title: PDX human in mouse tumor resection sample, GEX modality

description: Library name: PDX2_rna

data_processing:
The raw reads from RNA sequencing outputs with single cell gene expression were aligned to both the hg38 human and mm10 mouse reference genome to correctly identify species transcripts, and then quantified by the CellRanger pipeline and human reads were thus seperated from mouse reads.
Assembly: hg38 and mm10
Supplementary files format and content: PDX2_sample_filtered_feature_bc_matrix.h5

source_name: PDX

extract_protocol:
PDX tumors from NOD/SCID mice were dissected, minced and digested in collagenase type I (Sigma) at 3.5 mg/ml in HBSS (Gibco) for 30 minutes and in DNase, trypsin and EDTA (5 mM) for other 30 minutes, at 37°C on a rocking plate. The digestion was stopped by adding FBS. The cell suspensions were rinsed in PBS supplemented with 10% FBS, filtered through a 70-μm cell strainer (BD Bioscience) and centrifuged at 1.000 rpm for 10 minutes at 4ºC. For antibody incubation, cells were resuspended in PBS supplemented with 2% FBS. Cells were incubated with FITC-conjugated anti-CD31 (rat, clone MEC 13.3, BD, 553372, dilution 1:100), FITC-conjugated anti-CD45 (rat, clone 30-F11, BD, 553079, dilution 1:100), FITC-conjugated anti-CD13 (rat, clone R3-242, BD, 558744, dilution 1:100), FITC-conjugated anti-CD45 (mouse, clone HI30, BD, 555482, dilution 1:50), APC-conjugated anti-EPCAM (mouse, clone EBA-1, BD, 347200, dilution 1:50), PE/Cy7- conjugated anti-CD298 (mouse, clone LNH-94, Biolegend, 341707, dilution 1:50) antibodies for 30 min at 4ºC protected from light.  After antibody staining, cell suspensions were washed with PBS supplemented with 2% FBS and centrifuged for 5 minutes. Cells were then resuspended in Hoechst 33342 trihydrochloride trihydrate (Invitrogen, H3570, dilution 1:4.000) and filtered through a 40-μm cell strainer (BD Bioscience). Living single tumor cells were selected by forward and side scatter, doublet discrimination and Hoechst dye exclusion. Tumor cells were selected based on CD298 expression and the exclusion of CD45, CD31 and CD13. EPCAM expression in tumor cells was then assessed on the CD298+ CD45- CD31- CD13- population.
PDX tumors were sorted as 100% CD298+ CD45- CD31- CD13-. Cells were collected in PBS, 0,04% filtered BSA, centrifuged at 250g, 5 min at 4ºC, resuspended in 50 μl PBS, 0,04% filtered BSA, counted and loaded on Chromium Single Cell 3′ microfluidic chips (10x Genomics). The libraries were prepared using GEM-X OCM 3' Chip Kit v4 4-plex, On-chip Multiplexing (OCM) was used (10x Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq.

value: PDX

value: tumor

value: PDX model - patient tumor grafted into NOD/SCID mouse

tag: library

value: mRNA


title: mNPC ES, MOF-dTAG, negative control, H4K5ac, rep2

status: Public on Jun 06 2026

type: SRA

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: neg_4h_mNPC_ES_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz

library_source: genomic

data_processing:
The data were processed using the snakePipes DNA-mapping (v2.1.2) (Bhardwaj et al. 2019). Illumina adaptors were removed using cutadapt (v2.8) (Martin 2011) with default settings. Reads were then mapped to the mm10 genome with Bowtie2 (v2.3.5.1) (Langmead and Salzberg 2012), using the modified options –local –very-sensitive-local –no-mixed –no-discordant –phred33 -I 60 -X 700. Reads mapping to blacklisted regions from the Encode Consortium (Amemiya, Kundaje, and Boyle 2019) were discarded. Finally, only properly paired mapped reads and reads with a mapping quality over 3 were retained for further analysis
Assembly: mm10
Supplementary files format and content: bigwig files from sequencing-depth normalized counts
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: mNPC

growth_protocol: NPCs were cultured in N2B27 medium supplemented with EGF and FGF on gelatin-coated plates.

extract_protocol:
DNA fragments were isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research) and eluted with 15 l elution buffer (provided by the kit). The library was prepared using 13 l DNA solution, mixed with 1 l of 10 M barcoded i5 and i7 primers separately, and 15 l NEBNext HiFi 2x PCR Master Mix. The PCR program included 72 °C for 5 minutes, 98 °C for 30 seconds, followed by 13 to 16 cycles of 98 °C for 10 seconds and 72 °C for 10 seconds, ending with 72 °C for 1 minute and holding at 8 °C. Ampure beads (39 l) were used for DNA purification.
CUT&Tag

treatment_protocol: MOF-dTAG cells were treated with dTAG13 (5 mg, Tocris) at 500nM, or with TSA at 330nM at different time points before proceeding the downstream experiments.

tag: cell type

value: mNPC

tag: genotype

value: MOF-dTAG

tag: treatment

value: negative control

tag: cut&tag antibody


title: mNPC LS, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep2

description:
Library name: dtag_4h_mNPC_LS_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample9

city: Duluth

first: Peter

last: Schumann

state: MN

address: 6201 Congdon Blvd

country: USA

institute: United States Environmental Protection Agency

description:
Chem3_B_D1_A04
Chem3_counts_matrix.txt

library_source: transcriptomic

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples

molecule: total RNA

organism: Pimephales promelas

source_name: whole body

growth_protocol: not applicable

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

treatment_protocol: High-throughput in vivo exposures were conducted in 1 mL 96-well deep well plates (NEST, Catalog #502162) for 24 h. Each exposure consisted of two chemicals tested in a 1/2 log dilution series with five replicates per treatment concentration on each of three plates (15 organisms exposed per concentration). Final exposure concentrations ranged from 66.67 – 0.021 µM for all data poor chemicals, except fipronil amide (56.43- 0.018 µM) and fexofenadine hydrochloride (32.2 – 0.011 µM). All chemical stocks were prepared in DMSO and had purities > 95%. For each exposure, a Tecan D300e Bioprinter (Corvallis, OR, USA) was used to prepare an initial chemical dosing plate containing 1800 µL/well of test solution diluted in UV-treated, filtered Lake Superior Water in a 2 mL 96-well deep well plate (NEST, Catalog #503162). The concentration of DMSO was normalized across all wells to match those of the highest % DMSO obtained with the chemical delivery (i.e., the highest exposure concentration; generally 0.34% DMSO). Using the bioprinter, the dosing solutions were arranged to evenly distribute replicate exposure groups along the edges of the plate to avoid confounding any edge effects, if present, with treatment. For each exposure, one organism was loaded with 150 µL of control water (UV-treated, filtered Lake Superior Water) to each well of the three 96-well plates. A multi-channel pipette was used to deliver 550 µL of dosing solution to each well for a final volume of 700 µL per well. Each assay included DMSO controls, with final in-well DMSO concentrations never exceeding 0.34% in the exposure plate wells.

tag: tissue

value: whole body

tag: developmental stage

value: larval


title: mNPC LS, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep1

description:
Library name: dtag_4h_mNPC_LS_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample8

description:
Chem3_A_D8_H04
Chem3_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample7

description:
Chem3_A_D7_G04
Chem3_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample16

description:
Chem4_B_D8_H05
Chem4_counts_matrix.txt

value: Gabapentin


title: whole larval P. promelas, Gabapentin, sample20

description:
Chem4_C_D4_D05
Chem4_counts_matrix.txt


title: mNPC G0_1, MOF-dTAG, negative control, H4K8ac, rep2

description:
Library name: neg_4h_mNPC_G0_1_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, Gabapentin, sample21

description:
Chem4_C_D5_E05
Chem4_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample6

description:
Chem3_A_D6_F04
Chem3_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample11

description:
Chem4_B_D3_C05
Chem4_counts_matrix.txt


title: mNPC G0_1, MOF-dTAG, negative control, H4K8ac, rep1

description:
Library name: neg_4h_mNPC_G0_1_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample5

description:
Chem3_A_D5_E04
Chem3_counts_matrix.txt


title: mNPC ES, MOF-dTAG, negative control, H4K8ac, rep2

description:
Library name: neg_4h_mNPC_ES_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample4

description:
Chem3_A_D4_D04
Chem3_counts_matrix.txt


title: mNPC ES, MOF-dTAG, negative control, H4K8ac, rep1

description:
Library name: neg_4h_mNPC_ES_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC G2_M, MOF-dTAG, negative control, H4K8ac, rep1

description:
Library name: neg_4h_mNPC_G2_M_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample3

description:
Chem3_A_D3_C04
Chem3_counts_matrix.txt


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample2

description:
Chem3_A_D2_B04
Chem3_counts_matrix.txt


title: mNPC G2_M, MOF-dTAG, negative control, H4K8ac, rep2

description:
Library name: neg_4h_mNPC_G2_M_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: bone marrow-derived Lin-Sca-1+c-Kit+  rep2

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

country: China

institute: Zhejiang University

data_processing:
The predefined gene sets representing the comprehensive biological processes are from the Molecular Signatures Database (MSigDB v7.0)
The sequencing data were compared with the reference genome using Hisat software
StringTie was used to determine the expression levels for mRNAs by calculating fragments per kilobase of transcript per million mapped reads (FPKM)
The differentially expressed mRNAs and genes were selected with log2 (fold change) > 1 or log2 (fold change) < − 1 and with statistical significance (P value < 0.05) by Ballgown
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from 2000 isolated single cells (Lin-Sca-1+c-Kit- cells from bone marrow of primary recipient transplanted with sorted CD144+ cell and Lin-Sca-1+c-Kit+ cells (LSK) from bone marrow of 6-8 weeks C57BL/6 mice) and reverse transcribed using the SMART-Seq v4 Ultra Low Input RNA kit
libraries were generated with the cDNAs using the Nextera XT DNA Library Preparation Kit (FC-131-1024, Illumina, San Diego, CA), and sequenced using the Illumina Hiseq XTEN platform at Novogene Co.Ltd  (Beijing,  China).

value: Bone marrow

tag: cell line

value: primary cell

value: hematopoietic cells

value: Wild type

value: untreated


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample24

description:
Chem2_C_D8_H03
Chem2_counts_matrix.txt

value: 3,4-Dichlorophenyl isocyanate


title: mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep1

description:
Library name: dtag_4h_mNPC_G0_1_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample1

description:
Chem3_A_D1_A04
Chem3_counts_matrix.txt


title: whole larval P. promelas, Gabapentin, sample3

description:
Chem4_A_D3_C05
Chem4_counts_matrix.txt


title: mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep2

description:
Library name: dtag_4h_mNPC_G0_1_H4K5ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC ES, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep2

description:
Library name: dtag_4h_mNPC_ES_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample23

description:
Chem2_C_D7_G03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample22

description:
Chem2_C_D6_F03
Chem2_counts_matrix.txt


title: mNPC ES, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep1

description:
Library name: dtag_4h_mNPC_ES_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), H4K5ac, rep1

description:
Library name: dtag_4h_mNPC_G2_M_H4K5ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample20

description:
Chem2_C_D4_D03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample19

description:
Chem2_C_D3_C03
Chem2_counts_matrix.txt


title: mNPC LS, MOF-dTAG, negative control, H4K8ac, rep2

description:
Library name: neg_4h_mNPC_LS_H4K8ac_2
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), H4K8ac, rep1

description:
Library name: dtag_4h_mNPC_G2_M_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample17

description:
Chem2_C_D1_A03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample18

description:
Chem2_C_D2_B03
Chem2_counts_matrix.txt


title: mNPC LS, MOF-dTAG, negative control, H4K8ac, rep1

description:
Library name: neg_4h_mNPC_LS_H4K8ac_1
bigwig_files_H4K5_8ac_CUTnTAG.tar.gz


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample16

description:
Chem2_B_D8_H03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample15

description:
Chem2_B_D7_G03
Chem2_counts_matrix.txt


title: siSetdb1_1

city: hangzhou city

first: qiang

last: chen

address: No. 1369, Wenyi West Road, Yuhang District

institute: Liangzhu Laboratory

description: Library name: Sample10

data_processing:
Trimmomatic (v0.39) – Raw sequencing reads were processed to remove adapters and low-quality reads (quality limit: 0.05).
STAR (v2.7.10a) – Clean reads were aligned to the mouse reference genome (GRCm38/mm10) using parameters: mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8.
featureCounts (v2.0.3) – Gene-level raw counts were quantified based on Ensembl annotation (release 102).
DESeq2 (v1.36.0) – Differential expression analysis between control and experimental groups. Genes with absolute log2 fold change > 1 and adjusted p-value (Benjamini-Hochberg) < 0.05 were considered significantly differentially expressed.
Assembly: GRCm38/mm10
Supplementary files format and content: CSV file  including FPKM for each sample

source_name: Brown  adipose tissue

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher Scientific, #15596018) according to manufacturer's protocol. RNA purity and concentration were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Kit.
Sequencing libraries were constructed using NEBNext Ultra II RNA Library Prep Kit (NEB, #E7770) following manufacturer's instructions. mRNA was enriched using oligo(dT) beads.

value: Brown  adipose tissue

value: primary brown adipocyte


title: siSetdb1_2

description: Library name: Sample11


title: siNC

description: Library name: Sample9

value: siNC


title: PC_A_KO

description: Library name: Sample7

value: 4-OHT (1 μM)


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample12

description:
Chem2_B_D4_D03
Chem2_counts_matrix.txt


title: PC_A_CTL

description: Library name: Sample5

value: ETOH vehicle


title: TN_CE_KO_2

description: Library name: Sample4

value: Setdb1 AKO (Setdb1 fl/fl; Adipoq-Cre+)


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample10

description:
Chem2_B_D2_B03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample9

description:
Chem2_B_D1_A03
Chem2_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample8

description:
Chem2_A_D8_H03
Chem2_counts_matrix.txt


title: TN_CE_CTL_2

description: Library name: Sample2

value: Control (Setdb1 fl/fl; Adipoq-Cre-)


title: whole larval P. promelas, 1(2H)-Phthalazinone, sample15

description:
Chem3_B_D7_G04
Chem3_counts_matrix.txt


title: YK184_Median_left_E15_5

status: Public on Jun 08 2026

city: Boston

first: Yuemeng

last: Jia

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description: Library name: YK184_Median_left_E15_5

data_processing:
The data was process with our customized software (https://gitlab.com/hormozlab/carlin)
Assembly: mm10
Supplementary files format and content: text files

source_name: Liver

extract_protocol:
RNA were extracted with Qiagen RNAeasy
RNA was reverse transcribed using a CARLIN-specific UMI-tagged primer. The DARLIN from Col1a1 was was then PCR amplified by nested PCR

value: Liver


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample7

description:
Chem2_A_D7_G03
Chem2_counts_matrix.txt

value: whole body


title: TN_CE_CTL_1

description: Library name: Sample1


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample6

description:
Chem2_A_D6_F03
Chem2_counts_matrix.txt

value: larval


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample5

description:
Chem2_A_D5_E03
Chem2_counts_matrix.txt


title: MSCs, TAC 4w, gene expression, biol rep 2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

description: Library name: TAC2_MSC

data_processing:
Reads were aligned to the mm10 mouse genome using STAR. Aligned read files were analyzed using HOMER. Differential expression analysis was performed using DESeq2. Gene set enrichment analysis was performed using GSEApy.
Assembly: Mouse mm10
Supplementary files format and content: UCSC bedGraph format files (genome coverage signal tracks, gzip compressed, compatible with UCSC Genome Browser and IGV)

source_name: Mesenchymal stromal cells

extract_protocol:
Tibiae, femurs, and pelvis were harvested from mice (3 sham-operated and 3 TAC mice) and processed separately for isolation of MSCs. Bone marrow was first collected by flushing with cell suspension medium (PBS containing 2% FBS) and digested with collagenase type II (1 mg/mL) and DNase I (25 U/mL) in HBSS for 30 min at 37 °C. Remaining bone fragments were then crushed and further digested with collagenase type I (2.5 mg/mL) and DNase I (25 U/mL) in HBSS for 45 min at 37 °C. Cell suspensions were washed, filtered through a 100 µm strainer, and subjected to red blood cell lysis using PharmLyse solution. Cells were depleted of hematopoietic and endothelial populations using Mouse CD45 MicroBeads, CD31 MicroBeads, and Lineage Cell Depletion Kit (Miltenyi Biotec) via autoMACS separation. The negatively selected cells were washed and maintained in FACS buffer supplemented with actinomycin D (2 µM). Cells were stained with antibodies against lineage markers (Ter119, CD45, CD71, CD144, CD31, CD41, CD61, CD11b, Gr1, CD45R, CD5) and Leptin receptor (Lepr). Lin-Lepr+ cells were sorted as MSCs.
RNA-seq libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocols.

treatment_protocol: Transverse aortic constriction (TAC) surgery was performed to induce cardiac stress. Sham-operated mice underwent identical surgical procedures without aortic constriction.

value: Mesenchymal stromal cells

value: TAC


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample4

description:
Chem2_A_D4_D03
Chem2_counts_matrix.txt


title: MSCs, TAC 4w, gene expression, biol rep 3

description: Library name: TAC3_MSC


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample2

description:
Chem2_A_D2_B03
Chem2_counts_matrix.txt


title: MSCs, control, gene expression, biol rep 2

description: Library name: control2_MSC

value: sham


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample3

description:
Chem2_A_D3_C03
Chem2_counts_matrix.txt


title: YK184_Median_right_E15_5

description: Library name: YK184_Median_right_E15_5


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample1

description:
Chem2_A_D1_A03
Chem2_counts_matrix.txt


title: whole larval P. promelas, cis-Nonachlordane, sample24

description:
Chem12_C_D8_H11
Chem12_counts_matrix.txt

value: cis-Nonachlordane


title: whole larval P. promelas, cis-Nonachlordane, sample23

description:
Chem12_C_D7_G11
Chem12_counts_matrix.txt


title: Female, MSCs, TAC 4w, gene expression

description:
Library name: TAC_MSC
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) and aligned to the mouse reference genome (GRCm39). Downstream analyses were performed primarily using Seurat (v4) and SCALA. For MSC datasets, cells with fewer than 586 UMIs or mitochondrial gene content >5% were excluded. To remove potential doublets, cells with high  unique molecular identifiers (UMIs) counts (>3,500) were also excluded. After filtering, 5,063 control cells and 2,956 TAC cells were retained. Datasets were integrated using the fastMNN algorithm to correct for batch effects. Clustering was performed using a graph-based approach with the Louvain modularity optimization algorithm. Uniform Manifold Approximation and Projection (UMAP) was used for dimensionality reduction and visualization.
Assembly: Mouse GRCm39
Supplementary files format and content: AnnData h5ad file (MSC.h5ad) containing gene expression count matrix, cell-level metadata (sample identity, cluster assignment, sex), and dimensionality reduction results (UMAP) for female MSCs (control and TAC).

extract_protocol:
Tibiae, femurs, and pelvis were harvested from mice (3 sham-operated and 3 TAC mice) and processed separately for isolation of HSPCs and MSCs. Bone marrow was first collected by flushing with cell suspension medium (PBS containing 2% FBS) and digested with collagenase type II (1 mg/mL) and DNase I (25 U/mL) in HBSS for 30 min at 37 °C. Remaining bone fragments were then crushed and further digested with collagenase type I (2.5 mg/mL) and DNase I (25 U/mL) in HBSS for 45 min at 37 °C. Cell suspensions were washed, filtered through a 100 µm strainer, and subjected to red blood cell lysis using PharmLyse solution. Cells were depleted of hematopoietic and endothelial populations using Mouse CD45 MicroBeads, CD31 MicroBeads, and Lineage Cell Depletion Kit (Miltenyi Biotec) via autoMACS separation. The negatively selected cells were washed and maintained in FACS buffer supplemented with actinomycin D (2 µM). Three biological replicates in each group were labeled with TotalSeq-B0301, B0311, B0312 (anti-mouse Hashtag 1,11,12). Cells were stained with antibodies against lineage markers (Ter119, CD45, CD71, CD144, CD31, CD41, CD61, CD11b, Gr1, CD45R, CD5) and Leptin receptor (Lepr). Lin-Lepr+ cells were sorted as MSCs. Hashtag-labeled cells were pooled within each experimental group.
Single-cell suspensions were processed using the 10x Genomics Chromium platform with the Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index) according to the manufacturer’s instructions. Feature Barcoding technology was used for cell hashing with oligonucleotide-labeled antibodies to enable sample multiplexing.


title: Female, MSCs, control, hashtag

description:
Library name: Hashtag250918_1
10x Genomics. Female samples demultiplexed using TotalSeq-B0301 (F_3), TotalSeq-B0311 (F_1), TotalSeq-B0312 (F_2).

library_source: other

molecule: protein


title: whole larval P. promelas, cis-Nonachlordane, sample22

description:
Chem12_C_D6_F11
Chem12_counts_matrix.txt


title: whole larval P. promelas, cis-Nonachlordane, sample21

description:
Chem12_C_D5_E11
Chem12_counts_matrix.txt


title: Female, MSCs, control, gene expression

description:
Library name: control_MSC
10x Genomics


title: MSCs, TAC 4w, hashtag

description:
Library name: HTO_MSC_2
TotalSeq-B hashtag oligo library. Demultiplexing: HTO_B0301=MSC_TAC4w_1, HTO_B0302=MSC_TAC4w_2, HTO_B0303=MSC_TAC4w_3, HTO_B0304=MSC_TAC4w_4, HTO_B0305=MSC_TAC4w_5, HTO_B0306=MSC_TAC4w_6, HTO_B0307=MSC_TAC4w_7, HTO_B0308=MSC_TAC4w_8.

data_processing:
Raw sequencing data were processed using Cell Ranger (10x Genomics) and aligned to the mouse reference genome (mm10). Downstream analyses were performed primarily using Seurat (v4) and SCALA. For HSPC datasets, cells were filtered based on quality control metrics: cells with fewer than 941 unique molecular identifiers (UMIs) or with mitochondrial gene content greater than 7% were excluded. To minimize the inclusion of potential doublets, cells with abnormally high UMI counts (>3,272) were also removed. After filtering, 10,351 control cells and 8,167 TAC cells were retained for downstream analyses. Datasets from control and TAC groups were integrated using the SCALA v4 standard integration workflow. For MSC datasets, cells with fewer than 586 UMIs or mitochondrial gene content ≥5% were excluded. To remove potential doublets, cells with high UMI counts (≥3,500) were also excluded. After filtering, 3,508 control cells and 4,477 TAC cells were retained. Datasets were integrated using the fastMNN algorithm to correct for batch effects. Clustering was performed using a graph-based approach with the Louvain modularity optimization algorithm. Uniform Manifold Approximation and Projection (UMAP) was used for dimensionality reduction and visualization.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separeted value files and matrix files

extract_protocol:
Tibiae, femurs, and pelvis were harvested from mice (3 sham-operated and 5 TAC mice) and processed separately for isolation of HSPCs and MSCs. For HSPC isolation, bone marrow cells were obtained by crushing bones in MACS buffer supplemented with actinomycin D (2 µM), which was included in all buffers throughout the procedure to minimize transcriptional changes during sample processing. Cells were filtered through a 70 µm strainer after passing through a 23-gauge needle. Red blood cells were lysed using PharmLyse solution, followed by washing and filtration through a 40 µm strainer. Cells were enriched for c-Kit+ populations using CD117 MicroBeads (Miltenyi Biotec) and autoMACS separation. Cells were maintained in FACS buffer containing actinomycin D (2 µM) and labeled with sample-specific hashtag oligonucleotides (TotalSeq-B, BioLegend) for multiplexing. For control samples, three biological replicates were labeled with TotalSeq-B0301–B0303 (anti-mouse Hashtag 1–3), and for TAC samples, eight biological replicates were labeled with TotalSeq-B0301–B0308 (anti-mouse Hashtag 1–8). Cells were stained with antibodies against CD45.2, Sca-1, c-Kit, CD34, CD135, CD48, CD150, and lineage markers (CD4, CD8a, CD11b, Ly6G, B220, CD127, Ter119). Lin-CD45.2+Sca-1+c-Kit+ (LSK) cells were sorted using a FACSAria Fusion (BD Biosciences). Hashtag-labeled cells were pooled within each experimental group. For MSC isolation, bone marrow was first collected by flushing with cell suspension medium (PBS containing 2% FBS) and digested with collagenase type II (1 mg/mL) and DNase I (25 U/mL) in HBSS for 30 min at 37 °C. Remaining bone fragments were then crushed and further digested with collagenase type I (2.5 mg/mL) and DNase I (25 U/mL) in HBSS for 45 min at 37 °C. Cell suspensions were washed, filtered through a 100 µm strainer, and subjected to red blood cell lysis using PharmLyse solution. Cells were depleted of hematopoietic and endothelial populations using Mouse CD45 MicroBeads, CD31 MicroBeads, and Lineage Cell Depletion Kit (Miltenyi Biotec) via autoMACS separation. The negatively selected cells were washed and maintained in FACS buffer supplemented with actinomycin D (2 µM), followed by labeling with sample-specific hashtag oligonucleotides (TotalSeq-B, BioLegend) consistent with the HSPC sample barcoding scheme. Cells were stained with antibodies against lineage markers (Ter119, CD45, CD71, CD144, CD31, CD41, CD61, CD11b, Gr1, CD45R, CD5) and Leptin receptor (Lepr). Lin−Lepr+ cells were sorted as MSCs. Hashtag-labeled cells were pooled within each experimental group.
Single-cell suspensions were processed using the 10x Genomics Chromium platform with the Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index) according to the manufacturer’s instructions. Feature Barcoding technology was used for cell hashing with oligonucleotide-labeled antibodies to enable sample multiplexing.


title: YJ774_Right_superior_E10

description: Library name: YJ774_Right_superior_E10


title: whole larval P. promelas, cis-Nonachlordane, sample20

description:
Chem12_C_D4_D11
Chem12_counts_matrix.txt


title: MSCs, control, hashtag

description:
Library name: HTO_MSC_1
TotalSeq-B hashtag oligo library. Demultiplexing: HTO_B0301=MSC_CTRL_1, HTO_B0302=MSC_CTRL_2, HTO_B0303=MSC_CTRL_3, HTO_B0304=MSC_TAC1w_1, HTO_B0305=MSC_TAC1w_2, HTO_B0306=MSC_TAC1w_3, HTO_B0307=MSC_TAC1w_4, HTO_B0308=MSC_TAC1w_5. MSC_TAC1w samples are not part of this submission.


title: whole larval P. promelas, cis-Nonachlordane, sample19

description:
Chem12_C_D3_C11
Chem12_counts_matrix.txt


title: MSCs, TAC 4w, gene expression

description:
Library name: GEX_MSC_2
10x Genomics 3' gene expression library. Contains MSC_TAC4w_1-8 (HTO_B0301-308) multiplexed cells.


title: MSCs, control, gene expression

description:
Library name: GEX_MSC_1
10x Genomics 3' gene expression library. Contains MSC_CTRL (HTO_B0301-303) and MSC_TAC1w (HTO_B0304-308) multiplexed cells. MSC_TAC1w samples are not part of this submission.


title: whole larval P. promelas, cis-Nonachlordane, sample17

description:
Chem12_C_D1_A11
Chem12_counts_matrix.txt


title: LSK cells, TAC 4w, hashtag

description:
Library name: HTO_LSK_2
TotalSeq-B hashtag oligo library. Demultiplexing: HTO_B0301=LSK_TAC4w_1, HTO_B0302=LSK_TAC4w_2, HTO_B0303=LSK_TAC4w_3, HTO_B0304=LSK_TAC4w_4, HTO_B0305=LSK_TAC4w_5, HTO_B0306=LSK_TAC4w_6, HTO_B0307=LSK_TAC4w_7, HTO_B0308=LSK_TAC4w_8.

source_name: Hematopoietic stem progenitor cells

value: Hematopoietic stem progenitor cells


title: whole larval P. promelas, cis-Nonachlordane, sample16

description:
Chem12_B_D8_H09
Chem12_counts_matrix.txt


title: LSK cells, control, hashtag

description:
Library name: HTO_LSK_1
TotalSeq-B hashtag oligo library. Demultiplexing: HTO_B0301=LSK_CTRL_1, HTO_B0302=LSK_CTRL_2, HTO_B0303=LSK_CTRL_3, HTO_B0304=LSK_TAC1w_1, HTO_B0305=LSK_TAC1w_2, HTO_B0306=LSK_TAC1w_3, HTO_B0307=LSK_TAC1w_4, HTO_B0308=LSK_TAC1w_5. LSK_TAC1w samples are not part of this submission.


title: LSK cells, control, gene expression

description:
Library name: GEX_LSK_1
10x Genomics 3' gene expression library. Contains LSK_CTRL (HTO_B0301-303) and LSK_TAC1w (HTO_B0304-308) multiplexed cells. LSK_TAC1w samples are not part of this submission.


title: whole larval P. promelas, cis-Nonachlordane, sample14

description:
Chem12_B_D6_F09
Chem12_counts_matrix.txt


title: LSK cells, TAC 4w, gene expression

description:
Library name: GEX_LSK_2
10x Genomics 3' gene expression library. Contains LSK_TAC4w_1-8 (HTO_B0301-308) multiplexed cells.


title: whole larval P. promelas, cis-Nonachlordane, sample13

description:
Chem12_B_D5_E09
Chem12_counts_matrix.txt


title: LSCs,Nynrin-KO4

city: Chongqing

first: Jianming

last: Wang

state: Chongqing

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing medical university

description: Library name: NH-8

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample …

source_name: Primary cell

extract_protocol:
About 10000 LSCs (GFP+c-Kit+Gr-1-) were isolated by FACS and the mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction RNA libraries were prepared for sequencing using standard Illumina protocols
The mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Leukemia stem cell

value: Nynrin-KO


title: whole larval P. promelas, cis-Nonachlordane, sample12

description:
Chem12_B_D4_D09
Chem12_counts_matrix.txt


title: LSCs,Nynrin-KO3

description: Library name: NH-7


title: whole larval P. promelas, cis-Nonachlordane, sample10

description:
Chem12_B_D2_B09
Chem12_counts_matrix.txt


title: whole larval P. promelas, cis-Nonachlordane, sample11

description:
Chem12_B_D3_C09
Chem12_counts_matrix.txt


title: LSCs,Nynrin-KO2

description: Library name: NH-6


title: LSCs,Nynrin-KO1

description: Library name: NH-5


title: YJ774_Left1_E10

description: Library name: YJ774_Left1_E10


title: YK184_Caudate_E15_5

description: Library name: YK184_Caudate_E15_5


title: LSCs,WT4

description: Library name: NH-4

value: WT


title: whole larval P. promelas, cis-Nonachlordane, sample8

description:
Chem12_A_D8_H05
Chem12_counts_matrix.txt


title: LSCs,WT3

description: Library name: NH-3


title: whole larval P. promelas, cis-Nonachlordane, sample7

description:
Chem12_A_D7_G05
Chem12_counts_matrix.txt


title: LSCs, WT2

description: Library name: NH-2


title: whole larval P. promelas, cis-Nonachlordane, sample6

description:
Chem12_A_D6_F05
Chem12_counts_matrix.txt


title: LSCs, WT1

description: Library name: NH-1


title: whole larval P. promelas, cis-Nonachlordane, sample5

description:
Chem12_A_D5_E05
Chem12_counts_matrix.txt


title: D-4N-E18.5-heart-sc

city: Kunming

first: Shu

last: Wei

address: No.17 Longxin Road, Ciba Subdistrict, Panlong District

department: Group of Non-human primates of reproductive and stem cell

institute: Kunming insititute of zoology

description:
Library name: SRHX250000444-1a
4N-treatment

data_processing:
We use fastp to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.If cleanreads is indispensable: Then, raw read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below: (1)Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW: 4:10)                                                                                (2)Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3)Remove adapters : there are two modes to remove the adapter sequence: alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa: 2: 30: 7) (4)Drop reads below the 26 bases long(5)Discard those reads that can not form pairedThe remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use fastp to perform basic statisticson the quality of the cleanreads.                                                                                Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
In detail: cellranger count takes FASTQ files performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature_x0002_barcode matrices, determine clusters, and perform gene expression analysis. The count pipeline can take input from multiple sequencing runs on the same GEM well. Add -–nosecondary option to skip secondary analysis of the feature-barcode matrix (dimensionality reduction, clustering and visualization) When doing large studies involving multiple GEM wells, run cellranger count on FASTQ data from each of the GEM wells individually, and then pool the results using cellranger aggr: cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data. The aggr pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis. Befor Secondary Analysis of Gene Expression we use Seurat Second QC it(as above). Subsequent analysis of cellranger reanalyze and Seurat were all performed basing on this output gene expression matrix .Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings. Seurat The Seurat package was used to normalise data, dimensionality reduction, clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6. Global Analysis Between Samples Based on filtered gene expression matrix by Seurat ,between samples differential expression analysis was carried out using the edgeR package ( McCarthy et al., 2012) to obtain zone-specific marker genes. Enrichment analysis of marker genes Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by marker gene. KEGG (Kanehisa M, 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We usedclusterProfiler R package to test the statistical enrichment of markergenes in KEGG pathways. Reactome pathway-based analysis of marker genes was implemented by the ReactomePA R package. REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database( https://reactome.org/) Protein-Protein Interaction networks(PPI) analysis of marker genes was implemented by the STRINGdb R package.
Assembly: mm10
Supplementary files format and content: fastq.gz

source_name: heart

growth_protocol: Normal mouse husbandry conditions

extract_protocol:
10x Genomics® Cell Preparation Guide describes best practices and general protocols for washing, counting and concentrating cells from both abundant and limited cell suspensions (greater than or less than 100000 total cells, respectively) in preparation for use in 10x Genomics Single Cell Protocols.
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10XGenomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’  v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina  NovaSeq6000  according to the manufacturer’s instructions (Illumina).

treatment_protocol: the tetraploid tissue (4N-heart) were obtained from E18.5 embryos (D-4N-E18.5-heart, n=1), which were Nkx2.5 lineage depletion injected with 4N-ESCs (td-Tomato positive) at blastocyst stage. The sc-RNA-seq content mainly needs to focus on the cell definition and the distribution and proportion of tdTomato-positive cells within the cell population

value: heart

value: tissue


title: whole larval P. promelas, cis-Nonachlordane, sample4

description:
Chem12_A_D4_D05
Chem12_counts_matrix.txt


title: B-4N-p180-liver-sc

description:
Library name: SRHX250000443-1a
4N-treatment

data_processing:
We use fastp to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence.If cleanreads is indispensable: Then, raw read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below: (1)Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW: 4:10)                                                                                (2)Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3)Remove adapters : there are two modes to remove the adapter sequence: alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa: 2: 30: 7) (4)Drop reads below the 26 bases long(5)Discard those reads that can not form pairedThe remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use fastp to perform basic statisticson the quality of the cleanreads.                                                                                Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
In detail: cellranger count takes FASTQ files performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature_x0002_barcode matrices, determine clusters, and perform gene expression analysis. The count pipeline can take input from multiple sequencing runs on the same GEM well. Add -–nosecondary option to skip secondary analysis of the feature-barcode matrix (dimensionality reduction, clustering and visualization) When doing large studies involving multiple GEM wells, run cellranger count on FASTQ data from each of the GEM wells individually, and then pool the results using cellranger aggr: cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data. The aggr pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis. Befor Secondary Analysis of Gene Expression we use Seurat Second QC it(as above). Subsequent analysis of cellranger reanalyze and Seurat were all performed basing on this output gene expression matrix .Secondary Analysis of Gene Expression cellranger cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings. Seurat The Seurat package was used to normalise data, dimensionality reduction, clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6. Global Analysis Between Samples Based on filtered gene expression matrix by Seurat ,between samples differential expression analysis was carried out using the edgeR package ( McCarthy et al., 2012) to obtain zone-specific marker genes. Enrichment analysis of marker genes Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by marker gene. KEGG (Kanehisa M, 2008) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We usedclusterProfiler R package to test the statistical enrichment of markergenes in KEGG pathways. Reactome pathway-based analysis of marker genes was implemented by the ReactomePA R package. REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database( https://reactome.org/) Protein-Protein Interaction networks(PPI) analysis of marker genes was implemented by the STRINGdb R package.
Assembly: mm10

source_name: liver

treatment_protocol: the tetraploid tissue (4N-liver) were obtained from E18.5 embryos (A-4N-E18.5-liver, n=1) and postnatal day 180 (B-4N-p180-liver, n=1), which were Hhex knockout and injected with 4N-ESCs (tdTomato-positive) at blastocyst stage. This sc-RNA-seq content mainly focus on the cell definition and the distribution and proportion of tdTomato-positive cells within the cell population.

value: liver


title: whole larval P. promelas, cis-Nonachlordane, sample3

description:
Chem12_A_D3_C05
Chem12_counts_matrix.txt


title: A-4N-E18.5-liver-sc

description:
Library name: SRHX250000442-1a
4N-treatment


title: whole larval P. promelas, cis-Nonachlordane, sample2

description:
Chem12_A_D2_B05
Chem12_counts_matrix.txt


title: WT-18.5-liver-14

description:
Library name: FRAS240369439-1r
control

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format (Cock P. et al, 2010), which contains sequence information and corresponding sequencing quality information.Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used Fastp (version 0.23.1)(Chen S. et al, 2018) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
Assembly: GRCm39
Supplementary files format and content: fastq.gz

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: the tetraploid tissue (4N-liver; n=3) were obtained from E18.5 mouse embryos (4N-E18.5) , which were Hhex knockout and injected with 4N-ESCs (td-Tomato positive) at blastocyst stage. While the tissue of control group (wild-type, WT-liver, n=2) were obtained from normal  E18.5 mouse embryos.


title: whole larval P. promelas, Fexofenadine, sample24

description:
Chem11_C_D8_H11
Chem11_counts_matrix.txt

value: Fexofenadine


title: whole larval P. promelas, cis-Nonachlordane, sample1

description:
Chem12_A_D1_A05
Chem12_counts_matrix.txt


title: 4N-18.5-liver-12

description:
Library name: FRAS240369437-1r
4N-treatment


title: YJ774_Right_inferior_E10

description: Library name: YJ774_Right_inferior_E10


title: whole larval P. promelas, Fexofenadine, sample23

description:
Chem11_C_D7_G11
Chem11_counts_matrix.txt


title: 4N-18.5-liver-11

description:
Library name: FRAS240369436-1r
4N-treatment


title: 4N-18.5-liver-10

description:
Library name: FRAS240369435-1r
4N-treatment


title: Control.d8.Ep-.sample2

city: Brussels

first: Gabriel

middle: Sölvi

last: Windels

address: 808, route de Lennik

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles (ULB)

description:
Library name: Control d8 Ep- sample2
Column name in normalised_counts.csv: Control.d8.Ep-.sample2

data_processing:
The multiplexed libraries (11 pM or 18 pM) were loaded onto flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a Novaseq 6000 (Illumina). Approximately 20 million paired end reads per sample were generated and quality checks were performed with FastQC.
The adapter sequences and low-quality regions were trimmed by Trimmomatic
Trimmed reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments.
Duplicated reads were removed by Picard MarkDuplicates.
After transcript assembly, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Assembly: mm10
Supplementary files format and content: csv file includes normalised counts for each sample

source_name: primary cell lines derived from Lgr5CreER/ KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ primary tumor and CRISPR/Cas9-derived cell lines

extract_protocol:
After FACS isolation, cultured cells were collected in for RNA extraction. RNA was extracted from FACS-isolated cells or culture cell lines using RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations. RNA quality was evaluated by Bioanalyzer 2100 (Agilent) before sequencing.
Indexed cDNA libraries were obtained using Ovation Solo RNA-seq Systems (NuGen) according to the manufacturer’s recommendations.

tag: time

tag: ko treatment

value: Control

tag: epcam condition

value: Neg

tag: batch


title: NH95TT cells, baseline

city: Chapel Hill

first: Michael

middle: P

last: East

state: NC

address: 120 Mason Farm Rd, GMB 4100C

department: Pharmacology

institute: UNC

description:
Library name: NH95TT
10X Genomics Multiome

data_processing:
Data matrices were created using 10X Genomics CellRanger and analyzed using the Seurat R package
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Breast

growth_protocol: PDO lines were grown in 300 uL domes of Cultrex Ultimatrix reduced growth factor basement membrane (Bio-Techne), and maintained in DMEM/F12 (Gibco), 10% R-Spondin1 conditioned media obtained from Cultrex® HA-R-Spondin1-Fc 293T Cells (Bio-Techne), B27 supplement (Gibco), 5 mM Nicotinamide (Sigma-Aldrich), 1.25 mM N-Acetylcysteine (Sigma-Aldrich), 50 ug/ml Primocin (InvivoGen), 100 ng/ml Noggin (PEPROTECH), 5 ng/ml hEGF (PEPROTECH), 37.5 ng/ul hHeregulin-beta (PEPROTECH) 5 ng/ml FGF-7 (PEPROTECH), 20 ng/ml FGF10 (PEPROTECH), 5uM Y-27632 (Abmole Bioscience), 500 nM SB202190 (Sigma-Aldrich), 500 nM A83-01 (Tocris).

extract_protocol:
Single-cell suspensions from patient-derived organoid lines were made by digesting Cultrex domes with TrypLE, washing with PBS + 0.04% BSA, and filtering through Flowmi 40 µm cell strainers. Cells were spun at 300 × g for 5 minutes at 4°C, then resuspended by pipette mixing in chilled lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% IGEPAL, 0.01% digitonin, 1% bovine serum albumin (BSA), 1 mM DTT, 1 U/uL RNase inhibitor) and incubated on ice for 5 minutes. Chilled wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/uL RNase inhibitor) was added to the samples, pipette mixed, and spun at 500 × g for 5 minutes at 4°C. The supernatant was discarded, and the pellet was washed twice with chilled wash buffer. The final nuclei pellet was resuspended in 1X Nuclei Buffer (10X Genomics) and immediately processed for library preparation
10X Genomics Chromium with the Single Cell Multiome ATAC + Gene Expression kit per the manufacturer’s protocol

value: Breast

value: Breast cancer


title: whole larval P. promelas, Fexofenadine, sample21

description:
Chem11_C_D5_E11
Chem11_counts_matrix.txt

value: whole body

value: larval


title: Cardiomyocyte-Specific Smad7 Knockout (CMS7KO) heart, 7-day post transverse aortic constriction, sample 4: CMS7KO4

city: New York

first: Claudio

middle: Diego

last: Humeres

state: New York

address: 2911 PEARSALL AVE

department: Medicine

institute: Albert Einstein College of Medicine

description:
Library name: Sample 8
Heart from Female Mice

data_processing:
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads by CASAVA base recognition (Base Calling).
The library preparations were sequenced on Illumina NovaSeq 6000 devices, generating 100 bp paired end reads. Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis
Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (December 2011 release of the mouse musculus reference genome (mm10; GRCm38.p6) from Ensembl) using TopHat2 algorithm alignment program v.2.0.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm. HTSeq software v.0.6.1 was used to count the number of reads mapped to each gene. Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM), was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length
Assembly: mm10
Supplementary files format and content: excel files including raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Whole Heart

growth_protocol: 3-4 old month male and female C56BL mice exposed to model of transverse aortic constriction (TAC) for 7] days in order to generate pressure overload in the heart

extract_protocol:
RNA was extracted with Trizol reagent.
RNA sequencing was performed by Novogene. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aortic banding was achieved by creating a constriction between the right innominate and left carotid arteries. The degree of pressure overload was assessed by measuring right-to-left carotid artery flow velocity ratio after constricting the transverse aorta. Experiments with a right to left carotid flow ratio< 3 or >25 were excluded.

value: Whole Heart

value: Cardiomyocyte-specific Smad7  Knockout

value: Transverse Aortic Constriction 7 days

tag: Sex

value: female


title: lpp-rgn-rnai,fat body,P.e,18h,rep3

city: Shanghai

first: Yi

last: Yang

state: Xuhui District

address: 320 Yueyang Road, Xuhui District, Shanghai, China

department: Gut Microenvironment and Health Research Group

institute: Shanghai lnstitute of lmmunity and Infection

description: Library name: p_lpp_rgn_rnai3

data_processing:
Raw reads were processed with Trim Galore to trim adaptors and remove low-quality reads, then mapped to the Drosophila melanogaster genome assembly dm6 (Ensembl version 109) using STAR (PMID: 23104886).
Gene expression was quantified with featureCounts, and differential expression analysis was conducted via DESeq2(PMID: 25516281).
Assembly: dm6
Supplementary files format and content: the counts of sequenced genes
Supplementary files format and content: the fpkm of sequenced genes

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: The flies were maintained on standard cornmeal fly food (1 L food contains 77.7 g cornmeal, 32.19 g yeast, 10.6 g agar, 0.726 g CaCl2, 31.62 g sucrose, 63.2 g glucose, 2 g potassium sorbate, and 15 mL 5% Tegosept).

extract_protocol:
The total RNA was extracted using the TRIzol method from fat bodies of adult flies with P. entomophila oral infection and control flies (fed with 5% sucrose solution) at 18hpi.
The sequencing was performed using the Illumina NovaSeq 6000 platform at Beijing Novogene Bioinformatics Technology Co., Ltd. Skewer (V0.2.2) was utilized for quality trimming and adapter trimming of the reads.

treatment_protocol: The fiies was treated with P. entomophila oral infection and control flies (fed with 5% sucrose solution) at 18hpi.

value: fat body

value: not collected

value: lpp-rgn-rnai

value: 20 fat bodies


title: lpp-rgn-rnai,fat body,P.e,18h,rep2

description: Library name: p_lpp_rgn_rnai2


title: lpp-rgn-rnai,fat body,P.e,18h,rep1

description: Library name: p_lpp_rgn_rnai1


title: whole larval P. promelas, Fexofenadine, sample19

description:
Chem11_C_D3_C11
Chem11_counts_matrix.txt


title: lpp,fat body,P.e,18h,rep3

description: Library name: p_lpp_w3

value: lpp


title: Cardiomyocyte-Specific Smad7 Knockout (CMS7KO) heart, 7-day post transverse aortic constriction, sample 2: CMS7KO2

description:
Library name: Sample 6
Heart from Male Mice

value: male


title: lpp,fat body,P.e,18h,rep2

description: Library name: p_lpp_w2


title: whole larval P. promelas, Fexofenadine, sample18

description:
Chem11_C_D2_B11
Chem11_counts_matrix.txt

value: Fexofenadine


title: lpp,fat body,P.e,18h,rep1

description: Library name: p_lpp_w1


title: Cardiomyocyte-Specific Smad7 Knockout (CMS7KO) heart, 7-day post transverse aortic constriction, sample 1: CMS7KO1

description:
Library name: Sample 5
Heart from Male Mice


title: whole larval P. promelas, Fexofenadine, sample17

description:
Chem11_C_D1_A11
Chem11_counts_matrix.txt


title: lpp-rgn-rnai,fat body,sucrose,18h,rep2

description: Library name: s_lpp_rgn_rnai2

value: sucrose


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 7-day post transverse aortic constriction, sample 4: ACRE4

description:
Library name: Sample 4
Heart from Female Mice

value: aMHC Cre Control+


title: whole larval P. promelas, Fexofenadine, sample16

description:
Chem11_B_D8_H08
Chem11_counts_matrix.txt


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 7-day post transverse aortic constriction, sample 3: ACRE3

description:
Library name: Sample 3
Heart from Female Mice


title: lpp,fat body,sucrose,18h,rep2

description: Library name: s_lpp_w2


title: whole larval P. promelas, Fexofenadine, sample15

description:
Chem11_B_D7_G08
Chem11_counts_matrix.txt


title: whole larval P. promelas, 4-Chlorophenyl methyl sulfoxide, sample11

description:
Chem8_B_D3_C09
Chem8_counts_matrix.txt

value: 4-Chlorophenyl methyl sulfoxide


title: lpp,fat body,sucrose,18h,rep1

description: Library name: s_lpp_w1


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 7-day post transverse aortic constriction, sample 2: ACRE2

description:
Library name: Sample 2
Heart from Male Mice


title: CUT&Tag of HCASMC: H3K27ac, DDIT4_OE, replicate 3

city: Guangzhou

first: Fengfeng

last: Li

address: 253 Gongye Dadao Zhong, Haizhu District

department: Department of Cardiovascular Medicine

institute: ZhuJiang Hospital, Southern Medical University

description: Library name: sample 12

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
adapters were removed from reads, and reads containing more than 10% of unknown nucleotides (N) or more than 50% of low quality (Q-value≤20) bases were discarded, discarding reads left with < 50bp using fastp v0.21.0
reads were aligned to the ensembl release111 hg38 genome using Bowtie2 version 2.4.4. Only uniquely mapping reads with were retained.
bigWig files were generated from mapping bam files using bamCoverage v3.5.1
Peaks were called uing MACS v2.1.2 with the significance cut-off pvalue < 1e-5;Peaks differential analysis were done by R package diffBind v2.8.0 with significance cut-off pvalue < 0.05 and |log2fc| > 1
Assembly: hg38
Supplementary files format and content: bigWig, narrow Peak
Library strategy: CUT&Tag

source_name: Homo sapiens coronary artery smooth muscle cell (HCASMC)

growth_protocol: Human coronary artery smooth muscle cells (HCASMCs) were cultured in Vascular Cell Basal Medium supplemented with Vascular Smooth Muscle Cell Growth Kit at 37°C in a humidified 5% CO₂ atmosphere. Cells were maintained under standard conditions until reaching approximately 80-90% confluence prior to experimental processing.

extract_protocol:
Chromatin extraction and tagmentation were performed using the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit. Briefly, 2×10⁵ cells per sample were immobilized on Concanavalin A-coated magnetic beads, permeabilized with digitonin, and incubated overnight at 4°C with specific antibodies: H3K9ac (Cell Signaling Technology, #9649) or H3K27ac (Abcam, ab177178). Following secondary antibody incubation, tagmentation was carried out using pA-Tn5 transposase. Fragmented DNA was subsequently extracted using Tagment DNA Extract Beads.
Libraries were constructed following the manufacturer's protocol for the NovoNGS CUT&Tag 4.0 High-Sensitivity Kit. The extracted DNA was amplified in a 50 µL PCR reaction containing 20 µL DNA, 2.5 µL each of i5 and i7 indexing primers, and 25 µL 2×HiFi Amplimix. PCR products were purified using NovoNGS DNA Clean Beads. Final libraries were quality-controlled and sequenced on an Illumina NovaSeq X Plus-25B platform with 150 bp paired-end reads.

treatment_protocol: HCASMCs were transduced with adenovirus encoding full-length human DDIT4 or empty adenoviral vector control at MOI 100 for 48 hours.

tag: antibody

value: H3K27ac (rabbit monoclonal, Abcam, catalog # ab177178)


title: NH87TT cells, baseline

description:
Library name: NH87TT
10X Genomics Multiome

value: Breast

value: Breast cancer


title: whole larval P. promelas, Fexofenadine, sample14

description:
Chem11_B_D6_F08
Chem11_counts_matrix.txt

value: whole body

value: larval


title: CUT&Tag of HCASMC: H3K27ac, DDIT4_OE, replicate 2

description: Library name: sample 11

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 7-day post transverse aortic constriction, sample 1: ACRE1

description:
Library name: Sample 1
Heart from Male Mice

value: Whole Heart

value: Transverse Aortic Constriction 7 days


title: whole larval P. promelas, Fexofenadine, sample13

description:
Chem11_B_D5_E08
Chem11_counts_matrix.txt


title: CUT&Tag of HCASMC: H3K27ac, control, replicate 3

description: Library name: sample 9

value: empty adenoviral vector


title: Cardiomyocyte-Specific Smad7 Knockout (CS7KO) heart, 56-day transverse aortic constriction, sample 4: CS7KO4

description:
Library name: Sample 8
CS7KO4

source_name: Heart from Female Mice

growth_protocol: 3-4 old month male and female C56BL mice exposed to model of transverse aortic constriction (TAC) for 56 days in order to generate pressure overload in the heart

value: female

value: Cardiomyocyte-specific Smad7  Knockout

value: Transverse Aortic Constriction 56 days


title: CUT&Tag of HCASMC: H3K27ac, control, replicate 2

description: Library name: sample 8


title: whole larval P. promelas, Fexofenadine, sample12

description:
Chem11_B_D4_D08
Chem11_counts_matrix.txt


title: Cardiomyocyte-Specific Smad7 Knockout (CS7KO) heart, 56-day transverse aortic constriction, sample 3: CS7KO3

description:
Library name: Sample 7
CS7KO3


title: CUT&Tag of HCASMC: H3K9ac, DDIT4_OE, replicate 3

description: Library name: sample 6

value: H3K9ac (rabbit monoclonal, Cell Signaling Technology, catalog #9649)


title: whole larval P. promelas, Fexofenadine, sample11

description:
Chem11_B_D3_C08
Chem11_counts_matrix.txt

value: Fexofenadine


title: CUT&Tag of HCASMC: H3K9ac, DDIT4_OE, replicate 2

description: Library name: sample 5


title: Cardiomyocyte-Specific Smad7 Knockout (CS7KO) heart, 56-day transverse aortic constriction, sample 2: CS7KO2

description:
Library name: Sample 6
CS7KO2

source_name: Heart from Male Mice

value: male


title: Rb2 plus D-galactose_3

city: Daejeon

first: Byeong-Don

last: Min

state: Daejeon

address: 99 Daehak-ro, Yuseong-gu

country: South Korea

institute: Chungnam National University

description:
Library name: Rb2-plus-D-gal-3
RNA-seq sample from treated differentiated C2C12 myotubes.

data_processing:
Raw sequencing reads were quality-checked using FastQC v0.11.9.
Adapter sequences and low-quality bases were removed using Trim Galore v0.6.10.
Trimmed reads were aligned to the Mus musculus reference genome GRCm38/mm10 using STAR v2.7.9a.
Gene-level expression quantification was performed using RSEM v1.3.3 with GRCm38.86 gene annotation.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: Tab-delimited text file containing a gene-level expected count matrix generated using RSEM.

growth_protocol: C2C12 murine skeletal muscle myoblasts were maintained in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. To induce myotube differentiation, cells were grown to 100% confluence and the medium was replaced with differentiation medium consisting of DMEM supplemented with 2% fetal bovine serum. Differentiation medium was replenished every 2 days for 5 to 7 days. Cells were cultured at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from C2C12 myotubes using the FavorPrep Total RNA Extraction Mini Kit according to the manufacturer's instructions. RNA quality and quantity were assessed prior to library preparation.
mRNA sequencing libraries were prepared from total RNA using the MGIEasy RNA Directional Library Prep Kit according to the manufacturer's instructions. Poly-A-containing mRNA was enriched, fragmented, reverse-transcribed, adapter-ligated, PCR-enriched, circularized, and converted into DNA nanoballs for sequencing on the DNBSEQ platform.

treatment_protocol: Fully differentiated C2C12 myotubes were pretreated with vehicle, Korean Red Ginseng water extract (100 ug/mL), saponin fraction (100 ug/mL), non-saponin fraction (100 ug/mL), or ginsenoside Rb2 (20 uM) for 12 h. After pretreatment, cells were exposed to D-galactose (20 mg/mL) for an additional 24 h to induce cellular aging.

value: myotube

value: Wildtype

value: Ginsenoside Rb2 20 uM pretreatment for 12 h followed by D-galactose 20 mg/mL for 24 h


title: whole larval P. promelas, Fexofenadine, sample10

description:
Chem11_B_D2_B08
Chem11_counts_matrix.txt

data_processing:
*library strategy: TempO-Seq (Templated Oligo-Sequencing)
Sample-specific TempO-Seq libraries were pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2 × 50 bp, single-end reads, NovaSeq X 10B reagent kits.
Sequence reads were then demultiplexed based on sample-specific barcodes, and a FASTQ file was generated for each sample using Illumina's bcl2fastq conversion software. Resulting TempO-Seq data were analyzed by Biospyder using TempO-SeqR software implemented in R.
The FASTQ files were aligned to the known transcript composition of the reduced transcriptome, and a count table (columns = samples, genes = rows) was generated.
Assembly: GCA_016745375.1
Supplementary files format and content: count matrices with rows as gene features and columns as samples


title: CUT&Tag of HCASMC: H3K9ac, DDIT4_OE, replicate 1

description: Library name: sample 4


title: Cardiomyocyte-Specific Smad7 Knockout (CS7KO) heart, 56-day transverse aortic constriction, sample 1: CS7KO1

description:
Library name: Sample 5
CS7KO1


title: Rb2 plus D-galactose_2

description:
Library name: Rb2-plus-D-gal-2
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fexofenadine, sample9

description:
Chem11_B_D1_A08
Chem11_counts_matrix.txt


title: CUT&Tag of HCASMC: H3K9ac, control, replicate 3

description: Library name: sample 3


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 56-day post transverse aortic constriction, sample 5: CRE5

description:
Library name: Sample 4
CRE5

value: aMHC Cre Control+


title: Rb2 plus D-galactose_1

description:
Library name: Rb2-plus-D-gal-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fexofenadine, sample8

description:
Chem11_A_D8_H04
Chem11_counts_matrix.txt


title: CUT&Tag of HCASMC: H3K9ac, control, replicate 2

description: Library name: sample 2


title: whole larval P. promelas, Fexofenadine, sample7

description:
Chem11_A_D7_G04
Chem11_counts_matrix.txt


title: WT-18.5-liver-13

description:
Library name: FRAS240369438-1r
control

value: liver

value: tissue

value: WT


title: whole larval P. promelas, Fexofenadine, sample22

description:
Chem11_C_D6_F11
Chem11_counts_matrix.txt

value: whole body

value: larval


title: CUT&Tag of HCASMC: H3K9ac, control, replicate 1

description: Library name: sample 1

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 56-day post transverse aortic constriction, sample 2: CRE2

description:
Library name: Sample 2
CRE2

value: Whole Heart


title: whole larval P. promelas, Fexofenadine, sample20

description:
Chem11_C_D4_D11
Chem11_counts_matrix.txt


title: Cardiomyocyte-Specific Smad7 Knockout (CMS7KO) heart, 7-day post transverse aortic constriction, sample 3: CMS7KO3

description:
Library name: Sample 7
Heart from Female Mice

value: Transverse Aortic Constriction 7 days

value: female


title: Rb2_2

description:
Library name: Rb2-20uM-2
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Ginsenoside Rb2 20 uM for 12 h


title: whole larval P. promelas, Fexofenadine, sample6

description:
Chem11_A_D6_F04
Chem11_counts_matrix.txt


title: STM2459_3

city: Fuzhou

first: Tian

last: Lin

address: No. 20, Chazhong Road

institute: The First Affiliated Hospital of Fujian Medical University

description: Library name: sample6

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or lowquality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by SOAPnuke (version 0.18 0).
Assembly: The quality of the original sequencing data was evaluated using tools such as FastQC, and the sequencing read segment was compared with the reference genome of human
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample. csv files include FPKM values for each Sample

source_name: SK-N-SH cells

extract_protocol:
The human SK-N-SH cells in each group were collected for RNA extraction by RNAiso Plus reagent
Sequencing libraries were generated using NEBNext® UltraTM RNALibrary Prep Kit for lllumina® (NEB, USA) following manufacturer's recommendationsand index codes were added to attribute sequences to each sample.

value: SK-N-SH cells

value: treatment with STM2457


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 56-day post transverse aortic constriction, sample 1: CRE1

description:
Library name: Sample 1
CRE1

value: male

value: Transverse Aortic Constriction 56 days


title: whole larval P. promelas, Fexofenadine, sample5

description:
Chem11_A_D5_E04
Chem11_counts_matrix.txt

source_name: whole body

extract_protocol:
Samples were prepared for transcriptomics analysis by homogenization in a protease lysis buffer as directed by BioSpyder Technologies, Inc. Pimephales promelas were homogenized in 75 µL/well with a 2.3 mm stainless steel bead (BioSpec) at 30 Hz for 2 min using a well plate homogenizer (Bead Ruptor 96, OMNI International). Plates were centrifuged for 3 min at 1000 rpm. Homogenates were pooled (excluding any mortalities) by treatment concentration within each plate, resulting in n=3 replicates per treatment, each containing five pooled organisms (Supplementary Figure 2B). The final plates containing pool homogenates were stored at -80ºC until shipped on dry ice to BioSpyder Technologies, Inc. (Carlsbad, CA) for TempO-seq analysis. Test acceptability criteria were met if control survival was >90 %.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification were performed with a DeNovix UV-visible spectrophotometer (DeNovix). Ligated transcripts were subjected to polymerase chain reaction amplification, which also introduces adaptors for sequencing and a sample-specific barcode.

value: Fexofenadine


title: Rb2_1

description:
Library name: Rb2-20uM-1
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: Wildtype


title: STM2459_2

description: Library name: sample5


title: lpp-rgn-rnai,fat body,sucrose,18h,rep3

description: Library name: s_lpp_rgn_rnai3

value: fat body

value: not collected

value: lpp-rgn-rnai

value: sucrose

value: 20 fat bodies


title: RPB1_CTD_AID_ESCs_EU_washoff_36h_rep3

city: Beijing

first: Xu

last: Jingzhao

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua university

data_processing:
Adapters and low-quality reads were removed and polyC tracts were cut from the reads by Trim_galore.
Reads from RNA-seq were mapped to the mouse genome (mm10) using hisat2 (version 2.1.0) and additionally to the Drosophila genome (dm6) using Bowtie2 (version 2.2.8).
Read counts of genes were calculated using featureCounts (version 2.0.1) with Gencode vM25 annotation (56,262 annotated genes).
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Pol II CTD-AID ESCs

growth_protocol: Pol II CTD-AID mESCs were maintained in DMEM, supplemented with 15% heat-inactivated fetal bovine serum (FBS), GlutaMAX, Penicillin-Streptomycin Solution, nonessential amino acids, nucleoside mix, Sodium Pyruvate, 0.1 mM 2-mercaptoethanol, 1000 U/ml recombinant leukemia inhibitory factor (LIF), 1 μM PD0325901, and 3 μM CHIR99021. The LIF and two inhibitors (2i) were added freshly before use. The mESCs were seeded onto 0.1% gelatin-coated dishes and cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA were extracted by TRIzol reagent according to manufacturer's instruction.
ESCs were labeled with 1 mM 5-EU for 10 minutes and harvested by TRIzol with the addition of RNA spike-ins (5-EU labeled S2 cells) for cell number control. Apply purified RNA to DNase I treatment, fragmentation, ethanol precipitation, and biotinylation. Purify biotinylated RNA by phenol-chloroform, followed by two rounds of biotin-affinity purification using M-280 Streptavidin Dynabeads. Eluted RNA was applied for cDNA synthesis and strand-specific library construction by ssDNA-seq Lib Prep Kit (Abclonal, Cat#: RK20222) following manufacturer’s protocols.

treatment_protocol: To induce reprogramming in Pol II CTD-AID ESCs, cells were pre-treated with 1 μg/ml doxycycline hyclate for 12 hours to induce TIR1 expression. Subsequently, cells were treated with 500 μM auxin analog indole-3-acetic acid (IAA) at various time points to truncate Pol II CTD. During this process, LIF and 2i were withdrawn from the ESC culture medium.

value: Pol II CTD-AID ESCs

value: mouse embryonic stem cell

value: IAA treatment 24 hour then wash off

value: 36 hour


title: alpha myosin heavy chain (aMHC) Cre+ Control heart, 56-day post transverse aortic constriction, sample 3: CRE3

description:
Library name: Sample 3
CRE3

value: Whole Heart

value: female

value: aMHC Cre Control+


title: NSFr plus D-galactose_3

description:
Library name: NSFr-plus-D-gal-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Non-saponin fraction 100 ug/mL pretreatment for 12 h followed by D-galactose 20 mg/mL for 24 h


title: whole larval P. promelas, Fexofenadine, sample4

description:
Chem11_A_D4_D04
Chem11_counts_matrix.txt

value: whole body

value: larval


title: STM2459_1

description: Library name: sample4

value: SK-N-SH cells

value: treatment with STM2457


title: lpp-rgn-rnai,fat body,sucrose,18h,rep1

description: Library name: s_lpp_rgn_rnai1

value: fat body


title: RPB1_CTD_AID_ESCs_EU_washoff_36h_rep2


title: NSFr plus D-galactose_2

description:
Library name: NSFr-plus-D-gal-2
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: Wildtype


title: whole larval P. promelas, Fexofenadine, sample3

description:
Chem11_A_D3_C04
Chem11_counts_matrix.txt

value: Fexofenadine


title: Rb2_3

description:
Library name: Rb2-20uM-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Ginsenoside Rb2 20 uM for 12 h


title: lpp,fat body,sucrose,18h,rep3

description: Library name: s_lpp_w3

value: not collected

value: lpp

value: sucrose

value: 20 fat bodies


title: control_3

description: Library name: sample3

value: no treatment


title: RPB1_CTD_AID_ESCs_EU_washoff_36h_rep1

value: Pol II CTD-AID ESCs

value: mouse embryonic stem cell

value: IAA treatment 24 hour then wash off

value: 36 hour


title: NSFr plus D-galactose_1

description:
Library name: NSFr-plus-D-gal-1
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Non-saponin fraction 100 ug/mL pretreatment for 12 h followed by D-galactose 20 mg/mL for 24 h


title: whole larval P. promelas, Fexofenadine, sample2

description:
Chem11_A_D2_B04
Chem11_counts_matrix.txt

value: whole body

value: larval


title: control_2

description: Library name: sample2

value: SK-N-SH cells


title: RPB1_CTD_AID_ESCs_EU_washoff_24h_rep3

value: 24 hour


title: NSFr_3

description:
Library name: NSFr-100ug-mL-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: Wildtype

value: Non-saponin fraction 100 ug/mL for 12 h


title: whole larval P. promelas, Fexofenadine, sample1

description:
Chem11_A_D1_A04
Chem11_counts_matrix.txt

value: Fexofenadine


title: control_1

description: Library name: sample1


title: NSFr_2

description:
Library name: NSFr-100ug-mL-2
RNA-seq sample from treated differentiated C2C12 myotubes.


title: RPB1_CTD_AID_ESCs_EU_washoff_24h_rep2


title: whole larval P. promelas, Fipronil amide, sample24

description:
Chem10_C_D8_H11
Chem10_counts_matrix.txt

value: Fipronil amide


title: snATACseq, In vivo stimulation, donor IVS_9

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

description:
Library name: IVS_STIM_9_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

library_source: genomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v7.0.0)
The “mkfastq” command was used to generate FASTQ files and the “cellranger-arc count” command was used to generate raw gene-cell expression matrices
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Human Genome hg38 was used for the alignment and gencode.v42 was used for gene annotation and coordinates
Seurat and Signac was used for downstream analysis
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz' contains barcodes, 'features.tsv.gz' containts gene symbols for RNA and chromatin regions for ATAC, 'matrix.mtx.gz' contains raw counts for RNA and ATAC respectively.

source_name: brain

growth_protocol: MEA stimulation: Using the Maxwell Biosystems MaxOne microelectrode array, stimulation was delivered at configurations of 32 randomly selected electrodes across the entire MEA chip. Stimulation occurred for 15 minutes at 300mv, with new electrode configurations being chosen after 5 bursts of stimulation pulses (bipolar square waves, positive first, 200us phase length, 50ms inter-pulse interval, 5s inter-burst interval). Stimulated slices were flash frozen 10-15 minutes after stimulation. Control samples did not receive stimulation and were instead resting in oxygenated normal artificial CSF (123mM NaCl, 4mM KCl, 25mM NaHCO3, 1.2mM NaH2PO4, 10mM D-Glucose, 1mM CaCl2, 1mM MgSO4, pH 7.3-7.4, 290-310 mOsm). Slices on the MEA were being bathed in oxygenated normal aCSF at 37 degrees Celsius.

extract_protocol:
Libraries were constructed using the 10x Genomics multiome kit and protocol (revision F) with the goal of targeting 10,000 nuclei per sample.
10X multiome

treatment_protocol:
In vivo stimulation: Intraoperative cortical mapping procedures of the premotor area (BA6/8) were completed according to clinical need. Stimulation was delivered for 2 minutes in 30s 60Hz bursts (bipolar square waves, positive first, 200us phase length) with current amplitudes from 2 to 10 mA according to clinical need. Control samples were adjacent (~2cm away) cortex that did not receive direct stimulation. Samples were flash frozen immediately after resection, within 10 to 20 minutes of stimulation.
Nuclei were extracted using a modified version of the 10x Genomics Nuclei Isolation from Complex Tissues demonstrated protocol (CG000375). A sucrose density gradient was used in place of nuclei sorting.

value: brain

value: In vivo stimulation

tag: brain region

value: premotor cortex

tag: sample id

tag: age

value: male

tag: hemisphere

value: L

tag: epilepsy duration_years


title: RPB1_CTD_AID_ESCs_EU_washoff_24h_rep1

value: Pol II CTD-AID ESCs

tag: cell type

value: mouse embryonic stem cell

value: IAA treatment 24 hour then wash off


title: NSFr_1

description:
Library name: NSFr-100ug-mL-1
RNA-seq sample from treated differentiated C2C12 myotubes.

tag: genotype

tag: treatment


title: whole larval P. promelas, Fipronil amide, sample23

description:
Chem10_C_D7_G11
Chem10_counts_matrix.txt

tag: tissue

value: whole body


title: snATACseq, In vivo stimulation, donor IVS_8

description:
Library name: IVS_STIM_8_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: female

value: R


title: SFr plus D-galactose_3

description:
Library name: SFr-plus-D-gal-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Saponin fraction 100 ug/mL pretreatment for 12 h followed by D-galactose 20 mg/mL for 24 h


title: RPB1_CTD_AID_ESCs_EU_washoff_12h_rep3

value: 12 hour


title: whole larval P. promelas, Fipronil amide, sample22

description:
Chem10_C_D6_F11
Chem10_counts_matrix.txt

tag: developmental stage

value: larval


title: snATACseq, In vivo stimulation, donor IVS_7

description:
Library name: IVS_STIM_7_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: RPB1_CTD_AID_ESCs_EU_washoff_12h_rep2

tag: cell line


title: SFr plus D-galactose_2

description:
Library name: SFr-plus-D-gal-2
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: Wildtype


title: snATACseq, In vivo stimulation, donor IVS_6

description:
Library name: IVS_STIM_6_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz


title: whole larval P. promelas, Fipronil amide, sample21

description:
Chem10_C_D5_E11
Chem10_counts_matrix.txt

value: Fipronil amide


title: RPB1_CTD_AID_ESCs_EU_washoff_12h_rep1

tag: time


title: SFr plus D-galactose_1

description:
Library name: SFr-plus-D-gal-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: CUT&Tag of HCASMC: H3K27ac, DDIT4_OE, replicate 1

description: Library name: sample 10

value: Homo sapiens coronary artery smooth muscle cell (HCASMC)

value: H3K27ac (rabbit monoclonal, Abcam, catalog # ab177178)


title: whole larval P. promelas, Fipronil amide, sample20

description:
Chem10_C_D4_D11
Chem10_counts_matrix.txt


title: snATACseq, In vivo stimulation, donor IVS_5

description:
Library name: IVS_STIM_5_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: brain

value: In vivo stimulation

value: premotor cortex


title: RPB1_CTD_AID_ESCs_EU_washoff_6h_rep3

value: Pol II CTD-AID ESCs

value: 6 hour


title: whole larval P. promelas, Fipronil amide, sample19

description:
Chem10_C_D3_C11
Chem10_counts_matrix.txt


title: snATACseq, In vivo stimulation, donor IVS_4

description:
Library name: IVS_STIM_4_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: L


title: SFr_2

description:
Library name: SFr-100ug-mL-2
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Saponin fraction 100 ug/mL for 12 h


title: RPB1_CTD_AID_ESCs_EU_washoff_6h_rep2

value: mouse embryonic stem cell

value: IAA treatment 24 hour then wash off


title: whole larval P. promelas, Fipronil amide, sample18

description:
Chem10_C_D2_B11
Chem10_counts_matrix.txt

value: whole body


title: SFr_3

description:
Library name: SFr-100ug-mL-3
RNA-seq sample from treated differentiated C2C12 myotubes.


title: RPB1_CTD_AID_ESCs_EU_washoff_6h_rep1


title: snATACseq, In vivo stimulation, donor IVS_3

description:
Library name: IVS_STIM_3_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: male


title: SFr_1

description:
Library name: SFr-100ug-mL-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: CUT&Tag of HCASMC: H3K27ac, control, replicate 1

description: Library name: sample 7

value: empty adenoviral vector


title: whole larval P. promelas, Fipronil amide, sample17

description:
Chem10_C_D1_A11
Chem10_counts_matrix.txt

value: larval


title: snATACseq, In vivo stimulation, donor IVS_2

description:
Library name: IVS_STIM_2_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: R


title: RPB1_CTD_AID_ESCs_EU_washoff_3h_rep3

value: 3 hour


title: RGW plus D-galactose_3

description:
Library name: RG-W-plus-D-gal-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: Wildtype

value: Korean Red Ginseng water extract 100 ug/mL pretreatment for 12 h followed by D-galactose 20 mg/mL for 24 h


title: whole larval P. promelas, Fipronil amide, sample16

description:
Chem10_B_D8_H07
Chem10_counts_matrix.txt

value: Fipronil amide


title: snATACseq, In vivo stimulation, donor IVS_1

description:
Library name: IVS_STIM_1_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: brain

value: In vivo stimulation

value: premotor cortex


title: RPB1_CTD_AID_ESCs_EU_washoff_3h_rep2

value: Pol II CTD-AID ESCs


title: RGW plus D-galactose_2

description:
Library name: RG-W-plus-D-gal-2
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fipronil amide, sample15

description:
Chem10_B_D7_G07
Chem10_counts_matrix.txt


title: snRNAseq, In vivo stimulation, donor IVS_9

description:
Library name: IVS_STIM_9_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: L


title: RPB1_CTD_AID_ESCs_EU_washoff_3h_rep1

value: mouse embryonic stem cell


title: RGW plus D-galactose_1

description:
Library name: RG-W-plus-D-gal-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fipronil amide, sample14

description:
Chem10_B_D6_F07
Chem10_counts_matrix.txt


title: snRNAseq, In vivo stimulation, donor IVS_8

description:
Library name: IVS_STIM_8_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: female


title: RPB1_CTD_AID_ESCs_EU_IAA_24h_rep2

value: IAA

value: 24 hour


title: RGW_3

description:
Library name: RG-W-100ug-mL-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Korean Red Ginseng water extract 100 ug/mL for 12 h


title: whole larval P. promelas, Fipronil amide, sample13

description:
Chem10_B_D5_E07
Chem10_counts_matrix.txt

value: whole body

value: larval


title: snRNAseq, In vivo stimulation, donor IVS_7

description:
Library name: IVS_STIM_7_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz


title: RPB1_CTD_AID_ESCs_EU_IAA_24h_rep1


title: RGW_2

description:
Library name: RG-W-100ug-mL-2
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fipronil amide, sample12

description:
Chem10_B_D4_D07
Chem10_counts_matrix.txt


title: snRNAseq, In vivo stimulation, donor IVS_6

description:
Library name: IVS_STIM_6_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: male


title: RGW_1

description:
Library name: RG-W-100ug-mL-1
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube


title: whole larval P. promelas, Fipronil amide, sample11

description:
Chem10_B_D3_C07
Chem10_counts_matrix.txt


title: RPB1_CTD_AID_ESCs_EU_IAA_12h_rep2

value: 12 hour


title: snRNAseq, In vivo stimulation, donor IVS_5

description:
Library name: IVS_STIM_5_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: R


title: RPB1_CTD_AID_ESCs_EU_IAA_12h_rep1


title: D-galactose_3

description:
Library name: D-gal-20mg-mL-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Wildtype

value: D-galactose 20 mg/mL for 24 h


title: whole larval P. promelas, Fipronil amide, sample10

description:
Chem10_B_D2_B07
Chem10_counts_matrix.txt

value: Fipronil amide


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample21

description:
Chem2_C_D5_E03
Chem2_counts_matrix.txt

value: 3,4-Dichlorophenyl isocyanate


title: snRNAseq, In vivo stimulation, donor IVS_4

description:
Library name: IVS_STIM_4_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: brain

value: In vivo stimulation

value: premotor cortex


title: RPB1_CTD_AID_ESCs_EU_IAA_6h_rep2

value: Pol II CTD-AID ESCs

value: mouse embryonic stem cell

value: 6 hour


title: D-galactose_2

description:
Library name: D-gal-20mg-mL-2
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fipronil amide, sample9

description:
Chem10_B_D1_A07
Chem10_counts_matrix.txt


title: snRNAseq, In vivo stimulation, donor IVS_3

description:
Library name: IVS_STIM_3_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: L


title: D-galactose_1

description:
Library name: D-gal-20mg-mL-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: whole larval P. promelas, Fipronil amide, sample8

description:
Chem10_A_D8_H03
Chem10_counts_matrix.txt

value: whole body


title: RPB1_CTD_AID_ESCs_EU_IAA_6h_rep1

value: IAA


title: Tumor_ctrl

city: Singapore

first: Cheng

last: Xu

address: 70 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description: Library name: Sample 2

data_processing:
Fastq files were trimmed and filtered based on quality and then mapped using the Spliced Transcripts.
Assembly: mouse mm10
Supplementary files format and content: xlsx files with counts for each sample

source_name: 4T1 tumor

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (Invitrogen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNAseq library was constructed via AccuraCode® RNA Library Construction Kit.

value: 4T1 tumor

value: Control


title: snRNAseq, In vivo stimulation, donor IVS_2

description:
Library name: IVS_STIM_2_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: male


title: Vehicle control_3

description:
Library name: vehicle-control-3
RNA-seq sample from treated differentiated C2C12 myotubes.

value: myotube

value: vehicle control


title: RPB1_CTD_AID_ESCs_EU_IAA_3h_rep2

value: 3 hour


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample14

city: Duluth

first: Peter

last: Schumann

address: 6201 Congdon Blvd

institute: United States Environmental Protection Agency

description:
Chem2_B_D6_F03
Chem2_counts_matrix.txt

value: larval


title: RPB1_CTD_AID_ESCs_EU_IAA_3h_rep1


title: snRNAseq, In vivo stimulation, donor IVS_1

description:
Library name: IVS_STIM_1_RNA
ivs_rna_barcodes.tsv.gz
ivs_rna_features.tsv.gz
ivs_rna_matrix.mtx.gz

value: R


title: Vehicle control_2

description:
Library name: vehicle-control-2
RNA-seq sample from treated differentiated C2C12 myotubes.

value: Wildtype


title: whole larval P. promelas, Fipronil amide, sample7

description:
Chem10_A_D7_G03
Chem10_counts_matrix.txt

value: Fipronil amide


title: whole larval P. promelas, Fipronil amide, sample6

description:
Chem10_A_D6_F03
Chem10_counts_matrix.txt


title: whole larval P. promelas, 34-Dichlorophenyl isocyanate, sample13

description:
Chem2_B_D5_E03
Chem2_counts_matrix.txt

value: 3,4-Dichlorophenyl isocyanate


title: RPB1_CTD_AID_ESCs_EU_IAA_0h_rep2

value: Pol II CTD-AID ESCs

value: 0 hour


title: snATACseq, In vivo control, donor IVS_9

description:
Library name: IVS_CTRL_9_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: brain

value: In vivo control

value: premotor cortex


title: whole larval P. promelas, Fipronil amide, sample5

description:
Chem10_A_D5_E03
Chem10_counts_matrix.txt

value: whole body


title: Vehicle control_1

description:
Library name: vehicle-control-1
RNA-seq sample from treated differentiated C2C12 myotubes.


title: snATACseq, In vivo control, donor IVS_8

description:
Library name: IVS_CTRL_8_ATAC
ivs_atac_barcodes.tsv.gz
ivs_atac_features.tsv.gz
ivs_atac_matrix.mtx.gz

value: female


title: RPB1_CTD_AID_ESCs_EU_IAA_0h_rep1

value: mouse embryonic stem cell