title: Sufficiency MPRA, Firefly, Soma Rep2

description: Library name: sufficiency_FFS2


title: OVCAR8_gCTRL_0nM_6h_rep2

status: Public on Jun 09 2026

type: SRA

city: Kyoto

first: Kosuke

last: Yusa

state: Kyoto

address: 53 Shogoin Kawaharacho, Sakyo-ku

department: Institue for Life and Medical Sciences

country: Japan

institute: Kyoto University

description: Library name: OVCAR8_gCTRL_0nM_6h_rep2

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to reference human genome hg38 using HISAT2 (v2.2.1), and converted to bam format using samtools(v1.14)
reads assigned to genes were counted using featureCounts (v2.0.3)
Differentially expressed genes were analyzed using DESeq2 (v1.38.2) with filtering out genes with low expression (average read counts in all conditions are less than 1)
Assembly: hg38
Supplementary files format and content: tab-delimited text

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: OVCAR8 cells were cultured in RMPI1640 supplemented with 10% FBS. MDA-MB-231 cells were cultured in DMEM/F12 supplemented with 10% FBS.

extract_protocol:
After PBS wash twice, cells were directly lysed on 10-cm dish with Buffer RLT. Lysate was collected and total RNA was extracted using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: 2 million cells were seeded to a 10-cm dish a day before treatment. On the following day, CTX-439 was added at the indicated concentration and incubated for the indicated duration.

tag: cell line

tag: cell type

value: Ovarian cancer cell line

tag: genotype

value: CDK10 wildtype

tag: treatment

value: DMSO for 6 h


title: Sufficiency MPRA, Firefly, Soma Rep1

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Colorado Anschutz Medical Campus

description: Library name: sufficiency_FFS1

data_processing:
MPRA oligos were extracted from sequencing reads and aligned against known oligo sequences using bowtie2. UMI deduplication was performed to minimize contributions from differences in PCR amplification efficiency.
Assembly: mm10
Supplementary files format and content: For each oligo, the number of reads containing that oligo and the number of unique UMIs seen in those reads are reported.

organism: Mus musculus

source_name: CAD

growth_protocol: Mouse CAD cells were grown in DMEM/F12 supplemented with 10% FBS and pen/strep. Reporter transcript expression was induced by adding 1 ug/mL doxycycline for 48 hours.

extract_protocol:
RNA was extracted from soma and neurite fractions using a QuickRNA micro kit (Zymo).
Targeted sequencing libraries, with UMIs, were constructed through RT-PCR of an amplicon of the reporter transcript used in the MPRA. To minimize effects due to a particular reporter RNA, two reporters RNAs were used. One encoded GFP while the other encoded firefly luciferase.

treatment_protocol: CAD cells were mechanically fractionated into soma and neurite fractions by growing them on porous membranes to allow neurite growth through the membrane followed by scraping of the top of the membrane to separate soma and neurites.

value: CAD

value: Sufficiency MPRA, Firefly, Soma


title: DSS-3

city: Fuzhou

first: xiuli

last: Zhang

address: No. 1 Qiuyang Road, Minhou Street, Fuzhou City, Fujian Province

country: China

institute: Fujian University of Chinese Medicine

description:
Library name: Sample 6
Mice were administered 2.5% DSS for 5 days followed by normal drinking water for 5 days, while simultaneously being given 7.60 g/kg/day of BXD, and this process was repeated for three cycles.

data_processing:
Utilize the bcl2fastq software to perform Base Calling on the original image files from Illumina high-throughput sequencing and convert them into original sequencing reads.
Use the FastQC software to analyze the base quality from 5' to 3' of the sequencing reads and assess the content of A, T, C, and G bases in the sequencing data, evaluating the base type ratio at each position from an overall level.
Utilize the fastp software to filter the raw data, removing reads that do not meet the analysis criteria, in order to obtain clean reads that can be used for subsequent alignment, statistics, and further analysis.
After quality control of the raw sequencing data, clean data is obtained. The clean data is then assessed to review the effectiveness of the quality control, and ultimately, the clean data is used for analysis.
Read count extraction and normalization were performed using RseQC software
Assembly: mm10

molecule: total RNA

source_name: colon

extract_protocol:
RNA was harvested using TRIzol® Reagent (invitrogen.). 1 µgof total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nebnext ultra-RNA library preparation kit following manufacturer's protocols.

tag: tissue

value: Intestine

value: Mus musculus

value: 2.5% DSS+ddH2O


title: Sufficiency MPRA, Firefly, Neurite Rep4

description: Library name: sufficiency_FFN4

value: Sufficiency MPRA, Firefly, Neurite


title: OVCAR8_gCTRL_0nM_6h_rep1

description: Library name: OVCAR8_gCTRL_0nM_6h_rep1


title: Sufficiency MPRA, Firefly, Neurite Rep3

description: Library name: sufficiency_FFN3


title: Sufficiency MPRA, Firefly, Neurite Rep2

description: Library name: sufficiency_FFN2


title: OVCAR8_gCDK10-1_90nM_48h_rep2

description: Library name: OVCAR8_gCDK10-1_90nM_48h_rep2

value: CDK10 knockout

value: CTX-439 90nM for 48h


title: DSS-1

description:
Library name: Sample 4
Mouse treated with 2.5% DSS for 5 days and then drank water normally for 5 days, repeating three cycles


title: Shuffle MPRA, GFP, Soma Rep4

description: Library name: shuffle_GFPS4

value: Shuffle MPRA, GFP, Soma


title: OVCAR8_gCDK10-1_90nM_48h_rep1

description: Library name: OVCAR8_gCDK10-1_90nM_48h_rep1


title: Shuffle MPRA, GFP, Soma Rep3

description: Library name: shuffle_GFPS3


title: Control-3

description:
Library name: Sample 3
Mouse treated with 2.5% DSS for 5 days and then drank water normally for 5 days, repeating three cycles


title: Control-2

description:
Library name: Sample 2
Mouse treated with ddH2O


title: OVCAR8_gCDK10-1_90nM_24h_rep1

description: Library name: OVCAR8_gCDK10-1_90nM_24h_rep1

value: CTX-439 90nM for 24h


title: Shuffle MPRA, GFP, Neurite Rep4

description: Library name: shuffle_GFPN4

value: Shuffle MPRA, GFP, Neurite


title: Shuffle MPRA, GFP, Neurite Rep3

description: Library name: shuffle_GFPN3


title: Control-1

description:
Library name: Sample 1
Mouse treated with ddH2O


title: OVCAR8_gCDK10-1_90nM_6h_rep2

description: Library name: OVCAR8_gCDK10-1_90nM_6h_rep2

value: CTX-439 90nM for 6h


title: Shuffle MPRA, GFP, Neurite Rep1

description: Library name: shuffle_GFPN1


title: Ctrl_3

city: Lanzhou

first: yan

last: wang

address: No. 199 Donggang West Road Chengguan District

department: The First School of Clinical Medicine

institute: Lanzhou University

description:
Library name: Ctrl_3
control group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: cell culture

value: KGN

value: control


title: Shuffle MPRA, Firefly, Soma Rep4

description: Library name: shuffle_FFS4

value: Shuffle MPRA, Firefly, Soma


title: Shuffle MPRA, Firefly, Soma Rep3

description: Library name: shuffle_FFS3


title: Ctrl_2

description:
Library name: Ctrl_2
control group, replicate biosample 2


title: DSS-2

description:
Library name: Sample 5
Mouse treated with 2.5% DSS for 5 days and then drank water normally for 5 days, repeating three cycles


title: Sufficiency MPRA, Firefly, Neurite Rep1

description: Library name: sufficiency_FFN1


title: Shuffle MPRA, Firefly, Soma Rep2

description: Library name: shuffle_FFS2


title: OVCAR8_gCDK10-1_0nM_6h_rep2

description: Library name: OVCAR8_gCDK10-1_0nM_6h_rep2

value: Ovarian cancer cell line

value: DMSO for 6 h


title: Shuffle MPRA, Firefly, Soma Rep1

description: Library name: shuffle_FFS1

value: CAD


title: Shuffle MPRA, GFP, Soma Rep2

description: Library name: shuffle_GFPS2


title: OVCAR8_gCDK10-1_90nM_24h_rep2

description: Library name: OVCAR8_gCDK10-1_90nM_24h_rep2


title: Shuffle MPRA, GFP, Soma Rep1

description: Library name: shuffle_GFPS1


title: Ctrl_1

description:
Library name: Ctrl_1
control group, replicate biosample 1


title: Shuffle MPRA, Firefly, Neurite Rep4

description: Library name: shuffle_FFN4

value: Shuffle MPRA, Firefly, Neurite


title: OVCAR8_gCDK10-1_0nM_6h_rep1

description: Library name: OVCAR8_gCDK10-1_0nM_6h_rep1


title: Shuffle MPRA, Firefly, Neurite Rep3

description: Library name: shuffle_FFN3


title: IAA_3

description:
Library name: IAA_3
IAA treatment, replcate biosample 3

value: IAA


title: Shuffle MPRA, Firefly, Neurite Rep2

description: Library name: shuffle_FFN2


title: Shuffle MPRA, Firefly, Neurite Rep1

description: Library name: shuffle_FFN1


title: OVCAR8_gCTRL_90nM_rep2

description: Library name: OVCAR8_gCTRL_90nM_rep2

value: CDK10 wildtype


title: IAA_2

description:
Library name: IAA_2
IAA treatment, replcate biosample 2


title: SHAPE MPRA, GFP, Soma Rep4

description: Library name: SHAPE_GFPS4

value: SHAPE MPRA, GFP, Soma


title: OVCAR8_gCTRL_90nM_rep1

description: Library name: OVCAR8_gCTRL_90nM_rep1


title: SHAPE MPRA, GFP, Soma Rep3

description: Library name: SHAPE_GFPS3


title: IAA_1

description:
Library name: IAA_1
IAA treatment, replcate biosample 1


title: OVCAR8_gCTRL_30nM_rep2

description: Library name: OVCAR8_gCTRL_30nM_rep2

value: CTX-439 30nM for 6h


title: SHAPE MPRA, GFP, Soma Rep2

description: Library name: SHAPE_GFPS2


title: HC46TR_Fut CRC-SC line

city: Kyoto city

first: Makoto

middle: Mark

last: Taketo

state: Kyoto prefecture

address: 53 Shogoin-Kawahara-cho Sakyo-ku

description:
Library name: HC46TR_Fut
Patient-derived CRC-SC spheroid

data_processing:
RNA-seq analysis was performed by Macrogen.
Prepared libraries were subjected to paired-end sequencing (2 × 100 bases) to a depth of ~40 million reads/sample using the Illumina HighSeq 2000 sequencer.
The sequence reads were processed with fastp to trim adaptors and filter low-quality reads.
Processed reads were alined on the reference genome (hg38) with HISAT2.
Alinements were assembled with StringTie to estimate geme expression levels (count and TPM).
Assembly: hg38
Supplementary files format and content: An Excel file containing count and TPM values for each sample which is provided as processed data.

source_name: Large intestine

growth_protocol: CRC-SC spheroids were suspended in Matrigel (Corning, NY, USA), and the cell-Matrigel mixture was placed at the center of each well of the 12-well cell-culture plate (30 μL/well). After polymerization of Matrigel at 37°C, cells were cultured with the cancer medium containing 50 ng/mL EGF (PeproTech, Cranbury, NJ, USA) and 100 ng/mL basic FGF (bFGF; PeproTech, Cranbury, NJ, USA). Cell line authentication was not applicable because all experiments used spheroids derived from primary cancer tissue. Spheroids were verified to be free from mycoplasma contamination using an enzyme-based assay (MycoAlert; Lonza, Basel, Switzerland).

extract_protocol:
Total RNA was purified from spheroid samples using the NucleoSpin RNA II Kit (Takara Bio, Kusatsu, Shiga, Japan) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: FGFR inhibitor-resistant derivatives were established from parental CRC-SC spheroid lines through continuous culture in cancer medium containing 100 nM erdafitinib or futibatinib. Other non-resistant CRC-SC spheroid lines were maintained in cancer medium supplemented with 50 ng/mL EGF (PeproTech, Cranbury, NJ, USA) and 100 ng/mL basic FGF (bFGF; PeproTech, Cranbury, NJ, USA).

value: Large intestine

tag: disease state

value: Colorectal cancer

value: RAS/RAF-wild-type

value: 100 nM futibatinib


title: OE3.IP

city: hangzhou

first: zhiqi

last: xie

address: huzhou street 51

institute: Hangzhou city university

description: Library name: SAMPLES18

data_processing:
For acRIP-seq,  Paired-end reads were harvested from sequencer, and were quality controlled by Q30 and FastQC. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes
Assembly: GRCh38
Supplementary files format and content: The .xlsx file contains the genomic coordinates of all acetylated RNA sites for each sample.

source_name: HaCat

extract_protocol:
Total RNA was extracted using Trizol reagent
RNA libraries for IP and input samples were constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.

value: HaCat

value: NAT10 overexpression plasmids

tag: batch

value: IP


title: OVCAR8_gCDK10-1_90nM_6h_rep1

description: Library name: OVCAR8_gCDK10-1_90nM_6h_rep1

value: CDK10 knockout

value: CTX-439 90nM for 6h


title: SHAPE MPRA, GFP, Soma Rep1

description: Library name: SHAPE_GFPS1


title: HC20TR_Fut CRC-SC line

description:
Library name: HC20TR_Fut
Patient-derived CRC-SC spheroid


title: OVCAR8_gCTRL_30nM_rep1

description: Library name: OVCAR8_gCTRL_30nM_rep1

value: Ovarian cancer cell line


title: OE2.IP

description: Library name: SAMPLES17


title: SHAPE MPRA, GFP, Neurite Rep4

description: Library name: SHAPE_GFPN4

value: SHAPE MPRA, GFP, Neurite


title: MDAMB231_gCTRL_90nM_24h_rep2

description: Library name: MDAMB231_gCTRL_90nM_24h_rep2

value: Breast cancer cell line

value: CTX-439 90nM for 24h


title: OVCAR8_gCTRL_10nM_rep2

description: Library name: OVCAR8_gCTRL_10nM_rep2

value: CTX-439 10nM for 6h


title: HC6TR_Fut CRC-SC line

description:
Library name: HC6TR_Fut
Patient-derived CRC-SC spheroid


title: C. difficile WT ATCC43255 24 hours post infection Mouse 6

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Reads were also analyzed with Kraken2 to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Assembly: C. difficile ATCC 43255 https://www.bv-brc.org/view/Genome/1496.5150, M. musculus GRCm39 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/
Supplementary files format and content: HTSeq CDS read counts per gene.

source_name: Mouse caecal contents

growth_protocol: 6-7 week-old male and female gnotobiotic (germ-free) mice were inoculated by gavage with10^3 C. difficile ATCC43255 wild-type or prdB mutant spores.

extract_protocol:
Mice were sacrificed at the indicated timepoint and dissected. Cecal contents were immediately cryogenically stored for RNA extraction.
Purified RNAs were rRNA depleted and eukaryotic (mouse) poly-A mrRNA depleted. Illumina NovaSeq S4-300 with paired-end 150 nucleotide runs were performed.

value: Mouse caecal contents

tag: agent


title: C. difficile WT ATCC43255 24 hours post infection Mouse 7


title: OE1.IP

description: Library name: SAMPLES16


title: SHAPE MPRA, GFP, Neurite Rep3

description: Library name: SHAPE_GFPN3

value: CAD


title: OVCAR8_gCTRL_10nM_rep1

description: Library name: OVCAR8_gCTRL_10nM_rep1

value: CDK10 wildtype


title: OE3.Input

description: Library name: SAMPLES15

value: Input


title: SHAPE MPRA, GFP, Neurite Rep2

description: Library name: SHAPE_GFPN2


title: OVCAR8_gCTRL_0nM_rep2

description: Library name: OVCAR8_gCTRL_0nM_rep2

value: DMSO for 6 h


title: HC97TR_Erd CRC-SC line

description:
Library name: HC97TR_Erd
Patient-derived CRC-SC spheroid

value: Large intestine

value: Colorectal cancer

value: RAS/RAF-wild-type

value: 100 nM erdafitinib


title: HC46TR_Erd CRC-SC line

description:
Library name: HC46TR_Erd
Patient-derived CRC-SC spheroid


title: OE2.Input

description: Library name: SAMPLES14

value: HaCat

value: NAT10 overexpression plasmids


title: HC20TR_Erd CRC-SC line

description:
Library name: HC20TR_Erd
Patient-derived CRC-SC spheroid


title: OVCAR8_gCTRL_0nM_rep1

description: Library name: OVCAR8_gCTRL_0nM_rep1


title: OE1.Input

description: Library name: SAMPLES13


title: SHAPE MPRA, GFP, Neurite Rep1

description: Library name: SHAPE_GFPN1


title: C. difficile WT ATCC43255 20 hours post infection Mouse 5


title: SHAPE MPRA, Firefly, Soma Rep4

description: Library name: SHAPE_FFS4

value: SHAPE MPRA, Firefly, Soma


title: OVCAR8_gCDK10-1_90nM_rep2

description: Library name: OVCAR8_gCDK10-1_90nM_rep2

value: Ovarian cancer cell line

value: CDK10 knockout

value: CTX-439 90nM for 6h


title: HC6TR_Erd CRC-SC line

description:
Library name: HC6TR_Erd
Patient-derived CRC-SC spheroid


title: C3.IP

description: Library name: SAMPLES12

value: empty vector control

value: IP


title: SHAPE MPRA, Firefly, Soma Rep3

description: Library name: SHAPE_FFS3


title: OVCAR8_gCDK10-1_90nM_rep1

description: Library name: OVCAR8_gCDK10-1_90nM_rep1


title: HC212T CRC-SC line

description:
Library name: HC212T
Patient-derived CRC-SC spheroid

value: Untreated


title: C2.IP

description: Library name: SAMPLES11


title: SHAPE MPRA, Firefly, Soma Rep2

description: Library name: SHAPE_FFS2

value: CAD


title: OVCAR8_gCDK10-1_30nM_rep2

description: Library name: OVCAR8_gCDK10-1_30nM_rep2

value: CTX-439 30nM for 6h


title: OVCAR8_gCTRL_90nM_48h_rep2

description: Library name: OVCAR8_gCTRL_90nM_48h_rep2

value: CDK10 wildtype

value: CTX-439 90nM for 48h


title: HC203T CRC-SC line

description:
Library name: HC203T
Patient-derived CRC-SC spheroid

value: Large intestine


title: C1.IP

description: Library name: SAMPLES10


title: SHAPE MPRA, Firefly, Soma Rep1

description: Library name: SHAPE_FFS1


title: OVCAR8_gCDK10-1_30nM_rep1

description: Library name: OVCAR8_gCDK10-1_30nM_rep1


title: HC201T CRC-SC line

description:
Library name: HC201T
Patient-derived CRC-SC spheroid

value: Colorectal cancer


title: C3.Input

description: Library name: SAMPLES9

value: Input


title: OVCAR8_gCDK10-1_10nM_rep2

description: Library name: OVCAR8_gCDK10-1_10nM_rep2

value: CTX-439 10nM for 6h


title: SHAPE MPRA, Firefly, Neurite Rep4

description: Library name: SHAPE_FFN4

value: SHAPE MPRA, Firefly, Neurite


title: HC189T CRC-SC line

description:
Library name: HC189T
Patient-derived CRC-SC spheroid

value: RAS/RAF-wild-type


title: C2.Input

description: Library name: SAMPLES8

value: HaCat


title: OVCAR8_gCTRL_90nM_24h_rep2

description: Library name: OVCAR8_gCTRL_90nM_24h_rep2

value: Ovarian cancer cell line

value: CTX-439 90nM for 24h


title: OVCAR8_gCDK10-1_10nM_rep1

description: Library name: OVCAR8_gCDK10-1_10nM_rep1

value: CDK10 knockout


title: SHAPE MPRA, Firefly, Neurite Rep3

description: Library name: SHAPE_FFN3


title: C1.Input

description: Library name: SAMPLES7

value: empty vector control


title: HC167T CRC-SC line

description:
Library name: HC167T
Patient-derived CRC-SC spheroid


title: OVCAR8_gCDK10-1_0nM_rep2

description: Library name: OVCAR8_gCDK10-1_0nM_rep2

value: DMSO for 6 h


title: SHAPE MPRA, Firefly, Neurite Rep2

description: Library name: SHAPE_FFN2


title: HC165T CRC-SC line

description:
Library name: HC165T
Patient-derived CRC-SC spheroid

value: Untreated


title: OE3

description: Library name: SAMPLES6

data_processing:
For RNA-seq, Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4). Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization. Differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: GRCh38
Supplementary files format and content: The .xlsx file contains raw read counts for each sample.

extract_protocol:
Total RNA was extracted using Trizol reagent
RNA libraries for RNA-seq were construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc.,Shanghai, China) by following manufacturer’s recommendations.

value: NAT10 overexpression plasmids


title: OVCAR8_gCDK10-1_0nM_rep1

description: Library name: OVCAR8_gCDK10-1_0nM_rep1


title: Shuffle MPRA, GFP, Neurite Rep2

description: Library name: shuffle_GFPN2

value: CAD

value: Shuffle MPRA, GFP, Neurite


title: HC159T CRC-SC line

description:
Library name: HC159T
Patient-derived CRC-SC spheroid


title: SHAPE MPRA, Firefly, Neurite Rep1

description: Library name: SHAPE_FFN1


title: Necessity MPRA, GFP, Soma Rep4

description: Library name: necessity_GFPS4

value: Necessity MPRA, GFP, Soma


title: retinal organoid; control 2 mg ml k Carrageenan; well H12

city: Trondheim

first: Aleksandr

last: Ianevski

address: Høgskoleringen 1

country: Norway

institute: NTNU

description:
Library name: H12_2_mg_ml_k_Carrageenan
iPSC-derived retinal organoid, plate well H12; demultiplexed by 12 bp cell barcode GTCTAAGGTAGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

data_processing:
Reads filtered for low-quality and adapter contamination.
Raw FASTQs demultiplexed per well by exact match of the 12 bp cell barcode (read 1, bases 1-12); reads merged across lanes and the two sequencing runs per sample.
Cell barcode (XC) and UMI (XM) tagged; SMART adapter and polyA trimmed (Drop-seq tools).
Aligned to GRCh38 with STAR v2.7.11b; gene tagging with refFlat annotation.
Per-well UMI-collapsed digital gene expression via Drop-seq DigitalExpression; edgeR v3.42 quasi-likelihood for differential expression (downstream).
Assembly: GRCh38
Supplementary files format and content: Expression_counts.txt: tab-delimited gene x 96-sample UMI count matrix; first column Gene_ID; column headers match sample library names.
Supplementary files format and content: DGE_final_Pool1.txt (cardiac) and DGE_final_Pool2.txt (retinal): per-pool DigitalExpression matrices.

source_name: iPSC-derived retinal organoid

growth_protocol: Cardiac and retinal organoids generated from human iPSCs using modified published cardiac (Hofbauer 2021) and retinal (Nakano 2012) protocols. iPSCs reprogrammed from human dermal fibroblasts (CytoTune-iPS 2.0 Sendai kit), maintained in Essential 8, passaged with 0.5 mM EDTA, orbital shaking throughout differentiation. Retinal and cardiac organoids collected on days 20 and 53 post-induction; one organoid per well of an ultralow-attachment 96-well plate in 100 ul medium.

extract_protocol:
Total RNA isolated with the NAxtra kit; mRNA enriched with oligo-dT beads, fragmented, reverse-transcribed.
3'-barcoded bulk RNA-seq (Drop-seq-style DGE): read 1 = 12 bp per-well cell barcode (bases 1-12) + 8 bp UMI (bases 13-20); read 2 = cDNA. Libraries adaptor-ligated, PCR-amplified, pooled per organoid. NOTE: manuscript states DNBSEQ but the delivered runs are Element AVITI.

treatment_protocol: Treated 24 h at 5 uM (submaximal) with the indicated psychotropic drug and/or neurotransmitter/co-treatment; vehicle/chemical-control wells received the indicated control agent.

value: iPSC-derived retinal organoid

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: vehicle/chemical control:2 mg ml k Carrageenan


title: OE2

description: Library name: SAMPLES5


title: HC145T CRC-SC line

description:
Library name: HC145T
Patient-derived CRC-SC spheroid

value: Large intestine

value: Colorectal cancer


title: OE1

description: Library name: SAMPLES4

value: HaCat


title: retinal organoid; control 2 mg ml k Carrageenan; well G12

description:
Library name: G12_2_mg_ml_k_Carrageenan
iPSC-derived retinal organoid, plate well G12; demultiplexed by 12 bp cell barcode CCTAGCTGCAAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt


title: Necessity MPRA, GFP, Soma Rep3

description: Library name: necessity_GFPS3


title: HC139T CRC-SC line

description:
Library name: HC139T
Patient-derived CRC-SC spheroid

value: RAS/RAF-wild-type


title: C3

description: Library name: SAMPLES3


title: Necessity MPRA, GFP, Soma Rep2

description: Library name: necessity_GFPS2


title: retinal organoid; xanomeline + serotonin; well F12

description:
Library name: F12_Xanomeline_Serotonin
iPSC-derived retinal organoid, plate well F12; demultiplexed by 12 bp cell barcode TTACTGATCGGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: xanomeline 5 uM, 24 h; serotonin


title: C2

description: Library name: SAMPLES2


title: Necessity MPRA, GFP, Soma Rep1

description: Library name: necessity_GFPS1


title: retinal organoid; quetiapine + serotonin; well E12

description:
Library name: E12_Quetiapine_Serotonin
iPSC-derived retinal organoid, plate well E12; demultiplexed by 12 bp cell barcode AAGTCTTAGGGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: quetiapine 5 uM, 24 h; serotonin


title: HC135T CRC-SC line

description:
Library name: HC135T
Patient-derived CRC-SC spheroid


title: Necessity MPRA, GFP, Neurite Rep4

description: Library name: necessity_GFPN4

value: Necessity MPRA, GFP, Neurite


title: retinal organoid; sertraline + serotonin; well D12

description:
Library name: D12_Sertaline_Serotonin
iPSC-derived retinal organoid, plate well D12; demultiplexed by 12 bp cell barcode GGCGCTCAGTAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: sertraline 5 uM, 24 h; serotonin


title: HC136T CRC-SC line

description:
Library name: HC136T
Patient-derived CRC-SC spheroid

value: Untreated


title: C1

description: Library name: SAMPLES1

value: empty vector control


title: HC134T CRC-SC line

description:
Library name: HC134T
Patient-derived CRC-SC spheroid


title: MELANOMA ICI 3

type: RNA

city: IRVINE

first: Devyani

last: swami

state: CA

address: 811 Health Sciences Road

department: Anatomy & Neurobiology

institute: UNIVERSITY OF CALIFORNIA IRVINE

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw images were processed using the MERSCOPE software pipeline to generate spatial genomics output files ready for downstream analysis. These outputs included detected transcripts and their three-dimensional spatial coordinates, provided as cell metadata (CSV), experiment metadata (JSON),
Cell_ID was used representing a unique index was assigned to each imaged cell in every experiment

label: unique barcodes

source_name: Mouse Hippocampus

label_protocol: Unique barcodes were prepared for each run

growth_protocol: For Spatial transcriptomics using MERFISH, whole brains were carefully harvested from mice following decapitation and immediately placed into tissue-embedding plastic molds

extract_protocol: 10 µm sections from the OCT-embedded tissue blocks were mounted onto slides and processed for probe hybridization and gel embedding according to the MERFISH protocol

treatment_protocol: Adult male wild-type (WT) mice aged 10–12 weeks were randomly assigned to one of the following experimental groups: (i) WT mice receiving isotype-matched control antibodies (intraperitoneal, i.p.); (ii) WT mice bearing D4M-3A.UV2 tumors and treated with isotype-matched control antibodies (i.p.); (iii) WT mice treated with immune checkpoint inhibitors (ICIs), including anti–CTLA-4 (1 mg per dose, three times weekly, i.p.) and anti–PD-1 (200 µg per dose, twice weekly, i.p.); and (iv) WT mice bearing D4M-3A.UV2 tumors treated with the same combination ICI regimen for three weeks.For tumor induction, mice in the cancer groups received bilateral intradermal injections of 5 × 10⁵ syngeneic D4M-3A.UV2 melanoma cells. Tumors were allowed to engraft for one week prior to initiating ITC or ICI treatments

tag: strain

value: Hippocampus

tag: sample group

value: MELANOMA ICI


title: Necessity MPRA, GFP, Neurite Rep3

description: Library name: necessity_GFPN3

value: CAD


title: retinal organoid; loxapine + serotonin; well C12

description:
Library name: C12_Loxaipne_Serotonin
iPSC-derived retinal organoid, plate well C12; demultiplexed by 12 bp cell barcode CCGAGCGCTATT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: loxapine 5 uM, 24 h; serotonin


title: Necessity MPRA, GFP, Neurite Rep2

description: Library name: necessity_GFPN2


title: MELANOMA ICI 2

description: Replicate 2


title: HC133T CRC-SC line

description:
Library name: HC133T
Patient-derived CRC-SC spheroid


title: retinal organoid; aripiprazole + serotonin; well B12

description:
Library name: B12_Aripiprazole_Serotonin
iPSC-derived retinal organoid, plate well B12; demultiplexed by 12 bp cell barcode TTCTGCGCATCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: aripiprazole 5 uM, 24 h; serotonin


title: HC131T CRC-SC line

description:
Library name: HC131T
Patient-derived CRC-SC spheroid

value: Large intestine

value: Colorectal cancer


title: Necessity MPRA, GFP, Neurite Rep1

description: Library name: necessity_GFPN1


title: retinal organoid; No_drug + serotonin; well A12

description:
Library name: A12_No_drug_Serotonin
iPSC-derived retinal organoid, plate well A12; demultiplexed by 12 bp cell barcode AAGCAGCGTACC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: No_drug 5 uM, 24 h; serotonin


title: MELANOMA ICI 1

description: Replicate 1


title: CONTROL ICI 3

description: Replicate 3

value: CONTROL ICI


title: Necessity MPRA, Firefly, Soma Rep4

description: Library name: necessity_FFS4

value: Necessity MPRA, Firefly, Soma


title: HC126T CRC-SC line

description:
Library name: HC126T
Patient-derived CRC-SC spheroid

value: RAS/RAF-wild-type


title: retinal organoid; control 2 uM Na4P2O7; well H11

description:
Library name: H11_2_uM_Na4P2O7
iPSC-derived retinal organoid, plate well H11; demultiplexed by 12 bp cell barcode CCTACTACGCGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: vehicle/chemical control:2 uM Na4P2O7


title: HC123T CRC-SC line

description:
Library name: HC123T
Patient-derived CRC-SC spheroid

value: Untreated


title: CONTROL ICI 2

description: Replicate 2


title: Necessity MPRA, Firefly, Soma Rep3

description: Library name: necessity_FFS3


title: retinal organoid; control 2 uM Na4P2O7; well G11

description:
Library name: G11_2_uM_Na4P2O7
iPSC-derived retinal organoid, plate well G11; demultiplexed by 12 bp cell barcode GGAGGCTCCGCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt


title: KS02

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

description: Library name: KS02

data_processing:
RNA-seq reads were preprocessed with fastp for adaptor trimming. The trimmed reads were first aligned to the human reference genome (GRCh38.p14) using STAR and the aligned reads were quantified with Salmon. The unmapped reads were then extracted and quantified against the KSHV reference transcriptome derived from NC_009333 using Salmon. Transcript abundance estimates in transcripts per million (TPM) and estimated read counts were generated for both human and KSHV alignments.
Assembly: GRCh38.p14, NC_009333
Supplementary files format and content: Clinical metadata annotations for each samples
Supplementary files format and content: Salmon quantification summarized in csv files for counts and/or TPM for KSHV and human genes

source_name: Tumor

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the FormaPure XL RNA Kit (Beckman Coulter) according to the manufacturer’s protocol. RNA quantity and purity were assessed by micro-volume spectrophotometry (NanoDrop 2000, Thermo Scientific), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche/KAPA Biosystems). Briefly, ribosomal RNA was depleted by hybridization to complementary DNA oligonucleotides followed by RNase H and DNase treatment. The remaining RNA was fragmented using heat and magnesium, followed by first-strand cDNA synthesis using random priming and second-strand synthesis incorporating dUTP to enable strand-specific sequencing. Adapters were ligated, and libraries were PCR-amplified. Library quality and fragment size distribution were assessed using the Agilent Bioanalyzer or LabChip GX, and libraries were quantified by qPCR.

value: Tumor

value: Kaposi sarcoma (KS)


title: HC121T CRC-SC line

description:
Library name: HC121T
Patient-derived CRC-SC spheroid


title: CONTROL ICI 1

description: Replicate 1

value: Hippocampus


title: Necessity MPRA, Firefly, Soma Rep2

description: Library name: necessity_FFS2

value: CAD


title: retinal organoid; xanomeline + retinoic acid; well F11

description:
Library name: F11_Xanomeline_Retinoic_acid
iPSC-derived retinal organoid, plate well F11; demultiplexed by 12 bp cell barcode TTGTAGCTCCAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: xanomeline 5 uM, 24 h; retinoic acid


title: MELANOMA 2

description: Replicate 2

value: MELANOMA


title: HC116T CRC-SC line

description:
Library name: HC116T
Patient-derived CRC-SC spheroid


title: Necessity MPRA, Firefly, Soma Rep1

description: Library name: necessity_FFS1


title: retinal organoid; quetiapine + retinoic acid; well E11

description:
Library name: E11_Quetiapine_Retinoic_acid
iPSC-derived retinal organoid, plate well E11; demultiplexed by 12 bp cell barcode AATAGCGAGTTT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: quetiapine 5 uM, 24 h; retinoic acid


title: HC115T CRC-SC line

description:
Library name: HC115T
Patient-derived CRC-SC spheroid

value: Large intestine

value: Colorectal cancer


title: MELANOMA 1

description: Replicate 1


title: Necessity MPRA, Firefly, Neurite Rep4

description: Library name: necessity_FFN4

value: Necessity MPRA, Firefly, Neurite


title: retinal organoid; sertraline + retinoic acid; well D11

description:
Library name: D11_Sertaline_Retinoic_acid
iPSC-derived retinal organoid, plate well D11; demultiplexed by 12 bp cell barcode GACGGGTTTCGA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: sertraline 5 uM, 24 h; retinoic acid


title: HC103T CRC-SC line

description:
Library name: HC103T
Patient-derived CRC-SC spheroid

value: RAS/RAF-wild-type


title: CONTROL3

description: Replicate 3

value: CONTROL


title: Necessity MPRA, Firefly, Neurite Rep3

description: Library name: necessity_FFN3


title: retinal organoid; loxapine + retinoic acid; well C11

description:
Library name: C11_Loxaipne_Retinoic_acid
iPSC-derived retinal organoid, plate well C11; demultiplexed by 12 bp cell barcode TAGCCCAATGCA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: loxapine 5 uM, 24 h; retinoic acid


title: CONTROL2

description: Replicate 2


title: HC96T CRC-SC line

description:
Library name: HC96T
Patient-derived CRC-SC spheroid

value: Untreated


title: Necessity MPRA, Firefly, Neurite Rep2

description: Library name: necessity_FFN2


title: CONTROL1

description: Replicate 1


title: retinal organoid; aripiprazole + retinoic acid; well B11

description:
Library name: B11_Aripiprazole_Retinoic_acid
iPSC-derived retinal organoid, plate well B11; demultiplexed by 12 bp cell barcode ACTGTTGGATCG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: aripiprazole 5 uM, 24 h; retinoic acid


title: HC84T CRC-SC line

description:
Library name: HC84T
Patient-derived CRC-SC spheroid


title: Necessity MPRA, Firefly, Neurite Rep1

description: Library name: necessity_FFN1


title: retinal organoid; No_drug + retinoic acid; well A11

description:
Library name: A11_No_drug_Retinoic_acid
iPSC-derived retinal organoid, plate well A11; demultiplexed by 12 bp cell barcode GGGACGTCGATT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: No_drug 5 uM, 24 h; retinoic acid


title: HC79T CRC-SC line

description:
Library name: HC79T
Patient-derived CRC-SC spheroid


title: Mutation MPRA, GFP, Soma Rep4

description: Library name: mutation_GFPS4

value: CAD

value: Mutation MPRA, GFP, Soma


title: retinal organoid; control 2 uM C8H16NaO8; well H10

description:
Library name: H10_2_uM_C8H16NaO8
iPSC-derived retinal organoid, plate well H10; demultiplexed by 12 bp cell barcode CGCTGGAACAGT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: vehicle/chemical control:2 uM C8H16NaO8


title: mRNA_TC5_lin-46(++)_14h

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample 30

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
tab-delimited text file with raw gene expression read counts
tab-delimited text file with normalized gene expression read counts
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Synchronized L1 animals were plated on 2% NGM plates seeded with OP50 E. coli bacteria and grown at 25°C.

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina Stranded mRNA-seq

value: whole organism

tag: time (h)


title: HC64T CRC-SC line

description:
Library name: HC64T
Patient-derived CRC-SC spheroid


title: mRNA_TC5_lin-46(++)_13h

description: Library name: Sample 29


title: Mutation MPRA, GFP, Soma Rep3

description: Library name: mutation_GFPS3


title: HC61T CRC-SC line

description:
Library name: HC61T
Patient-derived CRC-SC spheroid


title: retinal organoid; control 2 uM C8H16NaO8; well G10

description:
Library name: G10_2_uM_C8H16NaO8
iPSC-derived retinal organoid, plate well G10; demultiplexed by 12 bp cell barcode GAGCCCTTGCTA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid


title: mRNA_TC5_lin-46(++)_12h

description: Library name: Sample 28


title: Mutation MPRA, GFP, Soma Rep2

description: Library name: mutation_GFPS2


title: retinal organoid; xanomeline + histamine; well F10

description:
Library name: F10_Xanomeline_Histamine
iPSC-derived retinal organoid, plate well F10; demultiplexed by 12 bp cell barcode CTGCTTCCGCAT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: xanomeline 5 uM, 24 h; histamine


title: mRNA_TC5_lin-46(++)_11h

description: Library name: Sample 27


title: HC57T CRC-SC line

description:
Library name: HC57T
Patient-derived CRC-SC spheroid

value: Large intestine

value: Colorectal cancer


title: HC56T CRC-SC line

description:
Library name: HC56T
Patient-derived CRC-SC spheroid


title: Mutation MPRA, GFP, Soma Rep1

description: Library name: mutation_GFPS1


title: retinal organoid; quetiapine + histamine; well E10

description:
Library name: E10_Quetiapine_Histamine
iPSC-derived retinal organoid, plate well E10; demultiplexed by 12 bp cell barcode GCAGAACCCGTA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: quetiapine 5 uM, 24 h; histamine


title: mRNA_TC5_lin-46(++)_10h

description: Library name: Sample 26


title: retinal organoid; sertraline + histamine; well D10

description:
Library name: D10_Sertaline_Histamine
iPSC-derived retinal organoid, plate well D10; demultiplexed by 12 bp cell barcode GTAGCTCCTTAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: sertraline 5 uM, 24 h; histamine


title: Mutation MPRA, GFP, Neurite Rep4

description: Library name: mutation_GFPN4

value: Mutation MPRA, GFP, Neurite


title: HC53T CRC-SC line

description:
Library name: HC53T
Patient-derived CRC-SC spheroid

value: RAS/RAF-wild-type


title: mRNA_TC5_lin-46(++)_9h

description: Library name: Sample 25


title: HC45T CRC-SC line

description:
Library name: HC45T
Patient-derived CRC-SC spheroid

value: Untreated


title: Mutation MPRA, GFP, Neurite Rep3

description: Library name: mutation_GFPN3


title: retinal organoid; loxapine + histamine; well C10

description:
Library name: C10_Loxaipne_Histamine
iPSC-derived retinal organoid, plate well C10; demultiplexed by 12 bp cell barcode TACTCCGGACGC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: loxapine 5 uM, 24 h; histamine


title: mRNA_TC5_lin-46(++)_8h

description: Library name: Sample 24


title: Mutation MPRA, GFP, Neurite Rep2

description: Library name: mutation_GFPN2


title: retinal organoid; aripiprazole + histamine; well B10

description:
Library name: B10_Aripiprazole_Histamine
iPSC-derived retinal organoid, plate well B10; demultiplexed by 12 bp cell barcode GTAGTTAACTCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: aripiprazole 5 uM, 24 h; histamine


title: HC41T CRC-SC line

description:
Library name: HC41T
Patient-derived CRC-SC spheroid


title: mRNA_TC5_lin-46(++)_7h

description: Library name: Sample 23


title: Mutation MPRA, GFP, Neurite Rep1

description: Library name: mutation_GFPN1

value: CAD


title: retinal organoid; No_drug + histamine; well A10

description:
Library name: A10_No_drug_Histamine
iPSC-derived retinal organoid, plate well A10; demultiplexed by 12 bp cell barcode TAGCAATTGAGT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: No_drug 5 uM, 24 h; histamine


title: HC38T CRC-SC line

description:
Library name: HC38T
Patient-derived CRC-SC spheroid


title: mRNA_TC5_lin-46(++)_6h

description: Library name: Sample 22


title: retinal organoid; control 2 uM NaNO2; well H9

description:
Library name: H9_2_uM_NaNO2
iPSC-derived retinal organoid, plate well H9; demultiplexed by 12 bp cell barcode GGTTGACGTCGA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: vehicle/chemical control:2 uM NaNO2


title: Mutation MPRA, Firefly, Soma Rep4

description: Library name: mutation_FFS4

value: Mutation MPRA, Firefly, Soma


title: Male Kidney Reperfusion_24h_DBA_Rep3

city: Bern

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

institute: University Hospital Bern

description: Library name: 4A_6_BEA23P181_MM_48_S48

data_processing:
Basecalling and demultiplexing were performed using Illumina bcl2fastq (v2.20.0).
Sequence data quality was assessed using FastQC (v0.11.8).
Counts for each gene were estimated using featureCounts (v1.5.1).
Assembly: Reads were aligned to the Ensembl GRCm38 reference genome using STAR (v2.7.9a).
Supplementary files format and content: tab-delimited text file contains raw counts for each sample.

source_name: kidney

extract_protocol:
RNA was extracted using Qiagen midi RNA extraction kit and purified.
Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA.

tag: Sex

value: male

value: kidney

tag: biol rep

value: normoxia-hyperoxia (reperfusion model)


title: mRNA_TC5_lin-46(++)_5h

description: Library name: Sample 21

value: whole organism


title: retinal organoid; control 10 uM NaNO2; well G9

description:
Library name: G9_10_uM_NaNO2
iPSC-derived retinal organoid, plate well G9; demultiplexed by 12 bp cell barcode CCAATAGCTGCA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: vehicle/chemical control:10 uM NaNO2


title: mRNA_TC5_lin-28(xe192)_14h

description: Library name: Sample 20


title: Male Kidney Reperfusion_24h_DBA_Rep2

description: Library name: 4A_5_BEA23P181_MM_47_S47


title: Mutation MPRA, Firefly, Soma Rep2

description: Library name: mutation_FFS2


title: Mutation MPRA, Firefly, Soma Rep3

description: Library name: mutation_FFS3


title: retinal organoid; xanomeline + dopamine; well F9

description:
Library name: F9_Xanomeline_Dopamine
iPSC-derived retinal organoid, plate well F9; demultiplexed by 12 bp cell barcode TTGGACTGATCG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: xanomeline 5 uM, 24 h; dopamine


title: Male Kidney Reperfusion_24h_DBA_Rep1

description: Library name: 4A_4_BEA23P181_MM_46_S46


title: mRNA_TC5_lin-28(xe192)_13h

description: Library name: Sample 19


title: Mutation MPRA, Firefly, Soma Rep1

description: Library name: mutation_FFS1


title: retinal organoid; quetiapine + dopamine; well E9

description:
Library name: E9_Quetiapine_Dopamine
iPSC-derived retinal organoid, plate well E9; demultiplexed by 12 bp cell barcode AAGGGTCTTAGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: quetiapine 5 uM, 24 h; dopamine


title: Male Kidney Reperfusion_24h_C57_Rep3

description: Library name: 4A_3_BEA23P181_MM_45_S45


title: mRNA_TC5_lin-28(xe192)_12h

description: Library name: Sample 18


title: Mutation MPRA, Firefly, Neurite Rep4

description: Library name: mutation_FFN4

value: Mutation MPRA, Firefly, Neurite


title: retinal organoid; sertraline + dopamine; well D9

description:
Library name: D9_Sertaline_Dopamine
iPSC-derived retinal organoid, plate well D9; demultiplexed by 12 bp cell barcode GGAACGCTCAGT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: sertraline 5 uM, 24 h; dopamine


title: Male Kidney Reperfusion_24h_C57_Rep2

description: Library name: 4A_2_BEA23P181_MM_44_S44


title: mRNA_TC5_lin-28(xe192)_11h

description: Library name: Sample 17


title: retinal organoid; loxapine + dopamine; well C9

description:
Library name: C9_Loxaipne_Dopamine
iPSC-derived retinal organoid, plate well C9; demultiplexed by 12 bp cell barcode CCTTGAGCGCTA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: loxapine 5 uM, 24 h; dopamine


title: Male Kidney Reperfusion_24h_C57_Rep1

description: Library name: 4A_1_BEA23P181_MM_43_S43


title: mRNA_TC5_lin-28(xe192)_10h

description: Library name: Sample 16


title: Mutation MPRA, Firefly, Neurite Rep2

description: Library name: mutation_FFN2

value: CAD


title: retinal organoid; aripiprazole + dopamine; well B9

description:
Library name: B9_Aripiprazole_Dopamine
iPSC-derived retinal organoid, plate well B9; demultiplexed by 12 bp cell barcode TTCCCTGCGCAT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: aripiprazole 5 uM, 24 h; dopamine


title: mRNA_TC5_lin-28(xe192)_9h

description: Library name: Sample 15


title: Male Kidney Ischemia_24h_DBA_Rep3

description: Library name: 3A_6_BEA23P181_MM_42_S42

value: normoxia (ischemia model)


title: Mutation MPRA, Firefly, Neurite Rep1

description: Library name: mutation_FFN1


title: retinal organoid; No_drug + dopamine; well A9

description:
Library name: A9_No_drug_Dopamine
iPSC-derived retinal organoid, plate well A9; demultiplexed by 12 bp cell barcode AACCGCAGCGTA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: No_drug 5 uM, 24 h; dopamine


title: mRNA_TC5_lin-28(xe192)_8h

description: Library name: Sample 14


title: Male Kidney Ischemia_24h_DBA_Rep2

description: Library name: 3A_5_BEA23P181_MM_41_S41

value: male


title: Tumor draining lymph nodes_Mock

city: Beijing

first: yujie

last: luo

state: Beijing

address: xueyuan road 38

institute: peking university

description:
Library name: sample4
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger  (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse
Supplementary files format and content: tumor NanoCa
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Tumor draining lymph nodes

extract_protocol:
The samples of tumors and draining lymph nodes (TDLNs) were harvested and cut into pieces approximately 500 mm3 in the RPMI-1640 medium with 10% bovine serum, and enzymatically. The dissociated cells were subsequently passed through then filtered 40 μM Cell-Strainer (BD) and centrifuged at 600 g for 6 minutes. After removing removed, supernatant, they were suspended in 2 mL red blood ml of lysis buffer (Solarbio) on ice for 5 min to lyse minutes blood cells. After washing twice with PBS (Solarbio), the cell pellets were resuspended in sorting buffer (PBS supplemented with 1% FBS). Single-cell suspensions collected from tumor samples and draining lymph nodes were stained with antibodies against CD45 for FACS sorting, which was performed on a BD Aria III instrument.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics).

treatment_protocol: NanoCa treatment

value: Tumor draining lymph nodes

value: immune cells

value: female

tag: age

value: 4-8 weeks old

value: no treatment


title: Male Kidney Ischemia_24h_DBA_Rep1

description: Library name: 3A_4_BEA23P181_MM_40_S40

value: kidney


title: Tumor draining lymph nodes_NanoCa treated

description:
Library name: sample3
10x Genomics

value: NanoCa


title: retinal organoid; control 10 uM NaCl; well G8

description:
Library name: G8_10_uM_NaCl
iPSC-derived retinal organoid, plate well G8; demultiplexed by 12 bp cell barcode CCGGTACTACGC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: vehicle/chemical control:10 uM NaCl


title: mRNA_TC5_lin-28(xe192)_7h

description: Library name: Sample 13

value: whole organism


title: Male Kidney Ischemia_24h_C57_Rep3

description: Library name: 3A_3_BEA23P181_MM_39_S39


title: mRNA_TC5_lin-28(xe192)_6h

description: Library name: Sample 12


title: Male Kidney Ischemia_24h_C57_Rep2

description: Library name: 3A_2_BEA23P181_MM_38_S38


title: tumor_Mock

description:
Library name: sample2
10x Genomics

source_name: tumor

value: tumor

value: Tumor infiltrating immune cells


title: retinal organoid; xanomeline + adrenaline; well F8

description:
Library name: F8_Xanomeline_Adrenaline
iPSC-derived retinal organoid, plate well F8; demultiplexed by 12 bp cell barcode TTAAGTAGCTCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: xanomeline 5 uM, 24 h; adrenaline


title: mRNA_TC5_lin-28(xe192)_5h

description: Library name: Sample 11


title: tumor_NanoCa treated

description:
Library name: sample1
10x Genomics


title: retinal organoid; quetiapine + adrenaline; well E8

description:
Library name: E8_Quetiapine_Adrenaline
iPSC-derived retinal organoid, plate well E8; demultiplexed by 12 bp cell barcode AATTTAGCGAGT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: quetiapine 5 uM, 24 h; adrenaline


title: Male Kidney Ischemia_24h_C57_Rep1

description: Library name: 3A_1_BEA23P181_MM_37_S37

value: male

value: normoxia (ischemia model)


title: mRNA_TC5_WT_14h

description: Library name: Sample 10

value: WT


title: Liver immune cells, intFXR KO or Ctrl-Flox, MASH; CMO

city: Lille

first: Simon

last: Peschard

address: 1, rue du professeur Calmette BP245

country: France

institute: INSERM UMR 1011

description:
Library name: Liver_ImmuneCells_cmo
10X Genomics

library_source: other

data_processing:
CellRanger v6.0.2 (10X Genomics, USA) was used to align reads (excluding intronic reads) to the mouse reference genome obtained from 10X Genomics and generate the UMI counts matrix.
Further analysis on the raw counts were performed in R software using the Seurat v.4.0.3 R package
Assembly: Mouse genome mm10-2020-A
Supplementary files format and content: For each mouse, processed files contains aligned and separated by CMO matrix, features and barcodes. These data are suitable for R importation to build seurat object and perform the analysis.

molecule: other

source_name: Liver

growth_protocol: Adult 8 weeks-old C57Bl6/J mice either Ctrl-flox or intFXR KO were maintained in accordance to ethical guidelines, with 12:12h light/dark cycle in a 21-24°C environment, with ad libitum access to food (MASH-inducing diet) and water.

extract_protocol:
Liver immune cell-enriched cell suspension were isolated after D collagenase digestion of the perfused liver of intFXR KO or Ctrl-flox mice, then labelled using one different CMO per mice. CD45+ cells were sorted using Influx cell sorter (BD) prior to single-cell encapsulation.. Sorted cells were loaded onto the 10x Genomics Chromium platform for single-cell partitioning and barcoding. Reverse transcription and subsequent library preparation steps were performed according to the manufacturer’s instructions.
Samples were prepared for single cell RNA-Sequencing with the Chromium Next GEM Single cell 3’ Reagent Kit (Dual Index) (10x genomics), according to the manufacturer's instructions. Cells from all mice were labelled using Cell Multiplexing Oligos then treated in multiplexing following 10X genomics protocols to construct library upon sequencing. Final sequencing to an average depth of 100k reds/cell was performed by BGI (Hong Kong).

value: Liver

value: 28-30 weeks

value: Leukocytes

value: intestinal FXR KO or control-flox mice

value: HFSC diet 20 weeks

tag: library type

value: CMO

tag: cmo

value: For intFXR KO mice:CMO301 for mouse 1, CMO302 for mouse 2; for Ctrl-flox mice:CMO304 for mouse 4, CMO305 for mouse 5, CMO306 for mouse 6.


title: Male nephrotoxicity_Cyclosporin 24h_DBA_Rep3

description: Library name: 2C_6_BEA23P181_MM_36_S36

value: kidney

value: cyclosporin A 24h


title: retinal organoid; sertraline + adrenaline; well D8

description:
Library name: D8_Sertaline_Adrenaline
iPSC-derived retinal organoid, plate well D8; demultiplexed by 12 bp cell barcode GACGTCGAGGTT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: sertraline 5 uM, 24 h; adrenaline


title: mRNA_TC5_WT_13h

description: Library name: Sample 9

value: whole organism


title: Liver immune cells, intFXR KO or Ctrl-Flox, MASH, RNA

description:
Library name: Liver_ImmuneCells_mRNA
10X Genomics

value: mRNA


title: retinal organoid; loxapine + adrenaline; well C8

description:
Library name: C8_Loxaipne_Adrenaline
iPSC-derived retinal organoid, plate well C8; demultiplexed by 12 bp cell barcode TAGCTGCACCAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: loxapine 5 uM, 24 h; adrenaline


title: Male nephrotoxicity_Cyclosporin 24h_DBA_Rep2

description: Library name: 2C_5_BEA23P181_MM_35_S35

value: male


title: retinal organoid; aripiprazole + adrenaline; well B8

description:
Library name: B8_Aripiprazole_Adrenaline
iPSC-derived retinal organoid, plate well B8; demultiplexed by 12 bp cell barcode ACTGATCGTTGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: aripiprazole 5 uM, 24 h; adrenaline


title: mRNA_TC5_WT_12h

description: Library name: Sample 8

value: WT


title: Male nephrotoxicity_Cyclosporin 24h_DBA_Rep1

description: Library name: 2C_4_BEA23P181_MM_34_S34


title: WT38.LPS.IL.4

city: Madison

first: Parth

middle: H

last: Khatri

state: WI

address: 1111 Highland Ave

department: Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

description: Library name: WT38.LPS.IL.4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Assembly: mm10
Supplementary files format and content: comma-delimited text files includes raw counts for each sample
Supplementary files format and content: csv files include TPM values for each sample

source_name: spleen

extract_protocol:
Total RNA was extracted from primary splenic B cells by GENEWIZ (Azenta Life Sciences) using standard RNA isolation protocols, followed by quality assessment using Bioanalyzer prior to library preparation.
RNA-seq libraries were prepared by GENEWIZ (Azenta Life Sciences) using Illumina-compatible protocols. Briefly, mRNA was enriched from total RNA, fragmented, and reverse transcribed to cDNA, followed by adaptor ligation and PCR amplification. Libraries were sequenced on an Illumina HiSeq platform to generate paired-end 150 bp reads.

treatment_protocol: CD40(2ug/mL)+IL-4(10ng/mL), or LPS (20ng/mL)+IL-4(10ng/mL) for 48 hours

value: spleen

value: primary

value: naive B cells


title: retinal organoid; No_drug + adrenaline; well A8

description:
Library name: A8_No_drug_Adrenaline
iPSC-derived retinal organoid, plate well A8; demultiplexed by 12 bp cell barcode GTCTTAGGAAGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: No_drug 5 uM, 24 h; adrenaline


title: mRNA_TC5_WT_11h

description: Library name: Sample 7


title: WT.35.LPS.IL.4

description: Library name: WT.35.LPS.IL.4


title: Male nephrotoxicity_Cyclosporin 24h_C57_Rep3

description: Library name: 2C_3_BEA23P181_MM_33_S33


title: mRNA_TC5_WT_10h

description: Library name: Sample 6


title: WT.35.CD40.IL.4

description: Library name: WT.35.CD40.IL.4


title: retinal organoid; control No drug; well H7

description:
Library name: H7_No_drug
iPSC-derived retinal organoid, plate well H7; demultiplexed by 12 bp cell barcode CGCTCAGTGGAA (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: vehicle/chemical control:No drug


title: Male nephrotoxicity_Cyclosporin 24h_C57_Rep2

description: Library name: 2C_2_BEA23P181_MM_32_S32

value: kidney


title: 2D_WT_shGFP_E2_veh_003

status: Public on Jun 10 2026

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

description: Library name: 2D_WT_shGFP_E2_veh_003

data_processing:
Quality scores across sequenced reads were assessed using FASTQC.
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using STAR
Sorted reads were counted using HTseq
Assembly: Hg38
Supplementary files format and content: raw counts data for each sample as text files

growth_protocol: For 2D conditions, T47D WT and Y537S ESR1 cells (shGFP and shPR) were plated in triplicate. For 3D conditions, cells were plated in triplicate into tumorsphere media in ULA plates and allowed to form for 6 days.

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen).
Purity of the total RNA samples was assessed using BioAnalyzer (Agilent) and samples with an RNA integrity score >8 were used for library construction by the University of Minnesota Genomics Core. Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Cells were hormone-starved for 24h, followed by treatment with E2 (1 nM, 48h) or R5020 (10 nM, 6h).

value: cancer

value: shGGP, E2


title: mRNA_TC5_WT_9h

description: Library name: Sample 5


title: retinal organoid; control No drug; well G7

description:
Library name: G7_No_drug
iPSC-derived retinal organoid, plate well G7; demultiplexed by 12 bp cell barcode GAGCGCTACCTT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid


title: WT.36.LPS.IL.4

description: Library name: WT.36.LPS.IL.4


title: Male nephrotoxicity_Cyclosporin 24h_C57_Rep1

description: Library name: 2C_1_BEA23P181_MM_31_S31

value: cyclosporin A 24h


title: mRNA_TC5_WT_8h

description: Library name: Sample 4

value: whole organism


title: WT.35

description: Library name: WT.35

value: untreated control


title: Male nephrotoxicity_Tunicamycin 24h_DBA_Rep3

description: Library name: 2B_6_BEA23P181_MM_30_S30

value: tunicamycin 24h


title: retinal organoid; xanomeline; well F7

description:
Library name: F7_Xanomeline_No_drug
iPSC-derived retinal organoid, plate well F7; demultiplexed by 12 bp cell barcode CTGCGCATTTCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: xanomeline 5 uM, 24 h


title: WT.36.CD40.IL.4

description: Library name: WT.36.CD40.IL.4

value: WT


title: Tn 4T1 cells-bearing tumor 6

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: Library name: T2

data_processing:
Raw paired-end RNA sequencing reads obtained from the tumor samples were initially subjected to quality assessment using FastQC to evaluate sequencing quality metrics, including per-base sequence quality, GC content distribution, sequence duplication levels, and adapter contamination. Subsequently, read preprocessing and filtering were performed using fastp (v0.23.x). During this step, Illumina adapter sequences were automatically detected and removed, low-quality bases were trimmed from both read ends, sequencing errors in paired-end reads were corrected when possible, and short or low-quality reads (PHRED<20) were excluded from downstream analyses. Only reads meeting predefined quality and length criteria were retained for transcriptomic processing. Quality control analyses were repeated after trimming to confirm improvements in read quality and overall dataset integrity.
Processed reads were aligned to the Mus musculus reference genome (GRCm39) using STAR version 2.7.11a. A two-pass alignment strategy was employed to improve splice junction detection sensitivity and mapping accuracy. Gene-level expression quantification was subsequently performed using featureCounts from the Subread package version 2.1.1. Reads were assigned to annotated exonic regions and summarized at the gene level based on the reference annotation file. Only properly paired reads mapping to exonic regions were considered for transcript abundance estimation.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: count matrix file with all samples

source_name: breast

extract_protocol:
Tumor tissues were processed for total RNA extraction using the miRNeasy Tissue/Cells Advanced Mini Kit (Qiagen) following mechanical homogenization in RLT buffer supplemented with β-mercaptoethanol.
Transcriptomic libraries were prepared using the Illumina Stranded mRNA Prep protocol with Illumina DNA/RNA UD Indexes Set B, including poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: murine 4T1 breast cancer cells carrying CRISPR/Cas9-mediated silencing of the Cosmc gene (Tn+) compared with parental wild-type 4T1 cells (WT)

value: breast

value: Tn


title: mRNA_TC5_WT_7h

description: Library name: Sample 3


title: retinal organoid; quetiapine; well E7

description:
Library name: E7_Quetiapine_No_drug
iPSC-derived retinal organoid, plate well E7; demultiplexed by 12 bp cell barcode GCAGCGTAAACC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: quetiapine 5 uM, 24 h


title: mRNA_TC5_WT_6h

description: Library name: Sample 2


title: WT.36

description: Library name: WT.36

value: spleen

value: primary

value: naive B cells


title: retinal organoid; sertraline; well D7

description:
Library name: D7_Sertaline_No_drug
iPSC-derived retinal organoid, plate well D7; demultiplexed by 12 bp cell barcode AGGCTCCGGGCC (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: sertraline 5 uM, 24 h


title: Male nephrotoxicity_Tunicamycin 24h_DBA_Rep1

description: Library name: 2B_4_BEA23P181_MM_28_S28

value: male

value: kidney


title: Male nephrotoxicity_Tunicamycin 24h_DBA_Rep2

description: Library name: 2B_5_BEA23P181_MM_29_S29


title: WT.38.CD40.IL.4

description: Library name: WT.38.CD40.IL.4


title: Male nephrotoxicity_Tunicamycin 24h_C57_Rep3

description: Library name: 2B_3_BEA23P181_MM_27_S27


title: mRNA_TC5_WT_5h

description: Library name: Sample 1


title: mRNA_TC4_lin-28(xe192)_6h

description: Library name: Sample 16

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts


title: WT.38

description: Library name: WT.38


title: retinal organoid; aripiprazole; well B7

description:
Library name: B7_Aripiprazole_No_drug
iPSC-derived retinal organoid, plate well B7; demultiplexed by 12 bp cell barcode AGGCGGCCTCCG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: retinal organoid

value: aripiprazole 5 uM, 24 h


title: retinal organoid; loxapine; well C7

description:
Library name: C7_Loxaipne_No_drug
iPSC-derived retinal organoid, plate well C7; demultiplexed by 12 bp cell barcode TACTACGCCCGG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: loxapine 5 uM, 24 h


title: mRNA_TC4_lin-28(xe192)_5h

description: Library name: Sample 15

value: whole organism


title: Male nephrotoxicity_Tunicamycin 24h_C57_Rep2

description: Library name: 2B_2_BEA23P181_MM_26_S26

value: tunicamycin 24h


title: DK.27.LPS.IL.4

description: Library name: DK.27.LPS.IL.4


title: retinal organoid; No_drug; well A7

description:
Library name: A7_No_drug_No_drug
iPSC-derived retinal organoid, plate well A7; demultiplexed by 12 bp cell barcode TAGCGAGTAATT (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: No_drug 5 uM, 24 h


title: Mutation MPRA, Firefly, Neurite Rep3

description: Library name: mutation_FFN3

data_processing:
MPRA oligos were extracted from sequencing reads and aligned against known oligo sequences using bowtie2. UMI deduplication was performed to minimize contributions from differences in PCR amplification efficiency.
Assembly: mm10
Supplementary files format and content: For each oligo, the number of reads containing that oligo and the number of unique UMIs seen in those reads are reported.

extract_protocol:
RNA was extracted from soma and neurite fractions using a QuickRNA micro kit (Zymo).
Targeted sequencing libraries, with UMIs, were constructed through RT-PCR of an amplicon of the reporter transcript used in the MPRA. To minimize effects due to a particular reporter RNA, two reporters RNAs were used. One encoded GFP while the other encoded firefly luciferase.

value: CAD

value: Mutation MPRA, Firefly, Neurite


title: Male nephrotoxicity_Tunicamycin 24h_C57_Rep1

description: Library name: 2B_1_BEA23P181_MM_25_S25


title: mRNA_TC4_lin-28(xe192)_4h

description: Library name: Sample 14


title: cardiac organoid; control 2 mg ml k Carrageenan; well H6

description:
Library name: H6_2_mg_ml_k_Carrageenan
iPSC-derived cardiac organoid, plate well H6; demultiplexed by 12 bp cell barcode GTCTAAGGTAGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

source_name: iPSC-derived cardiac organoid

value: iPSC-derived cardiac organoid

value: cardiac organoid

value: vehicle/chemical control:2 mg ml k Carrageenan


title: Male nephrotoxicity_control 24h_DBA_Rep3

description: Library name: 2A_6_BEA23P181_MM_24_S24

value: control 24h


title: DK.27.CD40.IL.4

description: Library name: DK.27.CD40.IL.4

value: spleen

value: primary

value: naive B cells


title: DK.27

description: Library name: DK.27

value: untreated control


title: mRNA_TC4_lin-28(xe192)_3h

description: Library name: Sample 13


title: cardiac organoid; control 2 mg ml k Carrageenan; well G6

description:
Library name: G6_2_mg_ml_k_Carrageenan
iPSC-derived cardiac organoid, plate well G6; demultiplexed by 12 bp cell barcode CCTAGCTGCAAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)


title: mRNA_TC4_WT_6h

description: Library name: Sample 12

value: WT


title: Male nephrotoxicity_control 24h_DBA_Rep2

description: Library name: 2A_5_BEA23P181_MM_23_S23

value: male

value: kidney


title: DK.28.LPS.IL.4

description: Library name: DK.28.LPS.IL.4


title: cardiac organoid; xanomeline + serotonin; well F6

description:
Library name: F6_Xanomeline_Serotonin
iPSC-derived cardiac organoid, plate well F6; demultiplexed by 12 bp cell barcode TTACTGATCGGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h; serotonin


title: retinal organoid; control 2 uM NaCl; well H8

description:
Library name: H8_2_uM_NaCl
iPSC-derived retinal organoid, plate well H8; demultiplexed by 12 bp cell barcode GGCCAGGCTCCG (Pool-2 i7 AAGAGGCA)
DGE_final_Pool2.txt

value: iPSC-derived retinal organoid

value: retinal organoid

value: vehicle/chemical control:2 uM NaCl


title: mRNA_TC4_WT_5h

description: Library name: Sample 11

value: whole organism


title: 2D_WT_shGFP_E2_veh_002

description: Library name: 2D_WT_shGFP_E2_veh_002

value: cancer

value: shGGP, E2


title: Male nephrotoxicity_control 24h_DBA_Rep1

description: Library name: 2A_4_BEA23P181_MM_22_S22


title: cardiac organoid; quetiapine + serotonin; well E6

description:
Library name: E6_Quetiapine_Serotonin
iPSC-derived cardiac organoid, plate well E6; demultiplexed by 12 bp cell barcode AAGTCTTAGGGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: cardiac organoid

value: quetiapine 5 uM, 24 h; serotonin


title: DK.28.CD40.IL.4

description: Library name: DK.28.CD40.IL.4

value: spleen

value: primary


title: Male nephrotoxicity_control 24h_C57_Rep3

description: Library name: 2A_3_BEA23P181_MM_21_S21

value: control 24h


title: DK.28

description: Library name: DK.28

value: naive B cells

value: untreated control


title: mRNA_TC4_WT_4h

description: Library name: Sample 10

value: WT


title: cardiac organoid; sertraline + serotonin; well D6

description:
Library name: D6_Sertaline_Serotonin
iPSC-derived cardiac organoid, plate well D6; demultiplexed by 12 bp cell barcode GGCGCTCAGTAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: sertraline 5 uM, 24 h; serotonin


title: Male nephrotoxicity_control 24h_C57_Rep2

description: Library name: 2A_2_BEA23P181_MM_20_S20

value: male

value: kidney


title: mRNA_TC4_WT_3h

description: Library name: Sample 9


title: cardiac organoid; loxapine + serotonin; well C6

description:
Library name: C6_Loxaipne_Serotonin
iPSC-derived cardiac organoid, plate well C6; demultiplexed by 12 bp cell barcode CCGAGCGCTATT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: loxapine 5 uM, 24 h; serotonin


title: DK.29.LPS.IL.4

description: Library name: DK.29.LPS.IL.4


title: Male nephrotoxicity_control 24h_C57_Rep1

description: Library name: 2A_1_BEA23P181_MM_19_S19


title: DK.29.CD40.IL.4

description: Library name: DK.29.CD40.IL.4


title: mRNA_TC3_lin-28(xe192)_6h

description: Library name: Sample 8

value: whole organism


title: cardiac organoid; aripiprazole + serotonin; well B6

description:
Library name: B6_Aripiprazole_Serotonin
iPSC-derived cardiac organoid, plate well B6; demultiplexed by 12 bp cell barcode TTCTGCGCATCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: aripiprazole 5 uM, 24 h; serotonin


title: Male nephrotoxicity_Cyclosporin 6h_DBA_Rep3

description: Library name: 1C_6_BEA23P181_MM_18_S18

value: cyclosporin A 6h


title: mRNA_TC3_lin-28(xe192)_5h

description: Library name: Sample 7


title: DK.29

description: Library name: DK.29


title: cardiac organoid; No_drug + serotonin; well A6

description:
Library name: A6_No_drug_Serotonin
iPSC-derived cardiac organoid, plate well A6; demultiplexed by 12 bp cell barcode AAGCAGCGTACC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: No_drug 5 uM, 24 h; serotonin


title: Male nephrotoxicity_Cyclosporin 6h_DBA_Rep2

description: Library name: 1C_5_BEA23P181_MM_17_S17


title: mRNA_TC3_lin-28(xe192)_4h

description: Library name: Sample 6


title: smallRNA_TC2_lin-28(xe192)_44h

description: Library name: Sample 42

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

growth_protocol: Synchronized L1 animals were grown in liquid culture (S-Basal supplemented with OP50; OD600 = 2.7; 1000 animals/ml) at 25°C shaking at 180 rpm.

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina TruSeq Small RNA Library Prep Kit


title: Male nephrotoxicity_Cyclosporin 6h_DBA_Rep1

description: Library name: 1C_4_BEA23P181_MM_16_S16


title: mRNA_TC3_lin-28(xe192)_3h

description: Library name: Sample 5


title: cardiac organoid; control 2 uM Na4P2O7; well H5

description:
Library name: H5_2_uM_Na4P2O7
iPSC-derived cardiac organoid, plate well H5; demultiplexed by 12 bp cell barcode CCTACTACGCGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: cardiac organoid

value: vehicle/chemical control:2 uM Na4P2O7


title: smallRNA_TC2_lin-28(xe192)_43h

description: Library name: Sample 41


title: cardiac organoid; control 2 uM Na4P2O7; well G5

description:
Library name: G5_2_uM_Na4P2O7
iPSC-derived cardiac organoid, plate well G5; demultiplexed by 12 bp cell barcode GGAGGCTCCGCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt


title: Male nephrotoxicity_Cyclosporin 6h_C57_Rep3

description: Library name: 1C_3_BEA23P181_MM_15_S15


title: mRNA_TC3_WT_6h

description: Library name: Sample 4


title: smallRNA_TC2_lin-28(xe192)_42h

description: Library name: Sample 40


title: cardiac organoid; xanomeline + retinoic acid; well F5

description:
Library name: F5_Xanomeline_Retinoic_acid
iPSC-derived cardiac organoid, plate well F5; demultiplexed by 12 bp cell barcode TTGTAGCTCCAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h; retinoic acid


title: mRNA_TC3_WT_5h

description: Library name: Sample 3


title: smallRNA_TC2_lin-28(xe192)_41h

description: Library name: Sample 39


title: Male nephrotoxicity_Cyclosporin 6h_C57_Rep2

description: Library name: 1C_2_BEA23P181_MM_14_S14


title: Male nephrotoxicity_Cyclosporin 6h_C57_Rep1

description: Library name: 1C_1_BEA23P181_MM_13_S13


title: cardiac organoid; quetiapine + retinoic acid; well E5

description:
Library name: E5_Quetiapine_Retinoic_acid
iPSC-derived cardiac organoid, plate well E5; demultiplexed by 12 bp cell barcode AATAGCGAGTTT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: quetiapine 5 uM, 24 h; retinoic acid


title: mRNA_TC3_WT_4h

description: Library name: Sample 2


title: smallRNA_TC2_lin-28(xe192)_40h

description: Library name: Sample 38


title: Male nephrotoxicity_Tunicamycin 6h_DBA_Rep3

description: Library name: 1B_6_BEA23P181_MM_12_S12

value: tunicamycin 6h


title: cardiac organoid; loxapine + retinoic acid; well C5

description:
Library name: C5_Loxaipne_Retinoic_acid
iPSC-derived cardiac organoid, plate well C5; demultiplexed by 12 bp cell barcode TAGCCCAATGCA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: loxapine 5 uM, 24 h; retinoic acid


title: Male nephrotoxicity_Tunicamycin 6h_DBA_Rep2

description: Library name: 1B_5_BEA23P181_MM_11_S11


title: mRNA_TC3_WT_3h

description: Library name: Sample 1

value: WT


title: smallRNA_TC2_lin-28(xe192)_38h

description: Library name: Sample 36


title: cardiac organoid; aripiprazole + retinoic acid; well B5

description:
Library name: B5_Aripiprazole_Retinoic_acid
iPSC-derived cardiac organoid, plate well B5; demultiplexed by 12 bp cell barcode ACTGTTGGATCG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: aripiprazole 5 uM, 24 h; retinoic acid


title: smallRNA_TC2_lin-28(xe192)_39h

description: Library name: Sample 37


title: mRNA_TC1_lin-28(xe192)_6h_rep1

description: Library name: Sample 16


title: Male nephrotoxicity_Tunicamycin 6h_DBA_Rep1

description: Library name: 1B_4_BEA23P181_MM_10_S10

value: male


title: mRNA_TC1_lin-28(xe192)_5h_rep1

description: Library name: Sample 15


title: smallRNA_TC2_lin-28(xe192)_37h

description: Library name: Sample 35


title: Male nephrotoxicity_Tunicamycin 6h_C57_Rep3

description: Library name: 1B_3_BEA23P181_MM_9_S9

value: kidney


title: mRNA_TC1_lin-28(xe192)_4h_rep1

description: Library name: Sample 14


title: smallRNA_TC2_lin-28(xe192)_36h

description: Library name: Sample 34


title: cardiac organoid; control 2 uM C8H16NaO8; well H4

description:
Library name: H4_2_uM_C8H16NaO8
iPSC-derived cardiac organoid, plate well H4; demultiplexed by 12 bp cell barcode CGCTGGAACAGT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: vehicle/chemical control:2 uM C8H16NaO8


title: Male nephrotoxicity_Tunicamycin 6h_C57_Rep2

description: Library name: 1B_2_BEA23P181_MM_8_S8


title: cardiac organoid; No_drug + retinoic acid; well A5

description:
Library name: A5_No_drug_Retinoic_acid
iPSC-derived cardiac organoid, plate well A5; demultiplexed by 12 bp cell barcode GGGACGTCGATT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: No_drug 5 uM, 24 h; retinoic acid


title: smallRNA_TC2_lin-28(xe192)_35h

description: Library name: Sample 33

value: whole organism


title: mRNA_TC1_lin-28(xe192)_3h_rep1

description: Library name: Sample 13


title: Male nephrotoxicity_Tunicamycin 6h_C57_Rep1

description: Library name: 1B_1_BEA23P181_MM_7_S7


title: mRNA_TC1_lin-28(n719)_6h_rep1

description: Library name: Sample 12


title: cardiac organoid; control 2 uM C8H16NaO8; well G4

description:
Library name: G4_2_uM_C8H16NaO8
iPSC-derived cardiac organoid, plate well G4; demultiplexed by 12 bp cell barcode GAGCCCTTGCTA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt


title: smallRNA_TC2_lin-28(xe192)_34h

description: Library name: Sample 32


title: cardiac organoid; xanomeline + histamine; well F4

description:
Library name: F4_Xanomeline_Histamine
iPSC-derived cardiac organoid, plate well F4; demultiplexed by 12 bp cell barcode CTGCTTCCGCAT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h; histamine


title: Male nephrotoxicity_control 6h_DBA_Rep3

description: Library name: 1A_6_BEA23P181_MM_6_S6

value: control 6h


title: cardiac organoid; quetiapine + histamine; well E4

description:
Library name: E4_Quetiapine_Histamine
iPSC-derived cardiac organoid, plate well E4; demultiplexed by 12 bp cell barcode GCAGAACCCGTA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: quetiapine 5 uM, 24 h; histamine


title: Male nephrotoxicity_control 6h_DBA_Rep2

description: Library name: 1A_5_BEA23P181_MM_5_S5


title: smallRNA_TC2_lin-28(xe192)_32h

description: Library name: Sample 30


title: mRNA_TC1_lin-28(n719)_4h_rep1

description: Library name: Sample 10


title: Male nephrotoxicity_control 6h_DBA_Rep1

description: Library name: 1A_4_BEA23P181_MM_4_S4


title: mRNA_TC1_lin-28(n719)_3h_rep1

description: Library name: Sample 9


title: cardiac organoid; sertraline + histamine; well D4

description:
Library name: D4_Sertaline_Histamine
iPSC-derived cardiac organoid, plate well D4; demultiplexed by 12 bp cell barcode AGGCGGCCTCCG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: cardiac organoid

value: sertraline 5 uM, 24 h; histamine


title: Male nephrotoxicity_control 6h_C57_Rep3

description: Library name: 1A_3_BEA23P181_MM_3_S3


title: smallRNA_TC2_lin-28(xe192)_31h

description: Library name: Sample 29


title: Male nephrotoxicity_control 6h_C57_Rep2

description: Library name: 1A_2_BEA23P181_MM_2_S2


title: cardiac organoid; aripiprazole + histamine; well B4

description:
Library name: B4_Aripiprazole_Histamine
iPSC-derived cardiac organoid, plate well B4; demultiplexed by 12 bp cell barcode GTAGTTAACTCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: aripiprazole 5 uM, 24 h; histamine


title: mRNA_TC1_WT_5h_rep2

description: Library name: Sample 7


title: cardiac organoid; No_drug + histamine; well A4

description:
Library name: A4_No_drug_Histamine
iPSC-derived cardiac organoid, plate well A4; demultiplexed by 12 bp cell barcode TAGCAATTGAGT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: No_drug 5 uM, 24 h; histamine


title: Male nephrotoxicity_control 6h_C57_Rep1

description: Library name: 1A_1_BEA23P181_MM_1_S1


title: mRNA_TC1_WT_4h_rep2

description: Library name: Sample 6


title: cardiac organoid; control 2 uM NaNO2; well H3

description:
Library name: H3_2_uM_NaNO2
iPSC-derived cardiac organoid, plate well H3; demultiplexed by 12 bp cell barcode GGTTGACGTCGA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: vehicle/chemical control:2 uM NaNO2


title: smallRNA_TC2_lin-28(xe192)_28h

description: Library name: Sample 26


title: Cd3_KO_rep2

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: Cd3_KO_rep2

data_processing:
Quality control of raw reads was performed with FastQC (v0.11.9), and sequences were aligned to the Mus musculus reference genome (mm10) using STAR (v2.7.10a). Read quantification was carried out using the featureCounts function of the Rsubread package (v2.12.3) at gene-level using GENCODE annotation retaining only uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: comma separated text file (.csv) of raw counts with all samples.

source_name: lung

extract_protocol:
Total RNA was isolated from FACS-sorted spleen and lung cells of WT and Dpp3−/− mice using QIAzol Lysis Reagent (QIAGEN) according to the manufacturer’s instructions. RNA concentration and purity were assessed prior to downstream applications.
total RNA was subjected to poly(A) mRNA sequencing using SMARTer-Stranded Total RNA Kit (Clontech), according to the manufacturer’s instructions.

value: lung

value: KO


title: mRNA_TC1_WT_3h_rep2

description: Library name: Sample 5

value: WT


title: cardiac organoid; control 10 uM NaNO2; well G3

description:
Library name: G3_10_uM_NaNO2
iPSC-derived cardiac organoid, plate well G3; demultiplexed by 12 bp cell barcode CCAATAGCTGCA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: vehicle/chemical control:10 uM NaNO2


title: Cd11b_KO_rep2

description: Library name: Cd11b_KO_rep2


title: mRNA_TC1_WT_6h_rep1

description: Library name: Sample 4


title: smallRNA_TC2_lin-28(xe192)_26h

description: Library name: Sample 24


title: Cd19_KO_rep2

description: Library name: Cd19_KO_rep2


title: mRNA_TC1_WT_5h_rep1

description: Library name: Sample 3


title: mRNA_TC1_WT_4h_rep1

description: Library name: Sample 2


title: cardiac organoid; quetiapine + dopamine; well E3

description:
Library name: E3_Quetiapine_Dopamine
iPSC-derived cardiac organoid, plate well E3; demultiplexed by 12 bp cell barcode AAGGGTCTTAGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: quetiapine 5 uM, 24 h; dopamine


title: smallRNA_TC2_lin-28(xe192)_24h

description: Library name: Sample 22


title: cardiac organoid; sertraline + dopamine; well D3

description:
Library name: D3_Sertaline_Dopamine
iPSC-derived cardiac organoid, plate well D3; demultiplexed by 12 bp cell barcode GGAACGCTCAGT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: sertraline 5 uM, 24 h; dopamine


title: mRNA_TC1_WT_3h_rep1

description: Library name: Sample 1

value: whole organism


title: smallRNA_TC2_WT_44h

description: Library name: Sample 21


title: cardiac organoid; loxapine + dopamine; well C3

description:
Library name: C3_Loxaipne_Dopamine
iPSC-derived cardiac organoid, plate well C3; demultiplexed by 12 bp cell barcode CCTTGAGCGCTA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: loxapine 5 uM, 24 h; dopamine


title: Cd19_rep2

description: Library name: Cd19_rep2


title: smallRNA_TC2_WT_43h

description: Library name: Sample 20


title: mRNA_RIPseq_lin-28(xe197)_antiGFP_rep3

description: Library name: Sample 12

growth_protocol: Approximately 4.5 millions of synchronized L1s of each genotype were plated on peptone-enriched 2% NGM agar XL plates seeded with E. coli OP50 bacteria (~ 500,000 L1s per plate) and grown for 6 hours at 25°C.

extract_protocol:
At the time of sample collection, animals were harvested, washed three times with M9 buffer, once with 0.1 M KCl and dry pellets were snap frozen in liquid nitrogen. Upon thawing, the pellets were lysed in extraction buffer (50 mM HEPES/KOH (pH 7.4 at 4°C), 150 mM KCl, 5 mM MgCl2, 0.1% (v/v) Triton X-100, 10% (w/v) glycerol, 1 mM PMSF, 1 tablet/10 ml cOmplete Mini Protease Inhibitor Tablets (EDTA-free; Roche, 11836170001), 200 U/ml RNaseOUT Recombinant Ribonuclease Inhibitor (Thermo Fisher Scientific, 10777019)), with mortar and pestle in the presence of liquid nitrogen. Anti-GFP IPs were performed by incubating 3 mg total protein with 50 µl of Dynabeads Protein G (Thermo Fisher Scientific, 10003D) bound to anti-GFP antibody (5 µg/IP; Abcam, ab290). The immunoprecipitated RNA was extracted by directly adding TRI Reagent (MRC, TR-118) to the beads and snap-freezing in liquid nitrogen. For each condition (N2 and HW2805), three IPs were performed in parallel as technical replicates. Three aliquots of input lysate each corresponding to 100 µg total protein were snap-frozen in liquid nitrogen upon addition of TRI Reagent for extraction of the input RNA. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062) according to the manufacturer’s protocol including the on column DNase digestion. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina Stranded mRNA-seq


title: cardiac organoid; sertraline + retinoic acid; well D5

description:
Library name: D5_Sertaline_Retinoic_acid
iPSC-derived cardiac organoid, plate well D5; demultiplexed by 12 bp cell barcode GACGGGTTTCGA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: sertraline 5 uM, 24 h; retinoic acid


title: Cd3_KO_rep1

description: Library name: Cd3_KO_rep1


title: cardiac organoid; aripiprazole + dopamine; well B3

description:
Library name: B3_Aripiprazole_Dopamine
iPSC-derived cardiac organoid, plate well B3; demultiplexed by 12 bp cell barcode TTCCCTGCGCAT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: aripiprazole 5 uM, 24 h; dopamine


title: mRNA_RIPseq_lin-28(xe197)_antiGFP_rep2

description: Library name: Sample 11


title: cardiac organoid; No_drug + dopamine; well A3

description:
Library name: A3_No_drug_Dopamine
iPSC-derived cardiac organoid, plate well A3; demultiplexed by 12 bp cell barcode AACCGCAGCGTA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: cardiac organoid

value: No_drug 5 uM, 24 h; dopamine


title: smallRNA_TC2_WT_42h

description: Library name: Sample 19


title: mRNA_RIPseq_lin-28(xe197)_antiGFP_rep1

description: Library name: Sample 10


title: smallRNA_TC2_WT_41h

description: Library name: Sample 18


title: cardiac organoid; control 2 uM NaCl; well H2

description:
Library name: H2_2_uM_NaCl
iPSC-derived cardiac organoid, plate well H2; demultiplexed by 12 bp cell barcode GGCCAGGCTCCG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: vehicle/chemical control:2 uM NaCl


title: mRNA_RIPseq_N2_antiGFP_rep3

description: Library name: Sample 9


title: smallRNA_TC2_WT_40h

description: Library name: Sample 17


title: cardiac organoid; control 10 uM NaCl; well G2

description:
Library name: G2_10_uM_NaCl
iPSC-derived cardiac organoid, plate well G2; demultiplexed by 12 bp cell barcode CCGGTACTACGC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: vehicle/chemical control:10 uM NaCl


title: Cd3_rep1

description: Library name: Cd3_rep1


title: mRNA_RIPseq_N2_antiGFP_rep2

description: Library name: Sample 8


title: cardiac organoid; xanomeline + adrenaline; well F2

description:
Library name: F2_Xanomeline_Adrenaline
iPSC-derived cardiac organoid, plate well F2; demultiplexed by 12 bp cell barcode TTAAGTAGCTCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h; adrenaline


title: mRNA_RIPseq_N2_antiGFP_rep1

description: Library name: Sample 7


title: smallRNA_TC2_WT_38h

description: Library name: Sample 15


title: cardiac organoid; quetiapine + adrenaline; well E2

description:
Library name: E2_Quetiapine_Adrenaline
iPSC-derived cardiac organoid, plate well E2; demultiplexed by 12 bp cell barcode AATTTAGCGAGT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: quetiapine 5 uM, 24 h; adrenaline


title: Cd19_rep1

description: Library name: Cd19_rep1

value: lung


title: mRNA_RIPseq_lin-28(xe197)_input_rep3

description: Library name: Sample 6


title: smallRNA_TC2_WT_37h

description: Library name: Sample 14


title: cardiac organoid; sertraline + adrenaline; well D2

description:
Library name: D2_Sertaline_Adrenaline
iPSC-derived cardiac organoid, plate well D2; demultiplexed by 12 bp cell barcode GACGTCGAGGTT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: sertraline 5 uM, 24 h; adrenaline