adding 10 µL of 2X BioSpyder Enhanced Lysis buffer.  Assay plates were then sealed, agitated for 30 seconds on the stage of a MultiFlo FX washer / dispenser and then placed in a hybridization oven at 37°C for 10 minutes. Plates were then immediately transferred to a -80°C freezer for storage. Plates were subsequently shipped frozen to BioSpyder Technologies (Carlsbad, CA) for analysis with the human whole transcriptome TempO-Seq assay.  The TempO-Seq assay was conducted directly on cell lysates with no RNA extraction step.
Plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the unattenuated TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The TempO-seq libraries were sequenced to a target read depth of 3.0x106 mapped reads per sample.

treatment_protocol: The experiments were carried out using the alginate immobilization of metabolic enzymes (AIME) technology. DMSO solubilized chemicals (120 nL) were dispensed into 384-well microplates. Locations of treatments were randomized by well coordinate on the 384-well plate. After chemical dispensing, 60 µL of assay medium charged with phase 1 and phase 2 metabolic co-factors (NADPH (1:11.4), uridine S’-diphosphoglucuronic acid trisodium salt (UDPGA; 0.5 mM), glutathione (GSH; 1 mM), and adenosine 3-phosphate 5-phosphosulfate lithium salt hydrate (PAPS; 2 µM)) was dispensed into each well and plates were shaken at 500 RPM for 7 minutes on an orbital shaker. AIME peg lids with hydrogels containing either hepatic rat S9 (AIME+ condition) or deionized water (AIME- condition) were inserted into the plates and incubated for 2 hours to create conditioned media. Then, 30 µL of conditioned media was transferred to assay plates containing VM7Luc4E2 cells and 30 µL of assay medium.  The final concentration of DMSO in all treatment wells was 0.1%. Assy plates were then incubated for 24 hours in a cell culture incubator (37°C and 5% CO2).

tag: cell line

value: 24h exposure of 11 uM of Ethylparaben

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: Ethylparaben

tag: chemical sample_id

tag: chemical concentration

value: 11 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: sample qc_issue

value: OK


title: Spatial Transcriptomics Sample 4-3

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

description: Library name: S8_R1

data_processing:
Libraries were sequenced using an Illumina NextSeq2000 at a reading depth of 100 million paired-end reads per sample using the following read metrics: Read1: 28bp; Index1: 10bp; Index2: 10bp; Read 2: 90bp. Raw FASTQ files were processed with Space Ranger 1.3.0 and aligned to mm10-2020-A reference genome (refdata-gex-mm10-2020-A).
Computational analysis was performed in R using a combination of Seurat Version 5.1.048 and custom scripts.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: RDS files that can be read into R as a Seurat Object via readRDS()
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Brain

extract_protocol:
Mice were anesthetized, the animal was decapitated, and brain extracted. The brain was subsequently flash frozen in OCT via isopentane and liquid nitrogen bath.
Processing of slices and library preparation were performed for Visium as recommended by the manufacturer (10x Genomics).

treatment_protocol: Mice underwent a CHIMERA TBI or sham TBI.

tag: tissue

value: Brain

value: FoxTRAP x Ai14

value: TBI


title: EC, 10d DSS, Intestine, biol. rep. 3

city: Wien

first: Cornelia

last: Vesely

state: Österreich

address: Schwarzspanierstr 17

department: Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description: Library name: 89

data_processing:
Quality Control: cutadapt: --nextseq-trim=30 --minimum-length=10
Adapter Trimming: cutadapt: -a  -A  --minimum-length=10
Mapping: Hisat2 (Standard configuration)
Editing Call: Jacusa2 (Standard configuration)
Assembly: GRCm39 from Ensemble, Mapper: Hisat2 (standard configuration)
Supplementary files format and content: Columns: Library Name, Sequence of Primers used to add barcodes, Number of raw or processed read, Cell Type, Tissue Type, Condition, counts of nucleotides at editing site and calculated editing ratio (%)

source_name: Intestine

extract_protocol:
The large intestine was removed from freshly sacrificed animals, cut open longitudinally and fecal contents were removed by vigorous shaking in PBS. Colon cells were incubated at 37°C for 20min in 4mL solution 1 (3% FCS, 20mM HEPES, 5mM EDTA, and 1mM DTT in RPMI (Gibco)) at 180rpm in a 6-well plate. Tissues were rinsed with 1xPBS, transferred to a fresh 6-well plate 700 containing 4mL of digest1 solution (0.8mg/ml Dispase, 20mM HEPES, 2mM EDTA in RPMI) and again incubated at 37°C at 180rpm for 5min. Next, tissues were agitated vigorously in digest1 solution before transferring them into digest2 solution (0.1mg/ml Liberase TL, 0.5mg/ml DNAseI, 20 mM HEPES in RPMI). After another incubation for 20min, tissue and solution were transferred into a gentleMACS™ M tube and dissociated in an octo-gentleMACS dissociator (Myltenyi Biotech, Germany). Suspensions were then filtered through a 100μM cell strainer, washed with 1xPBS containing 2% FCS to remove remaining enzymes. immune cells, B cells (CD45+, CD19+), T cells (CD45+, CD19-, CD3+), neutrophils (CD45+,CD3-, CD19-, Ly-6G+, CD11b+) and a myeloid cell-enriched fraction (CD45+, CD3-, CD19-, Ly-6G-, CD11b+) were sorted directly into RNA lysis buffer. Endothelial cells and a fibroblast/SMC-enriched fraction, cells were stained with anti-CD31, anti-EpCAM and anti-CD45 antibodies and sorted into RNA lysis buffer (endothelial cells: CD45-, EpCam-, CD31+, fibroblast/SMC fraction: CD45-, EpCam-, CD31-). RNA was extracted using the NucleoSpin 96 RNA Core Kit (Macherey-Nagel). CarrierRNA (Macherey-Nagel) was added to samples with cell counts <104 cells. cDNA was synthesized using the LunaScript RT Mastermix (NEB).
cDNA was subjected to a 2-step PCR: In a first round, Flna editing site primers (amplification of the region around the editing site) and Q5 High-Fidelity DNA Polymerase (NEB) were used to perform 25 cycles. 2μl of this PCR served as a template for PCR2: Using the ampSeq barcoding primers for 15 cycles, thereby adding Illumina-compatible adapters with dual-indices. PCR products were gel-eluted using the Monarch DNA Gel Extraction Kit (NEB) followed by quantification by Qubit Fluorometry (Thermo Fisher Scientific). A maximum of 96 samples were pooled into one multiplex for sequencing on an Illumina Nova-Seq instrument.

treatment_protocol: DSS-colitis was induced in 8-10-week-old mice by adding 2-2.5% DSS in the drinking water for 2,5 or 10 days

value: Intestine

value: EC

value: WT

value: 10d DSS


title: Macrophage, Ctrl, Intestine

description: Library name: 101

value: Macrophage

value: Ctrl


title: Met_transstilbene_139939_1_0.001uM_TC00003602_C11

description:
Library name: TC00003602_C11
TC00003602_C11

value: 24h exposure of 0.001 uM of trans-Stilbene

value: trans-Stilbene


title: G5TM_2

city: Kunming

first: Juhua

last: Dan

address: 727 of Jingming Road

country: China

institute: Kunming University of science and technology

description: Library name: sample 14

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: Mus_musculus_Ensemble_90
Supplementary files format and content: tab-delimited text files include gene count for each Sample
Supplementary files format and content: cvs files include FPKM values for each Sample

molecule: polyA RNA

source_name: MEF cell

growth_protocol: The MEF cells derived from the mice were harvested on e13.5 days and cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) at 37℃ with 5% CO2 and 3% O2.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: different genotype

value: MEF cell

value: Mouse Embryonic Fibroblasts

value: MEF cells from G5 mTR-/-Wrn-/-p53N236S/N236S mice


title: G5TM_3

description: Library name: sample 15


title: G5TM_1

description: Library name: sample 13


title: EC, 10d DSS, Intestine, biol. rep. 1

description: Library name: 87


title: Met_transstilbene_139939_5_11uM_TC00003602_C10

description:
Library name: TC00003602_C10
TC00003602_C10

value: 24h exposure of 11 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium


title: Met_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003602_C09

description:
Library name: TC00003602_C09
TC00003602_C09

value: 24h exposure of 0.865 uM of Ethylparaben

value: Ethylparaben

value: OK


title: Spatial Transcriptomics Sample 4-1

description: Library name: S7_R1

value: Brain

value: FoxTRAP x Ai14

value: TBI


title: Met_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003602_D09

description:
Library name: TC00003602_D09
TC00003602_D09

value: 24h exposure of 3.73 uM of Ethylparaben


title: Spatial Transcriptomics Sample 4-2

description: Library name: S7_R2


title: Spatial Transcriptomics Sample 3-4

description: Library name: S6_R2


title: EC, Ctrl, Intestine, biol. rep. 2

description: Library name: 86

value: Intestine

value: EC

value: WT


title: G5DM_3

description: Library name: sample 12

value: MEF cells from G5 mTR-/-Wrn-/-p53WT mice


title: Met_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003602_B12

description:
Library name: TC00003602_B12
TC00003602_B12

value: 24h exposure of 26.1 uM of Ethylparaben


title: Spatial Transcriptomics Sample 3-3

description: Library name: S6_R1


title: G5DM_2

description: Library name: sample 11

value: MEF cell


title: Met_daidzein_D7802_5_11uM_TC00003602_B11

description:
Library name: TC00003602_B11
TC00003602_B11

value: 24h exposure of 11 uM of Daidzein

value: Daidzein

value: 11 uM


title: G5DM_1

description: Library name: sample 10

value: Mouse Embryonic Fibroblasts


title: B-Cell, 5d DSS, Blood, biol. rep. 2

description: Library name: 84

source_name: Blood

value: Blood

value: B-Cell

value: 5d DSS


title: Met_DMSO_0_0uM_TC00003602_B10

description:
Library name: TC00003602_B10
TC00003602_B10

value: 0.5% DMSO vehicle control

value: VM7Luc4E2 Assay Medium

value: DMSO

value: 0 uM

value: OK


title: EC, Ctrl, Intestine, biol. rep. 1

description: Library name: 85

value: Intestine

value: EC

value: Ctrl


title: Spatial Transcriptomics Sample 3-2

description: Library name: S5_R2

value: Brain

value: FoxTRAP x Ai14

value: TBI


title: Spatial Transcriptomics Sample 3-1

description: Library name: S5_R1


title: B-Cell, 5d DSS, Blood, biol. rep. 1

description: Library name: 83

value: WT


title: Met_transstilbene_139939_7_53.5uM_TC00003602_B09

description:
Library name: TC00003602_B09
TC00003602_B09

value: 24h exposure of 53.5 uM of trans-Stilbene

value: trans-Stilbene


title: Spatial Transcriptomics Sample 2-4

description: Library name: S4_R2

value: Sham


title: G3TM_3

description: Library name: sample 9

value: MEF cell

value: Mouse Embryonic Fibroblasts

value: MEF cells from G3 mTR-/-Wrn-/-p53N236S/N236S mice


title: EC, 10d DSS, Intestine, biol. rep. 2

description: Library name: 88

value: 10d DSS


title: Met_daidzein_D7802_4_3.73uM_TC00003602_A12

description:
Library name: TC00003602_A12
TC00003602_A12

value: 24h exposure of 3.73 uM of Daidzein

value: VM7Luc4E2 Assay Medium

value: Daidzein


title: Myeloid Cell, 5d DSS, Blood, biol. rep. 2

description: Library name: 82

value: Blood

value: Myeloid Cell

value: 5d DSS


title: Spatial Transcriptomics Sample 2-3

description: Library name: S4_R1

value: Brain


title: G3TM_1

description: Library name: sample 7


title: G3TM_2

description: Library name: sample 8


title: Met_daidzein_D7802_1_0.001uM_TC00003602_A11

description:
Library name: TC00003602_A11
TC00003602_A11

value: 24h exposure of 0.001 uM of Daidzein

value: OK


title: Spatial Transcriptomics Sample 2-2

description: Library name: S3_R2

value: FoxTRAP x Ai14


title: G3DM_2

description: Library name: sample 6

value: MEF cells from G3 mTR-/-Wrn-/-p53WT mice


title: Met_DMSO_0_0uM_TC00003602_A10

description:
Library name: TC00003602_A10
TC00003602_A10

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: Myeloid Cell, 5d DSS, Blood, biol. rep. 1

description: Library name: 81

value: WT


title: Neutrophil, 5d DSS, Blood, biol. rep. 1

description: Library name: 79

value: Neutrophil


title: Spatial Transcriptomics Sample 2-1

description: Library name: S3_R1

value: Sham


title: Met_bestradiol_E2758_1_0.0001uM_TC00003602_A09

description:
Library name: TC00003602_A09
TC00003602_A09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: Spatial Transcriptomics Sample 1-4

description: Library name: S2_R2


title: T-Cell, 5d DSS, Blood, biol. rep. 2

description: Library name: 78

value: T-Cell


title: G1TM_2

description: Library name: sample 4

value: MEF cell

value: Mouse Embryonic Fibroblasts

value: MEF cells from G1 mTR-/-Wrn-/-p53N236S/N236S mice


title: Neutrophil, 5d DSS, Blood, biol. rep. 2

description: Library name: 80

value: Blood

value: 5d DSS


title: T-Cell, 5d DSS, Blood, biol. rep. 1

description: Library name: 77


title: Spatial Transcriptomics Sample 1-3

description: Library name: S2_R1

value: Brain


title: NoMet_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003599_H11

description:
Library name: TC00003599_H11
TC00003599_H11

value: 24h exposure of 53.5 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

value: OK


title: NoMet_daidzein_D7802_5_11uM_TC00003599_H12

description:
Library name: TC00003599_H12
TC00003599_H12

value: 24h exposure of 11 uM of Daidzein

value: Daidzein

value: 11 uM


title: G1TM_1

description: Library name: sample 3


title: Spatial Transcriptomics Sample 1-2

description: Library name: S1_R2

value: FoxTRAP x Ai14


title: NoMet_transstilbene_139939_4_3.73uM_TC00003599_H10

description:
Library name: TC00003599_H10
TC00003599_H10

value: 24h exposure of 3.73 uM of trans-Stilbene

value: trans-Stilbene


title: B-Cell, 5d DSS, Bone Marrow, biol. rep. 3

description: Library name: 76

source_name: Bone Marrow

value: Bone Marrow

value: B-Cell

value: WT


title: B-Cell, 5d DSS, Bone Marrow, biol. rep. 2

description: Library name: 75


title: NoMet_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003599_H09

description:
Library name: TC00003599_H09
TC00003599_H09

value: 24h exposure of 0.001 uM of Ethylparaben


title: G1DM_1

description: Library name: sample 1

value: MEF cell

value: Mouse Embryonic Fibroblasts

value: MEF cells from G1 mTR-/-Wrn-/-p53WT mice


title: G1DM_2

description: Library name: sample 2


title: Spatial Transcriptomics Sample 1-1

description: Library name: S1_R1

value: Brain

value: Sham


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003599_G12

description:
Library name: TC00003599_G12
TC00003599_G12

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

value: VM7Luc4E2 Assay Medium


title: G3DM_1

description: Library name: sample 5

value: MEF cells from G3 mTR-/-Wrn-/-p53WT mice


title: NoMet_DMSO_0_0uM_TC00003599_G11

description:
Library name: TC00003599_G11
TC00003599_G11

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

value: OK


title: Myeloid Cell, 5d DSS, Bone Marrow, biol. rep. 3

description: Library name: 73

value: Myeloid Cell

value: 5d DSS


title: Myeloid Cell, 5d DSS, Bone Marrow, biol. rep. 2

description: Library name: 72

value: Bone Marrow


title: NoMet_ethyl4hydroxybenzoate_111988_8_100uM_TC00003599_G10

description:
Library name: TC00003599_G10
TC00003599_G10

value: 24h exposure of 100 uM of Ethylparaben

value: Ethylparaben


title: NoMet_daidzein_D7802_2_0.093uM_TC00003599_G09

description:
Library name: TC00003599_G09
TC00003599_G09

value: 24h exposure of 0.093 uM of Daidzein

value: Daidzein


title: Myeloid Cell, 5d DSS, Bone Marrow, biol. rep. 1

description: Library name: 71

value: WT


title: 22RV1_NMYC_T13_REP2

type: genomic

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

description:
T13 Timepoint Replicate 2
22Rv1 MYCN overexpressing

hyb_protocol: hybing was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

scan_protocol: scanning was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

data_processing: The raw intensity data extracted from the CEL files were normalized with cyclic loess normalization and log transformed.

label: biotin

molecule: genomic DNA

source_name: Prostate

label_protocol: labeling was done as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

growth_protocol: Cells were collected as describled in the manuscript Walke et al.

extract_protocol: genomic DNA was extracted as described in Blakely et al. Methods in Molecular Biology. 2011 PMID: 2187728

treatment_protocol: cell were treated as described in the manuscript Walke et al.


title: Neutrophil, 5d DSS, Bone Marrow, biol. rep. 3

description: Library name: 70

value: Neutrophil


title: sample.Min6_PT_2

city: Athens

first: Craig

last: Nunemaker

state: OH

address: 228 Irvine Hall

department: Biomedical Sciences

institute: Ohio University

description: Library name: LIB033265

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Assembly: mouse reference genome (Ensembl GRCm38.101)
Supplementary files format and content: tab separated value (tsv) file containing read counts for each sample

growth_protocol: MIN6 cells were maintained in DMEM, supplemented with 10%. FBS and 1% penicillin/streptomycin. Media was changed every other day and cells were placed in 37C

extract_protocol:
RNA was extracted using Rneasy quiagen mini kit
Samples were prepared according to library kit manufacturer’s protocol

treatment_protocol: Upon confluency in 6-well plates, cells were transfected with PTHrP or empty vector DS red using lipofectamine 2000

value: pancreatic beta cell

value: Lipofectamine transfection


title: sample.Min6_DS_3

description: Library name: LIB033269


title: NoMet_daidzein_D7802_6_26.1uM_TC00003599_F12

description:
Library name: TC00003599_F12
TC00003599_F12

value: 24h exposure of 26.1 uM of Daidzein

value: VM7Luc4E2 Assay Medium


title: sample.Min6_DS_1

description: Library name: LIB033267


title: sample.Min6_PT_3

description: Library name: LIB033266


title: sample.Min6_PT_1

description: Library name: LIB033264


title: B-Cell, 5d DSS, Bone Marrow, biol. rep. 1

description: Library name: 74

value: B-Cell


title: NoMet_transstilbene_139939_2_0.093uM_TC00003599_F11

description:
Library name: TC00003599_F11
TC00003599_F11

value: 24h exposure of 0.093 uM of trans-Stilbene

value: trans-Stilbene


title: Neutrophil, 5d DSS, Bone Marrow, biol. rep. 2

description: Library name: 69


title: Neutrophil, 5d DSS, Bone Marrow, biol. rep. 1

description: Library name: 68


title: sample.Min6_DS_2

description: Library name: LIB033268


title: 22RV1_NMYC_T7_REP2

description:
T7 Timepoint Replicate 2
22Rv1 MYCN overexpressing


title: NoMet_daidzein_D7802_1_0.001uM_TC00003599_F10

description:
Library name: TC00003599_F10
TC00003599_F10

value: 24h exposure of 0.001 uM of Daidzein

value: OK


title: Mouse ovary, 12hr post-hCG (DEF)

city: West Lebanon

first: Ruixu

last: Huang

state: New Hampshire

address: 4 Sachem Circle

institute: Dartmouth College

description:
Library name: Sample 6 (12h)
10X Genomics

data_processing:
Raw sequencing data was demultiplexed using Cell Ranger from 10x Genomics, converting the raw data into FASTQ format.
Cell Ranger was also used for the alignment of the FASTQ files to the reference genome and counting the number of reads from each cell that aligned to each gene.
R version 4.2.2 and Seurat version 4 were used for all downstream analyses unless specified otherwise.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values and matrix values

source_name: Ovary

extract_protocol:
One ovary from each mouse was pooled for single-cell isolation, with a total of three ovaries per suspension (labeled ABC or DEF). The pooled ovaries were cut into quarters using insulin syringe needles and enzymatically digested in 2 mL aMEM-Glutamax supplemented with 1 mg/mL bovine serum albumin (BSA; Sigma-Aldrich, #A3311) and 1x insulin-transferrin-selenium (Sigma-Aldrich, #1884) containing 40 µg/L liberase DH (Sigma-Aldrich, #05401089001), 0.4mg/mL collagenase IV (Sigma-Aldrich, #C5138), and 0.2 mg/mL DNAse I (Sigma-Aldrich, #9003-98-9) for 15 minutes with gently agitation at 37°C and 5% CO2 for 15 minutes. Ovaries were then mechanically digested via trituration using a 1000P wide bore tip, and the suspension was strained through a pre-wet 30 µm strainer directly into aMEM-Glutamax containing 10% FBS to quench the enzymes. Any remaining pieces of ovary were returned to the incubator in 2 mL fresh digestion media for another 15 minutes, followed by repeat mechanical digestion and straining. Once the enzymatic and mechanical digestions were complete, the cell suspension was centrifuged at 300g for 10 minutes at 4℃. The supernatant was removed, and the remaining cell pellet was resuspended in 100 µL Red Blood Cell Lysis solution (Miltenyi Biotec, #130-107-677) and incubated for 10 min at 4°C. After red blood cell removal, the suspension was centrifuged again at 300g for 10 minutes at 4°C. Following supernatant removal, the resulting pellet was resuspended in 100μL of 0.025% BSA in phosphate-buffered saline without calcium or magnesium, and transferred to lo-bind Eppendorf tubes.
Cell number and viability were analyzed using Nexcelom Cellometer Auto2000 with AOPI fluorescent staining method. Sixteen thousand cells were loaded into the Chromium iX Controller (10X Genomics, PN-1000328) on a Chromium Next GEM Chip G (10X Genomics, PN-1000120), and processed to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol. The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual. Quality control for the constructed library was performed by Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, 5067-4626) and Qubit DNA HS assay kit for qualitative and quantitative analysis, respectively. The multiplexed libraries were pooled and sequenced on Illumina Novaseq6000 sequencer with 100 cycle kits using the following read length: 28 bp Read1 for cell barcode and UMI, and 90 bp Read2 for transcript. The single-cell library preparation and sequencing were performed at the Northwestern University NUseq core facility with the support of an NIH Grant (1S10OD025120).

treatment_protocol: Treatment with human chorionic gonadotropin (hCG)

value: Ovary

tag: strain

tag: Sex

value: Female

tag: age

value: 6-12 weeks old

value: human chorionic gonadotropin (hCG)

tag: batch

value: DEF


title: T-Cell, 5d DSS, Bone Marrow, biol. rep. 3

description: Library name: 67

value: Bone Marrow

tag: cell type

value: T-Cell

tag: genotype

value: 5d DSS


title: Mouse ovary, 12hr post-hCG (ABC)

description:
Library name: Sample 5 (12h)
10X Genomics

tag: treatment

value: ABC


title: NoMet_ethyl4hydroxybenzoate_111988_5_11uM_TC00003599_F09

description:
Library name: TC00003599_F09
TC00003599_F09

tag: cell line

value: 24h exposure of 11 uM of Ethylparaben

tag: media

value: Ethylparaben

value: 11 uM


title: 22RV1_NMYC_T13_REP1

description:
T13 Timepoint Replicate 1
22Rv1 MYCN overexpressing


title: 22RV1_NMYC_T0

description:
T0 Timepoint
22Rv1 MYCN overexpressing


title: Mouse ovary, 4hr post-hCG (DEF)

description:
Library name: Sample 4 (4h)
10X Genomics


title: T-Cell, 5d DSS, Bone Marrow, biol. rep. 2

description: Library name: 66

value: WT


title: 22RV1_T13_REP2

description:
T13 Timepoint Replicate 2
22Rv1 Parental


title: 22RV1_T13_REP1

description:
T13 Timepoint Replicate 1
22Rv1 Parental


title: 22RV1_NMYC_T7_REP1

description:
T7 Timepoint Replicate 1
22Rv1 MYCN overexpressing


title: NoMet_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003599_E12

description:
Library name: TC00003599_E12
TC00003599_E12

value: 24h exposure of 26.1 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

tag: chemical name

tag: chemical sample_id


title: 22RV1_T7_REP1

description:
T7 Timepoint Replicate 1
22Rv1 Parental


title: Chlamydomonas_Nanopore_dRNAseq used for SingleMod training

city: Guangzhou

first: Yingyuan

last: Xie

state: GuangDong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
raw signals were basecalled using Guppy (v6.3.7) with default parameters and converted into fastq format
Reads that passed the quality threshold (7) and had a length greater than 25bp were then aligned to the reference genome using Minimap2 (v2.22-r1101)
Nanopolish (v0.13.2) eventalign module was used to align raw signals to 5mer bases with the parameter settings "--scale-events --samples --signal-index".
sam2tsv was used to extract bases quality and alignment results for each read from bam files
In-house python scripts were used to extract and organize current features and base quality features for each 39 motif within each read.
These features were then used as inputs for SingleMod for training or prediction.
Assembly: Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, methylation rate of all As in 39 motifs predicted by SingleMod

organism: Chlamydomonas reinhardtii

source_name: cells

extract_protocol:
After extracting total RNA from the samples using TRIzol (Thermo Fisher Scientifific, 15596026), mRNA was isolated via a Dynabeads mRNA Purifification Kit (Thermo Fisher Scientifific, 61006) with genomic DNA removal using TuRBO DNase kit (Thermo Fisher, AM2238).
Nanopore direct RNA sequencing was conducted following instructions provided by Oxford Nanopore Technologies (Oxford, UK) using DRS kits (SQK-RNA002) and MinION flowcells (FLO-MIN106D, R9.4.1 pore).

value: cells


title: SMC, 5d DSS, Intestine, biol. rep. 3

description: Library name: 64

value: Intestine

value: SMC


title: T-Cell, 5d DSS, Bone Marrow, biol. rep. 1

description: Library name: 65


title: NoMet_transstilbene_139939_5_11uM_TC00003599_E11

description:
Library name: TC00003599_E11
TC00003599_E11

value: 24h exposure of 11 uM of trans-Stilbene

value: trans-Stilbene

tag: chemical concentration

tag: dose level

value: OK


title: Mouse ovary, 0hr post-hCG (DEF)

description:
Library name: Sample 2 (0h)
10X Genomics

value: Ovary

value: Female

value: 6-12 weeks old

value: DEF


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003599_E09

description:
Library name: TC00003599_E09
TC00003599_E09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: exposure time

tag: assay plate


title: NoMet_DMSO_0_0uM_TC00003599_D12

description:
Library name: TC00003599_D12
TC00003599_D12

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: assay plate_well

tag: sample qc_issue


title: A549, NDV, 24h, rep3

city: Shanghai

first: Yingjie

last: Sun

address: 518 Ziyue Road

institute: Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science

description: Library name: NDV_24h_3

data_processing:
Raw reads were quality-controlled by fastp and aligned to the reference genome via HISAT2. Mapped reads were assembled using StringTie. Differentially expressed genes (DEGs) were identified using DESeq2 or DEGseq, with thresholds of |log2FC|≥1 and FDR<0.05 (DESeq2) or FDR<0.001 (DEGseq). Functional enrichment analysis was also performed to interpret biological significance.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using TRIzol® Reagent following the manufacturer’s protocol. RNA quality was assessed via 5300 Bioanalyser and NanoDrop ND-2000, with only high-quality RNA (OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) used for sequencing library construction.
RNA-seq libraries were prepared at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. using the Illumina® Stranded mRNA Prep, Ligation protocol. PolyA-selected mRNA was fragmented, reverse-transcribed into cDNA, end-repaired, and adapter-ligated, followed by PCR amplification and size selection (300 bp). Libraries were sequenced on the NovaSeq X Plus platform.

tag: tissue

value: Lung

value: epithelial cell

value: NDV, 24h


title: Mouse ovary, 0hr post-hCG (ABC)

description:
Library name: Sample 1 (0h)
10X Genomics

tag: strain

tag: Sex

value: ABC


title: SMC, 5d DSS, Intestine, biol. rep. 1

description: Library name: 62

value: Intestine

value: WT

value: 5d DSS


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 2

description: Library name: 61

value: Endothelial Cells


title: NoMet_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003599_E10

description:
Library name: TC00003599_E10
TC00003599_E10

value: 24h exposure of 0.865 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

value: OK


title: A549, NDV, 24h, rep2

description: Library name: NDV_24h_2


title: AD-3

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
Samples were demultiplexed using bcl2fastq Conversion Software (Illumina, San Diego, CA)
FASTQ files were filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic]. Transcript-level mapping and quantification were performed by Salmon using the mouse transcriptome database (Gencode version M32). Flags -seqBias and -gcBias were applied during mapping to correct systematic biases commonly present in batch RNA-seq data. Quality of RNA-seq, mapping and quantification was assessed using FastQC (Babraham Bioinformatics, UK) and MultiQC tools
Gene-level quantification and annotation were done using Tximeta utility. Gene count matrices were normalized and differential expression analysis were done in DESeq2.
Assembly: GRCm39/Gencode M32
Supplementary files format and content: tab-delimited text file includes Salmon aligner quantification.
Supplementary files format and content: Columns: Name — This is the name of the target transcript provided in the input transcript database (FASTA file). Length —the length of the target transcript in nucleotides. EffectiveLength —the computed effective length of the target transcript. It takes into account all factors being modeled that will effect the probability of sampling fragments from this transcript, including the fragment length distribution and sequence-specific and gc-fragment bias. TPM —salmon’s estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads —salmon’s estimate of the number of reads mapping to each transcript that was quantified.

source_name: hippocampus

growth_protocol: PSAPP-transgenic (Tg) mice were used (APPSwePS1d9; The Jackson Laboratory, Bar Harbor, ME, USA). Transgene (TG) negative mice from PSAPP strain were used as controls (WT), C57/BL6J mice were used for control groups. All animal use protocols (#20-030) were approved by the Veterans Administration San Diego Healthcare System Institutional Animal Care and Use Committee (IACUC) before procedures were performed. Mice were housed under normal conditions with a sufficient supply of water and food.

extract_protocol:
Mice were perfused with ice cold saline and the hippocampal tissue was dissected and stored in -80 before RNA extraction. Total RNA was extracted and assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used.
RNA sequencing libraries were generated using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). 500 ng of RNA was used for each sample and processed following manufacturer’s instructions.
libraries were multiplexed and sequenced with 100 basepair (bp) Paired End reads (PE100) to a depth of approximately 25 millionreads per sample on an Illumina NovaSeq 6000.

treatment_protocol: 6-month-old PSAPP mice were used for SynCav1 delivery, considering that impaired long-term memory was already detected by this age [20]. TG negative, and PSAPP mice were allocated to 3 groups randomly: WT-Sham, PSAPP-Sham, and PSAPP-SynCav1 to receive hippocampal stereotactic injections of either AAV9-SynCav1 viral vector or sham surgery. WT control sham surgery received a needle path at same coordinates at 6 m. For transcriptome analyses, either SynRFP or SynCav1 was delivered to the hippocampus to correct for potential AAV9 effects on gene expression

value: hippocampus

value: PSAPP

value: Ctrl virus


title: AD-2


title: A549, NDV, 24h, rep1

description: Library name: NDV_24h_1


title: Mouse ovary, 4hr post-hCG (ABC)

description:
Library name: Sample 3 (4h)
10X Genomics

value: Ovary

value: Female

tag: age

value: 6-12 weeks old

value: human chorionic gonadotropin (hCG)

tag: batch


title: Endothelial Cells, 5d DSS, Intestine, biol. rep. 1

description: Library name: 60

tag: cell type

tag: genotype


title: NoMet_daidzein_D7802_4_3.73uM_TC00003599_D11

description:
Library name: TC00003599_D11
TC00003599_D11

tag: cell line

tag: treatment

value: 24h exposure of 3.73 uM of Daidzein

value: Daidzein


title: NoMet_transstilbene_139939_3_0.865uM_TC00003599_D10

description:
Library name: TC00003599_D10
TC00003599_D10

value: 24h exposure of 0.865 uM of trans-Stilbene

tag: media

tag: chemical name

value: trans-Stilbene


title: 22RV1_T7_REP2

description:
T7 Timepoint Replicate 2
22Rv1 Parental


title: 22RV1_T0

description:
T0 Timepoint
22Rv1 Parental


title: Chlamydomonas_Nanopore_dRNAseq

data_processing:
raw signals were basecalled using Guppy (v6.3.7) with default parameters and converted into fastq format
Reads that passed the quality threshold (7) and had a length greater than 25bp were then aligned to the reference genome using Minimap2 (v2.22-r1101)
Nanopolish44 (v0.13.2) eventalign module was used to align raw signals to 5mer bases with the parameter settings "--scale-events --samples --signal-index".
sam2tsv was used to extract bases quality and alignment results for each read from bam files
In-house python scripts were used to extract and organize current features and base quality features for each DRACN motif within each read.
These features were then used as inputs for SingleMod for training or prediction.
Assembly: mm10, TAIR10, Creinhardtii_281_v5.0
Supplementary files format and content: tab-delimited text file, quantification of m6A in all As with coverage >= 15.
Supplementary files format and content: tab-delimited text file, methylation rate of all As in DRACN motifs predicted by SingleMod

value: cells


title: ADCAV-4


title: A549, Mock, 24h, rep3

description: Library name: Mock_24h_3

value: Lung

value: epithelial cell

value: Mock, 24h


title: NoMet_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003599_D09

description:
Library name: TC00003599_D09
TC00003599_D09

value: 24h exposure of 3.73 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

tag: chemical sample_id

tag: chemical concentration


title: B-Cell, 5d DSS, Intestine, biol. rep. 3

description: Library name: 59

value: Intestine

value: B-Cell

value: WT

value: 5d DSS


title: A549, Mock, 24h, rep2

description: Library name: Mock_24h_2


title: ADCAV-3

value: hippocampus

value: PSAPP


title: NoMet_transstilbene_139939_6_26.1uM_TC00003599_C10

description:
Library name: TC00003599_C10
TC00003599_C10

value: 24h exposure of 26.1 uM of trans-Stilbene

tag: dose level

tag: exposure time

value: OK


title: AD-1

value: Ctrl virus


title: B-Cell, 5d DSS, Intestine, biol. rep. 1

description: Library name: 57


title: B-Cell, 5d DSS, Intestine, biol. rep. 2

description: Library name: 58


title: NoMet_transstilbene_139939_8_100uM_TC00003599_C12

description:
Library name: TC00003599_C12
TC00003599_C12

value: 24h exposure of 100 uM of trans-Stilbene

value: trans-Stilbene

tag: assay plate

tag: assay plate_well


title: A549, NDV, 18h, rep3

description: Library name: NDV_18h_3

tag: tissue

value: Lung

value: NDV, 18h


title: A549, Mock, 24h, rep1

description: Library name: Mock_24h_1

value: epithelial cell

value: Mock, 24h


title: Myeloid Cell, 5d DSS, Intestine, biol. rep. 1

description: Library name: 54

value: Myeloid Cell


title: WT-2

value: Needle pass sham surgery


title: A549, NDV, 18h, rep2

description: Library name: NDV_18h_2


title: NoMet_daidzein_D7802_3_0.865uM_TC00003599_C09

description:
Library name: TC00003599_C09
TC00003599_C09

value: 24h exposure of 0.865 uM of Daidzein

value: VM7Luc4E2 Assay Medium

value: Daidzein

tag: sample qc_issue


title: Myeloid Cell, 5d DSS, Intestine, biol. rep. 2

description: Library name: 55

value: Intestine

value: WT

value: 5d DSS


title: ADCAV-1

value: hippocampus

value: PSAPP


title: A549, NDV, 18h, rep1

description: Library name: NDV_18h_1


title: NoMet_transstilbene_139939_7_53.5uM_TC00003599_B12

description:
Library name: TC00003599_B12
TC00003599_B12

value: 24h exposure of 53.5 uM of trans-Stilbene

value: OK


title: A549, Mock, 18h, rep3

description: Library name: Mock_18h_3

value: Mock, 18h


title: Neutrophil, 5d DSS, Intestine, biol. rep. 3

description: Library name: 53

value: Neutrophil


title: WT-1


title: NoMet_daidzein_D7802_8_100uM_TC00003599_B11

description:
Library name: TC00003599_B11
TC00003599_B11

value: 24h exposure of 100 uM of Daidzein


title: A549, Mock, 18h, rep2

description: Library name: Mock_18h_2

value: Lung

value: epithelial cell


title: NoMet_daidzein_D7802_7_53.5uM_TC00003599_C11

description:
Library name: TC00003599_C11
TC00003599_C11

value: 24h exposure of 53.5 uM of Daidzein


title: ADCAV-2


title: WT-3

value: Needle pass sham surgery


title: D4M-3A_NfkbizKO_3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v22.0.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

growth_protocol: D4M-3A cells were maintained in RPMI-1640 medium supplemented with 10% FCS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, Cat. 79306), followed by DNase I digestion to remove contaminating DNA. 1.2 µg of total RNA was used for the construction of sequencing libraries.
Total RNA was isolated using Qiazol. Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Total RNA (RIN>8) was sent to Novogene (Cambridge, UK) for library preparation and sequencing (PE150) on a NovaSeq 6000 (Illumina).

value: melanoma cells

value: NFKBIZ knock out


title: A549, Mock, 18h, rep1

description: Library name: Mock_18h_1


title: NoMet_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003599_B10

description:
Library name: TC00003599_B10
TC00003599_B10

value: 24h exposure of 0.093 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben


title: Myeloid Cell, 5d DSS, Intestine, biol. rep. 3

description: Library name: 56

value: Intestine

value: Myeloid Cell

value: WT

value: 5d DSS


title: Neutrophil, 5d DSS, Intestine, biol. rep. 2

description: Library name: 52


title: SMC, 5d DSS, Intestine, biol. rep. 2

description: Library name: 63

value: SMC


title: Neutrophil, 5d DSS, Intestine, biol. rep. 1

description: Library name: 51


title: A549, NDV, 12h, rep3

description: Library name: NDV_12h_3

value: NDV, 12h


title: NoMet_DMSO_0_0uM_TC00003599_B09

description:
Library name: TC00003599_B09
TC00003599_B09

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

value: OK


title: NoMet_DMSO_0_0uM_TC00003599_A12

description:
Library name: TC00003599_A12
TC00003599_A12


title: D4M-3A_NfkbizKO_2


title: T-Cell, 5d DSS, Intestine, biol. rep. 3

description: Library name: 50

value: T-Cell


title: NoMet_transstilbene_139939_1_0.001uM_TC00003599_A11

description:
Library name: TC00003599_A11
TC00003599_A11

value: 24h exposure of 0.001 uM of trans-Stilbene

value: trans-Stilbene


title: T-Cell, 5d DSS, Intestine, biol. rep. 1

description: Library name: 48


title: NoMet_DMSO_0_0uM_TC00003599_A10

description:
Library name: TC00003599_A10
TC00003599_A10


title: A549, NDV, 12h, rep2

description: Library name: NDV_12h_2

value: Lung

value: epithelial cell


title: T-Cell, 5d DSS, Intestine, biol. rep. 2

description: Library name: 49


title: A549, NDV, 12h, rep1

description: Library name: NDV_12h_1


title: A549, Mock, 12h, rep3

description: Library name: Mock_12h_3

value: Mock, 12h


title: D4M-3A_Ctrl_1

value: melanoma cells

value: Ctrl


title: D4M-3A_Ctrl_2


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003599_A09

description:
Library name: TC00003599_A09
TC00003599_A09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

value: VM7Luc4E2 Assay Medium


title: EC, 5d DSS, Intestine, biol. rep. 3

description: Library name: 47

value: Intestine

value: EC

value: WT

value: 5d DSS


title: A549, Mock, 12h, rep2

description: Library name: Mock_12h_2


title: EC, 5d DSS, Intestine, biol. rep. 2

description: Library name: 46


title: A549, Mock, 12h, rep1

description: Library name: Mock_12h_1


title: L144162

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
10x Genomics
L144162

data_processing:
The barcode processing, gene counting, and aggregation were done using Cellranger version 7.1.0
Ambient RNA was removed using cellblender, doublet were removed using scrublet
Removed cells with less than 200 genes
Assembly: GRCm39.109
Supplementary files format and content: h5ad files containing count matrix and meta information for homeostatic and fibrotic condition

source_name: Fibrotic-like cell ratio periportal organoids, grown 18 days (LT) scRNAseq Repeat1

growth_protocol: Periportal assembloids are produced by rocking 1000 dissociated cholangiocytes, 250 or 2500 portal mesenchymal cells and 10 hepatocyte organoids for up to 24hrs in low attachment plate on a shaker (0.5ml of media) and then seeded in matrigel for the following 7 or 18 (long term, LT) days. The experiment was scaled up 50 times for this scRNAseq material.

extract_protocol:
The assembloids or organoids were dissociated to single cells using TrypLE 1x for 10min at 37°C. The cells were resuspended in PBS with 0.04% BSA, 0.2U/μL RNAse inhibitor (Merck, #3335399001) and 10μM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503) in BSA-coated tubes. The cells were filtered with 100 μm strainer, cell suspensions (1 000 – 20 000) were loaded into Chromium Next GEM ChipG and processed as specified in manufacturer’s instructions.
Single-cell RNA-Seq libraries were prepared using Single Cell 3ʹ v3.1 Gel Bead kit (10X Genomics) as per manufacturer’s instructions

treatment_protocol: Grown in the MM media for 7 or 18 (long term, LT) days; MM media was first described in Cordero-Espinoza et al., 2021, and consists of AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165), supplemented with WNT CM (30%) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503). EM cholangiocyte media was described previously (Huch et al., 2013) and consist of AdDMEM/F12 medium containing 1% HEPES, 1% Penicillin/Streptomycin, Glutamax, 1x B27 and 1.25 mM N-acetylcysteine supplemented with 10 nM gastrin (Merck/Sigma, #G9145), 50 ng/mL mEGF (ThermoFisher, #PMG8043), 5% RSPO1 conditioned medium (homemade), 100 ng/mL FGF10 (Peprotech, #100-26), 10 mM nicotinamide (Merck/Sigma, #N0636) and 50 ng/mL HGF (Peprotech, #100-39). HM-Wnt hepatocyte organoid media is described in this study as the previously published media (Hu et al., 2018) supplemented with 30% Wnt conditioned medium. The full composition contains AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165) –referred to as Basal medium–, which was further supplemented with 10 nM gastrin (Merck/Sigma, #G9145), 50 ng/mL mEGF (ThermoFisher, #PMG8043), 15% RSPO1 conditioned medium (homemade), 100 ng/mL FGF10 (Peprotech, #100-2), 50 ng/mL FGF7 (Peprotech, #100-19-50), 10 mM nicotinamide (Merck/Sigma, #N0636), 25 ng/mL HGF (Peprotech, #100-39), 3 μMCHIR9902 (Tocris, #4423), 1 μMA83-01(Tocris, #2939) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503), 30% WNT3a conditioned medium (WntCM) (homemade).

value: Liver

value: Primary

value: Cholangiocytes (nuclear tdTomato), Hepatocytes (WT), Mesenchyme (nuclear EGFP)

tag: mouse background

tag: mouse strain_for_cholangiocytes

tag: mouse strain_for_mesenchymal_cells

tag: time

value: day18 of culture


title: EC, 5d DSS, Intestine, biol. rep. 1

description: Library name: 45

tag: cell type

tag: genotype


title: D4M-3A_NfkbizKO_1

tag: cell line

value: NFKBIZ knock out


title: A549, NDV, 6h, rep3

description: Library name: NDV_6h_3

tag: treatment

value: NDV, 6h


title: Met_DMSO_0_0uM_TC00003597_H11

description:
Library name: TC00003597_H11
TC00003597_H11

value: 0.5% DMSO vehicle control

tag: media

tag: chemical name

value: DMSO

value: 0 uM

value: OK


title: D4M-3A_Ctrl_3

value: melanoma cells

value: Ctrl


title: B-Cell, 2d DSS, Blood, biol. rep. 4

description: Library name: 44

value: Blood

value: B-Cell

value: 2d DSS


title: B-Cell, 2d DSS, Blood, biol. rep. 3

description: Library name: 43

value: WT


title: Met_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003597_H09

description:
Library name: TC00003597_H09
TC00003597_H09

value: 24h exposure of 3.73 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

tag: chemical sample_id

tag: chemical concentration


title: A549, NDV, 6h, rep1

description: Library name: NDV_6h_1

value: Lung

value: epithelial cell


title: L144166

description:
10x Genomics
L144166

source_name: Matched controls of Msc, CholOrg and HepOrg grown separately in MM media Repeat3

value: Liver

value: Primary

value: Cholangiocytes (nuclear tdTomato), Hepatocytes (WT), Mesenchyme (nuclear EGFP)

value: day 7 of culture


title: Met_daidzein_D7802_5_11uM_TC00003597_G12

description:
Library name: TC00003597_G12
TC00003597_G12

value: 24h exposure of 11 uM of Daidzein

value: Daidzein

value: 11 uM

tag: dose level

tag: exposure time


title: L144165

description:
10x Genomics
L144165

source_name: Fibrotic-like cell ratio periportal organoids, scRNAseq Repeat3


title: L144164

description:
10x Genomics
L144164

source_name: Healthy cell ratio periportal organoids, scRNAseq Repeat3


title: Met_DMSO_0_0uM_TC00003597_G11

description:
Library name: TC00003597_G11
TC00003597_G11

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: assay plate

tag: assay plate_well

value: OK


title: B-Cell, 2d DSS, Blood, biol. rep. 2

description: Library name: 42

tag: tissue

value: Blood

value: B-Cell

value: WT

value: 2d DSS


title: B-Cell, 2d DSS, Blood, biol. rep. 1

description: Library name: 41


title: L144160

description:
10x Genomics
L144160

source_name: Other cell controls grown separately; Msc grown on plastic in MM media, CholOrg grown in expansion media (EM) and HepOrg grown in HM-Wnt media, Repeat 1

tag: mouse background


title: Met_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003597_G10

description:
Library name: TC00003597_G10
TC00003597_G10

value: 24h exposure of 0.865 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben

tag: sample qc_issue


title: Met_daidzein_D7802_7_53.5uM_TC00003597_H12

description:
Library name: TC00003597_H12
TC00003597_H12

value: 24h exposure of 53.5 uM of Daidzein


title: L144161

description:
10x Genomics
L144161

source_name: Healthy cell ratio periportal organoids, grown 18 days (LT) scRNAseq Repeat1

value: Liver

value: Primary

value: Cholangiocytes (nuclear tdTomato), Hepatocytes (WT), Mesenchyme (nuclear EGFP)

tag: mouse strain_for_cholangiocytes

tag: mouse strain_for_mesenchymal_cells

value: day18 of culture


title: A549, Mock, 6h, rep2

description: Library name: Mock_6h_2

value: Lung

tag: cell type

value: epithelial cell

value: Mock, 6h


title: A549, Mock, 6h, rep1

description: Library name: Mock_6h_1


title: Met_daidzein_D7802_4_3.73uM_TC00003597_H10

description:
Library name: TC00003597_H10
TC00003597_H10

value: 24h exposure of 3.73 uM of Daidzein

value: Daidzein


title: L144159

description:
10x Genomics
L144159

source_name: Matched controls of Msc, CholOrg and HepOrg grown separately in MM media Repeat2

tag: time

value: day 7 of culture


title: A549, NDV, 6h, rep2

description: Library name: NDV_6h_2

tag: cell line

value: NDV, 6h


title: L144167

description:
10x Genomics
L144167

source_name: Other cell controls grown separately; Msc grown on plastic in MM media, CholOrg grown in expansion media (EM) and HepOrg grown in HM-Wnt media, Repeat 2


title: Tree Swallow, Male 7

city: Bloomington

first: Kimberly

middle: A

last: Rosvall

state: IN

address: Dept of Biology, Indiana Univ., 1001 E. 3rd St, Jordan Hall

institute: Indiana University

data_processing:
Sequence reads were trimmed for adapters and low quality bases using Trimmomatic v0.36 (Bolger et al. 2014) and fastp v0.20.1 (Chen et al. 2019).
Transcriptomes from species-specific reads were assembled using Trinity v2.13.2 (Grabherr et al. 2011)
Assembled transcripts were aligned to the zebra finch proteome using tblastn v2.2.9 (Gertz et al. 2006)
Transcript abundance was quantified using Bowtie2 v2.4.4 (Langmead and Salzberg 2012)
Reads were sorted and indexed using Samtools v1.10 (Li et al. 2009)
Orthologous reads were assigned to zebra finch proteins using featureCounts from the Subread package v2.02z (Liao et al. 2014)
Assembly: GCF_003957565.2_bTaeGut1.4.pri_protein.faa (Rhie et al. 2021)
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample

organism: Tachycineta bicolor

source_name: Ventromedial telencephalon

extract_protocol:
RNA was isolated from brain tissue using a phenol chloroform extraction
TruSeq Stranded mRNA HT sample preparation kit (Illumina)

treatment_protocol: Nesting strategies included obligate cavity nesting, facultative cavity nesting, and open cup nesting. Adult females and males were sampled during territorial establishment and nest-building phases, before egg laying, in the Midwestern United States

tag: family

value: Hirundinidae

value: Ventromedial telencephalon

tag: treatment

value: Obligate cavity nester


title: Met_DMSO_0_0uM_TC00003597_G09

description:
Library name: TC00003597_G09
TC00003597_G09

value: 0.5% DMSO vehicle control

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: DMSO

value: 0 uM

value: OK


title: Myeloid Cell, 2d DSS, Blood, biol. rep. 4

description: Library name: 40

value: Blood

value: Myeloid Cell

tag: genotype

value: WT

value: 2d DSS


title: Met_ethyl4hydroxybenzoate_111988_2_0.093uM_TC00003597_F12

description:
Library name: TC00003597_F12
TC00003597_F12

value: 24h exposure of 0.093 uM of Ethylparaben

value: Ethylparaben

tag: chemical sample_id

tag: chemical concentration

tag: dose level


title: Myeloid Cell, 2d DSS, Blood, biol. rep. 3

description: Library name: 39


title: A549, Mock, 6h, rep3

description: Library name: Mock_6h_3

value: Lung

value: epithelial cell

value: Mock, 6h


title: Tree Swallow, Male 5

value: Hirundinidae


title: Myeloid Cell, 2d DSS, Blood, biol. rep. 2

description: Library name: 38


title: L144158

description:
10x Genomics
L144158

source_name: Fibrotic-like cell ratio periportal organoids, scRNAseq Repeat2

value: Liver

value: Primary

value: Cholangiocytes (nuclear tdTomato), Hepatocytes (WT), Mesenchyme (nuclear EGFP)

value: day 7 of culture


title: Myeloid Cell, 2d DSS, Blood, biol. rep. 1

description: Library name: 37

source_name: Blood


title: Met_transstilbene_139939_5_11uM_TC00003597_F11

description:
Library name: TC00003597_F11
TC00003597_F11

value: 24h exposure of 11 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene

value: 11 uM

tag: exposure time

tag: assay plate

tag: assay plate_well


title: L124779

description:
10x Genomics
L124779

source_name: Matched controls of Msc, CholOrg and HepOrg grown separately in MM media Repeat1

tag: tissue

tag: mouse background


title: Neutrophil, 2d DSS, Blood, biol. rep. 4

description: Library name: 36

value: Blood

value: Neutrophil


title: Tree Swallow, Male 3

value: Ventromedial telencephalon

value: Obligate cavity nester


title: Met_transstilbene_139939_3_0.865uM_TC00003597_F10

description:
Library name: TC00003597_F10
TC00003597_F10

value: 24h exposure of 0.865 uM of trans-Stilbene

tag: sample qc_issue

value: OK


title: Tree Swallow, Male 4


title: L124778

description:
10x Genomics
L124778

source_name: Fibrotic-like cell ratio periportal organoids, scRNAseq Repeat1

tag: cell type

tag: mouse strain_for_cholangiocytes

tag: mouse strain_for_mesenchymal_cells


title: Neutrophil, 2d DSS, Blood, biol. rep. 3

description: Library name: 35

value: WT

value: 2d DSS


title: Met_daidzein_D7802_1_0.001uM_TC00003597_F09

description:
Library name: TC00003597_F09
TC00003597_F09

tag: cell line

value: 24h exposure of 0.001 uM of Daidzein

value: Daidzein


title: Tree Swallow, Male 2

tag: family

value: Hirundinidae

tag: treatment


title: L124777

description:
10x Genomics
L124777

source_name: Healthy cell ratio periportal organoids, scRNAseq Repeat1

value: Liver

value: Primary

value: Cholangiocytes (nuclear tdTomato), Hepatocytes (WT), Mesenchyme (nuclear EGFP)

tag: time


title: Neutrophil, 2d DSS, Blood, biol. rep. 2

description: Library name: 34

tag: genotype


title: Met_daidzein_D7802_6_26.1uM_TC00003597_E12

description:
Library name: TC00003597_E12
TC00003597_E12

value: 24h exposure of 26.1 uM of Daidzein

tag: media

value: VM7Luc4E2 Assay Medium

tag: chemical name

tag: chemical sample_id


title: Tree Swallow, Male 1


title: Neutrophil, 2d DSS, Blood, biol. rep. 1

description: Library name: 33


title: Fibrosis-like assembloid 2.5 weeks Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146587

data_processing:
alignment  of reads and and read counting was done using STAR
TPM were calculated from raw counts using a custom R script
Assembly: GRCm39.109
Supplementary files format and content: tsv file with raw count and TPM values

source_name: Liver

growth_protocol: Periportal assembloids are produced by rocking 1000 dissociated cholangiocytes, 250 or 2500 portal mesenchymal cells and 10 hepatocyte organoids for up to 24hrs in low attachment plate on a shaker (0.5ml of media) and then seeded in matrigel for the following 7 or 18 days (2.5 weeks, long term). HepOrg are grown by plating primary hepatocytes in HM-Wnt media, and then if indicated - switching HepOrg at passage 2 to MM media.

extract_protocol:
Collected in PicoPure Extraction buffer and processed according to PicoPure RNA isolation protocol manufacturer's instructions (ThermoFisher, #KIT0204); RNA eluted in H2O
Illumina Nextera according to manufacturer's instructions.

treatment_protocol: Grown in the MM media for 7days, 14 days or 18 (long term, LT) days; MM media was first described in Cordero-Espinoza et al., 2021, and consists of AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165), supplemented with WNT CM (30%) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503). HM-Wnt hepatocyte organoid media is described in this study as the previously published media (Hu et al., 2018) supplemented with 30% Wnt conditioned medium. The full composition contains AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165) –referred to as Basal medium–, which was further supplemented with 10 nM gastrin (Merck/Sigma, #G9145), 50 ng/mL mEGF (ThermoFisher, #PMG8043), 15% RSPO1 conditioned medium (homemade), 100 ng/mL FGF10 (Peprotech, #100-2), 50 ng/mL FGF7 (Peprotech, #100-19-50), 10 mM nicotinamide (Merck/Sigma, #N0636), 25 ng/mL HGF (Peprotech, #100-39), 3 μMCHIR9902 (Tocris, #4423), 1 μMA83-01(Tocris, #2939) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503), 30% WNT3a conditioned medium (WntCM) (homemade).

value: periportal assembloids

tag: background strain

value: MM Media

tag: time of_culture

value: 18 days


title: Tree Swallow, Female 13

value: Ventromedial telencephalon


title: T-Cell, 2d DSS, Blood, biol. rep. 4

description: Library name: 32

value: Blood

value: T-Cell


title: Met_transstilbene_139939_1_0.001uM_TC00003597_E11

description:
Library name: TC00003597_E11
TC00003597_E11

value: 24h exposure of 0.001 uM of trans-Stilbene

value: trans-Stilbene

tag: chemical concentration

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

value: OK


title: Met_bestradiol_E2758_1_0.0001uM_TC00003597_E10

description:
Library name: TC00003597_E10
TC00003597_E10

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: sample qc_issue


title: Fibrosis-like assembloid 2.5 weeks Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146585

tag: tissue

tag: cell type

value: WT


title: Fibrosis-like assembloid 2.5 weeks Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146586

tag: cell line


title: L144157

description:
10x Genomics
L144157

source_name: Healthy cell ratio periportal organoids, scRNAseq Repeat2

tag: mouse background

tag: mouse strain_for_cholangiocytes

tag: mouse strain_for_mesenchymal_cells

value: day 7 of culture


title: Met_transstilbene_139939_7_53.5uM_TC00003597_E09

description:
Library name: TC00003597_E09
TC00003597_E09

tag: treatment

value: 24h exposure of 53.5 uM of trans-Stilbene

tag: media


title: Homeostasis assembloid 2.5 weeks Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146584

value: Liver

value: Primary

tag: genotype


title: Tree Swallow, Female 12

tag: family

value: Hirundinidae

value: Obligate cavity nester


title: Tree Swallow, Female 8


title: T-Cell, 2d DSS, Blood, biol. rep. 3

description: Library name: 31

value: 2d DSS


title: T-Cell, 2d DSS, Blood, biol. rep. 2

description: Library name: 30


title: T-Cell, 2d DSS, Blood, biol. rep. 1

description: Library name: 29


title: Met_ethyl4hydroxybenzoate_111988_8_100uM_TC00003597_D11

description:
Library name: TC00003597_D11
TC00003597_D11

value: 24h exposure of 100 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

tag: chemical name

value: Ethylparaben

tag: chemical sample_id


title: Tree Swallow, Female 5

value: Ventromedial telencephalon


title: Met_daidzein_D7802_2_0.093uM_TC00003597_D12

description:
Library name: TC00003597_D12
TC00003597_D12

value: 24h exposure of 0.093 uM of Daidzein

value: Daidzein

tag: chemical concentration

tag: dose level


title: Homeostasis assembloid 2.5 weeks Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146583

value: periportal assembloids

tag: background strain

value: MM Media

tag: time of_culture

value: 18 days


title: B-Cell, 2d DSS, Bone Marrow, biol. rep. 4

description: Library name: 28

source_name: Bone Marrow

value: Bone Marrow

value: B-Cell

value: WT


title: Met_ethyl4hydroxybenzoate_111988_1_0.001uM_TC00003597_D10

description:
Library name: TC00003597_D10
TC00003597_D10

value: 24h exposure of 0.001 uM of Ethylparaben

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: sample qc_issue

value: OK


title: Fibrosis-like assembloid 1 week Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146581

tag: tissue

value: Liver

tag: cell line

value: Primary

tag: cell type

value: 7 days


title: Tree Swallow, Female 4

value: Hirundinidae

tag: treatment

value: Obligate cavity nester


title: Met_bestradiol_E2758_1_0.0001uM_TC00003597_D09

description:
Library name: TC00003597_D09
TC00003597_D09

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: media

value: VM7Luc4E2 Assay Medium


title: Tree Swallow, Female 3

value: Ventromedial telencephalon


title: Fibrosis-like assembloid 1 week Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146580

tag: genotype


title: B-Cell, 2d DSS, Bone Marrow, biol. rep. 2

description: Library name: 26

value: 2d DSS


title: Met_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003597_C12

description:
Library name: TC00003597_C12
TC00003597_C12

value: 24h exposure of 26.1 uM of Ethylparaben

value: Ethylparaben


title: Tree Swallow, Female 7

tag: family


title: B-Cell, 2d DSS, Bone Marrow, biol. rep. 1

description: Library name: 25


title: Met_transstilbene_139939_6_26.1uM_TC00003597_C11

description:
Library name: TC00003597_C11
TC00003597_C11

value: 24h exposure of 26.1 uM of trans-Stilbene

tag: chemical name

value: trans-Stilbene


title: Fibrosis-like assembloid 1 week Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146579

value: periportal assembloids

value: MM Media


title: Myeloid Cell, 2d DSS, Bone Marrow, biol. rep. 4

description: Library name: 24

value: Bone Marrow

value: Myeloid Cell

value: WT


title: humanized mouse liver, AAV mixture, 1x10e12, rep 1

city: Seattle

first: Pavitra

last: Roychoudhury

state: Washington

address: 1100 Fairview Ave N, PO Box 19024, E5-110

institute: University of Washington

description:
Library name: Sample2
sequencing strategy was 28 x 8 x 494 (Read1 x i7 index x Read 2)

data_processing:
Raw bcls were demultiplexed using bcl-convert (v 4.0.3, Illumina) and count matrices were generated using CellRanger (v7.1.0, 10X Genomics) against human (GRCh38) and mouse (mm10) references separately. The resulting count matrices were processed using Seurat v5.0.1, and human vs mouse cells were distinguished based on the number of reads mapping to each reference transcriptome.
Assembly: GRCh38 and mm10
Supplementary files format and content: filtered count matrices from cell ranger are provided

organism:
Homo sapiens
Mus musculus

growth_protocol: 6–10 week old NSG-PiZ mice were humanized by administration of 1E6 primary human hepatocytes following pretreatment with the hepatotoxin monocrotaline (MCT, 50 mg/kg) according to the method of Borel et al and modifications of Colon-Thillet et al.

extract_protocol:
Mice were perfused with 20mL perfusion buffer (1X HBSS w/o Ca and Mg, 0.5mM EDTA, 25mM HEPES) followed by 20mL of digestion buffer (1X HBSS with Ca and Mg, 25mM HEPES, 1mg/mL collagenase type IV). Livers were then dissociated in 5mL digestion buffer before passing through a 70mm cell strainer. Cell were centrifuged, washed and resuspended in 1X HBSS with Ca and Mg, and counted.
2,000 cells from each of 8 animals (4 control, 4 AAV treated) were pooled by sample type (control or treated) to create 2 libraries with 8,000 cells each. Cells were prepared for sequencing with the 10X Genomics 3' Gene Expression Kit 3.1 following the manufacturer's protocol (CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D) precisely.

treatment_protocol: Treatment group mice were transduced with mixture of AAV8 (2E11 vgs/mouse), AAV9 (2E11 vgs/mouse), AAVrh10 (2E11 vgs/mouse), AAVDJ/8 (2E11 vgs/mouse) and AAV.LK03 (2E11 vgs/mouse) vectors for a total dose of 1E12 vgs by retroorbital IV injection. The AAVs carried a sc AAV genome and a barcoded GFP gene or mCherry specific to each serotype.

value: Liver

value: primary human hapatocytes

value: AAV


title: Met_transstilbene_139939_8_100uM_TC00003597_C10

description:
Library name: TC00003597_C10
TC00003597_C10

value: 24h exposure of 100 uM of trans-Stilbene

tag: chemical sample_id

value: OK


title: Myeloid Cell, 2d DSS, Bone Marrow, biol. rep. 3

description: Library name: 23


title: Homeostasis assembloid 2.5 weeks Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146582

value: Primary

value: 18 days


title: humanized mouse liver, no AAV, rep 1

description:
Library name: Sample1
sequencing strategy was 28 x 8 x 494 (Read1 x i7 index x Read 2)

value: primary human hepatocytes

value: Control


title: Homeostasis assembloid 1 week Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146577

value: 7 days


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, G1 phase, biorep 3

city: Raleigh

first: Emily

last: Markham

address: 851 Main Campus Dr

institute: NCSU

description: Library name: B73_seminal_G1_BR3

library_source: genomic

data_processing:
Sequencing data from both primary and seminal root types were merged for each biorep in the processed files. For example, primary root biorep 1 was merged with seminal root biorep 1.
Sequenced reads were trimmed using trimmomatic v0.39, with the parameters -phred33 -validatePairs and ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20
Trimmed reads were mapped to the genome assembly using bowtie2 v2.5.1, with the parameter --very-sensitive
Duplicate reads were removed using sambamba v1.0.0, with default parameters. Reads that were not properly paired or had a MAPQ value less than 6 were removed using samtools v1.9, with parameters -bf 0x2 and-q 6. Reads that mapped to scaffolds or plastids were also removed.
Spikes in the data were removed by calculated coverage in non-overlapping 10kb bins and the 0.25% highest coverage bins were removed. A low mappability drop list was created to remove regions of the genome where low read coverage could be due to poor inherent refrence genome mappability.
Read coverage was calculated in the remaining non-overlapping 10kb bins and normalized to 1X reads per genomic content (RPGC) using DeepTools bamCoverage with parameters -of bedgraph -bs 10000 --effectiveGenomeSize 2071945143 --normalizeUsing RPGC --ignoreDuplicates --extendReads, and with a --blackListFileName bed file that included the 0.25% spikes in coverage and low mappability regions from previous step. The effective genome size was calculated by subtracting the number of bp in the --blackListFileName file from the number of bp in the chromosomal fasta file.
The ratio of S coverage to G1 coverage for each biological replicate was calculated for each bin.
The S/G1 ratio data in non-overlapping 10kb bins was haar wavelet smoothed at level 2.
Assembly: B73v5, Zm-B73-REFERENCE-NAM-5.0, see https://maizegdb.org/NAM_project
Supplementary files format and content: bigWig

organism: Zea mays

source_name: terminal 1 mm of seminal root tips

growth_protocol: B73 seeds were surface sterilized in 1% NaClO; 0.05% Tween-20, imbibed overnight with stirring and aeration, and surface sterilized again but this time in 0.5% NaClO; 0.05% Tween-20. Seeds were germinated in magenta boxes with paper towels dampened with autoclaved dH2O. Seedlings were grown in a growth chamber for 3 days with constant dim LED light at 28 C.

extract_protocol:
A phenol:cholorform:IAA extraction was used to isolate DNA from each sorted nuclei population.
DNA-seq libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) in combination with NEB Unique Dual Index UMI Adaptors (NEB #E7395S). The libraries were constructed using 100 ng DNA input; the adapter dilution was 1:10 and the size selection protocol for obtaining 350-450 bp sequenceable inserts was followed. The libraries were amplified using 7 PCR cycles. The final average library size ranged from 503-540 bp (353-390 bp sequenceable insert + 150 bp adapters). The libraries were sequenced using the Illumina Novaseq 6000, 150 bp paired end.

treatment_protocol: The 3-day old seedlings were EdU-labeled and the terminal 1 mm of the root tips excised and nuclei isolated. S phase nuclei were collected by fluorescence activated nuclei sorting (FANS) based on their DNA content and EdU incorporation. G1 phase nuclei were collected based on their 2C DNA content and lack of EdU incorporation.

value: terminal 1 mm of seminal root tips

value: flow sorted G1 phase from seminal roots


title: Hepatocytes (isolated) WT Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146572

value: hepatocytes

value: freshly isolated


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, G1 phase, biorep 2

description: Library name: B73_seminal_G1_BR2


title: Met_transstilbene_139939_4_3.73uM_TC00003597_C09

description:
Library name: TC00003597_C09
TC00003597_C09

data_processing:
Read alignment: Each FASTQ file was aligned to the probe sequences in the hWTv2 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Probe counts: Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv2
Supplementary files format and content: aime_prepilot_count_data.csv.gz: A table of probe counts in CSV format, with rows corresponding to TempO-seq probe IDs (see httr_aime_prepilot-probe_manifest.csv file for probe ID mapping information) and columns corresponding to sample IDs.
Supplementary files format and content: httr_aime_prepilot-probe_manifest.csv: For each probe ID listed in the table of probe counts (aime_prepilot_count_data.csv.gz), a corresponding mapping of probe sequence, Entrez ID, and gene symbol are listed.

value: 24h exposure of 3.73 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene

tag: chemical concentration


title: Homeostasis assembloid 1 week Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146578

value: Liver

value: periportal assembloids

value: MM Media

value: WT


title: Myeloid Cell, 2d DSS, Bone Marrow, biol. rep. 1

description: Library name: 21

value: Bone Marrow

value: Myeloid Cell

value: 2d DSS


title: Met_DMSO_0_0uM_TC00003597_B11

description:
Library name: TC00003597_B11
TC00003597_B11

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: dose level

value: OK


title: Met_bestradiol_E2758_1_0.0001uM_TC00003597_B12

description:
Library name: TC00003597_B12
TC00003597_B12

value: 24h exposure of 1e-04 uM of 17beta-Estradiol


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, S phase, biorep 3

description: Library name: B73_seminal_S_BR3

value: terminal 1 mm of seminal root tips

value: flow sorted S phase from seminal roots


title: Myeloid Cell, 2d DSS, Bone Marrow, biol. rep. 2

description: Library name: 22


title: B-Cell, 2d DSS, Bone Marrow, biol. rep. 3

description: Library name: 27

value: B-Cell


title: Neutrophil, 2d DSS, Bone Marrow, biol. rep. 4

description: Library name: 20

value: Neutrophil


title: Homeostasis assembloid 1 week Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146576

value: Primary

tag: background strain

value: 7 days


title: Met_ethyl4hydroxybenzoate_111988_7_53.5uM_TC00003597_B10

description:
Library name: TC00003597_B10
TC00003597_B10

value: 24h exposure of 53.5 uM of Ethylparaben

value: VM7Luc4E2 Assay Medium

value: Ethylparaben


title: HepOrg p2 HMWnt 2 weeks Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146562

value: Liver

value: hepatocyte organoids

value: HM-Wnt Media

value: WT

tag: time of_culture

value: 14 days


title: Hepatocytes (isolated) WT Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146571

value: hepatocytes

value: freshly isolated


title: Neutrophil, 2d DSS, Bone Marrow, biol. rep. 3

description: Library name: 19

value: Bone Marrow

value: 2d DSS


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, S phase, biorep 1

description: Library name: B73_seminal_S_BR1

value: terminal 1 mm of seminal root tips

value: flow sorted S phase from seminal roots


title: Met_DMSO_0_0uM_TC00003597_B09

description:
Library name: TC00003597_B09
TC00003597_B09

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: exposure time

value: OK


title: HepOrg p2 HMWnt 2 weeks Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146561

value: Primary


title: Neutrophil, 2d DSS, Bone Marrow, biol. rep. 1

description: Library name: 17

value: Neutrophil


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, G1 phase, biorep 1

description: Library name: B73_seminal_G1_BR1

value: flow sorted G1 phase from seminal roots


title: Met_transstilbene_139939_2_0.093uM_TC00003597_A12

description:
Library name: TC00003597_A12
TC00003597_A12

value: 24h exposure of 0.093 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene

tag: assay plate


title: Met_daidzein_D7802_3_0.865uM_TC00003597_A11

description:
Library name: TC00003597_A11
TC00003597_A11

value: 24h exposure of 0.865 uM of Daidzein

value: Daidzein

tag: assay plate_well


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, G1 phase, biorep 2

description: Library name: B73_primary_G1_BR2

source_name: terminal 1 mm of primary root tip

value: terminal 1 mm of primary root tip

value: flow sorted G1 phase from primary roots


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, G1 phase, biorep 3

description: Library name: B73_primary_G1_BR3


title: HepOrg p2 HMWnt 2 weeks Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146560

value: Liver

value: hepatocyte organoids

value: HM-Wnt Media

value: WT

value: 14 days


title: T-Cell, 2d DSS, Bone Marrow, biol. rep. 4

description: Library name: 16

value: Bone Marrow

value: T-Cell

value: 2d DSS


title: Met_daidzein_D7802_8_100uM_TC00003597_A10

description:
Library name: TC00003597_A10
TC00003597_A10

value: 24h exposure of 100 uM of Daidzein

tag: sample qc_issue

value: OK


title: HepOrg p2 HMWnt 1 week Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146558

tag: tissue

value: Primary

value: 7 days


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, G1 phase, biorep 1

description: Library name: B73_primary_G1_BR1


title: HepOrg p2 HMWnt 1 week Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146559

tag: cell line


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, S phase, biorep 3

description: Library name: B73_primary_S_BR3

tag: cell type

value: flow sorted S phase from primary roots


title: T-Cell, 2d DSS, Bone Marrow, biol. rep. 3

description: Library name: 15

tag: treatment


title: T-Cell, 2d DSS, Bone Marrow, biol. rep. 2

description: Library name: 14


title: NoMet_ethyl4hydroxybenzoate_111988_3_0.865uM_TC00003594_H12

description:
Library name: TC00003594_H12
TC00003594_H12

value: 24h exposure of 0.865 uM of Ethylparaben

tag: media

value: VM7Luc4E2 Assay Medium

value: Ethylparaben


title: HepOrg p2 HMWnt 1 week Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146557

tag: genotype


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, S phase, biorep 2

description: Library name: B73_primary_S_BR2

value: terminal 1 mm of primary root tip


title: Zea mays B73, seminal root tips (0-1mm) DNA copy number, S phase, biorep 2

description: Library name: B73_seminal_S_BR2

value: terminal 1 mm of seminal root tips

value: flow sorted S phase from seminal roots


title: HepOrg p2 MM 2 weeks Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146556

value: Liver

value: hepatocyte organoids

value: MM Media


title: T-Cell, 2d DSS, Bone Marrow, biol. rep. 1

description: Library name: 13

value: Bone Marrow

value: WT


title: NoMet_daidzein_D7802_5_11uM_TC00003594_H11

description:
Library name: TC00003594_H11
TC00003594_H11

value: 24h exposure of 11 uM of Daidzein

value: Daidzein

value: 11 uM


title: Zea mays B73, primary root tips (0-1mm) DNA copy number, S phase, biorep 1

description: Library name: B73_primary_S_BR1


title: Neutrophil, 2d DSS, Bone Marrow, biol. rep. 2

description: Library name: 18

value: Neutrophil

value: 2d DSS


title: HepOrg p2 MM 2 weeks Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146555

value: Primary

value: 14 days


title: SMC, 2d DSS, Intestine, biol. rep. 4

description: Library name: 12

source_name: Intestine

value: Intestine

value: SMC


title: NoMet_daidzein_D7802_3_0.865uM_TC00003594_H10

description:
Library name: TC00003594_H10
TC00003594_H10

value: 24h exposure of 0.865 uM of Daidzein

value: VM7Luc4E2 Assay Medium

value: OK


title: HepOrg p2 MM 2 weeks Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146554

value: Liver


title: IMR90 ER:Ras +4OHT sin-lncRNA KD rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

data_processing:
Data were aligned to the genome assembly hg19 using Bowtie2 (Langmead & Salzberg, 2012)
Reads in each gene were counted with featureCounts (Liao et al., 2014) with default parameters
Assembly: hg19
Supplementary files format and content: one tab-delimited text matrix including raw counts values of each gene in each sample

growth_protocol: IMR90 cells were groen in DMEM medium (GIBCO), supplemented with 10% fetal bovine serum (GIBCO) and 1x penicillin/streptomycin (Lonza). Cells were maintained at 37 °C in the presence of 5% CO2 and tested for mycoplasma contamination regularly, using the MycoAlert Mycoplasma Detection Kit (Lonza).

extract_protocol:
RNA was extracted using TRI reagent (Sigma), purified and treated with DNAse I using RNAeasy mini Kit (Qiagen)
1μg of RNA polyA+ was used for library preparation at the EMBL genomic core
The libraries were sequenced on Illumina HiSeq 2000 (33×106 reads per sample, 50bp single-end sequencing modality) at the EMBL genomic core

treatment_protocol: Cells were treated with vehicle or 200nM of 4-hydroxy-tamoxifen (4OHT) for three days

tag: sirna

value: sin-lncRNA KD

value: 4-hydroxitamoxifen (4OHT)


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003594_H09

description:
Library name: TC00003594_H09
TC00003594_H09

extract_protocol:
At 24 hours after treatment with condition media, assay plates were removed from the incubator, assay wells were washed twice with 1X phosphate-buffered saline and the final PBS wash was aspirated from each well leaving a residual volume of 10 µL.  Cells were subsequently lysed by adding 10 µL of 2X BioSpyder Enhanced Lysis buffer.  Assay plates were then sealed, agitated for 30 seconds on the stage of a MultiFlo FX washer / dispenser and then placed in a hybridization oven at 37°C for 10 minutes. Plates were then immediately transferred to a -80°C freezer for storage. Plates were subsequently shipped frozen to BioSpyder Technologies (Carlsbad, CA) for analysis with the human whole transcriptome TempO-Seq assay.  The TempO-Seq assay was conducted directly on cell lysates with no RNA extraction step.
Plates containing cell lysates were shipped to BioSpyder, Inc. frozen (on dry ice) using overnight priority shipping. Cell lysates were then analyzed by BioSpyder using the unattenuated TempO-Seq human whole transcriptome version 2 (hWTv2) assay, which includes 22,537 probes covering 19,703 genes. 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv2 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 h. Excess oligos were then removed via nuclease digestion (90 min at 37°C), and hybridized detector oligos were ligated (1 h at 37°C) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured, and 10 µL of each ligation product were transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were pooled into sequencing libraries, distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA). The TempO-seq libraries were sequenced to a target read depth of 3.0x106 mapped reads per sample.

value: 24h exposure of 1e-04 uM of 17beta-Estradiol

tag: chemical name


title: HepOrg p2 MM 1 week Rep3

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146553

value: hepatocyte organoids

value: MM Media

value: WT

value: 7 days


title: IMR90 ER:Ras +4OHT sin-lncRNA KD rep2


title: SMC, 2d DSS, Intestine, biol. rep. 3

description: Library name: 11

data_processing:
Quality Control: cutadapt: --nextseq-trim=30 --minimum-length=10
Adapter Trimming: cutadapt: -a  -A  --minimum-length=10
Mapping: Hisat2 (Standard configuration)
Editing Call: Jacusa2 (Standard configuration)
Assembly: GRCm39 from Ensemble, Mapper: Hisat2 (standard configuration)
Supplementary files format and content: Columns: Library Name, Sequence of Primers used to add barcodes, Number of raw or processed read, Cell Type, Tissue Type, Condition, counts of nucleotides at editing site and calculated editing ratio (%)


title: SMC, 2d DSS, Intestine, biol. rep. 2

description: Library name: 10


title: IMR90 ER:Ras +4OHT sin-lncRNA KD rep1


title: HepOrg p2 MM 1 week Rep2

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146552


title: NoMet_ethyl4hydroxybenzoate_111988_6_26.1uM_TC00003594_G12

description:
Library name: TC00003594_G12
TC00003594_G12

value: 24h exposure of 26.1 uM of Ethylparaben

value: Ethylparaben

tag: chemical sample_id


title: SMC, 2d DSS, Intestine, biol. rep. 1

description: Library name: 9

value: 2d DSS


title: NoMet_bestradiol_E2758_1_0.0001uM_TC00003594_G11

description:
Library name: TC00003594_G11
TC00003594_G11

tag: chemical concentration


title: IMR90 ER:Ras +4OHT SCRAMBLE rep 3

value: siSCR


title: Met_ethyl4hydroxybenzoate_111988_5_11uM_TC00003597_A09

description:
Library name: TC00003597_A09
TC00003597_A09

value: 24h exposure of 11 uM of Ethylparaben

value: 11 uM

tag: dose level


title: HepOrg p2 MM 1 week Rep1

description:
SmartSeq-2
bulk_count_tpm.tsv
library name:
L146551

value: Primary

tag: background strain


title: IMR90 ER:Ras +4OHT SCRAMBLE rep 2


title: B-Cell, 2d DSS, Intestine

description: Library name: 8

value: Intestine

value: B-Cell


title: Myeloid Cell, 2d DSS, Intestine

description: Library name: 7

value: Myeloid Cell


title: NoMet_daidzein_D7802_6_26.1uM_TC00003594_G10

description:
Library name: TC00003594_G10
TC00003594_G10

value: 24h exposure of 26.1 uM of Daidzein

value: VM7Luc4E2 Assay Medium

value: Daidzein

value: OK


title: NoMet_daidzein_D7802_7_53.5uM_TC00003594_G09

description:
Library name: TC00003594_G09
TC00003594_G09

value: 24h exposure of 53.5 uM of Daidzein


title: IMR90 ER:Ras +4OHT SCRAMBLE rep 1

value: 4-hydroxitamoxifen (4OHT)


title: Neutrophil, 2d DSS, Intestine

description: Library name: 6

value: Neutrophil

value: WT


title: NoMet_DMSO_0_0uM_TC00003594_F12

description:
Library name: TC00003594_F12
TC00003594_F12

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM


title: LOX-IMVI_shNFKBIZ_3

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v24.0.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCh38 genome.
Default settings: Reference type = Genome annotated with genes and transcripts; Reference sequence = Homo sapiens (GRCh38); Gene track = Homo sapiens (GRCh38.109)  (Gene); mRNA track = Homo sapiens (GRCh38.109)  (RNA); Use spike-in controls = no; Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0,8; Similarity fraction = 0,8; Global alignment = No; Strand specific = Reverse; Library type = Bulk; Maximum number of hits for a read = 10; Count paired reads as two = No; Ignore broken pairs = Yes; Expression value = TPM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

source_name: LOX-IMVI

growth_protocol: LOX-IMVI cells were maintained in RPMI-1640 medium supplemented with 10% FCS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

value: LOX-IMVI

value: melanoma cells

value: NFKBIZ knock down


title: shJmjd1a plus WT, Day 2, Rep 2

city: Maebashi

first: Tetsuro

last: Komatsu

address: 3-39-15 Showa-machi

country: Japan

institute: Gunma University

data_processing:
FASTQ files were pre-processed using fastp with the default setting (Galaxy Version 0.23.2+galaxy0).
Reads were aligned to the mm9 mouse genome using HISAT2 with the default setting (Galaxy Version 2.2.1+galaxy1).
Read counting was performed using featureCounts with the default setting (Galaxy Version 2.0.3+galaxy2, paired-end and count them as 1 single fragment).
Assembly: mm9
Supplementary files format and content: txt, raw read counts

source_name: 3T3-L1 preadipocyte cell line

growth_protocol: Cells were maintained in DMEM-HG (high glucose), 10% CS until reaching confluent. 2 days before differentiation induction, the medium was replaced with fresh DMEM-HG, 10% CS. On day of differentiation induction (Day 0), the medium was replaced with DMEM-HG, 10% FBS supplemented with 1.67 uM insulin, 1 uM dexamethasone, and 115 ug/mL of IBMX.

extract_protocol:
Total RNA was purified from cells using RNeasy Lipid Tissue Mini Kit (QIAGEN, 74804).
Library construction was done using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530).

treatment_protocol: Knockdown and exogenous expression were carried out using the pMXs-based retroviral vector system.

value: 3T3-L1 preadipocyte cell line


title: shJmjd1a plus WT, Day 2, Rep 1


title: T-Cell, 2d DSS, Intestine

description: Library name: 5

extract_protocol:
The large intestine was removed from freshly sacrificed animals, cut open longitudinally and fecal contents were removed by vigorous shaking in PBS. Colon cells were incubated at 37°C for 20min in 4mL solution 1 (3% FCS, 20mM HEPES, 5mM EDTA, and 1mM DTT in RPMI (Gibco)) at 180rpm in a 6-well plate. Tissues were rinsed with 1xPBS, transferred to a fresh 6-well plate 700 containing 4mL of digest1 solution (0.8mg/ml Dispase, 20mM HEPES, 2mM EDTA in RPMI) and again incubated at 37°C at 180rpm for 5min. Next, tissues were agitated vigorously in digest1 solution before transferring them into digest2 solution (0.1mg/ml Liberase TL, 0.5mg/ml DNAseI, 20 mM HEPES in RPMI). After another incubation for 20min, tissue and solution were transferred into a gentleMACS™ M tube and dissociated in an octo-gentleMACS dissociator (Myltenyi Biotech, Germany). Suspensions were then filtered through a 100μM cell strainer, washed with 1xPBS containing 2% FCS to remove remaining enzymes. immune cells, B cells (CD45+, CD19+), T cells (CD45+, CD19-, CD3+), neutrophils (CD45+,CD3-, CD19-, Ly-6G+, CD11b+) and a myeloid cell-enriched fraction (CD45+, CD3-, CD19-, Ly-6G-, CD11b+) were sorted directly into RNA lysis buffer. Endothelial cells and a fibroblast/SMC-enriched fraction, cells were stained with anti-CD31, anti-EpCAM and anti-CD45 antibodies and sorted into RNA lysis buffer (endothelial cells: CD45-, EpCam-, CD31+, fibroblast/SMC fraction: CD45-, EpCam-, CD31-). RNA was extracted using the NucleoSpin 96 RNA Core Kit (Macherey-Nagel). CarrierRNA (Macherey-Nagel) was added to samples with cell counts <104 cells. cDNA was synthesized using the LunaScript RT Mastermix (NEB).
cDNA was subjected to a 2-step PCR: In a first round, Flna editing site primers (amplification of the region around the editing site) and Q5 High-Fidelity DNA Polymerase (NEB) were used to perform 25 cycles. 2μl of this PCR served as a template for PCR2: Using the ampSeq barcoding primers for 15 cycles, thereby adding Illumina-compatible adapters with dual-indices. PCR products were gel-eluted using the Monarch DNA Gel Extraction Kit (NEB) followed by quantification by Qubit Fluorometry (Thermo Fisher Scientific). A maximum of 96 samples were pooled into one multiplex for sequencing on an Illumina Nova-Seq instrument.

value: Intestine

value: T-Cell

value: 2d DSS


title: NoMet_transstilbene_139939_6_26.1uM_TC00003594_F11

first: Monique

last: Hazemi

address: 109 T.W. Alexander Dr

institute: US EPA

description:
Library name: TC00003594_F11
TC00003594_F11

value: 24h exposure of 26.1 uM of trans-Stilbene

value: VM7Luc4E2 Assay Medium

value: trans-Stilbene


title: LOX-IMVI_shNFKBIZ_2


title: NoMet_ethyl4hydroxybenzoate_111988_4_3.73uM_TC00003594_F10

description:
Library name: TC00003594_F10
TC00003594_F10

value: 24h exposure of 3.73 uM of Ethylparaben

value: Ethylparaben

value: OK


title: EC, 2d DSS, Intestine, biol. rep. 3

description: Library name: 3

value: EC

value: WT


title: NoMet_DMSO_0_0uM_TC00003594_F09

description:
Library name: TC00003594_F09
TC00003594_F09

value: 0.5% DMSO vehicle control

value: DMSO


title: EC, 2d DSS, Intestine, biol. rep. 4

description: Library name: 4


title: shJmjd1a plus Mut, Day 2, Rep 2


title: shJmjd1a plus Mut, Day 2, Rep 1


title: LOX-IMVI_shNFKBIZ_1

value: LOX-IMVI


title: LOX-IMVI_shCtrl_3

value: melanoma cells

value: Ctrl


title: EC, 2d DSS, Intestine, biol. rep. 2

description: Library name: 2


title: NoMet_transstilbene_139939_2_0.093uM_TC00003594_E12

description:
Library name: TC00003594_E12
TC00003594_E12

value: 24h exposure of 0.093 uM of trans-Stilbene


title: EC, 2d DSS, Intestine, biol. rep. 1

description: Library name: 1

value: Intestine


title: shJmjd1a plus LacZ, Day 2, Rep 3

value: 3T3-L1 preadipocyte cell line


title: NoMet_transstilbene_139939_1_0.001uM_TC00003594_E11

description:
Library name: TC00003594_E11
TC00003594_E11

value: 24h exposure of 0.001 uM of trans-Stilbene


title: LOX-IMVI_shCtrl_2