title: AO2246_0-5_R1_P5

description: Library name: s397

value: Mammary


title: patient5

status: Public on Jul 01 2026

type: other

city: Memphis

first: Kyle

middle: S

last: Smith

state: TN

address: 262 Danny Thomas Pl

country: USA

institute: St. Jude Children's Research Hospital

description: Brain tumor patient

hyb_protocol: Bisulphite converted DNA was amplified and hybridized to human MethylationHM450 BeadChip

scan_protocol: Array were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing: Minfi R package (v1.58)

label: Cy3 and Cy5

molecule: other

organism: Homo sapiens

source_name: Brain tumor

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from samples using Qiagen Kit according to standard instructions

tag: Sex

value: Female

tag: age

tag: mstage

tag: risk group

value: Average

tag: subgroup

tag: g34 subtype

value: II

tag: tissue

value: Brain tumor


title: HepG2.batch2.DIQ.rep3.E01

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: HepG2_Batch2_DIQ_3_E01

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: liver

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: cell line

tag: treatment


title: patient4

description: Brain tumor patient


title: RDY280 ChEC-seq, 25 min IAA, rep A

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

description: Library name: RDHTS772

library_source: genomic

data_processing:
Paired-end 150 bp reads were preprocessed using bbduk (BBMap version 39.06) and aligned using Bowtie 2 (version 2.5.0). BAM files were created, sorted, and indexed using Samtools (version 1.18). Genome coverage was calculated and normalized by counts per million (CPM) using deepTools2 (version 3.5.4). Average genome coverage across replicates was calculated using BEDTools (version 2.30.0) and bedGraphToBigWig. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/ChEC-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Processed data (counts per million [CPM] normalized genome coverage) are provided in bigwig (.bw) format.
Library strategy: ChEC-seq

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.

extract_protocol:
DNA was purified using a ChIP DNA Clean and Concentrator kit (Zymo Research). Cleaved DNA was selected based on size using Sera-Mag Speedbeads (Cytiva) prepared as described (dx.doi.org/10.17504/protocols.io.x54v9p7b1g3e/v2).
Libraries were constructed using a Next Ultra II DNA Library Prep kit (New England Biolabs) as described (https://doi.org/10.1371/journal.pgen.1010945) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.5. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in Buffer A, permeabilized, and treated with calcium chloride to induce DNA cleavage.

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD5:TRP1

value: 25 min IAA treatment


title: patient3

description: Brain tumor patient

value: Male


title: AO2246_0-1_R1_P5

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description: Library name: s396

library_source: transcriptomic

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

molecule: total RNA

source_name: Mammary

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia) were cultured in 10 cm dishes (Corning Falcon No. 353003, Corning, New York) with Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Waltham, Massachusetts) containing 10% fetal bovine serum (FBS; Wisent Bioproducts, Saint-Jean Baptiste, QC, Canada), and 1% penicillin and streptomycin (P/S; Wisent), at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells were washed with phosphate-buffered saline (PBS) and the media were replaced with phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) to eliminate estrogens present in commercial media and serum (Atlas et al. 2003) for 24 h. Cells were then seeded into clear 96-well plates (Corning Falcon No. 353075) at a density of 2.0 x 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS and 1% P/S. After 24 h, the medium was removed and replaced with phenol red-free DMEM containing 5% CD-FBS and 1% P/S and chemicals of interest. Cells were exposed for 48 h, in quadruplicates, to BPA, the 12 chemicals of interest at eight different concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM), 17β-estradiol (E2; 0.1, 1 nM) as a positive control, and at least four plate-matched solvent controls (0.1% DMSO).

value: Epithelial

value: WT

value: chemical exposure

tag: chemical

value: antioxidant 2246

tag: dose

tag: batch


title: RDY280 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS775

value: 25 min DMSO treatment


title: HepG2.batch2.DIQ.rep3.D01

description: Library name: HepG2_Batch2_DIQ_3_D01


title: RDY280 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS773


title: RDY280 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS771


title: HepG2.batch2.DIQ.rep3.C01

description: Library name: HepG2_Batch2_DIQ_3_C01


title: AO2246_0-01_R1_P5

description: Library name: s394

value: Mammary


title: HepG2.batch2.DIQ.rep3.B01

description: Library name: HepG2_Batch2_DIQ_3_B01


title: patient1

description: Brain tumor patient

value: VIII


title: patient2

description: Brain tumor patient

value: High


title: RDY294 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS1057

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD22:TRP1


title: AO2246_0-05_R1_P5

description: Library name: s395


title: HepG2.batch2.DIQ.rep3.A01

description: Library name: HepG2_Batch2_DIQ_3_A01


title: AO2246_5_R1_P5

description: Library name: s399


title: BM from Allergic, Cre Positive

city: Ann Arbor

first: Ramon

last: Ocadiz Ruiz

state: Michigan

address: 109 Zina Pitcher, BSRB

institute: University of Michigan

description:
Library name: BM_AA_Cre+
10X Genomics

library_source: transcriptomic single cell

data_processing:
Downstream analyses were conducted in R (v4.1.0) using Seurat. Cells with 200–5,000 detected genes and <20% mitochondrial transcripts were retained. Data were log-normalized and scaled prior to dimensionality reduction and clustering using a graph-based approach.
Assembly: Raw sequencing data were processed with Cell Ranger using the mm10 mouse reference genome to generate gene–barcode matrices.
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Bone marrow from allergic and control Kitlfl/fl-UBC-cre-ERT mice was collected by flushing the femur and tibia of the hind legs with RPMI 1640 supplemented with 10% fetal calf serum (FCS), L-glutamine, penicillin/streptomycin, non-essential amino acids, and sodium pyruvate.We combined bone marrow samples from 3 mice per group and sequenced them to assess sample heterogeneity. To enrich the stem precursor cells and mesenchymal population in the bone marrow samples, we magnetically isolated mature l cells, including T cells, B cells, monocytes/macrophages, granulocytes, erythrocytes, and their committed precursors, using a Direct Lineage Cell Depletion Kit, and following the manufacturer’s instructions (Miltenyi Biotec). Subsequently, one-third of the isolated Lineage+ cells were reintroduced into the original sample.
scRNA-seq was performed on ~10,000 cells per sample using the Chromium Next GEM Single Cell 3′ v3.1 platform (10x Genomics) at the University of Michigan Advanced Genomics Core.

value: Bone Marrow

value: Cre Positive

value: Mixed cells


title: AO2246_0-001_R1_P5

description: Library name: s393


title: HepG2.batch2.DIQ.rep2.H01

description: Library name: HepG2_Batch2_DIQ_2_H01

value: liver

value: hepatocyte

value: cell line


title: HepG2.batch2.DIQ.rep2.G01

description: Library name: HepG2_Batch2_DIQ_2_G01


title: BM from Naïve, Cre Positive

description:
Library name: BM_Naive_Cre+
10X Genomics


title: AO425_5_R1_P5

description: Library name: s391

value: antioxidant 425


title: AO425_1_R1_P5

description: Library name: s390


title: HepG2.batch2.DIQ.rep2.E01

description: Library name: HepG2_Batch2_DIQ_2_E01


title: AO425_0-5_R1_P5

description: Library name: s389


title: RDY294 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS1054

value: yeast cell


title: HepG2.batch2.DIQ.rep2.D01

description: Library name: HepG2_Batch2_DIQ_2_D01


title: AO425_0-1_R1_P5

description: Library name: s388

value: Epithelial


title: RDY294 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS1052


title: Sort-purified (live/CD8a+/NRP-V7 tetramer+) IGRP-specific CD8 T cells isolated from the pLN, ATAC

city: New York

first: Andrea

last: Schietinger

state: NY

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: KH-2254_Tetramer_CD8_pooled ATAC
ATAC: read1 contains genomic insert; read2 contains genomic insert; read3 contains cell barcode (16bp)
KH-2254_Tetramer_CD8_pooled_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
GEX and ATAC libraries were processed jointly using cellranger-arc count (v2.0.2) with the cellranger-arc-mm10-2020-A-2.0.0 reference genome
Assembly: mm10
Supplementary files format and content: *_filtered_feature_bc_matrix.h5: CellRanger ARC output, filtered feature-barcode matrix containing GEX counts for called cells
Supplementary files format and content: *_atac_fragments.tsv.gz: CellRanger ARC output, ATAC fragment file with genomic coordinates, cell barcodes, and read counts

source_name: pancreatic lymph node

extract_protocol:
Cells were sorted from the pancreatic lymph node (IGRP-specific CD8 T cells) or from spleens of LCMV-clone 13 infected mice (GP33 specific CD8 T cells) into 0.01% BSA prior to freezing down in Bambanker media. Frozen cells were thawed and prior to nuclei extraction following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow.
ATAC libraries were constructed using sample indexing PCR with 10x Genomics reagents, followed by dual-sided SPRI size selection. cDNA was amplified, cleaned, fragmented, end-repaired, A-tailed, and ligated using 10x Genomics reagents, with SPRI-based purifications throughout. Final gene expression libraries were indexed using 10x Genomics dual-index reagents and purified with SPRIselect.

treatment_protocol: For GP33-specific CD8+ T cells: Non-obese diabetic mice were depleted of CD4 T cells (200µg/mouse anti-CD4, Clone GK1.5) two days prior to infection with LCMV clone 13 (2 x 106 PFU/mouse; i.v.).

value: pancreatic lymph node

value: CD8 T cell

value: NOD WT mice

tag: library type

value: ATAC


title: AO425_0-05_R1_P5

description: Library name: s387

value: Mammary

value: WT

value: chemical exposure


title: HepG2.batch2.DIQ.rep2.B01

description: Library name: HepG2_Batch2_DIQ_2_B01


title: Sort-purified (live/CD8a+/NRP-V7 tetramer+) IGRP-specific CD8 T cells isolated from the pLN, GEX

description:
Library name: KH-2254_Tetramer_CD8_pooled RNA
GEX: read1 contains cell barcode (16bp) + UMI (12bp); read2 contains cDNA sequence

value: mRNA


title: RDY291 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS743

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD17:TRP1

value: 25 min DMSO treatment


title: RDY291 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS741


title: HepG2.batch2.DIQ.rep1.G01

description: Library name: HepG2_Batch2_DIQ_1_G01


title: PC_B_R4_P4

description: Library name: s383

value: technical control

value: brain RNA


title: mNSC, control R1

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

country: Germany

institute: Ludwig Maximilians University

description:
Library name: EKDL250034814
reads_psite_list_th_all.csv

data_processing:
sequencing primers and adpaters were removed with Cutadapt v5.2
UMIs were processed with UMI-tools v1.1.6
reads were aligned with STAR v2.7.10b
psites were obtained using RiboWaltz
Assembly: GRCm39 M35 primary assembly
Supplementary files format and content: contains number of psites for all genes and all samples
Library strategy: Ribo-Seq

source_name: Neural Stem Cells

extract_protocol:
Total RNA and Ribosomoe pulldown was done by Immagina biotechnology
library preparation was done by Immagina biotechnology using LACEseq library preparation

value: Neural Stem Cells

value: GF, control


title: HepG2.batch2.PER.rep1.E02

description: Library name: HepG2_Batch2_PER_1_E02

value: liver

value: hepatocyte

value: cell line


title: PC_UH_R4_P4

description: Library name: s384

value: Epithelial

value: universal human RNA


title: HepG2.batch2.DIQ.rep1.D01

description: Library name: HepG2_Batch2_DIQ_1_D01


title: tg(Grm1)Epv, BSO, biological replicate 5

city: Innsbruck

first: Patrizia

last: Stoitzner

address: Anichstraße 35

department: Department of Dermatology, Venereology and Allergology

country: Austria

institute: Medical University of Innsbruck

description: Library name: SD24

data_processing:
Nf-core RNA-seq 3.14
Genes with names starting with “Gm” or “Rp” or ending with “rik” were not considered for the downstream analysis. Duplicated gene names were removed. In addition, genes were required to have at least "n" raw counts in at least “M” samples, where “M” was the size of the smallest group considered in the comparison. For the comparison BSO+DC boost vs DC boost, "n" was set equal to 10 and the design was based on the treatment. Differential gene expression analysis was performed with DESeq2 (1.44.0; R 4.4.1). Differentially expressed genes (DEGs) were selected, imposing a threshold on p-values adjusted for multiple testing with Benjamini and Hochberg of 0.05.
Assembly: GRCm39, M30
Supplementary files format and content: Tab-delimited text files, including raw, normalized for all samples
Supplementary files format and content: DE table for the comparison BSO+DC boost vs DC boost, comma separated files

source_name: ear skin, melanoma

extract_protocol:
For RNA-sequencing (RNA-seq) analysis, EPv tumor/ear samples were weighed and processed using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Frozen samples were disrupted and homogenized on ice in an appropriate volume of lysis buffer according to the manufacturers’ recommendations by using a Tissue Ruptor (Omni TH Tissue Homogenisierer).
Lexogen QuantSeq 3’-mRNA libraries were prepared at the MultiOmics Sequencing Core Facility (Medical University of Innsbruck) following the manufacturer’s instructions (Lexogen GmbH, Vienna, Austria), quality validated, multiplexed and sequenced with a Illumina NovaSeq sequencer (Azenta, Leipzig, Germany) at 150 bp read length.

value: ear skin, melanoma

value: BSO


title: tg(Grm1)Epv, BSO+DC boost, biological replicate 5

description: Library name: SD23

value: BSO+DC boost


title: BM from Allergic, Cre Negative

description:
Library name: BM_AA_Cre-
10X Genomics

value: Bone Marrow

value: Cre Negative

value: Mixed cells


title: RDY294 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS1056

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD22:TRP1


title: HepG2.batch2.DIQ.rep2.F01

description: Library name: HepG2_Batch2_DIQ_2_F01


title: HepG2.batch2.DIQ.rep2.C01

description: Library name: HepG2_Batch2_DIQ_2_C01


title: Sort-purified (live/CD8a+/GP33 tetramer+) GP33-specific CD8 T cells splenocytes from LCMV clone 13 infected mice, GEX

description:
Library name: KH-2685_8 RNA
GEX: read1 contains cell barcode (16bp) + UMI (12bp); read2 contains cDNA sequence

source_name: spleen

value: spleen

value: CD8 T cell

value: NOD WT mice

value: LCMV Clone 13

value: mRNA


title: BM from Naïve, Cre Negative

description:
Library name: BM_Naive_Cre-
10X Genomics


title: RDY291 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS740

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD17:TRP1

value: 25 min IAA treatment


title: Sort-purified (live/CD8a+/GP33 tetramer+) GP33-specific CD8 T cells splenocytes from LCMV clone 13 infected mice, ATAC

description:
Library name: KH-2685_8 ATAC
ATAC: read1 contains genomic insert; read2 contains genomic insert; read3 contains cell barcode (16bp)
KH-2685_8_multiome_filtered_feature_bc_matrix.h5

value: ATAC


title: HepG2.batch2.DIQ.rep1.C01

description: Library name: HepG2_Batch2_DIQ_1_C01

value: liver

value: hepatocyte

value: cell line


title: AO425_0-001_R1_P5

description: Library name: s385

value: Mammary

value: Epithelial

value: WT

value: chemical exposure

value: antioxidant 425


title: tg(Grm1)Epv, PBS, biological replicate 5

description: Library name: SD22

value: ear skin, melanoma

value: PBS


title: HepG2.batch2.DIQ.rep1.H01

description: Library name: HepG2_Batch2_DIQ_1_H01


title: RDY290 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS933

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD16:TRP1

value: 25 min DMSO treatment


title: HepG2.batch2.DIQ.rep1.B01

description: Library name: HepG2_Batch2_DIQ_1_B01


title: mNSC, gRNA R2

description:
Library name: EKDL250034815
reads_psite_list_th_all.csv

value: Neural Stem Cells

value: GF, gRNA


title: DMSO_0-1_R36_P4

description: Library name: s378

value: vehicle control

value: dimethyl sulfoxide


title: HepG2.batch2.DIQ.rep1.F01

description: Library name: HepG2_Batch2_DIQ_1_F01

value: liver


title: RDY291 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS739

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD17:TRP1


title: DMSO_0-1_R35_P4

description: Library name: s377


title: tg(Grm1)Epv, PBS, biological replicate 3

description: Library name: SD19


title: tg(Grm1)Epv, PBS, biological replicate 4

description: Library name: SD20


title: NC_R8_P4

description: Library name: s376

value: technical control

value: lysis buffer


title: RDY290 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS929


title: RDY289 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS732

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD15:TRP1

value: 25 min IAA treatment


title: tg(Grm1)Epv, PBS, biological replicate 2

description: Library name: SD18


title: HepG2.batch2.DIP.rep3.G07

description: Library name: HepG2_Batch2_DIP_3_G07

value: hepatocyte

value: cell line


title: NC_R7_P4

description: Library name: s375

value: Mammary

value: Epithelial

value: WT


title: RDY290 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS934

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD16:TRP1


title: RDY290 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS932


title: tg(Grm1)Epv, PBS, biological replicate 1

description: Library name: SD17

value: ear skin, melanoma

value: PBS


title: RDY289 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS730


title: HepG2.batch2.DIP.rep3.F07

description: Library name: HepG2_Batch2_DIP_3_F07


title: tg(Grm1)Epv, BSO, biological replicate 4

description: Library name: SD16

value: BSO


title: DMSO_0-1_R34_P4

description: Library name: s374

value: vehicle control

value: dimethyl sulfoxide


title: RDY289 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS728


title: HepG2.batch2.DIP.rep3.E07

description: Library name: HepG2_Batch2_DIP_3_E07

value: liver


title: DMSO_0-1_R33_P4

description: Library name: s373


title: tg(Grm1)Epv, BSO, biological replicate 3

description: Library name: SD15


title: RDY289 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS731

value: 25 min DMSO treatment


title: HepG2.batch2.DIP.rep3.D07

description: Library name: HepG2_Batch2_DIP_3_D07


title: DMSO_0-1_R32_P4

description: Library name: s372


title: tg(Grm1)Epv, BSO, biological replicate 2

description: Library name: SD13


title: RDY289 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS729


title: DMSO_0-1_R31_P4

description: Library name: s371


title: tg(Grm1)Epv, BSO, biological replicate 1

description: Library name: SD12


title: RDY290 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS930


title: RDY289 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS727


title: E2_1_R4_P4

description: Library name: s370

value: chemical exposure


title: tg(Grm1)Epv, DC boost, biological replicate 5

description: Library name: SD11

value: DC boost


title: HepG2.batch2.DIP.rep3.A07

description: Library name: HepG2_Batch2_DIP_3_A07


title: RDY301 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS806

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD68:TRP1

value: 25 min IAA treatment


title: E2_0-1_R4_P4

description: Library name: s369


title: RDY301 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS804


title: HepG2.batch2.DIP.rep2.H07

description: Library name: HepG2_Batch2_DIP_2_H07

value: hepatocyte

value: cell line


title: tg(Grm1)Epv, DC boost, biological replicate 3

description: Library name: SD9


title: RDY301 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS802


title: HepG2.batch2.DIP.rep2.G07

description: Library name: HepG2_Batch2_DIP_2_G07


title: BPA_10_R4_P4

description: Library name: s367

value: Mammary

value: Epithelial

value: bisphenol A


title: RDY301 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS805

value: yeast cell


title: tg(Grm1)Epv, DC boost, biological replicate 2

description: Library name: SD7

value: ear skin, melanoma


title: HepG2.batch2.DIP.rep2.F07

description: Library name: HepG2_Batch2_DIP_2_F07


title: tg(Grm1)Epv, DC boost, biological replicate 1

description: Library name: SD6


title: RDY301 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS803


title: BPA_5_R4_P4

description: Library name: s366

value: WT


title: HepG2.batch2.DIP.rep2.E07

description: Library name: HepG2_Batch2_DIP_2_E07


title: BPA_1_R4_P4

description: Library name: s365


title: tg(Grm1)Epv, BSO+DC boost, biological replicate 4

description: Library name: SD5

value: BSO+DC boost


title: RDY301 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS801


title: HepG2.batch2.DIP.rep2.D07

description: Library name: HepG2_Batch2_DIP_2_D07


title: BPA_0-5_R4_P4

description: Library name: s364


title: tg(Grm1)Epv, BSO+DC boost, biological replicate 3

description: Library name: SD4


title: RDY180 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS648

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD2:TRP1


title: HepG2.batch2.DIP.rep2.C07

description: Library name: HepG2_Batch2_DIP_2_C07


title: tg(Grm1)Epv, BSO+DC boost, biological replicate 2

description: Library name: SD3


title: BPA_0-1_R4_P4

description: Library name: s363


title: BPA_0-001_R4_P4

description: Library name: s362


title: HepG2.batch2.DIP.rep2.B07

description: Library name: HepG2_Batch2_DIP_2_B07


title: tg(Grm1)Epv, BSO+DC boost, biological replicate 1

description: Library name: SD2


title: RDY180 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS768


title: HepG2.batch2.DIP.rep2.A07

description: Library name: HepG2_Batch2_DIP_2_A07


title: RDY180 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS766


title: RDY180 ChEC-seq, 25 min DMSO, rep C

description: Library name: RDHTS647


title: BPA_0-01_R4_P4

description: Library name: s361


title: CD11b- cells from IRI-6h mice

city: Sendai

first: Kosuke

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku University

description: Library name: PR4106_02_a

data_processing:
Sample demultiplexing, barcode processing, single cell 3' and 5' gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Barcodes (Tab-separated values files)
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Features (Tab-separated values files)
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Matrix (matrix files)

source_name: Small intestine

extract_protocol:
Small intestinal lamina propria cells were collected utilizing a Lamina Propria Dissociation Kit (Miltenyi Biotec) following the manufacturer’s protocol, followed by density gradient separation using Percoll (Cytiva). Single-cell suspensions were obtained from gradient layers between 30 % and 70 % Percoll. Live CD11b- cells were enriched using Dead Cell Removal Kit and CD11b Microbeads (Miltenyi Biotec), and fixed for 19 hours at 4 °C with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).
For each fixed sample, the detection probe of the Chromium Fixed RNA Kit was hybridized to RNA in the cells, and a ligation reaction performed to bind adjacent hybridized probes. After mixing each sample, barcode primer beads and the cells were encapsulated, annealing the probes and the primers, and an extension reaction performed to add a cell identification adapter sequence to the detection probe using ChromiumX. To construct the library, samples were amplified and purified by polymerase chain reaction using index primers.

value: Small intestine


title: TBPB_50_R4_P4

description: Library name: s360

value: tetrabromophenol blue


title: HepG2.batch2.DIP.rep1.H07

description: Library name: HepG2_Batch2_DIP_1_H07

value: liver


title: tg(Grm1)Epv, DC boost, biological replicate 4

description: Library name: SD10


title: RDY294 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS1055

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD22:TRP1


title: AO425_10_R1_P5

description: Library name: s392

value: chemical exposure

value: antioxidant 425


title: RDY180 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS767

value: 25 min DMSO treatment


title: HepG2.batch2.DIP.rep1.G07

description: Library name: HepG2_Batch2_DIP_1_G07

value: hepatocyte


title: HepG2.batch2.DIP.rep3.B07

description: Library name: HepG2_Batch2_DIP_3_B07

value: cell line


title: CD11b- cells from Sham-6h mice

description: Library name: PR4106_01_a


title: RDY294 ChEC-seq, 25 min IAA, rep A

description: Library name: RDHTS1053

value: 25 min IAA treatment


title: 4-1BBL KO B cells, VDJ

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

description: Library name: 4-1BBLKO_B_VDJ

data_processing:
scRNA-seq, CITE-seq and V(D)J-seq were processed using Cell Ranger Multi v9.0.1
V, D and J genes were assigned using IgBLAST.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: sample_filtered_feature_bc_matrix.h5
Supplementary files format and content: IgBLAST output: BCR_data_sequences_igblast_db-pass.tsv
Library strategy: BCR-Seq

source_name: Spleen

extract_protocol:
Total B cells were flow sorted and run on the 10X Chromium (10X Genomics).
Library preparation was performed according to the manufacturer’s protocol for Chromium GEM-X Single Cell 5’ Reagent Kit v3 with Feature Barcode technology and V(D)J amplification for mouse B cells (10X Genomics).

value: Spleen

value: B cells

value: 4-1BBL KO


title: TBPB_10_R4_P4

description: Library name: s359

value: Mammary

value: Epithelial


title: HepG2.batch2.DIP.rep1.F07

description: Library name: HepG2_Batch2_DIP_1_F07


title: RDY180 ChEC-seq, 25 min DMSO, rep A

description: Library name: RDHTS765

value: yeast cell


title: 4-1BB KO B cells, VDJ

description: Library name: 4-1BBKO_B_VDJ

value: 4-1BB KO


title: HepG2.batch2.DIP.rep1.E07

description: Library name: HepG2_Batch2_DIP_1_E07


title: RDY215 ChEC-seq, no treatment, rep C

description: Library name: RDHTS105

value: no treatment


title: TBPB_1_R4_P4

description: Library name: s357

value: WT

value: tetrabromophenol blue


title: RDY215 ChEC-seq, no treatment, rep B

description: Library name: RDHTS104


title: HepG2.batch2.DIP.rep1.D07

description: Library name: HepG2_Batch2_DIP_1_D07

value: liver


title: TBPB_0-5_R4_P4

description: Library name: s356

value: chemical exposure


title: TBPB_0-1_R4_P4

description: Library name: s355


title: HepG2.batch2.DIP.rep1.C07

description: Library name: HepG2_Batch2_DIP_1_C07


title: HepG2.batch2.DIP.rep1.B07

description: Library name: HepG2_Batch2_DIP_1_B07


title: 4-1BB KO B cells, ADT

description: Library name: 4-1BBKO_B_ADT

data_processing:
scRNA-seq, CITE-seq and V(D)J-seq were processed using Cell Ranger Multi v9.0.1
V, D and J genes were assigned using IgBLAST.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: sample_filtered_feature_bc_matrix.h5
Supplementary files format and content: IgBLAST output: BCR_data_sequences_igblast_db-pass.tsv
Library strategy: CITE-seq

molecule: protein


title: RDY388 SLAM-seq, ET overexpression, IAA, rep C

description: Library name: RDHTS1163

data_processing:
Paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) and bbduk (BBMap version 39.06). Forward reads were processed using SLAM-DUNK (version 0.4.3), where reads were aligned against the Saccharomyces cerevisiae genome or the spike-in Schizosaccharomyces pombe genome using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 2 T>C conversions was used to define T>C read counts. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/SLAM-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2); Schizosaccharomyces pombe strain 972h- version ASM294v2 (RefSeq Assembly GCF_000002945.1)
Supplementary files format and content: Raw read count tables are provided in tab-separated values (.tsv) format. *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for Saccharomyces cerevisiae. *_spom_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions for Schizosaccharomyces pombe.

extract_protocol:
Schizosaccharomyces pombe cells were combined with Saccharomyces cerevisiae cells in mass-to-mass ratio of 1:19 based on OD600. RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer’s recommendations with minor modifications. Reagents used during RNA purification were supplemented with DTT to maintain reducing conditions. RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. Samples were protected from light when possible.
Libraries were constructed as previously described in detail (https://doi.org/10.1186/s44330-024-00008-1) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.45. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4-thiouracil (4tU) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 4 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at –80°C.

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pJR15:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment, ET overexpression


title: RDY388 SLAM-seq, ET overexpression, IAA, rep B

description: Library name: RDHTS1161


title: WT B cells, ADT

description: Library name: WT_B_ADT


title: HepG2.batch2.DIP.rep1.A07

description: Library name: HepG2_Batch2_DIP_1_A07

value: hepatocyte


title: 4-1BBL KO B cells, GEX

description: Library name: 4-1BBLKO_B_GEX

data_processing:
scRNA-seq, CITE-seq and V(D)J-seq were processed using Cell Ranger Multi v9.0.1
V, D and J genes were assigned using IgBLAST.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: sample_filtered_feature_bc_matrix.h5
Supplementary files format and content: IgBLAST output: BCR_data_sequences_igblast_db-pass.tsv


title: HepG2.batch2.DIP.rep3.C07

description: Library name: HepG2_Batch2_DIP_3_C07

value: cell line


title: TBPB_0-001_R4_P4

description: Library name: s353


title: HepG2.batch2.DIC.rep3.H06

description: Library name: HepG2_Batch2_DIC_3_H06


title: RDY388 SLAM-seq, ET overexpression, IAA, rep A

description: Library name: RDHTS1159


title: PRed_50_R4_P4

description: Library name: s352

value: phenol red


title: 4-1BB KO B cells, GEX

description: Library name: 4-1BBKO_B_GEX

value: Spleen


title: RDY388 SLAM-seq, ET overexpression, DMSO, rep C

description: Library name: RDHTS1162

value: 25 min DMSO treatment, 4 min 4tU treatment, ET overexpression


title: HepG2.batch2.DIC.rep3.G06

description: Library name: HepG2_Batch2_DIC_3_G06


title: RDY388 SLAM-seq, ET overexpression, DMSO, rep B

description: Library name: RDHTS1160


title: WT B cells, GEX

description: Library name: WT_B_GEX

value: B cells


title: HepG2.batch2.DIC.rep3.F06

description: Library name: HepG2_Batch2_DIC_3_F06


title: PRed_5_R4_P4

description: Library name: s350

value: Mammary


title: RWZ179_STR_dSVA_F

first: Weimin

last: Zhang

address: 435 E 30th street

department: Institute for Systems Genetics

institute: NYU Langone Health

description:
Library name: RWZ179_STR_dSVA_F
100 Cycle Flowcell

data_processing:
Adapters and low-quality bases were trimmed using Trimmomatic (v0.36).
Sequencing reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.7.3). Alignments were guided by a Gene Transfer Format (GTF) file.
The mean read insert sizes and their standard deviations were calculated using Picard tools (v.2.18.20).
The genes-samples counts matrix was generated using featureCounts (v1.6.3), normalized based on their library size factors using DEseq2, and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using deepTools (v.3.1.0). Data were visualized using GraphPad Prism or Rstudio.
Assembly: mm10
Supplementary files format and content: Raw count txt files
Supplementary files format and content: Normalized csv file

source_name: Striatum

growth_protocol:
For mESCs, the culture medium consisted of ES medium (85% (v/v) KnockOut DMEM (Fisher Scientific, 10829018), 15% (v/v) Fetal Bovine Serum (Hyclone, SH30070.03), 0.5 mg/ml Penicillin-Streptomycin-Glutamine (Gibco, 10378016), 7 μL 2-Mercaptoethanol (Sigma-Aldrich, M6250), 0.1 mM MEM Non-Essential Amino Acids (Gibco, 11140050) and 1 U/ml LIF (EMD Millipore, ESG1107), 3 µM CHIR99021 and 1 µM PD0325901). Tissue culture treated plates were coated with 0.1% gelatin solution before use. All cells were grown in a humidified tissue culture incubator at 37°C supplied with 5% CO2.
For mouse striatum, progeny of NesCre and PC-XDP crossing were euthanized at week 3. Striatal cells were dissected for total RNA extraction.

extract_protocol:
Total RNA from mESCs and strial cells were extracted using A RNeasy miniplus kit (QIAGEN, 74136)
Total RNA quality and quantity were examined using a Bioanalyzer (Agilent 2100, RNA 6000 nano kit). Sequencing libraries were constructed using a TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, 20020599).

value: Striatum

tag: strain

value: MSN


title: RDY388 SLAM-seq, ET overexpression, DMSO, rep A

description: Library name: RDHTS1158

value: yeast cell


title: HepG2.batch2.DIC.rep3.E06

description: Library name: HepG2_Batch2_DIC_3_E06


title: PRed_1_R4_P4

description: Library name: s349

value: Epithelial


title: RDY73 SLAM-seq, control, IAA, rep C

description: Library name: RDHTS1157

value: 25 min IAA treatment, 4 min 4tU treatment


title: RWZ156_STR_XDP

description:
Library name: RWZ156_STR_XDP
100 Cycle Flowcell


title: HepG2.batch2.DIC.rep3.D06

description: Library name: HepG2_Batch2_DIC_3_D06


title: RHLA293_conv-dSVA_F&D

description:
Library name: RHLA293_conv-dSVA_F_D
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv

source_name: mESC

value: mESC


title: HepG2.batch2.DIC.rep3.C06

description: Library name: HepG2_Batch2_DIC_3_C06

value: liver


title: RDY73 SLAM-seq, control, IAA, rep B

description: Library name: RDHTS1155


title: PRed_0-1_R4_P4

description: Library name: s347

value: WT

value: chemical exposure


title: RHLA290_conv-dSVA_F&D

description:
Library name: RHLA290_conv-dSVA_F_D
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv


title: RDY73 SLAM-seq, control, IAA, rep A

description: Library name: RDHTS1153


title: PRed_0-01_R4_P4

description: Library name: s346


title: HepG2.batch2.DIC.rep3.B06

description: Library name: HepG2_Batch2_DIC_3_B06


title: RDY73 SLAM-seq, control, DMSO, rep C

description: Library name: RDHTS1156

value: 25 min DMSO treatment, 4 min 4tU treatment


title: RHLA291_conv-dSVA_D

description:
Library name: RHLA291_conv-dSVA_D
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv


title: HepG2.batch2.DIC.rep3.A06

description: Library name: HepG2_Batch2_DIC_3_A06

value: hepatocyte


title: PRed_0-001_R4_P4

description: Library name: s345


title: RHLA287_conv-dSVA_D

description:
Library name: RHLA287_conv-dSVA_D
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv


title: HepG2.batch2.DIC.rep2.H06

description: Library name: HepG2_Batch2_DIC_2_H06

value: cell line


title: RDY73 SLAM-seq, control, DMSO, rep B

description: Library name: RDHTS1154


title: THPE_50_R4_P4

description: Library name: s344


title: RHLA289_conv-dSVA_F

description:
Library name: RHLA289_conv-dSVA_F
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv


title: RDY73 SLAM-seq, control, DMSO, rep A

description: Library name: RDHTS1152


title: HepG2.batch2.DIC.rep2.G06

description: Library name: HepG2_Batch2_DIC_2_G06


title: THPE_10_R4_P4

description: Library name: s343


title: RHLA288_conv-dSVA_F

description:
Library name: RHLA288_conv-dSVA_F
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv


title: RDY251 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS720

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.2. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 3 h. Immediately after IAA treatment, cultures were treated with 5 mM 4-thiouracil (4tU) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 6 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at –80°C.

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD46:TRP1

value: 3 h IAA treatment, 6 min 4tU treatment


title: HepG2.batch2.DIC.rep2.F06

description: Library name: HepG2_Batch2_DIC_2_F06


title: THPE_5_R4_P4

description: Library name: s342


title: RWZ235_preconv-XDP

description:
Library name: RWZ235_preconv-XDP
100 Cycle Flowcell


title: RDY251 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS718


title: HepG2.batch2.DIC.rep2.E06

description: Library name: HepG2_Batch2_DIC_2_E06


title: THPE_1_R4_P4

description: Library name: s341


title: RHLA295_MK6

description:
Library name: RHLA295_MK6
100 Cycle Flowcell
Normalized_counts_for_DEseq2.csv

value: Wild type


title: HepG2.batch2.DIC.rep2.D06

description: Library name: HepG2_Batch2_DIC_2_D06


title: RDY251 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS716


title: THPE_0-5_R4_P4

description: Library name: s340


title: RDY251 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS719

value: 3 h DMSO treatment, 6 min 4tU treatment


title: 32D Jak2V617F cells, GLUT1/3 KO, clone 3

city: Aachen

first: Patrick

last: Weiand

state: NRW

address: Pauwelsstraße 19

department: Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation

institute: RWTH Aachen University

description:
Library name: VFK3
Column name in gene_fpkm.csv: VFK3

data_processing:
fastp (1.0.1) for filtering, HISAT2 (2.2.1) for alignment to reference genome , featureCounts (2.0.6) to count the reads numbers mapped to each gene.
The sequenced reads (fastq format) contain low quality reads and adapters, which affect the analysis quality. It's necessary to filter the raw reads to get clean reads. The filtering process is as follows: First, remove reads containing adapters. Then remove reads containing N > 10% (N represents the base cannot be determined). Finally, remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
The original raw data from Illumina platform are transformed to Sequenced Reads, known as Raw Data or RAW Reads, by base calling. Raw data are recorded in a FASTQ file, which contains sequencing reads and corresponding sequencing quality.
Assembly: mm39
Supplementary files format and content: csv file includes FPKM values for each samples

growth_protocol: 32D cells were cultured in RPMI1640 supplemented with 10% fetal calf serum, 1% penicillin/streptomycin and 10% supernatant of WEHI-3B cells as a source of murine interleukin-3 (IL-3) in 37 °C and 5% CO2 in a incubator.

extract_protocol:
RNA was isolated using a NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) and following manufactureres instructions. 20 µL of RNA elution with a concentration of at least 200 ng/µL RNA per sample were sent to NovoGene (NovoGene Germany, Munich, Germany) for sequencing.
mRNA library preparation (poly A enrichment: polyA capture and reverse transcription into cDNA, followed by quality assessment) was performed by NovoGene ((NovoGene Germany, Munich, Germany).

treatment_protocol: Cells were maintained in RPMI-1640 with 5 mM glucose, 1 mM L-glutamine, 10% FCS, 1% penicillin/streptomycin, 2 ng/ml IL-3 to 24 hours. Cells were washed twice with PBS prior to RNA isolation.

value: myeloblast-like bone marrow cell line

value: Jak2V617F Slc2a1/3dKO

value: low-supplement media


title: HepG2.batch2.DIC.rep2.C06

description: Library name: HepG2_Batch2_DIC_2_C06


title: THPE_0-1_R4_P4

description: Library name: s339

value: Mammary


title: 32D Jak2V617F cells, GLUT1/3 KO, clone 1

description:
Library name: VFK1
Column name in gene_fpkm.csv: VFK1


title: HepG2.batch2.DIC.rep2.B06

description: Library name: HepG2_Batch2_DIC_2_B06


title: THPE_0-01_R4_P4

description: Library name: s338

value: Epithelial


title: 32D Jak2V617F cells, GLUT1/3 WT, clone 3

description:
Library name: VFT3
Column name in gene_fpkm.csv: VFT3

value: Jak2V617F Slc2a1/3WT


title: RDY251 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS715

value: yeast cell


title: HepG2.batch2.DIC.rep2.A06

description: Library name: HepG2_Batch2_DIC_2_A06

value: liver


title: THPE_0-001_R4_P4

description: Library name: s337

value: WT


title: 32D Jak2V617F cells, GLUT1/3 WT, clone 1

description:
Library name: VFT1
Column name in gene_fpkm.csv: VFT1


title: RDY249 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS1139

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD44:TRP1


title: HepG2.batch2.DIC.rep1.H06

description: Library name: HepG2_Batch2_DIC_1_H06


title: PA08_10_R4_P4

description: Library name: s336

value: chemical exposure

value: plastic additive 08


title: 32D Jak2WT cells, GLUT1/3 KO, clone 3

description:
Library name: WK3
Column name in gene_fpkm.csv: WK3

value: Jak2WT Slc2a1/3dKO


title: RDY249 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS1137


title: HepG2.batch2.DIC.rep1.G06

description: Library name: HepG2_Batch2_DIC_1_G06

value: hepatocyte

value: cell line


title: PA08_5_R4_P4

description: Library name: s335


title: 32D Jak2WT cells, GLUT1/3 KO, clone 1

description:
Library name: WK1
Column name in gene_fpkm.csv: WK1


title: RDY249 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS1135

value: 3 h IAA treatment, 6 min 4tU treatment


title: HepG2.batch2.DIC.rep1.F06

description: Library name: HepG2_Batch2_DIC_1_F06


title: PA08_1_R4_P4

description: Library name: s334


title: 32D Jak2WT cells, GLUT1/3 WT, clone 3

description:
Library name: WT3
Column name in gene_fpkm.csv: WT3

value: Jak2WT Slc2a1/3WT


title: HepG2.batch2.DIC.rep1.E06

description: Library name: HepG2_Batch2_DIC_1_E06


title: PA08_0-5_R4_P4

description: Library name: s333


title: RDY249 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS1138

value: 3 h DMSO treatment, 6 min 4tU treatment


title: 32D Jak2WT cells, GLUT1/3 WT, clone 1

description:
Library name: WT1
Column name in gene_fpkm.csv: WT1

value: myeloblast-like bone marrow cell line


title: RDY249 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS1136


title: HepG2.batch2.DIC.rep1.D06

description: Library name: HepG2_Batch2_DIC_1_D06


title: PA08_0-1_R4_P4

description: Library name: s332


title: 2-5-8W-KO-CCL4

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

country: China

institute: Wuhan University

description: Library name: sample 12

data_processing:
Raw sequencing reads (FASTQ) were subjected to standard quality control. Low-quality bases and adapter contamination were removed when necessary. Clean reads were aligned to the mouse reference genome (mm10) using a splice-aware aligner. Gene-level expression quantification was performed based on a corresponding mouse gene annotation, generating count matrices for downstream analyses (e.g., normalization and differential expression).
Assembly: mm10
Supplementary files format and content: FPKM
Supplementary files format and content: Processed data files include alignment files (BAM/BAI), gene-level expression matrices (raw counts; TSV/CSV), and summary QC/mapping statistics (TXT/TSV). If provided, normalized expression tables (e.g., TPM/FPKM) and differential expression result tables are included in tab-delimited/CSV format.

source_name: liver

extract_protocol:
Total RNA was extracted from mouse whole liver tissue using TRIzol reagent following the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and RNA integrity was evaluated prior to library preparation.
mRNA libraries were prepared from total RNA using a KAPA mRNA library preparation kit (poly(A) selection–based) according to the manufacturer’s protocol. Libraries were indexed, quality-checked, and sequenced on an Illumina platform to generate paired-end reads.


title: RDY249 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS1134


title: HepG2.batch2.DIC.rep1.C06

description: Library name: HepG2_Batch2_DIC_1_C06


title: RDY251 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS717

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD46:TRP1


title: PA08_0-05_R4_P4

description: Library name: s331

value: Mammary


title: 2-2-8W-KO-CCL4

description: Library name: sample 11


title: TBPB_5_R4_P4

description: Library name: s358

value: Epithelial

value: tetrabromophenol blue


title: WT B cells, VDJ

description: Library name: WT_B_VDJ

value: Spleen

value: B cells


title: RDY247 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS1145

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD42:TRP1


title: 4-1BBL KO B cells, ADT

description: Library name: 4-1BBLKO_B_ADT

value: 4-1BBL KO


title: PA08_0-01_R4_P4

description: Library name: s330

value: WT

value: chemical exposure

value: plastic additive 08


title: 2-4-8W-CCL4

description: Library name: sample 10

value: liver


title: HepG2.batch2.DIC.rep1.B06

description: Library name: HepG2_Batch2_DIC_1_B06

value: hepatocyte

value: cell line


title: RDY247 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS1143

value: 3 h IAA treatment, 6 min 4tU treatment


title: HepG2.batch2.DIC.rep1.A06

description: Library name: HepG2_Batch2_DIC_1_A06


title: RDY215 ChEC-seq, no treatment, rep A

description: Library name: RDHTS103

value: no treatment


title: PA08_0-001_R4_P4

description: Library name: s329


title: 2-3-8W-CCL4

description: Library name: sample 9


title: TBPB_0-01_R4_P4

description: Library name: s354


title: RDY247 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS1141


title: HepG2.batch2.control.rep3.D12

description: Library name: HepG2_Batch2_control_3_D12


title: TBBPS_50_R4_P4

description: Library name: s328

value: tetrabromo bisphenol S


title: HepG2.batch2.control.rep3.C12

description: Library name: HepG2_Batch2_control_3_C12


title: TBBPS_10_R4_P4

description: Library name: s327

value: Mammary


title: RDY247 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS1144

value: 3 h DMSO treatment, 6 min 4tU treatment


title: 3-1-8W-Sj-KO

description: Library name: sample 8


title: RDY247 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS1142


title: 2-1-8W-Sj-KO

description: Library name: sample 7


title: TBBPS_5_R4_P4

description: Library name: s326

value: Epithelial


title: 3-1-8W-Sj

description: Library name: sample 6


title: RDY247 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS1140


title: HepG2.batch2.control.rep3.B12

description: Library name: HepG2_Batch2_control_3_B12


title: HepG2.batch2.control.rep2.D11

description: Library name: HepG2_Batch2_control_2_D11


title: TBBPS_1_R4_P4

description: Library name: s325


title: HepG2.batch2.control.rep3.A12

description: Library name: HepG2_Batch2_control_3_A12


title: 2-2-8W-Sj

description: Library name: sample 5


title: RDY237 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS714

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD32:TRP1


title: HepG2.batch2.control.rep2.C11

description: Library name: HepG2_Batch2_control_2_C11


title: PRed_10_R4_P4

description: Library name: s351

value: phenol red


title: RDY237 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS712

value: yeast cell


title: 3-2-8W-KO-NC

description: Library name: sample 4


title: TBBPS_0-1_R4_P4

description: Library name: s323


title: TBBPS_0-5_R4_P4

description: Library name: s324


title: RDY237 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS710


title: 2-2-8W-KO-NC

description: Library name: sample 3


title: 3-1-8W-NC

description: Library name: sample 2


title: TBBPS_0-01_R4_P4

description: Library name: s322


title: HepG2.batch2.control.rep2.B11

description: Library name: HepG2_Batch2_control_2_B11


title: 1-1-8W-NC

description: Library name: sample 1


title: HepG2.batch2.control.rep1.D10

description: Library name: HepG2_Batch2_control_1_D10


title: TBBPS_0-001_R4_P4

description: Library name: s321


title: HepG2.batch2.control.rep2.A11

description: Library name: HepG2_Batch2_control_2_A11


title: PRed_0-5_R4_P4

description: Library name: s348


title: RDY237 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS713


title: RDY237 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS711


title: DABPA_10_R4_P4

description: Library name: s320

value: diallyl bisphenol A


title: Brain,rebound sleep,total RNA(Input)_ rep#4

city: Beijing

first: Hong

last: Jiang

address: No. 38, Xueyuan Road, Haidian District, Beijing

institute: School of Basic Medical Sciences Peking University

description: Library name: RS4Input

data_processing:
Preprocessing and Quality Control:Raw FASTQ files were performed data filtering and quality control using fastp, which included quality control of raw reads to assess sequencing quality and remove low-quality bases or adapter sequences.
Gene-Level Quanitification:And then aligned to the Ensembl GRCm39 reference genome using HISAT2. Using StringTie to assemble the reads on the alignment to create all the transcripts present in all samples. Per-gene transcripts were quantified with StringTie to produce a raw gene expression matrix and use the FPKM value (Fragments Per Kilobase Million) to evaluate the correlation of gene expression characteristics within and between groups.
Differential Gene Expression Analysis:  For the differential gene expression analysis, the DESeq2 package, version 1.38.3,42 implemented in R, was employed. Raw counts were normalized, and statistical models were applied to identify differentially expressed genes across experimental conditions: Control-IP vs Control-Input, RS-IP vs RS-Input, and RS-IP vs Control-IP.
Enrichment Analysis: Differentially expressed genes from the RS-IP vs Control-IP genes (adjusted p value<0.05) were filtered to retain only those enriched in FosL10a neurons based on the enrichment criteria.
Filtering for Differentially Expressed Genes:A gene was considered to be enriched in FosL10a neurons if it exhibited differential expression under one of two conditions: (1) Control-IP vs Control-Input or (2) RS-IP vs RS-Input (adjusted p value<0.05). Differentially expressed genes due to RS were identified by comparing RS-IP vs Control-IP (adjusted p value<0.05 and its log2fold-change ≥ |1|) and filtered for enrichment in FosL10a -expressing neurons.
Assembly: GRCm39 reference genome
Supplementary files format and content: Supplementary files format and content: merged.gene_count_matrix.csv :Gene Counts
Supplementary files format and content: Supplementary files format and content: merged.gene_fpkm_matrix.csv : Normalized Gene Counts
Supplementary files format and content: Supplementary files format and content: deseq2_results_combined.csv :DESeq2 results

source_name: Brain, Hypothalamus

extract_protocol:
Mice were killed at 12 weeks of age in a random-fed state by decapitation. Whole PVN were obtained using a mouse brain slicer matrix and snap frozen in liquid nitrogen until translating ribosome affinity purification (TRAP). One day before TRAP, 375 µl of Dynal Protein G magnetic beads (Invitrogen) was washed three times (1 ml) and resuspended in 275µl of IP wash buffer (20 mM HEPES (pH 7.4), 150 mM KCl, 5 mM MgCl2 and 1% NP-40). Then, 50µg of two monoclonal anti-GFP antibodies (HtzGFP-19C8 and HtzGFP-19F7) from the Memorial Sloan-Kettering Cancer Center was added to the magnetic beads and incubated with slow end-over-end mixing overnight at 4 °C. On the day of TRAP, Dynal Protein G magnetic beads were washed three times (1 ml) and resuspended in 200µl IP buffer (20 mM HEPES (pH 7.4), 150 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol and 100 mg ml−1 cycloheximide) to remove unbound anti-GFP. Ice-cold polysome extraction buffer (20 mM HEPES (pH 7.4), 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 U ml−1 cycloheximide, protease inhibitors and 40 U ml−1 recombinant RNasin Ribonuclease inhibitor) was added to the samples containing mouse hypothalamic and homogenized with a motor-driven Teflon glass homogenizer. Homogenates were centrifuged at 4 °C for 10 min at, 2000g to pellet cell debris. Supernatant was transferred to a new microcentrifuge tube and NP-40 (Applichem) and 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC; Avanti Polar Lipids) were added to the supernatant at a final concentration of 1% and 30 mM, respectively. After incubation on ice for 5 min, the clarified lysate was centrifuged for 10 min at 13,000g to pellet insoluble material. Next, 30µl of supernatant (input) was snap frozen in liquid nitrogen until RNA extraction as a comparison to the immunoprecipitated sample. Then, 200µl of anti-GFP-coated Dynal protein G magnetic beads were added to the supernatant, and the mixture was incubated at 4 °C with end-over-end rotation for 1 hr. Beads were subsequently collected on a MagnaRack (Invitrogen), washed four times with high-salt polysome wash buffer (20 mM HEPES (pH 7.4), 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol and 100 mg·ml−1 cycloheximide). Input and IP beads were resuspended and incubated in RLT buffer (RNAeasy micro kit, Qiagen) for 5 mins at RT. Supernatant was removed from the IP beads and RNA extraction was performed according to Qiagen’s protocol, including in-column DNase digestion. RNA was resuspended in 10 μl nuclease-free water. RNA quantity and quality of input and IP were determined with a Qubit Fluorometer (Invitrogen) and Agilent 4200 TapeStation System.
Briefly, anchored oligo-dT VN primer was added to the RNA lysis buffer, denatured at 72 °C for 3 min and immediately placed on ice. The reverse transcription reaction was performed using SMARTScribe (Takara Bio, Otsu, Japan) and LNA-TSO (GeneDesign, Osaka, Japan) at 42°C for 120 min followed by 70 °C for 10 min. The first strand cDNA synthesis product was added to the PCR amplification reaction system. The number of amplification cycles was set according to the sample volume, and full-length cDNA amplification was performed using a PCR instrument. The cDNA amplification products were purified using magnetic beads. An aliquot of the purified sample was used to check the library size distribution using the Agilent 2100 Bioanalyzer and High Sensitivity DNA Chip. Transposase digestion, end repair, and ligating of 1 ng purified cDNA were performed to construct a sequencing library specifically designed for the Illumina high-throughput sequencing platform. After magnetic bead sorting, the sequencing library underwent quality control using the Agilent 2100 Bioanalyzer. Pooled libraries were sequenced on Illumina NovaSeq X Plus sequencer with 150-bp Paired-End chemistry (Illumina) at the IIHG core.

value: Brain, Hypothalamus

value: rebound sleep


title: HepG2.batch2.control.rep1.C10

description: Library name: HepG2_Batch2_control_1_C10


title: RDY237 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS709


title: DABPA_5_R4_P4

description: Library name: s319

value: WT

value: chemical exposure


title: RDY236 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS708

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD31:TRP1


title: DABPA_1_R4_P4

description: Library name: s318


title: Brain,rebound sleep,total RNA(Input)_ rep#3

description: Library name: RS3Input


title: HepG2.batch2.control.rep1.B10

description: Library name: HepG2_Batch2_control_1_B10

value: liver

value: hepatocyte


title: HepG2.batch2.control.rep1.A10

description: Library name: HepG2_Batch2_control_1_A10

value: cell line


title: RDY236 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS706

value: 3 h IAA treatment, 6 min 4tU treatment


title: RDY236 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS704


title: HepG2.batch2.CAR.rep3.H04

description: Library name: HepG2_Batch2_CAR_3_H04


title: Brain,rebound sleep,pulldown RNA(IP)_ rep#4

description: Library name: RS4_IP


title: Brain,rebound sleep,pulldown RNA(IP)_ rep#3

description: Library name: RS3_IP


title: DABPA_0-1_R4_P4

description: Library name: s316


title: Brain,rebound sleep,total RNA(Input)_ rep#2

description: Library name: RS2Input


title: RDY236 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS707


title: DABPA_0-05_R4_P4

description: Library name: s315


title: HepG2.batch2.DIQ.rep1.E01

description: Library name: HepG2_Batch2_DIQ_1_E01


title: HepG2.batch2.CAR.rep3.G04

description: Library name: HepG2_Batch2_CAR_3_G04


title: RDY236 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS705


title: DABPA_0-01_R4_P4

description: Library name: s314


title: Brain,rebound sleep,total RNA(Input)_ rep#1

description: Library name: RS1Input


title: HepG2.batch2.CAR.rep3.F04

description: Library name: HepG2_Batch2_CAR_3_F04


title: Brain,rebound sleep,pulldown RNA(IP)_ rep#2

description: Library name: RS2_IP


title: HepG2.batch2.CAR.rep3.E04

description: Library name: HepG2_Batch2_CAR_3_E04


title: Brain,rebound sleep,pulldown RNA(IP)_ rep#1

description: Library name: RS1_IP


title: DABPA_0-001_R4_P4

description: Library name: s313


title: RDY236 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS703


title: RDY235 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS702

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD30:TRP1


title: BPK_50_R4_P4

description: Library name: s312

value: Mammary

value: bisphenol K


title: HepG2.batch2.CAR.rep3.D04

description: Library name: HepG2_Batch2_CAR_3_D04


title: RDY235 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS700


title: HepG2.batch2.CAR.rep3.C04

description: Library name: HepG2_Batch2_CAR_3_C04


title: Brain,control sleep,pulldown RNA(IP)_ rep#5

description: Library name: C5_IP

value: control sleep


title: BPK_10_R4_P4

description: Library name: s311

value: Epithelial


title: Brain,control sleep,total RNA(Input)_ rep#5

description: Library name: C5_Input


title: BPK_5_R4_P4

description: Library name: s310


title: HepG2.batch2.CAR.rep3.B04

description: Library name: HepG2_Batch2_CAR_3_B04


title: Brain,control sleep,pulldown RNA(IP)_ rep#4

description: Library name: C4_IP


title: RDY235 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS701

value: 3 h DMSO treatment, 6 min 4tU treatment


title: BPK_1_R4_P4

description: Library name: s309


title: HepG2.batch2.CAR.rep3.A04

description: Library name: HepG2_Batch2_CAR_3_A04


title: Brain,control sleep,total RNA(Input)_ rep#4

description: Library name: C4_Input


title: RDY235 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS699

value: yeast cell


title: HepG2.batch2.CAR.rep2.H04

description: Library name: HepG2_Batch2_CAR_2_H04


title: Brain,control sleep,pulldown RNA(IP)_ rep#3

description: Library name: C3_IP


title: BPK_0-1_R4_P4

description: Library name: s307


title: HepG2.batch2.CAR.rep2.G04

description: Library name: HepG2_Batch2_CAR_2_G04


title: RDY235 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS697


title: Brain,control sleep,total RNA(Input)_ rep#3

description: Library name: C3_Input


title: HepG2.batch2.CAR.rep2.F04

description: Library name: HepG2_Batch2_CAR_2_F04


title: BPK_0-01_R4_P4

description: Library name: s306


title: RDY234 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS696

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1


title: BPK_0-5_R4_P4

description: Library name: s308


title: Brain,control sleep,pulldown RNA(IP)_ rep#2

description: Library name: C2_IP

value: Brain, Hypothalamus


title: RDY234 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS694


title: Brain,control sleep,total RNA(Input)_ rep#2

description: Library name: C2_Input


title: HepG2.batch2.CAR.rep2.E04

description: Library name: HepG2_Batch2_CAR_2_E04


title: BPK_0-001_R4_P4

description: Library name: s305


title: HepG2.batch2.CAR.rep2.D04

description: Library name: HepG2_Batch2_CAR_2_D04


title: RDY234 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS692


title: Brain,control sleep,pulldown RNA(IP)_ rep#1

description: Library name: C1_IP


title: RDY234 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS695


title: HepG2.batch2.CAR.rep2.C04

description: Library name: HepG2_Batch2_CAR_2_C04


title: BPM_5_R4_P4

description: Library name: s303

value: bisphenol M


title: BPM_10_R4_P4

description: Library name: s304

value: WT


title: RDY234 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS693


title: Brain,control sleep,total RNA(Input)_ rep#1

description: Library name: C1_Input


title: HepG2.batch2.CAR.rep2.B04

description: Library name: HepG2_Batch2_CAR_2_B04


title: DABPA_0-5_R4_P4

description: Library name: s317

value: chemical exposure

value: diallyl bisphenol A


title: BPM_1_R4_P4

description: Library name: s302


title: RDY234 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS691


title: HepG2.batch2.CAR.rep2.A04

description: Library name: HepG2_Batch2_CAR_2_A04

value: liver


title: BPM_0-5_R4_P4

description: Library name: s301


title: BMDM, biol rep 5, TRα1PV, M2

city: Amsterdam

first: Esmée

last: Hoen

address: Meibergdreef 9

department: Department of Laboratory Medicine

country: Netherlands

institute: Amsterdam UMC

description: Library name: Run_5_pv_m2

data_processing:
RNA sequencing: Paired-End, 150 bp Trimmed for adapter sequences using Trimmomatic v0.39 (parameters: "ILLUMINACLIP:./adapters_list_v7.fa:2:40:15 MINLEN:15" ) Aligned using HISAT2 (v2.2.1) (default parameters; -p 4 --dta-cufflinks --rna-strandness RF; genome: GRCm39v105)
Counts obtained using HTSeq v1.99.2 parameters: -m union -f bam -r name -s reverse -a 10 -t exon GTF: Mus_musculus.GRCm39.105.gtf  QC performed using FastQC v0.11.9 QC performed using dupRadar v1.12.1
Count tabel made using HTSeq Filtering: Genes with more than 2 count-per-million reads (CPM) in 4 or more of the samples were kept. Normalization: TMM (edgeR), weighted trimmed mean of M-values (to the reference) is used (Robinson & Oshlack, 2010). No refColumn specified, so library whose upper quartile is closest to the mean upper quartile is used. Annotation: Genes were reannotated using biomaRt, using Ensembl (v113). The count data was transformed to log2-counts per million (logCPM) using voom, estimating the mean-variance relationship. Differential expression was assessed using a moderated t-test using the linear model framework from the limma package.
Benjamini-Hochberg false discovery rate to correct for multiple testing of the resulting p-values Analysis was performed using R v4.3.2 and Bioconductor v3.18
Assembly: GRCm39v105
Supplementary files format and content: COUNT file containing Ensembl Gene ID and raw counts per samples

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow from WT mice and transgenic mice with a TRα1 mutation (TRαPV) was cultured in DMEM/F12 with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin–neomycin (PSN), 1% GlutaMAX and 15 or 20% L929-conditioned medium for 7 days. During this culture time the monocytes from the bone marrow have differentiated into marrow derived macrophages (BMDMs).

extract_protocol:
RNA was isolated with the Roche High Pure RNA isolation kit according to the manufacturer’s instructions. 1,25 ug total RNA was used for the construction of sequence libraries.
The KAPA mRNA Hyperprep Kit was used to produce cDNA libraries from the RNA.

treatment_protocol: BMDMs were left unstimulated (unpolarized, M0) or polarized into a pro-inflammatory phenotype (M1) or immunomodulatory phenotype (M2). BMDMs were stimulated with either 20 ng/mL lipopolysaccharide (LPS) and 20 ng/mL interferon (IFN)-γ for M1 polarization or 20 ng/mL interleukin (IL)-4 for M2 polarization.

value: Bone marrow derived macrophages

value: Biol rep 5


title: BMDM, biol rep 5, TRα1PV, M1

description: Library name: Run_5_pv_m1


title: RDY73 SLAM-seq, 3 h IAA, rep C

description: Library name: RDHTS1133

value: 3 h IAA treatment, 6 min 4tU treatment


title: HepG2.batch2.CAR.rep1.H04

description: Library name: HepG2_Batch2_CAR_1_H04

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

value: hepatocyte

value: cell line


title: BPM_0-1_R4_P4

description: Library name: s300

value: Mammary


title: BMDM, biol rep 5, TRα1PV, M0

description: Library name: Run_5_pv_m0


title: RDY73 SLAM-seq, 3 h IAA, rep B

description: Library name: RDHTS1131


title: HepG2.batch2.CAR.rep1.G04

description: Library name: HepG2_Batch2_CAR_1_G04


title: RDY235 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS698

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD30:TRP1


title: BPM_0-05_R4_P4

description: Library name: s299

value: Epithelial


title: BMDM, biol rep 5, WT, M2

description: Library name: Run_5_wt_m2


title: HepG2.batch2.CAR.rep1.F04

description: Library name: HepG2_Batch2_CAR_1_F04


title: BMDM, biol rep 5, WT, M1

description: Library name: Run_5_wt_m1


title: RDY73 SLAM-seq, 3 h DMSO, rep C

description: Library name: RDHTS1132

value: 3 h DMSO treatment, 6 min 4tU treatment


title: RDY73 SLAM-seq, 3 h IAA, rep A

description: Library name: RDHTS1129

value: yeast cell


title: BPM_0-01_R4_P4

description: Library name: s298


title: BPM_0-001_R4_P4

description: Library name: s297


title: BMDM, biol rep 5, WT, M0

description: Library name: Run_5_wt_m0


title: RDY73 SLAM-seq, 3 h DMSO, rep B

description: Library name: RDHTS1130


title: HepG2.batch2.CAR.rep1.D04

description: Library name: HepG2_Batch2_CAR_1_D04


title: HepG2.batch2.CAR.rep1.E04

description: Library name: HepG2_Batch2_CAR_1_E04


title: BPE_50_R4_P4

description: Library name: s296

value: bisphenol E


title: BMDM, biol rep 4, TRα1PV, M2

description: Library name: Run_4_pv_m2

value: Biol rep 4


title: RDY73 SLAM-seq, 3 h DMSO, rep A

description: Library name: RDHTS1128


title: HepG2.batch2.CAR.rep1.C04

description: Library name: HepG2_Batch2_CAR_1_C04


title: BMDM, biol rep 4, TRα1PV, M1

description: Library name: Run_4_pv_m1


title: BPE_10_R4_P4

description: Library name: s295


title: HepG2.batch2.CAR.rep1.B04

description: Library name: HepG2_Batch2_CAR_1_B04


title: BPE_5_R4_P4

description: Library name: s294


title: BMDM, biol rep 4, TRα1PV, M0

description: Library name: Run_4_pv_m0


title: HepG2.batch2.CAR.rep1.A04

description: Library name: HepG2_Batch2_CAR_1_A04


title: RDY251 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS416

data_processing:
Paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) and bbduk (BBMap version 39.06). Forward reads were processed using SLAM-DUNK (version 0.4.3), where reads were aligned against the Saccharomyces cerevisiae genome using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 2 T>C conversions was used to define T>C read counts. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/SLAM-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Raw read count tables are provided in tab-separated values (.tsv) format. *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions.

extract_protocol:
RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer’s recommendations with minor modifications. Reagents used during RNA purification were supplemented with DTT to maintain reducing conditions. RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. Samples were protected from light when possible.
Libraries were constructed as previously described in detail (https://doi.org/10.1186/s44330-024-00008-1) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD46:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: RDY251 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS415


title: BPE_1_R4_P4

description: Library name: s293

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

value: WT

value: chemical exposure


title: HepG2.batch2.AMPA.rep3.H05

description: Library name: HepG2_Batch2_AMPA_3_H05

value: liver


title: BMDM, biol rep 4, WT, M2

description: Library name: Run_4_wt_m2

value: Bone marrow derived macrophages


title: RDY251 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS414


title: BPE_0-5_R4_P4

description: Library name: s292


title: BMDM, biol rep 4, WT, M1

description: Library name: Run_4_wt_m1


title: RDY251 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS413

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch2.AMPA.rep3.G05

description: Library name: HepG2_Batch2_AMPA_3_G05


title: BPE_0-1_R4_P4

description: Library name: s291


title: RDY251 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS412


title: HepG2.batch2.AMPA.rep3.F05

description: Library name: HepG2_Batch2_AMPA_3_F05


title: BMDM, biol rep 4, WT, M0

description: Library name: Run_4_wt_m0


title: BPE_0-01_R4_P4

description: Library name: s290


title: HepG2.batch2.AMPA.rep3.E05

description: Library name: HepG2_Batch2_AMPA_3_E05


title: BMDM, biol rep 3, TRα1PV, M2

description: Library name: Run_3_pv_m2

value: Biol rep 3


title: RDY251 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS411


title: BPE_0-001_R4_P4

description: Library name: s289


title: RDY249 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS290

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD44:TRP1


title: HepG2.batch2.AMPA.rep3.D05

description: Library name: HepG2_Batch2_AMPA_3_D05

value: hepatocyte

value: cell line


title: BMDM, biol rep 3, TRα1PV, M1

description: Library name: Run_3_pv_m1


title: PC_UH_R3_P3

description: Library name: s288

value: Mammary

value: technical control

value: universal human RNA


title: BMDM, biol rep 3, TRα1PV, M0

description: Library name: Run_3_pv_m0


title: RDY249 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS289

value: yeast cell


title: HepG2.batch2.AMPA.rep3.C05

description: Library name: HepG2_Batch2_AMPA_3_C05


title: PC_B_R3_P3

description: Library name: s287

value: Epithelial

value: brain RNA


title: BMDM, biol rep 3, WT, M2

description: Library name: Run_3_wt_m2


title: RDY249 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS288


title: HepG2.batch2.AMPA.rep3.B05

description: Library name: HepG2_Batch2_AMPA_3_B05


title: DMSO_0-1_R30_P3

description: Library name: s286

value: vehicle control

value: dimethyl sulfoxide


title: HepG2.batch2.AMPA.rep3.A05

description: Library name: HepG2_Batch2_AMPA_3_A05


title: BMDM, biol rep 3, WT, M1

description: Library name: Run_3_wt_m1

value: WT


title: RDY249 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS287


title: BMDM, biol rep 3, WT, M0

description: Library name: Run_3_wt_m0


title: DMSO_0-1_R29_P3

description: Library name: s285


title: RDY249 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS286


title: HepG2.batch2.AMPA.rep2.H05

description: Library name: HepG2_Batch2_AMPA_2_H05


title: BMDM, biol rep 2, TRα1PV, M2

description: Library name: Run_2_pv_m2

value: Biol rep 2


title: RDY249 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS285


title: DMSO_0-1_R27_P3

description: Library name: s283


title: HepG2.batch2.AMPA.rep2.G05

description: Library name: HepG2_Batch2_AMPA_2_G05

value: liver


title: DMSO_0-1_R28_P3

description: Library name: s284


title: RDY250 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS296

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD45:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: BMDM, biol rep 2, TRα1PV, M1

description: Library name: Run_2_pv_m1

value: Bone marrow derived macrophages


title: RDY250 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS295


title: DMSO_0-1_R26_P3

description: Library name: s282


title: HepG2.batch2.AMPA.rep2.F05

description: Library name: HepG2_Batch2_AMPA_2_F05


title: BMDM, biol rep 2, TRα1PV, M0

description: Library name: Run_2_pv_m0


title: DMSO_0-1_R25_P3

description: Library name: s281


title: HepG2.batch2.AMPA.rep2.E05

description: Library name: HepG2_Batch2_AMPA_2_E05


title: BMDM, biol rep 2, WT, M2

description: Library name: Run_2_wt_m2


title: RDY250 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS294


title: NC_R6_P3

description: Library name: s280

value: lysis buffer


title: RDY250 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS293

value: 25 min DMSO treatment, 4 min 4tU treatment


title: BMDM, biol rep 2, WT, M1

description: Library name: Run_2_wt_m1


title: HepG2.batch2.AMPA.rep2.C05

description: Library name: HepG2_Batch2_AMPA_2_C05

value: hepatocyte

value: cell line


title: HepG2.batch2.AMPA.rep2.D05

description: Library name: HepG2_Batch2_AMPA_2_D05


title: NC_R5_P3

description: Library name: s279

value: Mammary

value: technical control


title: BMDM, biol rep 2, WT, M0

description: Library name: Run_2_wt_m0


title: HepG2.batch2.AMPA.rep2.B05

description: Library name: HepG2_Batch2_AMPA_2_B05


title: RDY250 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS292

value: yeast cell


title: DMSO_0-1_R24_P3

description: Library name: s278

value: Epithelial


title: RDY250 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS291


title: BMDM, biol rep 1, TRα1PV, M2

description: Library name: Run_1_pv_m2

value: Biol rep 1


title: DMSO_0-1_R23_P3

description: Library name: s277

value: vehicle control


title: HepG2.batch2.AMPA.rep2.A05

description: Library name: HepG2_Batch2_AMPA_2_A05


title: BMDM, biol rep 1, TRα1PV, M1

description: Library name: Run_1_pv_m1


title: RDY241 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS386

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD36:TRP1


title: HepG2.batch2.AMPA.rep1.H05

description: Library name: HepG2_Batch2_AMPA_1_H05


title: DMSO_0-1_R22_P3

description: Library name: s276

value: WT

value: dimethyl sulfoxide


title: BMDM, biol rep 1, TRα1PV, M0

description: Library name: Run_1_pv_m0


title: RDY241 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS385


title: HepG2.batch2.AMPA.rep1.G05

description: Library name: HepG2_Batch2_AMPA_1_G05

value: liver


title: DMSO_0-1_R21_P3

description: Library name: s275


title: BMDM, biol rep 1, WT, M2

description: Library name: Run_1_wt_m2


title: RDY241 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS384


title: E2_1_R3_P3

description: Library name: s274

value: chemical exposure


title: HepG2.batch2.AMPA.rep1.F05

description: Library name: HepG2_Batch2_AMPA_1_F05


title: RDY241 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS383


title: HepG2.batch2.AMPA.rep1.E05

description: Library name: HepG2_Batch2_AMPA_1_E05


title: E2_0-1_R3_P3

description: Library name: s273


title: BMDM, biol rep 1, WT, M1

description: Library name: Run_1_wt_m1


title: RDY241 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS382


title: BMDM, biol rep 1, WT, M0

description: Library name: Run_1_wt_m0


title: HepG2.batch2.AMPA.rep1.D05

description: Library name: HepG2_Batch2_AMPA_1_D05


title: BPA_50_R3_P3

description: Library name: s272

value: bisphenol A


title: 3-week, No stress, mouse 5, replicate 2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Library name: 3wNS_5_rep2

data_processing:
Illumina NovaSeq X plus with double-end 150-nt read was used to sequence each library, generating ~15 million reads for each sample.
Read trimming was performed using default settings by Trim Galore!
Raw RNA-seq reads were then mapped to mouse mm10 genome (GRCm38) using Hisat2.
FeatureCounts was used to count reads. Genes for which more than 6 libraries (out of 10-12 libraries per condition) had fewer than 20 counts were excluded from downstream analysis.
The differentially expressed genes (DEGs) were determined by pairwise comparison using DESeq2 (34) with FDR < 0.05. The gene expression was normalized by variance stabilizing transformation (VST) from the DESeq2 and, DEGs were separated into two groups using k-means clustering.then the heatmap showing the gene expression of DEGs were plotted by ComplexHeatmap (2.16.0). The Gene Ontology (GO) analysis was conducted based on DEGs using ShinyGO 0.77 with FDR <0.05. The expression pattern of all the genes in each comparison was shown in the volcano plot by using ggplot2 (3.5.2). Volcano plot illustrating gene expression differences between each pairwise comparison. Genes upregulated at 1-week group are highlighted in red, while genes upregulated in the 3-week group are highlighted in blue. Significantly differentially expressed genes (|log2(fold change)| > 1 and -log10 adjusted p-value > 1.3) are labeled.
Assembly: mm10
Supplementary files format and content: Raw reads count (.csv)

source_name: Nucleus Accumbens

extract_protocol:
Bilateral NAc tissue (2.0 mm punch) samples were collected, frozen, and randomized before processing to prevent batch effects. Nuclei were isolated via dounce homogenization of NAc tissue in a cold extraction buffer, followed by filtration and iodixanol gradient centrifugation. NeuN+ nuclei were labeled with an Alexa Fluor 488-conjugated antibody (MAB377X, EMD Millipore Sigma) and sorted using FACS (BD Biosciences) (PMID: 35402909; PMID: 38508188; PMID: 34686347).
~8000 NeuN+ nuclei were used to produce one RNA-seq library and two technical replicates were generated on each NAc sample. RNA was extracted from sorted NeuN+ nuclei (RNeasy Mini Kit 74104, Qiagen), and cDNA were reverse transcribed using Smart-seq3 protocol (PMID: 32518404) with minor modifications. We used a tagmentation-based protocol to construct RNA-seq libraries(PMID: 40164799). The library fragment size was checked using high sensitivity DNA analysis kit (5067-4626, Agilent) on a TapeStation system (4150, Agilent), and any primer-dimers were removed using SPRIselect beads purification. Library was pooled based on the concentrations examined quantified by  using a KAPA library quantification kit (KK4824,Roche).

treatment_protocol: Male C57BL/6 (B6) mice were exposed daily to aggressive male CD-1 mice to induce CSDS first, then the mice were classified either stress-susceptible or resilient based on social interaction test. The nucleus accumbens (NAc) of susceptible and resilient mice, along with non-stressed control mice was collected at 1 week and 3 weeks after CSDS, resulting in six distinct experimental groups: 1wRES, 1wSUS, 1wNS, 3wRES, 3wSUS and 3wNS (n=5-6 per group).

value: Nucleus Accumbens

value: Neuron

value: male

value: 3-week, No Stress


title: RDY241 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS381

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch2.AMPA.rep1.C05

description: Library name: HepG2_Batch2_AMPA_1_C05

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

value: hepatocyte

value: cell line


title: 3-week, No stress, mouse 5, replicate 1

description: Library name: 3wNS_5_rep1


title: BPA_10_R3_P3

description: Library name: s271

value: Mammary


title: RDY240 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS326

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD35:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: BPA_5_R3_P3

description: Library name: s270

value: Epithelial


title: HepG2.batch2.AMPA.rep1.B05

description: Library name: HepG2_Batch2_AMPA_1_B05


title: 3-week, No stress, mouse 4, replicate 2

description: Library name: 3wNS_4_rep2


title: HepG2.batch2.AMPA.rep1.A05

description: Library name: HepG2_Batch2_AMPA_1_A05


title: BPA_1_R3_P3

description: Library name: s269


title: RDY240 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS325


title: 3-week, No stress, mouse 4, replicate 1

description: Library name: 3wNS_4_rep1


title: RDY240 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS324


title: HepG2.batch1.THX.rep3.H08

description: Library name: HepG2_Batch1_THX_3_H08


title: BPA_0-5_R3_P3

description: Library name: s268

value: WT


title: 3-week, No stress, mouse 3, replicate 2

description: Library name: 3wNS_3_rep2


title: RDY240 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS323


title: 3-week, No stress, mouse 3, replicate 1

description: Library name: 3wNS_3_rep1


title: BPA_0-1_R3_P3

description: Library name: s267


title: RDY240 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS322


title: HepG2.batch1.THX.rep3.G08

description: Library name: HepG2_Batch1_THX_3_G08


title: BPA_0-001_R3_P3

description: Library name: s266


title: HepG2.batch1.THX.rep3.F08

description: Library name: HepG2_Batch1_THX_3_F08


title: HepG2.batch1.THX.rep3.E08

description: Library name: HepG2_Batch1_THX_3_E08


title: BPA_0-01_R3_P3

description: Library name: s265


title: RDY240 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS321


title: 3-week, No stress, mouse 2, replicate 2

description: Library name: 3wNS_2_rep2


title: 3-week, No stress, mouse 2, replicate 1

description: Library name: 3wNS_2_rep1


title: RDY239 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS404

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD34:TRP1


title: TBPB_50_R3_P3

description: Library name: s264

value: tetrabromophenol blue


title: HepG2.batch1.THX.rep3.D08

description: Library name: HepG2_Batch1_THX_3_D08

value: liver


title: 3-week, No stress, mouse 1, replicate 2

description: Library name: 3wNS_1_rep2


title: RDY239 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS403


title: TBPB_10_R3_P3

description: Library name: s263

value: chemical exposure


title: 3-week, No stress, mouse 1, replicate 1

description: Library name: 3wNS_1_rep1

value: Nucleus Accumbens


title: RDY239 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS402


title: HepG2.batch1.THX.rep3.C08

description: Library name: HepG2_Batch1_THX_3_C08


title: TBPB_5_R3_P3

description: Library name: s262


title: HepG2.batch1.THX.rep3.A08

description: Library name: HepG2_Batch1_THX_3_A08


title: HepG2.batch1.THX.rep3.B08

description: Library name: HepG2_Batch1_THX_3_B08


title: RDY239 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS401


title: 1-week, No stress, mouse 6, replicate 2

description: Library name: 1wNS_6_rep2

value: Neuron

value: 1-week, No Stress


title: TBPB_1_R3_P3

description: Library name: s261


title: 1-week, No stress, mouse 6, replicate 1

description: Library name: 1wNS_6_rep1

value: male


title: RDY239 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS400

value: 25 min DMSO treatment, 4 min 4tU treatment


title: TBPB_0-5_R3_P3

description: Library name: s260


title: HepG2.batch1.THX.rep2.H08

description: Library name: HepG2_Batch1_THX_2_H08

value: hepatocyte


title: 1-week, No stress, mouse 5, replicate 2

description: Library name: 1wNS_5_rep2


title: RDY239 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS399


title: HepG2.batch1.THX.rep2.G08

description: Library name: HepG2_Batch1_THX_2_G08

value: cell line


title: TBPB_0-1_R3_P3

description: Library name: s259

value: Mammary


title: 1-week, No stress, mouse 5, replicate 1

description: Library name: 1wNS_5_rep1


title: HepG2.batch1.THX.rep2.F08

description: Library name: HepG2_Batch1_THX_2_F08


title: RDY238 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS398

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD33:TRP1


title: TBPB_0-01_R3_P3

description: Library name: s258


title: HepG2.batch1.THX.rep2.E08

description: Library name: HepG2_Batch1_THX_2_E08


title: TBPB_0-001_R3_P3

description: Library name: s257


title: 1-week, No stress, mouse 4, replicate 1

description: Library name: 1wNS_4_rep1


title: RDY238 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS397

value: 25 min IAA treatment, 4 min 4tU treatment


title: HepG2.batch1.THX.rep2.D08

description: Library name: HepG2_Batch1_THX_2_D08


title: 1-week, No stress, mouse 4, replicate 2

description: Library name: 1wNS_4_rep2


title: PRed_50_R3_P3

description: Library name: s256

value: Epithelial

value: phenol red


title: RDY238 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS395


title: PRed_10_R3_P3

description: Library name: s255

value: WT


title: HepG2.batch1.THX.rep2.C08

description: Library name: HepG2_Batch1_THX_2_C08


title: 1-week, No stress, mouse 3, replicate 2

description: Library name: 1wNS_3_rep2


title: RDY238 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS396


title: 1-week, No stress, mouse 3, replicate 1

description: Library name: 1wNS_3_rep1


title: RDY238 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS393


title: HepG2.batch1.THX.rep2.B08

description: Library name: HepG2_Batch1_THX_2_B08


title: RDY238 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS394


title: PRed_1_R3_P3

description: Library name: s253


title: HepG2.batch1.THX.rep2.A08

description: Library name: HepG2_Batch1_THX_2_A08


title: 1-week, No stress, mouse 2, replicate 2

description: Library name: 1wNS_2_rep2


title: PRed_5_R3_P3

description: Library name: s254


title: 1-week, No stress, mouse 2, replicate 1

description: Library name: 1wNS_2_rep1


title: RDY237 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS422

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD32:TRP1


title: HepG2.batch1.THX.rep1.H08

description: Library name: HepG2_Batch1_THX_1_H08

value: liver


title: PRed_0-5_R3_P3

description: Library name: s252

value: chemical exposure


title: 1-week, No stress, mouse 1, replicate 2

description: Library name: 1wNS_1_rep2

value: Nucleus Accumbens


title: HepG2.batch1.THX.rep1.G08

description: Library name: HepG2_Batch1_THX_1_G08


title: PRed_0-1_R3_P3

description: Library name: s251


title: RDY237 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS421


title: 1-week, No stress, mouse 1, replicate 1

description: Library name: 1wNS_1_rep1

value: Neuron


title: RDY237 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS420


title: PRed_0-01_R3_P3

description: Library name: s250


title: HepG2.batch1.THX.rep1.F08

description: Library name: HepG2_Batch1_THX_1_F08


title: 3-week, Resilient, mouse 6, replicate 2

description: Library name: 3wRES_6_rep2

value: 3-week, Resilient


title: HepG2.batch1.THX.rep1.E08

description: Library name: HepG2_Batch1_THX_1_E08


title: RDY237 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS419


title: PRed_0-001_R3_P3

description: Library name: s249


title: 3-week, Resilient, mouse 6, replicate 1

description: Library name: 3wRES_6_rep1

value: male


title: HepG2.batch1.THX.rep1.D08

description: Library name: HepG2_Batch1_THX_1_D08


title: RDY237 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS418

value: 25 min DMSO treatment, 4 min 4tU treatment


title: THPE_50_R3_P3

description: Library name: s248


title: 3-week, Resilient, mouse 5, replicate 2

description: Library name: 3wRES_5_rep2


title: RDY237 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS417


title: THPE_10_R3_P3

description: Library name: s247


title: 3-week, Resilient, mouse 5, replicate 1

description: Library name: 3wRES_5_rep1


title: RDY236 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS278

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD31:TRP1


title: HepG2.batch1.THX.rep1.C08

description: Library name: HepG2_Batch1_THX_1_C08

value: hepatocyte

value: cell line


title: THPE_5_R3_P3

description: Library name: s246

value: Mammary


title: RDY236 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS277

value: yeast cell


title: HepG2.batch1.THX.rep1.B08

description: Library name: HepG2_Batch1_THX_1_B08


title: HepG2.batch1.THX.rep1.A08

description: Library name: HepG2_Batch1_THX_1_A08


title: THPE_1_R3_P3

description: Library name: s245


title: 3-week, Resilient, mouse 4, replicate 2

description: Library name: 3wRES_4_rep2


title: 3-week, Resilient, mouse 4, replicate 1

description: Library name: 3wRES_4_rep1


title: RDY236 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS276

value: 25 min IAA treatment, 4 min 4tU treatment


title: THPE_0-5_R3_P3

description: Library name: s244

value: Epithelial


title: HepG2.batch1.MET.rep3.H07

description: Library name: HepG2_Batch1_MET_3_H07


title: 3-week, Resilient, mouse 3, replicate 2

description: Library name: 3wRES_3_rep2


title: THPE_0-1_R3_P3

description: Library name: s243


title: RDY236 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS275


title: 3-week, Resilient, mouse 3, replicate 1

description: Library name: 3wRES_3_rep1


title: HepG2.batch1.MET.rep3.G07

description: Library name: HepG2_Batch1_MET_3_G07


title: HepG2.batch1.MET.rep3.F07

description: Library name: HepG2_Batch1_MET_3_F07


title: THPE_0-01_R3_P3

description: Library name: s242


title: 3-week, Resilient, mouse 2, replicate 2

description: Library name: 3wRES_2_rep2


title: RDY236 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS274


title: RDY236 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS273


title: HepG2.batch1.MET.rep3.E07

description: Library name: HepG2_Batch1_MET_3_E07


title: 3-week, Resilient, mouse 2, replicate 1

description: Library name: 3wRES_2_rep1


title: RDY235 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS272

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD30:TRP1


title: THPE_0-001_R3_P3

description: Library name: s241

value: WT


title: HepG2.batch1.MET.rep3.D07

description: Library name: HepG2_Batch1_MET_3_D07


title: PA08_10_R3_P3

description: Library name: s240

value: plastic additive 08


title: HepG2.batch1.MET.rep3.C07

description: Library name: HepG2_Batch1_MET_3_C07

value: liver


title: RDY235 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS271