title: Wild Type T-24h_replicate C

description:
Biological replicate 2 of 3 of timepoint T-24h of sexual reproduction time course
2C_T-24

tag: biosource 3

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: MILDd15_REP1

status: Public on Jun 30 2025

type: SRA

city: Catanzaro

first: Barbara

last: Puccio

address: Viale Europa

department: Dept of Surgical and Medical Sciences

country: Italy

institute: Magna Graecia University of Catanzaro

description:
Library name: Sample 19
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  MILDd15_1

library_source: transcriptomic

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
After quality control, paired-end clean reads were aligned to the reference genome (Homo Sapiens(GRCh38/hg38)) using Hisat2 v2.0.5.
Assembly: GRCh38/hg38
Supplementary files format and content: xls file includes gene counts for each Sample
Supplementary files format and content: xls file includes fpkm values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cell derived neurons

extract_protocol:
Total RNA was extracted by using TRIzol Reagents (Invitrogen, 15596026), according to the manufacturer’s protocol.
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.

tag: cell type


title: SEVd45_REP3

description:
Library name: Sample 18
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd45_3

value: induced pluripotent stem cell derived neurons


title: BM_PC_WT_3

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Removal of low-quality reads and adapter-trimming with TrimGalore (v0.6.6).
Mapping of reads to genome reference with STAR (v2.6.1d)
Quantification of aligned reads with Salmon (v1.4.0) and gene-level summarization
Assembly: GRCm38
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample from Spikevax immunization
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample from non-immunized mice (steady state)

organism: Mus musculus

source_name: bone marrow

growth_protocol: Mice were immunized with mRNA-1273 (Spikevax) subcutaneously on day 0 and boosted day 70. On day 77, bone marrow plasma cells (CD138+ TACI+) were sorted and lysed for total RNA isolation.

extract_protocol:
Plasma cells were FACS-purified (CD138+ TACI+) and sorted directly into beta-mercaptoethanol-containing RLT (Qiagen) Lysis buffer. Total RNA was isolated with the RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Plus kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

tag: tissue

value: bone marrow

value: plasma cell (CD138+ TACI+)

tag: genotype

tag: treatment

value: steady state


title: Basal epithelial cells transfected with stealth control siRNA (Rep-3)

city: Cincinnati

first: Satish

middle: Kumar

last: Madala

state: Ohio

address: 3235 Eden Ave

department: Internal Medicine

country: USA

institute: University of Cincinnati

description:
Library name: PP3
18378_Ctrl_3_raw_counts_All_Sample.xlsx

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Assembly: hg19
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

source_name: Lung

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: cell line

value: Primary cells

value: Basal epithelial cells

value: control siRNA


title: Wild Type T-24h_replicate A

type: RNA

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description:
Biological replicate 1 of 3 of timepoint T-24h of sexual reproduction time course
2A_T-24

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: To facilitate biological materials collecting, S strains from both mating types were grown on cheesecloth (Sefar Nitex 03-48/31 Heiden) or cellophane sheet (cat#1650193, BioRad laboratories, Hercules) previously placed on Petri-dishes containing M2 medium. S mat- strain has been used as male gamete donor and S mat+ as female. the S mat+ strains were grown on M2 Petri-dishes plus cheesecloth.  For each ten points of the time course materials, number of Petri-dishes has been adjusted (5 were used for T-24h, T0h, T6h, T18h, T24h, 4 for T30h, 2 for T42h, 1 for T54h and T96h) to collect 20 to 100 mg of biological. All the time points were grown on cheesecloth except the T-24h (on cellophane sheet). One to five Petri-dishes per time course experiment were thus inoculated simultaneously with a growing S mat- strain and conidia were collected by washing with 1.5 ml of H2O 6 days later. The collected conidia (around 104 microconidies per ml) were pooled and then used to fertilize corresponding number of Petri-dishes of the S mat+ strain which was growing since 4 days. Time just prior the fertilization process was considered as the T0 (0h). The biological material was then collected 6h, 12h, 18h, 24h, 30h, 42h, 54h and 96h hours after fertilization. An additional time point 24h prior fertilization was taken. Three biological replicates issued from three independent time course have been collected for all time points. The RNA pool used as a reference was assembled by combining equal amount of RNA issued from various growth and crosses conditions and has already been described (Bidard et al., BMC research notes, 2010).

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: strain

value: Wild type S mat +

tag: growth condition

value: harvested after 72h at 28°C, on M2 media covered with cellophane sheet (24 hours before fertilization)

tag: mating type

value: mat-

tag: time (post-fertilization)

source_name: Common reference (4 biosources)

tag: biosource 1

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 1

tag: biosource 2

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: name of biosource 2

tag: name of biosource 3

tag: biosource 4

tag: name of biosource 4


title: BM_PC_KO_2


title: HiCAR_H1-WT_HiCAR_R2

city: Durham

first: Tongyu

last: Sun

state: NC

address: 307 research drive

institute: Duke university

library_source: genomic

data_processing:
library strategy: HiCAR
The reads were trimmed using cutadapt and mapped to the hg38 genome using BWA-MEM, and then pairs were detected with the pairtools. Only reads with MAPQ>30 were retained. The hic files and mcool files were created with the juicer and the cool tool separately.
Assembly: hg38
Supplementary files format and content: hic

molecule: genomic DNA

source_name: H1 hESCs

growth_protocol: Human pluripotent stem cells are maintained in the mTseR plus medium(Stemcell Tech, 100-0276) according to manufacturer's instructions and detached using EDTA/PBS or accutase.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine at room temperature.
Crosslinked cells were lysed with 400 μL NPB buffer (5% BSA, 1mM DTT, 0.2% IGEPAL, Roche Complete Protease Inhibitor) on ice for 15 min to isolate the nuclei. For tagmentation, the nuclei were resuspended in 50 μL 2X TB buffer (66mM Tris-AC pH 7.8, 132mM KCl-AC, 20mM Mg-AC, 32% DMF), 45 μL molecular biology grade water and 5 μL assembled Tn5 transposase, and rotated at 37°C for 1 h. Then the nuclei were treated by MseI or CviQI for the first digestion, followed by in situ ligation with T4 DNA ligase. The second restriction enzyme digestion was performed using NlaIII, followed by the circularization and PCR amplification.

value: H1 hESCs


title: HiCAR_H1-WT_HiCAR_R1


title: SEVd45_REP2

description:
Library name: Sample 17
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd45_2


title: CUT&RUN_H1_YAP-KO_CTCF_R2

data_processing:
library strategy: CUT&RUN
RAW reads were trimmed using fastp (0.20.0) using default settings.
Trimmed reads were aligned to the hg38 genome using Bowtie version 2.4.4. Only uniquely mapping reads without mismatches were retained.
To create coverage plots, bam files were converted to bigwig files using bamCoverage and renormalized using RPKM.
Peaks were called uing MACS2 v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: Human pluripotent stem cells are maintained in the mTseR plus medium(Stemcell Tech, 100-0276) according to manufacturer's instructions and detached using  EDTA/PBS or accutase.

extract_protocol:
Cells were collected at RT and slightly crosslinked in 0.1% formaldehyde.
Cells were treated with primary antibodies and pAG-Mnase. DNA was purified and PCR amplified.

tag: sample group


title: Basal epithelial cells transfected with stealth control siRNA (Rep-2)

description:
Library name: PP2
18377_Ctrl_2_raw_counts_All_Sample.xlsx

tag: cell type


title: BM_PC_KO_4

tag: tissue


title: BM_PC_WT_1

tag: genotype


title: SEVd45_REP1

description:
Library name: Sample 16
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd45_1


title: Basal epithelial cells transfected with stealth control siRNA (Rep-1)

description:
Library name: PP1
18376_Ctrl_1_raw_counts_All_Sample.xlsx

tag: treatment


title: BMPC_KO_SpikeVax_10

value: mRNA-1273 (Spikevax) immunization


title: SEVd15_REP3

description:
Library name: Sample 15
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd15_3


title: BMPC_WT_SpikeVax_9


title: CUT&RUN_H1_YAP-KO_CTCF_R1

tag: cell line


title: CUT&RUN_H1_WT_CTCF_R2


title: MM84

city: Seattle

first: Carl

last: Murie

state: Washington

institute: Institute of System Biology

data_processing:
STAR alignment to HG38
Assembly: STAR alignment to HG38
Supplementary files format and content: csv text file of TPM values for each sample

source_name: CD138+ purified plasma cells

extract_protocol: Bone marrow plasma cell samples were obtained from 23 multiple myeloma patients at various stages of disease from the Seattle Cancer Care Institute. RNASeq gene expression profiling was applied to CD138+ purified plasma cells.

tag: disease

value: multiple myeloma

value: CD138+ purified plasma cells


title: MM83


title: BMPC_KO_SpikeVax_8


title: SEVd15_REP1

description:
Library name: Sample 13
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd15_1

value: induced pluripotent stem cell derived neurons


title: MM68


title: CUT&RUN_TEAD1-KO_BRD4_R2


title: BMPC_WT_SpikeVax_7

value: bone marrow


title: MM80


title: GSd45_REP3

description:
Library name: Sample 12
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd45_3


title: CUT&RUN_TEAD1-KO_BRD4_R1


title: BMPC_WT_SpikeVax_5

value: plasma cell (CD138+ TACI+)


title: GSd45_REP2

description:
Library name: Sample 11
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd45_2


title: MM59


title: BMPC_KO_SpikeVax_6


title: GSd45_REP1

description:
Library name: Sample 10
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd45_1


title: MM26


title: MM48


title: GSd15_REP3

description:
Library name: Sample 9
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd15_3


title: BMPC_KO_SpikeVax_4


title: CUT&RUN_YAP-KO_BRD4_R1


title: SEVd15_REP2

description:
Library name: Sample 14
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  SEVd15_2


title: GSd15_REP2

description:
Library name: Sample 8
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd15_2


title: BMPC_WT_SpikeVax_3


title: MM209


title: CUT&RUN_H1_WT_CTCF_R1


title: CUT&RUN_H1-WT_BRD4_R1


title: GSd15_REP1

description:
Library name: Sample 7
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GSd15_1


title: MM194


title: TCR DNR-plus-anti-PD-1 bio rep3-4

city: Shanghai

first: Qinlan

last: Wang

address: Chongqingnan R.280

country: China

institute: Shanghai Jiaotong University

description: two CD45+ samples from B16F10-bearing mouse tumor

library_source: transcriptomic single cell

data_processing:
The scRNA-seq reads were aligned to the mm10 reference genome and quantified using cellranger count (10x Genomics, v6.0.1). TCR reads were aligned to the mm10 reference genome and consensus TCR annotation was performed using cellranger vdj (10x Genomics, v6.0.1).
Assembly: mm10
Supplementary files format and content: barcodes.tsv(cell barcode counts);               features.tsv(genes files);             matrix.mtx(gene-barcode counts);

source_name: melanoma tumor

extract_protocol:
The tumor tissues were minced and dissociated into single-cell suspensions using a tissue dissociation kit (Miltenyi Biotec). Cells were washed and re-suspended in PBS and stained with a Viability Dye and CD45, the alive CD45 TILs were sorted on a MACS sorter. Sorted cells were collected into cold PBS plus 2% FBS, and used for the scRNA-seq.
Cells were loaded between 10,000 and 15,000 cells/chip position using the 10x Chromium Single Cell V(D)J Reagent Kits v1.1. Library was performed according to the manufacter's instructions (single cell 5' v1+TCR protocol).

value: melanoma tumor

value: Tumor infiltrated lymphocytes

value: CD45+ TILs

value: DNR + anti-PD-1


title: TCR DNR-plus-anti-PD-1 bio rep1-2


title: CUT&RUN_YAP-KO_BRD4_R2


title: CUT&RUN_H1-WT_YAP_R2


title: GCd45_REP3

description:
Library name: Sample 6
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd45_3


title: TCR anti-PD-1 bio rep3-4

value: Vehicle + anti-PD-1


title: GCd45_REP2

description:
Library name: Sample 5
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd45_2


title: CUT&RUN_H1-WT_YAP_R1


title: jazDcdk8-1_rep 3

city: East Lansing

first: Qiang

last: Guo

state: MI

address: 612 Wilson Rd

department: MSU-DOE Plant Research Laboratory

institute: Michigan State University

data_processing:
Reads assessed for quality and filtered with FASTX toolkit (http://hannonlab.cshl.edu /fastx_toolkit/).
RSEM v1.2.25 (Li and Dewey, BMC Bioinformatics, 2011) used to map reads to the Arabidopsis genome using the Illumina iGenomes TAIR10 index with default parameters. Transcript abundances expressed as transcripts per million (TPM; reads per kilobase of model per million mapped reads normalized to transcript coverage).
Assembly: TAIR10
Supplementary files format and content: expression data (jazDcdk8_expression.txt) in tab-delimited matrix table for TPM (transcripts per million) values for all samples, as determined by RSEM
Supplementary files format and content: count data (jazDcdk8_counts.txt) in tab-delimited matrix table for read counts for all samples, as determined by RSEM

organism: Arabidopsis thaliana

source_name: whole rosette

growth_protocol: Seeds were sowed on peat pellets and grown for 18 days. Peat pellets were then transferred into soil and grown for another 7 days. Plants were maintained under a 16-h light (100 μE m-2 s-1) and 8-h dark photoperiod at 20 ºC

extract_protocol:
For each replicate sample, approximately 20 plants (whole rosette, excluding roots) per genotype were pooled and immediately frozen in liquid nitrogen and stored at -80 ºC until processing. Wild-type Col-0 and mutant plants were grown in the same tray to minimize tray-to-tray variation. Three independent samples (biological replicates) were sequenced per genotype. Total RNA was isolated using a Qiagen RNeasy kit with Qiagen on-column DNase treatment to remove genomic DNA. RNA integrity was assessed with a 2100 Bioanalyzer (Agilent Bioanalyzer) and all samples had an integrity score of at least 7.0.
Sequencing libraries were prepared using the BGI Transcriptome Library kit according to the manufacturer's instructions.

value: whole rosette


title: MM173


title: TCR anti-PD-1 bio rep1-2


title: TCR DNR  bio rep3-4

value: DNR + Isotype


title: MM184


title: MM160


title: jazDcdk8-1_rep 2


title: GCd15_REP3

description:
Library name: Sample 3
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd15_3


title: jazD_rep 3

value: jazD


title: jazDcdk8-1_rep 1


title: GCd45_REP1

description:
Library name: Sample 4
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd45_1


title: GCd15_REP2

description:
Library name: Sample 2
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd15_2


title: MM154


title: TCR Vehicle bio rep1-2

value: Vehicle and Isotype


title: 9944-25


title: GCd15_REP1

description:
Library name: Sample 1
Column name in gene_count.xlsx AND gene_fpkm.xlsx:  GCd15_1


title: Control 3

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: c9

data_processing:
Adaptor sequences and low quality reads removed
Mapped to C elegans genome (version WBcel235)
DEG determined using DESeq2
Assembly: WBcel235
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Caenorhabditis elegans

source_name: Whole organism

extract_protocol:
total RNA was extracted using TRIZOL reagent, followed by chrloroform treatment and isopropanol precipiation
Standard Illumina

value: Whole organism


title: TCR DNR  bio rep1-2


title: DNR-plus-anti-PD-1 bio rep3-4 scRNAseq


title: jazD_rep 1


title: CUT&RUN_H1-WT_BRD4_R2

value: H1 hESCs


title: MM144


title: cdk8-1_rep 3


title: 9944-21


title: jazD_rep 2


title: TCR Vehicle bio rep3-4


title: DNR-plus-anti-PD-1 bio rep1-2 scRNAseq


title: Control 2

description: Library name: c8


title: MM137


title: Magnolol 3

description: Library name: c6


title: cdk8-1_rep 2


title: anti-PD-1 bio rep3-4 scRNAseq


title: cdk8-1_rep 1


title: anti-PD-1 bio rep1-2 scRNAseq


title: Col-0_rep 3

value: wildtype


title: DNR  bio rep3-4 scRNAseq


title: 9944-04

value: multiple myeloma


title: DNR  bio rep1-2 scRNAseq


title: Magnolol 1

description: Library name: c4


title: 9944-10

value: CD138+ purified plasma cells


title: Honokiol 1

description: Library name: c1


title: Vehicle bio rep3-4 scRNAseq


title: 9944-02


title: 9944-01


title: Control 1

description: Library name: c7


title: Col-0_rep 1


title: Neuronal (NeuN+) sample from individual IM1979

status: Public on Jun 29 2025

city: New York City

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads from each sample were aligned on gender specific hg19 reference genome (pseudoautosomal region was masked on the chromosome Y for males) using the STAR aligner (v2.5.0) with the following parameters: --alignIntronMax 1, --outFilterMismatchNmax 100, --alignEndsType EndToEnd, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads. We excluded reads that: (1) mapped to more than one locus; (2) were duplicated; and (3) mapped to the mitochondrial genome. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw count values (file count_matrix / hg19) and annotations of peaks (files peaks_description_hg19/38.tsv; first 4 columns are standard BED coordinates, the following one is an annotation for the closest gene).

source_name: orbitofrontal cortex

extract_protocol:
50mg of frozen brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Mg(Ace)2, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to ultracentrifugation at 24,000 rpm for 1 hour at 4°C. Pellets were thoroughly resuspended in 500µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore) under rotation for 1 hour, at 4 °C, in the dark. Prior to FANS sorting, DAPI (Thermoscientific) was added to a final concentration of 1µg/ml. DAPI positive neuronal (NeuN+) and non-neuronal (NeuN-) nuclei were sorted into tubes pre-coated with 5%BSA using a BD-FACSAria flow cytometer (BD Biosciences) equipped with a 70μm nozzle.
ATAC-seq reactions were performed using an established protocol (Buenrostro 2013) with minor modifications. Following FANS, 50,000 sorted nuclei were centrifuged at 500 ×g
for 10 min, 4°C. Pellets were re-suspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Samples were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204) according to manufacturer’s instructions. Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), under the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute for a total of 5 cycles. In order to prevent saturation due to over-amplification, a 5µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 μL reaction. The additional number of cycles was determined as follows: (1) Plot linear Rn vs. Cycle
(2) Calculate the # of cycle that is corresponded to 1⁄4 of maximum fluorescent intensity. In general, we found adding 4-6 cycles to this estimate yielded optimal ATACseq libraries, as determined by analysis on Bioanalyzer High Sensitivity DNA Chips (Agilent technologies Cat#5067-4626). Libraries were amplified for a total of 13–19 cycles. Following PCR, ATACseq libraries were resolved on 2% agarose gels and fragments ranging in size from 100bp-1Kbp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Libraries were quantified by by quantitiative PCR (KAPA Biosystems Cat#KK4873) prior to sequencing. Libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

value: orbitofrontal cortex

tag: person id

value: neuronal (NeuN+)

tag: gender

value: Female

tag: age of death

tag: postmortem interval (hours)

tag: ph

tag: rin

tag: ethnicity

value: Caucasian

tag: diagnosis

value: Control


title: 9944-20


title: Non-neuronal (NeuN-) from individual IM1978

value: non-neuronal (NeuN-)

value: MDD


title: Neuronal (NeuN+) sample from individual IM1978


title: 9944-14


title: Neuronal (NeuN+) sample from individual IM1975

value: Male


title: Neuronal (NeuN+) sample from individual IM1977


title: Non-neuronal (NeuN-) from individual IM1977


title: Non-neuronal (NeuN-) from individual IM1975


title: Non-neuronal (NeuN-) from individual IM1973


title: Non-neuronal (NeuN-) from individual IM1979


title: Neuronal (NeuN+) sample from individual IM1973


title: Non-neuronal (NeuN-) from individual IM1974


title: Col-0_rep 2

value: whole rosette


title: Magnolol 2

description: Library name: c5


title: Honokiol 2

description: Library name: c3


title: Non-neuronal (NeuN-) from individual IM1972


title: Neuronal (NeuN+) sample from individual IM1970


title: Non-neuronal (NeuN-) from individual IM1970


title: Neuronal (NeuN+) sample from individual IM1966


title: Neuronal (NeuN+) sample from individual IM1968


title: Vehicle bio rep1-2 scRNAseq

value: melanoma tumor

value: Tumor infiltrated lymphocytes

value: CD45+ TILs


title: Non-neuronal (NeuN-) from individual IM1966


title: Neuronal (NeuN+) sample from individual IM1965


title: Non-neuronal (NeuN-) from individual IM1965


title: Neuronal (NeuN+) sample from individual IM1960


title: Non-neuronal (NeuN-) from individual IM1962


title: Non-neuronal (NeuN-) from individual IM1964


title: Non-neuronal (NeuN-) from individual IM1960


title: Non-neuronal (NeuN-) from individual IM1959


title: Neuronal (NeuN+) sample from individual IM1958


title: Neuronal (NeuN+) sample from individual IM1963


title: Neuronal (NeuN+) sample from individual IM1957


title: Neuronal (NeuN+) sample from individual IM1959


title: Non-neuronal (NeuN-) from individual IM1957


title: Neuronal (NeuN+) sample from individual IM1972


title: Non-neuronal (NeuN-) from individual IM1958


title: Neuronal (NeuN+) sample from individual IM1955


title: Neuronal (NeuN+) sample from individual IM1962


title: Non-neuronal (NeuN-) from individual IM1956


title: Neuronal (NeuN+) sample from individual IM1954


title: Neuronal (NeuN+) sample from individual IM1956


title: Neuronal (NeuN+) sample from individual IM1953


title: Neuronal (NeuN+) sample from individual IM1961


title: Non-neuronal (NeuN-) from individual IM1954


title: Non-neuronal (NeuN-) from individual IM1953


title: Non-neuronal (NeuN-) from individual IM1952


title: Non-neuronal (NeuN-) from individual IM1955


title: Neuronal (NeuN+) sample from individual IM1951


title: Neuronal (NeuN+) sample from individual IM1974


title: Neuronal (NeuN+) sample from individual IM1952


title: HCT116, chromatin, replicate 2 (input)

city: Dallas

first: David

middle: Reid

last: Corey

state: Texas

address: 6001 Forest Park Rd.

department: Pharmacology

institute: UT Southwestern Medical Center

description: Library name: WT_chromatin 2_input

data_processing:
Samples were processed with Eclipsebio's prorietary analysis pipeline (v1)
UMIs were pruned using umi_tools (v1.1.1) and 3' adapters were trimmed using cutadapt (v3.2)
Non-repeat reads were mapped to hg38 genome using STAR (v2.7.7a) and PCR duplicates were removed with umi_tools (v1.1.1)
miRNAs were reverse mapped to reads that did not map to repetitive elements or the genome using bowtie (v1.2.3). miRNA portion of read was trimmed and remainder of read was mapped to the genome using STAR (v2.7.7a).
AGO2 eCLIP peaks and miRNA target clusters were identified using CLIPper (v2.0.1)
Assembly: hg38
Supplementary files format and content: bigwig files contain RPM normalized AGO2 eCLIP reads

growth_protocol: Cells were cultured in McCoy's 5A medium supplemented with 10% FBS. Growth conditions were 37C, 5% CO2.

extract_protocol:
Cells were UV-crosslinked (254 nm, 400mJ/cm2) and collected in PBS. Cell pellets were flash frozen and subcellular lysates were isolated by fractionation. All samples were lysed and sonicated prior to immunoprecipitation. AGO2 immunoprecipitation was performed with mouse monoclonal AGO2/EIF2C2 antibody (Santa Cruz Biotechnology).
Libraries were prepared as previously described (PMID:27018577).

value: WT

tag: subcelullar fraction

value: chromatin


title: HCT116, chromatin, replicate 2 (IP)

description: Library name: WT_chromatin 2_IP


title: Neuronal (NeuN+) sample from individual IM1949


title: Non-neuronal (NeuN-) from individual IM1951


title: HCT116, chromatin, replicate 1 (input)

description: Library name: WT_chromatin 1_input


title: HCT116, cytoplasm, replicate 2 (IP)

description: Library name: WT_cytoplasm 2_IP

value: cytoplasm


title: HCT116, cytoplasm, replicate 2 (input)

description: Library name: WT_cytoplasm 2_input


title: Non-neuronal (NeuN-) from individual IM1944


title: Non-neuronal (NeuN-) from individual IM1949


title: HCT116, chromatin, replicate 1 (IP)

description: Library name: WT_chromatin 1_IP


title: Neuronal (NeuN+) sample from individual IM1944


title: HCT116, cytoplasm, replicate 1 (input)

description: Library name: WT_cytoplasm 1_input


title: Neuronal (NeuN+) sample from individual IM1943


title: NLS-AGO2, whole cell, replicate 2 (IP)

description: Library name: NLS-AGO2_whole cell 2_IP

value: whole cell


title: NLS-AGO2, whole cell, replicate 2 (input)

description: Library name: NLS-AGO2_whole cell 2_input


title: Non-neuronal (NeuN-) from individual IM1942


title: Non-neuronal (NeuN-) from individual IM1943


title: Neuronal (NeuN+) sample from individual IM1942


title: NLS-AGO2, whole cell, replicate 1 (input)

description: Library name: NLS-AGO2_whole cell 1_input


title: Neuronal (NeuN+) sample from individual IM1938


title: Day21_vHuman_Samll_Intestine_Organoid

first: Minzhe

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics 3' (v3.1)

data_processing:
Sequencing reads were preprocessed, aligned, and quantified using 10x Genomics Cell Ranger software (v6.1.2).
Cell Ranger filtered feature-barcode count matrix was used as input for downstream QC and analysis using Seurat v4.
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5

source_name: Organoid derived from iPSC

extract_protocol:
Day-3 meso-endoderm spheroids and day-7 vascularized AFG and MHG organoids were dissociated with TrypLE Express Enzyme (1X) (Invitrogen) at 37oC for 7 – 12 mins. The reactions were stopped by adding N2B27 basal medium and centrifuged and filtered with 40um strainer. Day-21 vascularized gut tube organoids were embedded in a Collagen-Matrigel mixture, so were dissociated with a different digestion cocktail. Briefly, the organoids from one trans-well insert were immersed in 1ml Cell Recovery Solution at 4oC for 5 mins and triturated with P1000 wide-bore tip to break the matrix. The solution was centrifuged and resuspended in 1ml pre-warmed Dispase (5mg/ml)/Liberase solution (0.5mg/ml), and the organoids were minced with scissors. The mixture was incubated at 37oC for 20 mins with gentle triturate every 5 – 7 mins. After the first 5 mins, 10ul Dnase I (60U/ml) was added to the reaction. To stop the reaction, 9ml of Knock-out DMEM/F12 containing 10% FBS was added and centrifuged and filtered with 40um strainer. Cell pellets were resuspended in N2B27 basal medium and loaded to 10X Chromium controller for 3’ single-cell RNA-seq (v3.1).
Library was performed according to the manufacturer's instructions (Single cell 3' v3.1, 10x Genomics).

value: Organoid derived from iPSC

value: Human iPSC

value: Normal


title: HCT116, cytoplasm, replicate 1 (IP)

description: Library name: WT_cytoplasm 1_IP


title: Day21_vHuman_Colon_Organoid

description: 10x Genomics 3' (v3.1)

value: Day21 vascularizedHuman_Colon_Organoid


title: Non-neuronal (NeuN-) from individual IM1938

value: orbitofrontal cortex

value: Caucasian


title: HCT116, whole cell, replicate 2 (IP)

description: Library name: WT_whole cell 2_IP


title: Non-neuronal (NeuN-) from individual IM1939

value: non-neuronal (NeuN-)

value: Control


title: Curioseeker Spatial Transcriptomics, vascularized human lung organoids (vHLuO)

description: Library name: vHLuO_ST

data_processing:
Sequencing reads of Curio Seeker spatial transcriptomics of vHLuO was processed using Curio Seeker bioinformatics pipeline (v3.0.0) with the pre-built human and mouse mixed genome reference (Reference ID: GRCh38_mm10) downloaded from Curio Bioscience.
Background noise was removed using the background removal R script from Curio Bioscience.
Beads with more than 20 UMIs mapped to mouse genes were excluded.
Downstream data visualization and analysis was performed using Seurat and CytoSignal.
Assembly: GRCh38_mm10
Supplementary files format and content: h5ad file of anndata object containing the barcodes and gene expression matrix; output file of the Curio Seeker bioinformatics pipeline
Supplementary files format and content: txt file mapping the barcodes and spatial coordinates; an input file to the Curio Seeker bioinformatics pipeline
Library strategy: Spatial Transcriptomics

source_name: lung organoids

growth_protocol: NSG mice were kept on antibiotic chow (275 p.p.m. Sulfamethoxazole and 1,365 p.p.m. Trimethoprim, Test Diet). Food and water were provided ad libitum before and after surgeries. A single vHLuO matured in vitro for 35 days, was removed from Matrigel and transplanted under the kidney capsule as previously described53,89,90. Briefly, the mice were anesthetized with 2% inhaled isoflurane, and the left side of the mouse was then prepped in sterile fashion with isopropyl alcohol and povidine-iodine. A small left-posterior subcostal incision was made to expose the kidney. A subcapsular pocket was created and the organoid was then placed into the pocket. The kidney was then returned to the peritoneal cavity and the mice were given an intraperitoneal (IP) flush of Zosyn (100 mg/kg.). The skin was closed in a double layer and the mice were given a subcutaneous injection with Buprenex (0.05 mg/kg). At 8-15 weeks following engraftment, the mice were then humanely euthanized and the resulting grafts were analyzed.

extract_protocol:
5 scrolls of tissue sections of 10um thickness were collected to derive an RNA integrity number (RIN) to test the tissue’s RNA quality. All organoids’ RIN numbers were higher than 8 to pass the quality test. One 10um thickness tissue section was placed on the Curio Seeker tile and mounted with 30um section of CryoCube. Then, the section was processed for hybridization, reverse transcription, and tissue clearance to yield Curio Seeker Bead resuspension, according to the manufacture's instruction.
11 cycles of PCR was utilized for second-string synthesis and cDNA amplification. The purified cDNA was applied for Tagmentation with Dual Indexing Primer V2 and consequent library cleanup and QC

treatment_protocol: No treatment was used in this dataset.

value: lung organoids

value: human iPSC/ESC


title: Normal, Rag1-/-, BM, B220+ cell sorted, SP3

city: Bethesda

first: Peter

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

description:
Library name: 12_RAG_Pool_SP3_BM_S12
12_RAG_Pool_SP3_BM_S12

data_processing:
Raw fastq reads were analyzed using Partek™ Flow™ software, v12.4.2. Analysis steps included base and adaptor trimming, STAR Alignment (using reference genome=mm10), quantification of aligned reads (using Partek E/M), and normalization of gene counts (using DESeq2(poscounts) + add0.01). Differential gene expression analysis was performed using DESeq2 method.
Assembly: mm10
Supplementary files format and content: csv file includes DESeq2 normalized value of all samples

source_name: BM

growth_protocol: All three mouse genotypes(Wild type, Idh2R140Q/NHD13 and SCL/LMO1) were maintained from birth in mice facility.

extract_protocol:
Total RNA was isolated from leukemic ATC treated Rag1-/- mice spleen cells, untreated non-leukemic Rag1-/- mice CD19+B220+ sorted BM cells and untreated non-leukemic Rag1-/- mice B220+ sorted BM cells using TRIzol reagent following the manufacturer’s recommended protocol
Total RNA was reverse transcribed and library prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit using manufacturers recommendated protocol.

treatment_protocol: For in vivo treatment Rag1 KO mice were treated with ATC (1mg/kg) or PBS (as control) once daily via intraperitoneal injection for 5 days per week for 2 weeks followed by 1-week rest and repeating this cycle again till the end point of treatment (euthanasia of moribund mouse or end of experiment)

value: BM

value: Normal BM

value: No treatment


title: Normal, Rag1-/-, BM, B220+ cell sorted, SP1

description:
Library name: 10_RAG_Pool_SP1_BM_S10
10_RAG_Pool_SP1_BM_S10


title: HCT116, whole cell, replicate 2 (input)

description: Library name: WT_whole cell 2_input

value: WT


title: Day7_vMHG_B3

description: 10x Genomics 3' (v3.1)

value: Day-7 vascularized anterior mid/hindgut


title: Neuronal (NeuN+) sample from individual IM1937

value: neuronal (NeuN+)

value: Female


title: Day7_vMHG_B2

description: 10x Genomics 3' (v3.1)

value: Organoid derived from iPSC


title: HCT116, whole cell, replicate 1 (IP)

description: Library name: WT_whole cell 1_IP

value: whole cell


title: Normal, Rag1-/-, BM, CD19+B220+ cell sorted, DP3

description:
Library name: 9_RAG_Pool_DP3_BM_S9
9_RAG_Pool_DP3_BM_S9


title: mitoDMS FASTKD5 knockout 2

city: Miami

first: Ahram

last: Ahn

state: FL

address: 1600 NW 10th Ave

department: Biochemistry and Molecular Biology

institute: University of Miami

description:
Library name: E
DMS treated isolated human FASTKD5-KO mitochondria, Bioreplicate 2

library_source: other

data_processing:
CutAdapt
Bowtie 2
SEISMIC-RNA
Assembly: GRCh38/hg38
Supplementary files format and content: Population Average Reactivities from the Heavy and Light strand, .txt files

molecule: other

source_name: Embryonic kidney

growth_protocol: HEK-293T cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS), 5 mL 100X antibiotic/antimycotic, 1 mM sodium pyruvate, 1 mM sodium formate, and 50 g/ml uridine, and 1x GlutaMAX (ThermoFisher Scientific; Waltham, MA) at 37°C under 5% CO2 in 1 L of liquid culture.

extract_protocol:
RNA was extracted following the TRIzol manufacturer’s specifications. The aqueous phase was transferred to a new tube, and an equal volume of 100% isopropanol and 3 μl of glycogen were added to precipitate the RNA. The samples were incubated at -80 oC for 1 hour and centrifuged at 15000 g for 20 min, at 4 °C. RNA was resuspended in 50 μl of RNase-free water and quantified by measuring absorbance at a wavelength of 260 nm with Nanodrop (Thermo Fisher Scientific). 10 μg of RNA was DNase-treated using the TURBO DNase kit (Thermo Fisher Scientific). After treatment, the RNA was purified using RNA Clean and Concentrator −5 kit (Zymo Research) according to the manufacturer’s protocol. DNase treatment and column purification were repeated two additional times to ensure the complete removal of all DNA.
Sequencing libraries were generated using the xGen Broad-range RNA library preparation kit from IDT, according to the manufacturer's instructions, with the following modifications. The RNA fragmentation step was conducted by combining 1 μg of RNA with 1 μl of reagent F1, 4 μl of F3, and 2 μl of F4, and incubating at 95 °C for 2 min. The samples were immediately placed on ice and combined with a mixture of 1 μl Induro Reverse Transcriptase (NEB), 1 μl R1 reagent, and 1 μl 0.1 M DTT. This mixture was incubated for 30 min at room temperature before adding 2 μl of reagent F2, and then placed in a thermocycler for 10 min at 20°C, 10 min at 42 °C, and 60 min at 55 °C. Then, 1 μl of 4M NaOH was added, and the samples were incubated at 95°C for 3 minutes. At this point, the sample was removed from the thermocycler and placed on ice, and 1 μl of 4M HCl and 27 μl of IDTE (10 mM Tris, 0.1 mM EDTA) were added. After the indexing PCR, the indexed libraries were resolved on an 8% TBE gel for 55 min at 180 V and size-selected for products ~300 nt. The products were sequenced using the NovaSeq X Plus platform (Illumina) with PE 150, 250M reads per sample.

treatment_protocol: Two 15-cm dishes of wild-type or HEK293T FASTKD5-KO cells, respectively, grown at 80% confluency, were inoculated into one liter of FreeStyle 293 expression medium supplemented with 50 ml FBS, 50 μg/ml uridine, and 10 ml of 100X antibiotic/antimycotic. Cells were grown at 37°C under 5% CO2, spinning at 63 RPM for four days. Mitochondria were isolated as previously described 27 and resuspended in 1 ml of STE buffer (0.32 M sucrose, 1 mM EDTA, and 10 mM Tris-HCl, pH 7.4). 3 mg of freshly prepared mitochondria were pelleted by centrifugation at 10000 g for 10 min at 4 °C. For one set of experiments, the pellet was resuspended in 150 μl of Na-cacodylate in organello translation buffer (300 mM Na-cacodylate pH 8.0, 100 mM mannitol, 10 mM sodium succinate, 80 mM KCl, 5 mM MgCl2, 1 mM Na-phosphate, 60 mg/ml of each of the 20 amino acids including methionine, 5 mM ATP, 20 mM GTP, 6 mM creatine phosphate, and 60 mg/ml creatine kinase) that had been preheated to 37 °C and incubated for 5 min at 37 °C. A freshly prepared and preheated mixture of 150 μl of the Na-cacodylate translation buffer plus 3 μl of dimethyl sulfate (DMS) was added to the mitochondria, resulting in a final DMS concentration of 1%. The samples were then incubated for 5 min at 37°C for DMS labelling. To quench the DMS reaction, 180 μl of β-mercaptoethanol were added to the mitochondria, the solution was mixed, and the samples were centrifuged at 10000 g for 5 min at 4 °C. The mitochondrial pellets were washed twice in 1 ml of glycerol wash buffer (10% glycerol, 0.15 mM MgCl2, 10 mM Tris-HCl pH 6.8), following the same centrifugation conditions indicated above and resuspended in 1 ml of TRIzol for RNA extraction.

value: Embryonic kidney

value: HEK 293

value: Epithelial-like

value: FASTKD5 knock out

value: 1% DMS


title: Neuronal (NeuN+) sample from individual IM1936

value: orbitofrontal cortex

value: Caucasian

value: Control


title: Non-neuronal (NeuN-) from individual IM1936

value: non-neuronal (NeuN-)


title: NLS-AGO2, whole cell, replicate 1 (IP)

description: Library name: NLS-AGO2_whole cell 1_IP


title: Normal, Rag1-/-, BM, CD19+B220+ cell sorted, DP2

description:
Library name: 8_RAG_Pool_DP2_BM_S8
8_RAG_Pool_DP2_BM_S8

value: BM

value: Normal BM


title: Day7_vAFG_B1

description: 10x Genomics 3' (v3.1)

value: Human iPSC

value: Day-7 vascularized anterior foregut

value: Normal


title: mitoDMS FASTKD5 knockout 1

description:
Library name: D
DMS treated isolated human FASTKD5-KO mitochondria, Bioreplicate 1


title: Day21_vHuman_Lung_Progenitor_Organoid

description: 10x Genomics 3' (v3.1)


title: Neuronal (NeuN+) sample from individual IM1935

value: neuronal (NeuN+)

value: Male


title: Leukemic, Rag1-/-, Spleen, 8662

description:
Library name: 6_8662_Spleen_S6
6_8662_Spleen_S6

source_name: Spleen

value: Spleen

value: BCP-ALL

value: ATC treated (in vivo)


title: Leukemic, Rag1-/-, Spleen, 8660

description:
Library name: 5_8660_Spleen_S5
5_8660_Spleen_S5


title: mitoDMS WT2

description:
Library name: C
DMS treated isolated human WT mitochondria, Bioreplicate 2

value: Embryonic kidney

value: HEK 293

value: Epithelial-like

value: WT


title: Non-neuronal (NeuN-) from individual IM1935

value: orbitofrontal cortex

value: Caucasian


title: Day3_BMP_2

description: 10x Genomics 3' (v3.1)

value: Organoid derived from iPSC

value: Day-3 meso-endoderm spheroids


title: Neuronal (NeuN+) sample from individual IM1933

value: Female

value: Control


title: Non-neuronal (NeuN-) from individual IM1937

value: non-neuronal (NeuN-)


title: Day7_vMHG_B1

description: 10x Genomics 3' (v3.1)

value: Human iPSC

value: Day-7 vascularized anterior mid/hindgut

value: Normal


title: DMS untreated WT

description:
Library name: A
DMS untreated isolated human WT mitochondria, Bioreplicate 1

value: 0% DMS


title: HCT116, whole cell, replicate 1 (input)

description: Library name: WT_whole cell 1_input

value: whole cell


title: Day3_BMP_1

description: 10x Genomics 3' (v3.1)


title: Non-neuronal (NeuN-) from individual IM1933


title: Leukemic, Rag1-/-, Spleen, 8656

description:
Library name: 4_8656_Spleen_S3
4_8656_Spleen_S3

value: Spleen

value: BCP-ALL

value: ATC treated (in vivo)


title: Leukemic, Rag1-/-, Spleen, 8661

description:
Library name: 3_8661_Spleen_S2
3_8661_Spleen_S2


title: sample5- Expanded CDX2mCherry pos p3

city: New York

first: Hina

last: Chaudhry

state: USA

department: Cardiology

institute: Mount Sinai Hospital

description: Library name: sample5- Expanded CDX2mCherry pos p3

data_processing:
Raw sequencing data in the form of .bcl files, generated from Illumina, were converted into FASTQ files and demultiplexed using the 10x Genomics' Cell Ranger mkfastq pipeline. Differential gene expression analysis was conducted interactively using the 10x Genomics Loupe Browser for data visualization and interpretation.
Assembly: mm10
Supplementary files format and content: Tab seperated values files and barcodes/features files

source_name: Term Placenta

extract_protocol:
Human CDX2mCherry-positive cell samples, both freshly isolated (n=2) and expanded at passage 3 (n=3), were thawed for analysis (total n=5). Cell counts were assessed using the Cellaca Cell Counter (Nexcelom Bioscience, Lawrence, MA, USA) in conjunction with NucBlue for staining cell nuclei and propidium iodide (PI) for identifying dead cells. Samples were then processed with the Chromium X platform (10x Genomics, Pleasanton, CA, USA), following the manufacturer’s protocols.
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3’ Gene Expression Kit. Library quality was assessed using the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified via Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Additional quantification was performed using qPCR (Applied Biosystems, Carlsbad, CA, USA) before sequencing on an Illumina platform, adhering to 10x Genomics' recommended sequencing configurations.

value: Term Placenta

value: Chorionic cells


title: Normal, Rag1-/-, BM, CD19+B220+ cell sorted, DP1

description:
Library name: 7_RAG_Pool_DP1_BM_S7
7_RAG_Pool_DP1_BM_S7

value: BM

value: Normal BM

value: No treatment


title: Neuronal (NeuN+) sample from individual IM1925

value: orbitofrontal cortex

value: neuronal (NeuN+)

value: Male

value: Caucasian


title: Day7_vAFG_B0

description: 10x Genomics 3' (v3.1)

value: Organoid derived from iPSC

value: Human iPSC

value: Day-7 vascularized anterior foregut


title: Day3_BMP_0

description: 10x Genomics 3' (v3.1)

value: Day-3 meso-endoderm spheroids

value: Normal


title: Leukemic, Rag1-/-, Spleen, 8658

description:
Library name: 1_8658_Spleen_S1
1_8658_Spleen_S1

value: Spleen


title: Leukemic, Rag1-/-, Spleen, 8650

description:
Library name: 2_8650_Spleen_S4
2_8650_Spleen_S4

value: BCP-ALL


title: mitoDMS WT1

description:
Library name: B
DMS treated isolated human WT mitochondria, Bioreplicate 1

value: Embryonic kidney

value: HEK 293

value: Epithelial-like

value: WT

value: 1% DMS


title: Non-neuronal (NeuN-) from individual IM1925

value: non-neuronal (NeuN-)

value: Control


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep3

city: Austin

first: Qiuxia

last: Zhao

address: 2415 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: ESC_HSL_698

data_processing:
Adapter removal (Truseq HT adapters) and genome mapping (WBcel235) and assignment to protein coding genes were accomplished by using NextFlow preprocessing pipeline, Riboflow.
The raw reads per gene were extracted from the output ribo file using RiboR.
These reads were then analyzed for significant differences with and without CHX using Deseq2 analysis.
Assembly: WBcel235
Supplementary files format and content: CSV file includes transcript counts for each Sample
Library strategy: Ribo-Seq

source_name: whole worm

growth_protocol: Animals were grew at 23˚C

extract_protocol:
Worm lysate was loaded onto 34% sucrose made with the lysis buffer, and spun at 70,000 rpm using TLA 100.3 rotor (Beckman Coulter) for 4 hours at 4 ℃. The resulting pellet was solubilized in 1 ml of TRIzol to extract RNA. Resulting RNA was resolved on 10% Acrylamide TBE-urea gel (ThermoFisher Scientific), fragments between 26-34 nucleotides were cut for RNA extraction.
Ribo-seq libraries were prepared using D-Plex Small RNA-seq Kit (diagenode) following manufacturer's protocols.

treatment_protocol: Put synchronized eggs on without or with CHX (500 µg/ml) NGM plates.

value: whole worm

tag: developmental stage

tag: Sex

value: hermaphrodite

value: rpl-36A(P55Q)/mIn1 heterozygotes

value: embryos, no CHX, 2 days


title: Neuronal (NeuN+) sample from individual IM1923

value: orbitofrontal cortex

tag: cell type

value: neuronal (NeuN+)

value: Male

value: Caucasian


title: Sample4- Fresh CDX2mCherry pos

description: Library name: Sample4- Fresh CDX2mCherry pos

tag: tissue

value: Term Placenta

value: Chorionic cells


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep3

description: Library name: ESC_HSL_700

tag: genotype

value: embryos, +CHX, 3 days


title: Day3_BMP_3

description: 10x Genomics 3' (v3.1)

value: Organoid derived from iPSC

value: Human iPSC

value: Day-3 meso-endoderm spheroids

value: Normal

tag: treatment


title: Non-neuronal (NeuN-) from individual IM1923

value: non-neuronal (NeuN-)


title: WT_mesentery_LEC

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description: Library name: ct_mes

data_processing:
Aligned reads were processed to generate cell-gene raw expression matrices. Then, low quality cells (expressing less than 1200 genes) and potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat (v3.1.1). After removing contaminating cells, dimensionality reduction and clusterings were performed to produce processed data files.
Identification of differentially expressed genes and downstream analysis were performed by Seurat.
Assembly: mm10
Supplementary files format and content: Seurat object file of LEC from each dataset after quality control,  dimensionality reduction and clustering.

molecule: polyA RNA

source_name: Mesentery

extract_protocol:
FACS sorted LEC were processed by 10X chromium v3.1 kit following the manufacturer's protocols.
10X v3.1 reagent kits (10X genomics) were used to generate cDNA libraries.

value: Mesentery

value: Lymphatic endothelial cell

value: WT


title: sample2- Expanded CDX2mCherry pos p3

description: Library name: sample2- Expanded CDX2mCherry pos p3


title: KO_mesentery_LEC

description: Library name: ko_mes

value: Prox1-Cre; Erg-fl/fl; Fli1-fl/fl


title: Sample1- Fresh CDX2mCherry pos

description: Library name: Sample1- Fresh CDX2mCherry pos


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep2

description: Library name: ESC_HSL_697

value: whole worm

value: hermaphrodite

value: rpl-36A(P55Q)/mIn1 heterozygotes

value: embryos, no CHX, 2 days


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep2

description: Library name: ESC_HSL_699


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep1

description: Library name: ESC_HSL_696


title: sample3- Expanded CDX2mCherry pos p3

description: Library name: sample3- Expanded CDX2mCherry pos p3


title: HASMCs, AngII6

city: Nanjing

first: Shanshan

last: Luo

state: Jiangsu province

address: Long Mian Avenue 109

department: Pharmacy

institute: 南京医科大学

description:
Library name: sample9
Column name in gene_count_matrix.txt:AngII_6

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each Samples
Supplementary files format and content: tab-delimited text file include FPKM values for each Samples

source_name: aorta

growth_protocol: Human aortic smooth muscle cells (HASMCs, 6110, ScienCell) purchased from ScienCell Research Laboratories were cultured in Smooth Muscle Cell Medium (SMCM, 1101, ScienCell).

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

treatment_protocol: HASMCs were starved in serum-free SMCM for 24 hs followed by Angiotensin II (Ang II, 10-6M) treatments.

value: aorta

tag: cell line

value: primary cell

value: smooth muscle cell

value: Ang II

tag: batch


title: 4Y-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

description: Library name: Sample 9

data_processing:
Fastp filters low-quality readings.
FastQC performs data quality control, Star performs reference genome alignment.
Screening and quantification of differentially expressed genes using Trinity and RSEM.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Calculate the number of reads in the open reading frame of coding genes using software RSEM, and normalize gene expression levels using FPKM method

organism: Bos grunniens

source_name: testis

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
Grind the frozen tissue into powder using a mortar and pestle in liquid nitrogen, and then dissolve it in 400 μ L lysis buffer. After RNA extraction from tissue samples, Nanodrop was used to detect RNA purity, and Qubit was used to accurately quantify RNA.
After passing the RNA sample detection, the Covaris ultrasonic disruptor is used to randomly interrupt the entire library preparation process, followed by end repair, addition of A tail, addition of sequencing adapter, purification, PCR amplification, and other steps. After passing the library detection, different libraries are pooled into Flow cells and cBOT clusters according to the requirements of effective concentration and target data volume. Then, Illumina NovaSeq high-throughput sequencing platform is used for sequencing.

treatment_protocol: Three 6-month-old (6M), 18-month-old (18M), 4-year-old (4Y) male yaks and 4-year-old (4Y)  cattle-yaks were selected from the same cooperative in Xiahe County, Gannan Tibetan Autonomous Prefecture, Gansu Province (N34 ° 51'50 ', E102 ° 26'9') for castration to collect testicular tissue

value: testis

value: sexual maturity


title: 4Y-2

institute: Chinese Academy of Agricultural Sciences

description: Library name: Sample 8


title: HASMCs, AngII5

description:
Library name: sample8
Column name in gene_count_matrix.txt:AngII_5


title: 4Y-1

description: Library name: Sample 7


title: E.coli K12 mcr-3, replicate3

city: Nagoya

first: Yihao

last: Zhang

state: Aichi

address: 65 Tsurumaichō, Showa Ward

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

description:
Library name: mcr-3-3
mcr-3

data_processing:
Bowtie2 for rRNA removal. STAR aligner for reads alignment. RSEM for read count.
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: The processed data is in txt format. First column is gene id. Following columns refer to three groups in three replicates. Annotated gene name, protein id and description are attached as well.

organism: Escherichia coli K-12

source_name: Bacteria

extract_protocol:
RNA is extracted by Trizol.
Library is constructed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: Bacteria


title: E.coli K12 mcr-3, replicate2

description:
Library name: mcr-3-2
mcr-3


title: Non-neuronal (NeuN-) from individual IM1963

value: orbitofrontal cortex

tag: person id

value: Male

value: Caucasian

value: MDD


title: HASMCs, AngII4

description:
Library name: sample7
Column name in gene_count_matrix.txt:AngII_4

value: WT


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep3 (50-80 nt)

description: Library name: ESC_HSL_706

data_processing:
Adapter removal (Truseq HT adapters) and genome mapping (WBcel235) and assignment to protein coding genes were accomplished by using NextFlow preprocessing pipeline, Riboflow.
The raw reads per gene were extracted from the output ribo file using RiboR.
These reads were then analyzed for significant differences with and without CHX using Deseq2 analysis.
Assembly: WBcel235
Supplementary files format and content: CSV file includes transcript counts for each Sample

extract_protocol:
Worm lysate was loaded onto 34% sucrose made with the lysis buffer, and spun at 70,000 rpm using TLA 100.3 rotor (Beckman Coulter) for 4 hours at 4 ℃. The resulting pellet was solubilized in 1 ml of TRIzol to extract RNA. Resulting RNA was resolved on 10% Acrylamide TBE-urea gel (ThermoFisher Scientific), fragments between 50-80 nucleotides were cut for RNA extraction.
Disome-seq libraries were prepared using D-Plex Small RNA-seq Kit (diagenode) following manufacturer's protocols.

value: embryos, +CHX, 3 days


title: E.coli K12 mcr-3, replicate1

description:
Library name: mcr-3-1
mcr-3


title: 18m-2

description: Library name: Sample 5

value: puberty


title: HASMCs, AngII3

description:
Library name: sample6
Column name in gene_count_matrix.txt:AngII_3


title: HASMCs, AngII2

description:
Library name: sample5
Column name in gene_count_matrix.txt:AngII_2


title: 18m-3

description: Library name: Sample 6


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep2 (50-80 nt)

description: Library name: ESC_HSL_704

value: whole worm

value: hermaphrodite


title: 18m-1

description: Library name: Sample 4


title: E.coli K12 mcr-1, replicate1

description:
Library name: mcr-1-1
mcr-1


title: E.coli K12 mcr-1, replicate3

description:
Library name: mcr-1-3
mcr-1


title: HASMCs, AngII1

description:
Library name: sample4
Column name in gene_count_matrix.txt:AngII_1


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep2 (50-80 nt)

description: Library name: ESC_HSL_703

value: rpl-36A(P55Q)/mIn1 heterozygotes

value: embryos, no CHX, 2 days


title: E.coli K12 control, replicate3

description:
Library name: control-3
control

value: control


title: HASMCs, Ctrl3

description:
Library name: sample3
Column name in gene_count_matrix.txt:Ctrl_3

value: aorta

value: primary cell

value: smooth muscle cell

value: PBS


title: rpl-36A(P55Q)/mIn1 heterozygotes, +CHX, 3-day, 23˚C, L4, Rep1 (50-80 nt)

description: Library name: ESC_HSL_702


title: 6m-2

description: Library name: Sample 2

value: testis

value: Juvenile stage


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep1

description: Library name: ESC_HSL_695


title: HASMCs, Ctrl2

description:
Library name: sample2
Column name in gene_count_matrix.txt:Ctrl_2


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep1 (50-80 nt)

description: Library name: ESC_HSL_701


title: HASMCs, Ctrl1

description:
Library name: sample1
Column name in gene_count_matrix.txt:Ctrl_1


title: lv_Mettl3_2

status: Public on Jun 28 2025

first: Yuhui

last: Zang

address: 163 Xianlin Road

institute: Nanjing University

description: Library name: Sample 4

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
RNA-seq reads were aligned to the rnor_6_0_gca_000001895_4 genome assembly using HISAT2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: RPKM values for each Sample
Supplementary files format and content: The file 'Lv_Mettl3vsLv_nc_deg_all.txt' lists all differentiated genes in the NRK-52E cell line Lv_Mettl3 relative to Lv_nc, while the file 'Lv_Mettl3vsLv_nc_deg.txt' only includes the differentially expressed genes complying with the following criteria: P <0.05 and fold change (FC) ≥2.0 or ≤−2.0.

organism: Rattus norvegicus

source_name: Kidney

growth_protocol: The cells maintained in DMEM(Invitrogen) containing 10% fetal calf serum, penicillin (100 units/ml) and streptomycin (100 μg/ml). All cells were incubated at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from NRK-52E subline cells with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The validated murine Mettl3 cDNA was cloned into the pLVX-IRES-Puro lentiviral vector to generate pLVX-IRES-Puro-Mettl3. The infectious virus particles were collected at 48 h after HEK 293T cells were transfected with pLVX-IRES-Puro-Mettl3, the packaging plasmid psPAX2 and the VSV-G envelope plasmid pMD2.G (Addgene, Cambridge, MA) using the Lipofectamine 2000 reagent. The NRK-52E cell line overexpressing METTL3 was established by infecting the cells with the lentivirus. After lentivirus infection, the stable cell lines were selected using 0.5 mg/ml of puromycin. The stable line was maintained in DMEM supplemented with 10% FBS and 0.25 mg/ml of puromycin.

value: Kidney

value: proximal tubular epithelial cell

value: untreated


title: E.coli K12 control, replicate1

description:
Library name: control-1
control

value: Bacteria


title: lv_Mettl3_1

description: Library name: Sample 3


title: E.coli K12 mcr-1, replicate2

description:
Library name: mcr-1-2
mcr-1


title: lv_nc_1

description: Library name: Sample 1


title: rpl-36A(P55Q)/mIn1 heterozygotes, -CHX, 2-day, 23˚C, L4, Rep3 (50-80 nt)

description: Library name: ESC_HSL_705


title: single nucleus RNA sequencing S37

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

description: Library name: S37_scRNA-seq

data_processing:
We used cellranger v7.0.1 (10X Genomics) to generate count matrices with default parameters but an optimized transcriptome reference v1.1 for GRCh38. CellBender v0.3.0 was used to remove background noise.
Assembly: GRCh38
Supplementary files format and content: Cellbender output file: raw_feature_bc_matrix_filtered.h5

source_name: sural nerve

extract_protocol:
Residual material from the sural nerve grafts were used for control samples in this study. In PNP patients, sural nerve biopsy was performed as part of the clinical diagnostic workup and a small portion of the nerve (approximately 0.2 cm) was used for this study. In Münster and Essen, the samples were immediately fresh-frozen after surgery in dry ice-cooled methylbutane and stored in liquid nitrogen (0 - 14 months) until nuclei extraction. In Würzburg, the samples were embedded into OCT embedding matrix (Roth) until nuclei extraction (33 - 77 months). In Essen and Münster samples were collected from newly recruited patients. In Würzburg, samples were collected from an existing biobank of OCT embedded cryo-preserved sural nerve biopsies collected between 2016 and 2020. For each patient, approximately 10 mg pieces (median of 13.9 mg) were cut on dry ice as starting material from the original samples. Nerve pieces were cut into smaller pieces and processed using the Miltenyi Biotec nuclei extraction protocol. In summary, samples were transferred to a gentleMACS C-tube (Cat.no. 130-093-237) containing 2 ml lysis buffer (nuclei extraction buffer (Cat. no. 130-128-024) + 0.2 U/µl RNase inhibitor (EO0381) and processed on a gentleMACS dissociator with program 4C_nuclei_1. After dissociation, the nuclei suspension was filtered through a pluriStrainer Mini 70-µm cell strainer (pluriSelect®) and washed in 200-400 µl resuspension buffer (PBS with 0.1% BSA and 0.2 U/μL RNase inhibitor (EO0381) depending on sample size and expected nuclei count. Nuclei suspension was then filtered through a pluriStrainer Mini 40-μm cell strainer (pluriSelect®), placed on a 1.5 ml DNA-LoBind tube (Merck). The nuclei suspension was stained with Trypan Blue to manually assess nuclei viability and count using a Fuchs-Rosenthal chamber. Equal volumes between samples were used for downstream application of single nucleus RNA seq.
Single nucleus suspensions were loaded into a Chromium Next GEM Chip G and placed into the Chromium X Single Cell Controller and processed with Chromium Next GEM Single Cell 3´ Kit v3.1 reagents (all 10X Genomics). Sequencing was performed on Illumina Nextseq 2000 and Novaseq 6000 with a 28-8-0-91 read setup. CellBender v0.3.0 was used to remove background noise. In CellBender, the number of expected cells and total droplets was based on the UMI curve and the learning rate was reduced based on the automated output report.

value: sural nerve

tag: material

value: OCT

tag: disease

value: CIDP

tag: center

value: Würzburg


title: lv_nc_2

description: Library name: Sample 2


title: single nucleus RNA sequencing S36

description: Library name: S36_scRNA-seq


title: single nucleus RNA sequencing S35

description: Library name: S35_scRNA-seq


title: single nucleus RNA sequencing S34

description: Library name: S34_scRNA-seq

value: CIAP


title: 6m-3

description: Library name: Sample 3


title: single nucleus RNA sequencing S31

description: Library name: S31_scRNA-seq


title: single nucleus RNA sequencing S30

description: Library name: S30_scRNA-seq

value: VN


title: single nucleus RNA sequencing S26

description: Library name: S26_scRNA-seq


title: single nucleus RNA sequencing S28

description: Library name: S28_scRNA-seq


title: single nucleus RNA sequencing S33

description: Library name: S33_scRNA-seq


title: single nucleus RNA sequencing S27

description: Library name: S27_scRNA-seq


title: single nucleus RNA sequencing S25

description: Library name: S25_scRNA-seq

value: fresh frozen

value: CTRL

value: Essen


title: single nucleus RNA sequencing S24

description: Library name: S24_scRNA-seq


title: E.coli K12 control, replicate2

description:
Library name: control-2
control

value: control


title: 6m-1

description: Library name: Sample 1


title: SL0536_CEv3_neratinib_48_2

city: Birmingham

first: Benjamin

last: Lin

state: AL

address: 401F Wallace Tumor Institute

department: Pathology

institute: The University of Alabama at Birmingham

description: Library name: SL0536

data_processing:
Aligned with STAR aligner and transcripts quantified with SALMON
Assembly: Gencode vM32 genome with vH43 EGFR
Supplementary files format and content: Transcripts quantified by SALMON

extract_protocol:
RNeasy kit (Qiagen, Hilden, Germany)
KAPA Stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA)

value: starve serum culture


title: single nucleus RNA sequencing S23

description: Library name: S23_scRNA-seq


title: SL0538_CEv3_neratinib_4_1

description: Library name: SL0538


title: SL0531_CEv3_neratinib_4_2

description: Library name: SL0531


title: single nucleus RNA sequencing S21

description: Library name: S21_scRNA-seq

value: ONIN


title: single nucleus RNA sequencing S20

description: Library name: S20_scRNA-seq

value: DPN


title: SL0530_CEv3_neratinib_24_2

description: Library name: SL0530


title: single nucleus RNA sequencing S17

description: Library name: S17_scRNA-seq


title: SL0522_CEv3_neratinib_24_1

description: Library name: SL0522


title: single nucleus RNA sequencing S22

description: Library name: S22_scRNA-seq


title: single nucleus RNA sequencing S18

description: Library name: S18_scRNA-seq


title: SL0528_CEv3_neratinib_24_3

description: Library name: SL0528


title: SL0516_CEv3_neratinib_48_1

description: Library name: SL0516


title: SL0523_CEv3_neratinib_48_3

description: Library name: SL0523


title: single nucleus RNA sequencing S19

description: Library name: S19_scRNA-seq


title: single nucleus RNA sequencing S32

description: Library name: S32_scRNA-seq


title: single nucleus RNA sequencing S15

description: Library name: S15_scRNA-seq


title: single nucleus RNA sequencing S16

description: Library name: S16_scRNA-seq

value: OIN


title: single nucleus RNA sequencing S29

description: Library name: S29_scRNA-seq


title: WT_plus

city: Tsukuba

first: Chigusa

last: Nakahashi-Oda

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

institute: University of Tsukuba

data_processing:
RNA-seq reads were aligned to the  genome assembly of GRCm39 using CLC genomics workbench 22.0 with the default settings.
A statistical differential expression test was used "Differential Expression for RNA-Seq tool" in the CLC software.
Assembly: GRCm39
Supplementary files format and content: statistic test and expression data.

source_name: heart

extract_protocol:
mice were perfused with 20 ml PBS under deep anesthesia. The hearts were collected and minced with scissor into about 0.5 mm in 5 mL of RPMI-1640 with 10% Fetal Bovine Serum (FBS). Then digested with Collagenase II (200 U/mL, WOR) and DNase I (60 U/ml, WOR) a 37°C incubator for 30 min with agitation on a rotator and stirred in the gentleMACS Program m_heart_01 of the gentleMACS Dissociator. The Incubation was again carried out for 30 min and stirred in gentleMACS Program m_heart_02. The homogenate of cardiac tissue was passed through a 70 µm cell strainer, added 10 ml of wash buffer (PBS supplemented with 1% FBS) and centrifuged at 400 x g for 10 min and resuspended in PBS. Single-cell suspension was stained with anti-CD45.2, CD11b, Ly6G, SiglecF. CD45.2+ CD11b+ Ly6G+ SiglecF+ neutrophils and CD45.2+ CD11b+ Ly6G+ SiglecF- neutrophils were isolated using FACS Aria II (BD Biosciences). For each sample, neutrophils from eight animals were pooled to make the cell numbers at least 2 × 104. RNA was extracted using ISOGEN (Nippon Gene).
Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina, and NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# E7770 and E7490; New England Biolabs).

value: heart

value: neutrophils

value: WT

value: 3 days after  myocardial ischemia and reperfusion


title: KO_minus

value: CD45.2+ CD11b+ Ly6G+ SiglecF- neutrophils


title: single nucleus RNA sequencing S11

description: Library name: S11_scRNA-seq

value: sural nerve

value: CIDP


title: WT_minus


title: P2 ipsRPE cells, line 82, 10-week-old_RNA-seq

city: Rensselaer

first: Farhad

last: Farjood

state: NY

address: 1 Discovery Drive

institute: Neural Stem Cell Institute

description: CITE-Seq with ICELL8 platform

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cogent software v1.0 (https://www.takarabio.com/products/next-generation-sequencing/bioinformatics-tools/cogent-ngs-analysis-pipeline)
Seurat package was used to make and integrate seurat objects for RNA-seq libraries. CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) Was used for demultiplexing and counting ADT libraries.
Assembly: hg38
Supplementary files format and content: rds, includes Seurat objects containing read counts and clustering results

source_name: RPE

growth_protocol: RPE cells were isolated from human donor eyes and CITE-Seq was performed on acutely isolated and cultured cells at passage 2. Cultured cells were maintained in RPE medium: DMEM F12 50/50 medium (Corning), MEM alpha modification medium (Sigma-Aldrich), 1.25 mL Glutamax (Gibco), 2.5 mL Sodium Pyruvate (Gibco), 2.5 mL Niacinamide (1M; Spectrum Chemical Inc., CA), 2.5 mL MEM NEAA (Gibco), 2% or 10% or 2% heat inactivated fetal bovine serum (FBS), supplemented with THT (Taurine, Hydrocortisone, Triiodo-thyronin), and 1.25 mL N1 medium supplement (Sigma-Aldrich). Cells were incubated in a humidified incubator at 37 oC and 5% CO2. RPE medium with 10% FBS was used until the cultures were confluent and 2% FBS was used after confluency. The medium was replaced every 3 days.

extract_protocol:
RNA isolation and cDNA sythesis were performed using the SMART-Seq ICELL8 Application Kit. ADTs were separated from the cDNA after RT-PCR using Ampure beads (1.8X), from which a separate ADT library was prepared.
Single cell library preparation was performed using the SMART-Seq ICELL8 Application Kit. ADT library prepration was performed with ADTs isolated from the cDNA and sparq hifi master mix (Quantbio)

value: RPE

tag: donor gender

value: not applicable

tag: donor age

tag: donor race

tag: time in_culture

value: 10 weeks


title: single nucleus RNA sequencing S14

description: Library name: S14_scRNA-seq

value: fresh frozen

value: CIAP


title: KO_plus

value: CD45.2+ CD11b+ Ly6G+ SiglecF+ neutrophils


title: single nucleus RNA sequencing S13

description: Library name: S13_scRNA-seq

value: Essen


title: SL0520_CEv3_neratinib_4_3

description: Library name: SL0520

value: starve serum culture


title: P2 ipsRPE cells, line 82, 10-week-old_ADT

description: CITE-Seq with ICELL8 platform


title: single nucleus RNA sequencing S10

description: Library name: S10_scRNA-seq

value: Münster


title: single nucleus RNA sequencing S07

description: Library name: S07_scRNA-seq


title: single nucleus RNA sequencing S09

description: Library name: S09_scRNA-seq


title: P2 RPE cells, line 322, 2- and 10-week-old_ADT

description: CITE-Seq with ICELL8 platform

value: female

value: caucasian

value: 2 or 10 weeks


title: P2 ipsRPE cells, lines 88 and 255, 10-week-old_ADT

description: CITE-Seq with ICELL8 platform


title: single nucleus RNA sequencing S06

description: Library name: S06_scRNA-seq


title: single nucleus RNA sequencing S04

description: Library name: S04_scRNA-seq


title: single nucleus RNA sequencing S03

description: Library name: S03_scRNA-seq

value: PPN


title: single nucleus RNA sequencing S02

description: Library name: S02_scRNA-seq


title: P2 ipsRPE cells, lines 88 and 255, 10-week-old_RNA-seq

description: CITE-Seq with ICELL8 platform


title: single nucleus RNA sequencing S01

description: Library name: S01_scRNA-seq


title: P2 RPE cells, lines 318 and 319, 10-week-old_ADT

description: CITE-Seq with ICELL8 platform

value: black / caucasian


title: single nucleus RNA sequencing S12

description: Library name: S12_scRNA-seq

value: ONIN


title: single nucleus RNA sequencing S08

description: Library name: S08_scRNA-seq

value: sural nerve


title: Tri_d100_Rep01_P3

city: Indianapolis

first: Andi

last: Dhroso

state: Indiana

address: 9330 Zionsville Rd

institute: Corteva

data_processing:
Adapter sequences remaining within the reads were trimmed (using parameters minlength=35 trimq=20 ktrim=r qtrim=rl k=23 mink=11 hdist=1) using the bbmap tool (v 38.18)
any reads aligning to Rattus norvegicus rRNA sequences were removed using the bbmap tool (v38.18) from the JGI bbtools software package.
Rattus norvegicus and Homo sapiens transcript abundances were calculated on a per sample basis using the Salmon software (v.1.2.0) 11 (with parameters “--seqBias --validateMappings --numBootstraps 100 --libType SR”) processed against the  Rattus norvegicus mRatBN7.2 and Homo sapiens GRCh38p13 reference genomes and annotation 4 downloaded from Ensembl
Following transcript level abundance estimation, gene level expression counts were summarized from the salmon output using the tximport package (v1.26) 12 in R
any protein coding gene with less than an abundance count of ten across all samples were removed from further analysis
Assembly: The DESeq2 analysis package (v1.34.0) in R 13 (version 4.1.3) was used for data normalization (using the variance stabilizing transformation (vst) method), and identification of differentially expressed genes between control groups and dose treatment groups for each molecule tested.
Supplementary files format and content: Rattus norvegicus mRatBN7.2 and Homo sapiens GRCh38p13 reference genomes
Supplementary files format and content: tab-delimited text file which includes raw gene count values for each Sample
Supplementary files format and content: tab-delimited text files include 1) raw gene count values for each Sample and 2) vst-normalized  (filtered for low expressing genes)

source_name: Rat primary hepatocytes

growth_protocol: Please refer to associated manuscript

extract_protocol: Total RNA was isolated from HepaRG and rat hepatocyte samples with the MagMax mirVana Total RNA isolation kit following the manufacturer’s protocol for cells using KingFisher™ flex magnetic particle processor (ThermoFisher, Waltham, MA). RNA samples had RNA Quality Scores ≥7 as determined with a 5200 Fragment Analyzer System (Agilent, Santa Clara, CA).

treatment_protocol: Please refer to associated manuscript

value: Rat primary hepatocytes

value: hepatocytes


title: Tri_d10_Rep03_P3


title: BLANK_Rep01_P3


title: Tri_d100_Rep03_P3


title: single nucleus RNA sequencing S05

description: Library name: S05_scRNA-seq

value: DPN


title: Tri_d100_Rep04_P3


title: Lu134A cells, CRISPR-Cas9 Negative control miRNA

city: Bunkyo-ku, Hongo

first: Hiroshi

last: Takumida

state: Tokyo

department: Respiratory Medicine

institute: Graduate School of Medicine, The University of Tokyo

data_processing:
CLC Genomics workbench v 24.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench
Trimmed sequence reads were mapped to GRCh38/hg38 and miRBase(v22)  using CLC genomics workbench
Read count extraction and normalization were performed using CLC genomics workbench.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts and TPM.

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen).
RNA libraries for RNA-Seq were prepared using NEBNext Ultra ll Directional RNA Library Prep Kit. And miRNA libraries for miRNA-Seq were prepared using NEBNext Multiplex Small RNA Library Prep Kit for Illumina.

value: small cell carcinoma

value: NC


title: Tri_d0.1_Rep02_P3


title: Lu134A cells, miRNA mimic hsa-miR-139-5p

value: miR-139-5p mimic


title: Lu134A cells, CRISPR-Cas9 Negative control RNA


title: Tri_d100_Rep02_P3


title: Tri_d1_Rep02_P3


title: Tri_d0.1_Rep01_P3


title: Tri_d1_Rep01_P3


title: Lu134A cells, miRNA mimic Negative control RNA


title: Tri_d0.1_Rep03_P3


title: Tri_d10_Rep02_P3


title: Tri_d0.01_Rep03_P3


title: Tri_d1_Rep03_P3


title: Lu134A cells, Wildtype miRNA

value: WT


title: Tri_d0.01_Rep02_P3


title: A549_con_VitC1

city: Guangzhou

first: Xiang-yu

last: Sun

state: Guangdong

address: China

institute: Nanfang Hospital,southern Medical University

data_processing:
1.Filtering of Clean Reads Reads obtained from the sequencing machines includes raw reads containing adapters or low  quality bases which will affect the following assembly and analysis. Thus, to get high quality  clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases. 2.Alignment with Ribosome RNA (rRNA) Short reads alignment tool Bowtie2(version 2.2.8) was used for mapping reads to  ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The  remaining clean reads were further used in assembly and gene abundance calculation. 3.Alignment with Reference Genome An index of the reference genome was built, and paired-end clean reads were mapped to the  reference genome using HISAT2 2.1.0 and other parameters set as a default. 4.Quantification of Gene Abundance The mapped reads of each sample were assembled by using StringTie v1.3.1 in a  reference-based approach. For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression  abundance and variations, using RSEM software.Given FPKM(i) to be the expression of gene i, C to be number of fragments mapped to  gene i, N to be total number of fragments that mapped to reference genes, and L to be  number of bases on gene i. The FPKM method is able to eliminate the influence of  different gene lengths and sequencing data amount on the calculation of gene expression.  Therefore, the calculated gene expression can be directly used for comparing the difference  of gene expression among samples. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a  reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase  of exon model per Million mapped reads) value was calculated to quantify its expression  abundance and variations, using RSEM software. Given TPM(i) to be the expression of gene i, N to be reads count of gene i, L to be number  of bases on gene i, and sum() to be total number of reads count of all genes after  normalization. The TPM method is able to eliminate the influence of different gene lengths  and sequencing data amount on the calculation of gene expression. Therefore, the calculated  gene expression can be directly used for comparing the difference of gene expression among  samples.
Assembly: Ensembl release106
Supplementary files format and content: genes.expression.xls

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according  to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer  (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel  electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by  Oligo(dT) beads(pronucleus:After total RNA was extracted, prokaryotic mRNA was enriched by  removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA).Then the  enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly  transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB  #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA  fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The  ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain  reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina  Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: pretreated with high-dose AA


title: Tri_d10_Rep01_P3


title: A549_con_PBS3

value: pretreated with PBS


title: Lu134A cells, CRISPR-Cas9 NEUROD1 KO RNA

value: NEUROD1 KO


title: Lu134A cells, CRISPR-Cas9 NEUROD1 KO miRNA


title: A549_con_PBS1


title: Myc_d10_Rep03_P3


title: A549_con_VitC3


title: Lu134A cells, Wildtype RNA


title: A549_con_VitC2


title: Myc_d100_Rep02_P3


title: A549_WT_VitC3


title: Myc_d100_Rep04_P3


title: Myc_d100_Rep01_P3


title: A549_con_PBS2


title: Tri_d0.01_Rep01_P3


title: A549_WT_VitC1


title: Pron_d0.1_Rep03_P3


title: Myc_d10_Rep02_P3


title: Myc_d10_Rep01_P3


title: A549_WT_VitC2


title: A549_WT_PBS3


title: Pron_d0.1_Rep02_P3


title: Myc_d100_Rep03_P3


title: Fenpicoxamid_0.1_Rep03_P3


title: Sulf_d100_Rep04_P3


title: A549_WT_PBS1


title: Pron_d1_Rep03_P3


title: A549_WT_PBS2


title: Myc_d300_Rep3_P3

source_name: Human HepaRG

value: Human HepaRG

value: HepaRG


title: Sulf_d1_Rep03_P3


title: PHB_50_Rep04_P3


title: Fen_d0.03_Rep2_P3


title: Myc_d3_Rep1_P3


title: Pro_d10_Rep1_P3


title: Fen_d0.03_Rep3_P3


title: Pron_d10_Rep03_P3


title: Tri_d100_Rep1_P3


title: 3MC_d0.3_Rep04_P3


title: DMSO_Rep06_P3


title: Myc_d3_Rep2_P3


title: Pron_d0.01_Rep03_P3


title: Fen_d3_Rep3_P3


title: Fenpicoxamid_0.01_Rep03_P3


title: Pro_d30_Rep3_P3


title: DMSO_Rep05_P3


title: Fenpicoxamid_1_Rep03_P3


title: Sul_d0.3_Rep3_P3


title: Myc_d0.01_Rep03_P3


title: Pro_d30_Rep1_P3


title: PHB_d500_Rep2_P3


title: Sulf_d10_Rep03_P3


title: Tri_d300_Rep4_P3


title: Fenpicoxamid_10_Rep04_P3


title: Sulf_d0.01_Rep03_P3


title: Pro_d30_Rep2_P3


title: Fenpicoxamid_0.001_Rep03_P3


title: Sul_d300_Rep1_P3


title: Pron_d1_Rep02_P3


title: Sul_d100_Rep2_P3


title: Sul_d0.3_Rep1_P3


title: Tri_d30_Rep3_P3


title: Myc_d3_Rep3_P3


title: Sulf_d10_Rep02_P3


title: Myc_d100_Rep3_P3


title: Pron_d100_Rep04_P3


title: Pro_d0.1_Rep2_P3


title: Pron_d0.01_Rep02_P3


title: 3MC_d1_Rep2_P3


title: Sul_d300_Rep2_P3


title: Sulf_d100_Rep03_P3


title: Sul_d30_Rep2_P3


title: Myc_d30_Rep3_P3


title: PHB_50_Rep03_P3


title: Pron_d10_Rep02_P3


title: Fen_d30_Rep2_P3


title: Myc_d0.1_Rep03_P3


title: 3MC_d0.3_Rep03_P3


title: 3MC_d1_Rep1_P3


title: Sul_d3_Rep3_P3


title: Fenpicoxamid_0.1_Rep02_P3


title: Myc_d0.3_Rep3_P3


title: DMSO_Rep07_P3


title: Pro_d1_Rep3_P3


title: Myc_d1_Rep03_P3


title: Myc_d300_Rep2_P3


title: Fenpicoxamid_10_Rep03_P3


title: 3MC_d1_Rep4_P3


title: Fenpicoxamid_0.001_Rep02_P3


title: DMSO_Rep03_P3


title: Tri_d300_Rep3_P3


title: 3MC_d0.3_Rep02_P3


title: Myc_d300_Rep4_P3


title: DMSO_Rep04_P3


title: Tri_d100_Rep2_P3


title: Sul_d300_Rep3_P3


title: Fenpicoxamid_0.01_Rep02_P3


title: Sulf_d0.01_Rep02_P3


title: Tri_d100_Rep3_P3


title: Myc_d0.3_Rep1_P3


title: Myc_d0.01_Rep02_P3


title: Pron_d100_Rep03_P3


title: Pro_d1_Rep2_P3


title: Pro_d100_Rep3_P3


title: Tri_d30_Rep2_P3


title: Sulf_d100_Rep02_P3


title: PHB_50_Rep02_P3


title: Myc_d0.1_Rep02_P3


title: Sulf_d1_Rep02_P3


title: Tri_d300_Rep1_P3


title: Fenpicoxamid_1_Rep02_P3


title: Fen_d0.3_Rep1_P3


title: Pro_d100_Rep2_P3


title: Pron_d0.1_Rep01_P3


title: Sulf_d0.1_Rep02_P3


title: PHB_d500_Rep1_P3


title: Fen_d30_Rep3_P3


title: PHB_d500_Rep3_P3


title: Myc_d300_Rep1_P3


title: Pron_d100_Rep02_P3


title: Myc_d1_Rep02_P3


title: Sulf_d10_Rep01_P3


title: 3MC_d0.3_Rep01_P3


title: Pro_d10_Rep3_P3


title: Pro_d100_Rep4_P3


title: 3MC_d1_Rep3_P3


title: Fenpicoxamid_0.1_Rep01_P3


title: Myc_d0.01_Rep01_P3


title: Myc_d30_Rep1_P3


title: Sulf_d0.01_Rep01_P3


title: Pron_d0.01_Rep01_P3


title: Pron_d1_Rep01_P3


title: Fen_d3_Rep2_P3


title: Fenpicoxamid_10_Rep02_P3


title: Sul_d30_Rep3_P3


title: Sulf_d0.1_Rep01_P3


title: Fenpicoxamid_0.01_Rep01_P3


title: DMSO_d0_Rep3_P3


title: DMSO_d0_Rep7_P3


title: Myc_d0.1_Rep01_P3


title: DMSO_Rep02_P3


title: Pron_d100_Rep01_P3


title: Tri_d3_Rep1_P3


title: Myc_d0.3_Rep2_P3


title: Fenpicoxamid_10_Rep01_P3


title: Fenpicoxamid_0.001_Rep01_P3


title: Fen_d10_Rep2_P3


title: DMSO_d0_Rep4_P3


title: Sulf_d1_Rep01_P3


title: Tri_d300_Rep2_P3


title: Fen_d30_Rep1_P3


title: Fen_d0.3_Rep2_P3


title: Myc_d30_Rep2_P3


title: DMSO_Rep01_P3


title: Myc_d1_Rep01_P3


title: Fen_d0.03_Rep1_P3


title: Fen_d3_Rep1_P3


title: Sulf_d100_Rep01_P3


title: Sul_d3_Rep2_P3


title: Tri_d0.3_Rep2_P3


title: Fen_d10_Rep1_P3


title: Pro_d100_Rep1_P3


title: Mef_d1_Rep03_P2


title: Tri_d3_Rep2_P3


title: Myc_d100_Rep2_P3


title: Fen_d0.3_Rep3_P3


title: BLANK_Rep01_P2


title: Tri_d0.3_Rep1_P3


title: Fen_d30_Rep4_P3


title: Gri_d10_Rep03_P2


title: Pron_d10_Rep01_P3


title: Fenpicoxamid_1_Rep01_P3


title: Ethio_d100_Rep04_P2


title: Tri_d30_Rep1_P3


title: Ethio_d0.01_Rep03_P2


title: PHB_50_Rep01_P3


title: Ket_d10_Rep04_P2


title: Ket_d0.001_Rep03_P2


title: DMSO_d0_Rep5_P3


title: Sul_d100_Rep3_P3


title: PHB_50_Rep04_P2


title: Phen_d0.1_Rep03_P2


title: DMSO_d0_Rep2_P3


title: Ethio_d100_Rep03_P2


title: Pro_d0.1_Rep3_P3


title: Gri_d100_Rep04_P2


title: Pro_d10_Rep2_P3


title: DMSO_Rep06_P2


title: Sul_d300_Rep4_P3


title: Phen_d0.01_Rep03_P2


title: Pro_d1_Rep1_P3


title: Mef_d0.1_Rep03_P2


title: Gri_d1_Rep03_P2


title: Myc_d100_Rep1_P3


title: Mef_d100_Rep04_P2


title: Pro_d0.1_Rep1_P3


title: Sul_d3_Rep1_P3


title: Ethio_d0.1_Rep03_P2


title: Tri_d3_Rep3_P3


title: DMSO_d0_Rep1_P3


title: Sul_d0.3_Rep2_P3


title: Sul_d30_Rep1_P3


title: Gri_d0.1_Rep03_P2


title: Ethio_d1_Rep03_P2


title: Ethio_d0.01_Rep02_P2


title: Tri_d0.3_Rep3_P3


title: DMSO_d0_Rep6_P3


title: Gri_d1_Rep02_P2


title: Phen_d100_Rep04_P2


title: 3MC_d0.3_Rep04_P2


title: Ethio_d10_Rep1_P2


title: Ethio_d1_Rep02_P2


title: Ket_d100_Rep4_P2


title: Mef_d0.03_Rep1_P2


title: Mef_d10_Rep03_P2


title: DMSO_Rep05_P2


title: Sul_d100_Rep1_P3


title: Ket_d0.01_Rep03_P2


title: Gri_d0.01_Rep03_P2


title: Fen_d10_Rep3_P3


title: Phen_d10_Rep03_P2


title: PHB_d500_Rep4_P3


title: PHB_d500_Rep1_P2


title: Mef_d10_Rep2_P2


title: Ket_d1_Rep03_P2


title: Gri_d10_Rep1_P2


title: Mef_d30_Rep1_P2


title: Ethio_d10_Rep02_P2


title: Mef_d0.01_Rep03_P2


title: Ethio_d0.1_Rep1_P2


title: Mef_d1_Rep02_P2


title: Ket_d10_Rep03_P2


title: Ket_d100_Rep1_P2


title: Phe_d3_Rep2_P2


title: Mef_d3_Rep3_P2


title: Phen_d0.01_Rep02_P2


title: PHB_50_Rep03_P2


title: Phen_d1_Rep03_P2


title: Gri_d100_Rep03_P2


title: Ket_d10_Rep02_P2


title: Phen_d100_Rep03_P2


title: Phe_d30_Rep2_P2


title: Gri_d1_Rep1_P2


title: DMSO_d0_Rep6_P2


title: 3MC_d0.3_Rep02_P2


title: Ket_d0.1_Rep1_P2


title: Mef_d0.03_Rep2_P2


title: 3MC_d0.3_Rep03_P2


title: Phe_d0.3_Rep2_P2


title: Mef_d30_Rep4_P2


title: Phe_d30_Rep1_P2


title: Gri_d10_Rep02_P2


title: Mef_d100_Rep03_P2


title: Ethio_d100_Rep02_P2


title: Ethio_d1_Rep3_P2


title: DMSO_Rep04_P2


title: Phe_d30_Rep3_P2


title: Phen_d10_Rep02_P2


title: DMSO_Rep07_P2


title: Mef_d100_Rep02_P2


title: Phe_d10_Rep2_P2


title: DMSO_Rep03_P2


title: Ethio_d1_Rep2_P2


title: Gri_d1_Rep3_P2


title: Phen_d1_Rep02_P2


title: Phe_d0.03_Rep1_P2


title: Ethio_d100_Rep3_P2


title: Mef_d10_Rep3_P2


title: Mef_d0.03_Rep3_P2


title: Mef_d0.1_Rep02_P2


title: 3MC_d1_Rep1_P2


title: Gri_d0.1_Rep02_P2


title: Ethio_d1_Rep1_P2


title: Ket_d0.01_Rep02_P2


title: Ket_d0.1_Rep2_P2


title: Phe_d30_Rep4_P2


title: Mef_d0.01_Rep02_P2


title: Gri_d100_Rep4_P2


title: Ethio_d0.1_Rep2_P2


title: Ket_d1_Rep02_P2


title: Phen_d0.1_Rep02_P2


title: Phe_d0.03_Rep3_P2


title: Gri_d100_Rep02_P2


title: Ethio_d30_Rep2_P2


title: Phen_d100_Rep02_P2


title: Ethio_d100_Rep1_P2


title: Ethio_d30_Rep3_P2


title: Mef_d0.1_Rep01_P2


title: DMSO_d0_Rep7_P2


title: Ethio_d0.1_Rep3_P2


title: Ket_d0.001_Rep02_P2


title: DMSO_d0_Rep2_P2


title: 3MC_d0.3_Rep01_P2


title: DMSO_d0_Rep4_P2


title: Mef_d10_Rep02_P2


title: Gri_d0.01_Rep02_P2


title: Phen_d0.01_Rep01_P2


title: Mef_d10_Rep1_P2


title: Phe_d10_Rep1_P2


title: Gri_d10_Rep01_P2


title: PHB_50_Rep02_P2


title: Ethio_d0.1_Rep02_P2


title: Ket_d0.1_Rep03_P2


title: Ket_d1_Rep3_P2


title: Gri_d10_Rep2_P2


title: Mef_d100_Rep01_P2


title: Ethio_d10_Rep01_P2


title: Ket_d0.1_Rep02_P2


title: Gri_d30_Rep1_P2


title: Ethio_d100_Rep01_P2


title: Ket_d30_Rep3_P2


title: DMSO_Rep02_P2


title: Ket_d10_Rep01_P2


title: Phen_d10_Rep01_P2


title: Ethio_d10_Rep3_P2


title: Mef_d0.01_Rep01_P2


title: Phe_d0.3_Rep1_P2


title: Ethio_d30_Rep1_P2


title: Ket_d0.01_Rep01_P2


title: Ket_d1_Rep1_P2


title: Gri_d1_Rep01_P2


title: Ethio_d0.01_Rep01_P2


title: Gri_d0.01_Rep01_P2


title: Gri_d100_Rep3_P2


title: Gri_d0.1_Rep1_P2


title: Mef_d10_Rep01_P2


title: DMSO_Rep01_P2


title: PHB_d500_Rep4_P2


title: Ket_d10_Rep3_P2


title: DMSO_d0_Rep1_P2


title: Phen_d100_Rep01_P2


title: Phen_d1_Rep01_P2


title: Ethio_d10_Rep03_P2


title: Phe_d3_Rep1_P2


title: Ket_d1_Rep01_P2


title: Gri_d100_Rep2_P2


title: Ethio_d0.1_Rep01_P2


title: Gri_d10_Rep3_P2


title: Ethio_d1_Rep01_P2


title: Ket_d0.001_Rep01_P2


title: PHB_d500_Rep3_P2


title: Mef_d1_Rep01_P2


title: Ket_d30_Rep1_P2


title: Ket_d100_Rep3_P2


title: Phe_d0.3_Rep3_P2


title: Gri_d0.1_Rep01_P2


title: Phen_d0.1_Rep01_P2


title: Gri_d100_Rep01_P2


title: DMSO_d0_Rep5_P2


title: Mef_d0.3_Rep2_P2


title: Amit_d0.001_Rep03_P1


title: Phe_d3_Rep3_P2


title: BLANK_Rep01_P1


title: Buc_d100_Rep04_P1


title: Gri_d0.1_Rep3_P2


title: Eth_d100_Rep04_P1


title: Ethio_d100_Rep2_P2


title: Gri_d0.1_Rep2_P2


title: Gri_d30_Rep3_P2


title: Col_d100_Rep04_P1


title: Ket_d10_Rep1_P2


title: Col_d100_Rep03_P1


title: Ket_d0.1_Rep3_P2


title: Ket_d0.1_Rep01_P2


title: Mef_d30_Rep2_P2


title: PHB_50_Rep01_P2


title: Phe_d10_Rep3_P2


title: Col_d1_Rep03_P1


title: 3MC_d1_Rep2_P2


title: Buc_d0.01_Rep03_P1


title: 3MC_d1_Rep4_P2


title: Amit_d1_Rep03_P1


title: Gri_d100_Rep1_P2


title: Benz_d0.316_Rep03_P1


title: Mef_d3_Rep2_P2


title: Amit_d0.001_Rep02_P1


title: Phe_d0.03_Rep2_P2


title: DMSO_d0_Rep3_P2


title: Mef_d30_Rep3_P2


title: 3MC_d1_Rep3_P2


title: Gri_d30_Rep2_P2


title: Mef_d3_Rep1_P2


title: DMSO_Rep06_P1


title: Eth_d1_Rep03_P1