title: TNBC7

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Human primary tumor from a non-metastatic TNBC patient

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were rinsed of excess probes in 2X SSCT for 1 min and were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing: Data preprocessing was conducted using the AtoMx Spatial Informatics Platform. Images were segmented to extract the transcript count matrix, cell boundaries (polygons), and corresponding cell metadata. The expression matrices, polygon coordinates, field of view (FOV) coordinates, and cell metadata were exported and loaded into R using LoadNanostring function of Seurat (version 5.0.3) in R 4.3.2. Each sample's raw data was normalized individually using the regularized negative binomial regression model implemented in Seurat SCTransform function. Before normalization, cells with low total transcript counts - based on the distribution of total counts across the dataset - were removed. Cell typing was performed in supervised mode using the insitutypeML function from the InSituType R package (v1.0.0; https://github.com/Nanostring-Biostats/InSituType; Danaher et al., 2022). As inputs, we used reference data from scRNA-seq, expression profiles, spatial context, and morphological features (e.g., cell size, shape, and immunofluorescence intensity for PanCK and CD45) of individual spatial transcriptomic samples. The cell types identified by insitutypeML were then manually refined, incorporating prior knowledge of marker genes specific to certain cell types.

source_name: primary TNBC

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 1:2,000 fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for CosMxTM SMI and tissue staining (IHC IF, ISH).

value: Primary Breast cancer

tag: Sex

value: Female

value: ER-negative, PR-negative, HER2-negative


title: TNBC6

status: Public on Mar 27 2026

type: RNA

description: Human primary tumor from a metastatic TNBC patient

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: napM-deleted biol rep 1

type: SRA

city: Wrocław

first: Kornel

last: Milcarz

address: Fryderyka Joliot-curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wrocław

library_source: transcriptomic

data_processing:
Unzipping the .gz file with gunzip function with Ubuntu Linux command line
seqencing adapter removal with Cutadapt software v.2.8 with parameters set cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -g TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -G AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15 && cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -G TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
Quality trimming was done with Sickle v.1.33 -pe script setting variable parameters as -t sanger -q 20 -l 20
Mapping reads to the reference genome with bowtie2 v.2.3.5.1 in pair end mode -1 -2
Sorting and indexing of the alignemnt files with Samtools v.1.10
Counting reads to features with HTSeq.count v.0.11.2 -t CDS -i Locus -m intersection-nonempty
Count matrix was build in excel by merging the HTSeq.count output files
Assembly: Assembly: NC_008596.1 (Mycolicibacterium smegmatis, MC2_v4.fasta) were used for mapping.
Supplementary files format and content: This file contains a tabular format with genes (MSMEG annotation) as rows and samples as columns. Each cell represents the number of reads mapped to a specific gene in a sample, providing a quantitative measurement of gene expression across all samples.

organism: Mycolicibacterium smegmatis

source_name: Bacterial culture

growth_protocol: 7H9 medium supplemented with 10% ADC and 0,05% Tween 80

extract_protocol:
RNA was isolated with the standard RNA isolation protocol, ribodepletion was performed using riboPools Pan-Bacteria (siTools Biotech GmbH), followed by sequencing library preparation using a KAPA-stranded RNA Seq kit (Roche Diagnostics).
Sequencing libraries were generated with a KAPA-stranded RNA Seq kit, according to the manufacturer's protocol.

value: Bacterial culture

tag: genotype

value: napM deletion


title: Wild type biol rep 2

value: WT


title: TNBC4


title: Wild type biol rep 1


title: TNBC5


title: TNBC3


title: TNBC2


title: TNBC1


title: Wild type biol rep 3


title: Young-Tension-CTRL-ATAC-seq_Replicate2

city: Villigen

last: Shivashankar

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institute

description: Library name: YRC2

library_source: genomic

data_processing:
Briefly, fastq files were trimmed based on adapter sequences by fastp --trim_front1 4 --trim_tail1 0  --average_qual 20 --max_len1 0 --max_len2 0 --trim_poly_x --poly_x_min_len 10 --length_required 30. Bowtie2 was used to align reads to the GRCh38.p13 reference genome with default parameters. Resulting BAM files were filtered to remove PCR duplicates using Picard (version 2.22.8). Mitochondrial reads were removed. ATAC shifts were corrected using alignmentSieve --ATACshift. Peaks were called using macs2 callpeak –bw 200 --keep-dup all --extsize 200 --binSize 10. Macs2 identified peaks from two biological replicates were initially combined using intersection (consensus_intersection). Combined peaks from different biological conditions were further merged using union (consensus_union). Counts tables of reads per peak (within either consensus_intersection or consensus_union) were generated using bam file (from bowtie2) for each sample and pysam package.
Assembly: GRCh38
Supplementary files format and content: peaks.bed

molecule: genomic DNA

growth_protocol: cells were cultured in complete medium consisting of Minimum Essential Medium supplemented with 15% (vol/vol) heat-inactivated fetal bovine serum, 1% nonessential amino acids, 1% GlutaMAX, and 1% penicillin-streptomycin.

extract_protocol: DNA library preparation using the ATAC-Seq Kit (Active Motif)

treatment_protocol: Fibroblasts embedded in the 3D collagen gel, with tension, were cultured in complete medium for 24 hours, followed by starvation in serum-free medium for 24 hours. Subsequently, cells were treated with 10 ng/mL TGF-β in serum-free medium for an additional 24 hours.

tag: cell line

value: primary dermal fibroblast

tag: age

value: young:10 years old

tag: treatment

value: tension without TGFb

tag: batch


title: Young-Tension-CTRL-ATAC-seq_Replicate1

description: Library name: YRC1


title: WT1

city: beijing

first: Hongyue

last: Wang

state: Beijing

address: Mentougou District Fuwai Hospital Western Hills scientific research base

country: China

institute: Fuwai Hospital

description: Library name: sample4

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com). Structure variation detection The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V4.1.2) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: RNA identification Bowtie2[5] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [6]. The heatmap was drawn by pheatmap (v1.0.12) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0）[9] or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001). Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [11].
Supplementary files format and content: all-gene.xls

extract_protocol:
Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: embryonic stem cell


title: Human brain metastasis from a HER2+BC patient

source_name: brain metastasis

value: Brain metastatic Breast cancer

value: 37 years

value: ER-positive, HER2-positive (3+)


title: KO2

description: Library name: sample2


title: Young-Tension-TGFb-ATAC-seq_Replicate1

description: Library name: YRT1

value: tesion with TGFb


title: Old-Tension-CTRL-ATAC-seq_Replicate2

description: Library name: ORC2

value: old:75 years old


title: Old-Tension-TGFb-ATAC-seq_Replicate1

description: Library name: ORT1


title: FUUR1_INPUT

city: Boston

first: Karl

last: Semaan

state: MA

address: Brookline Ave 450

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: FUUR1_INPUT

data_processing:
ChIP-seq and MeDIP-seq reads were aligned to the hg19 human genome build using Burrows–Wheeler Aligner version 0.7.1740. Non-uniquely mapping and redundant reads were discarded. MACS version 2.1.1.2014061641 was used for ChIP-seq peak calling with a q value (false discovery rate (FDR)) threshold of 0.01. Fragment locations were converted to BED files using BEDTools (version 2.29.2) bamtobed with the -bedpe flag set. For analyses involving overlap with genomic regions, fragments were imported as GRanges objects and collapsed to 1 bp at the center of the fragment location to ensure that a fragment can map to only one site. LPWGS data were used to estimate ctDNA using ichorCNA with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
MeDIP was performed using the MagMeDIP kit from Diagenode.Samples were purified using the iPure Kit v2 from Diagenode
ChIP-seq libraries were generated from purified input and IP sample DNA using the ThruPLEX DNA-seq Kit from TakaraBio. Libraries were sequenced using 150-base paired-end reads on an Illumina platform. MeDIP-Seq libraries were generated using the KAPA HyperPrep Kit, complemented by end-repair, A-tailing, and ligation of NEBNext adaptors. 10 ng of DNA was used as starting material.Libraries were sequenced using 150-base paired-end reads on an Illumina platform.

tag: immunoprecipitation and_sequencing

value: INPUT

tag: genome build


title: UOK146_INPUT

description: Library name: UOK146_INPUT


title: Old-Tension-CTRL-ATAC-seq_Replicate1

description: Library name: ORC1


title: UOK146_H3K4me3

description: Library name: UOK146_H3K4me3

value: H3K4me3 ChIP-seq


title: FUUR1_H3K4me3

description: Library name: FUUR1_H3K4me3


title: cm_ipsc_Lysate_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description: Library name: cm_ipsc_Lysate_3_MKDL250010856-1A_22YHCGLT4_L3

data_processing:
Deduplication via czid-dedup (paired-end mode)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

molecule: polyA RNA

source_name: not applicable

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

value: not applicable

value: iPSC-derived cardiomyocyte differentiation sample

tag: rna origin

value: Lysate

value: iPSC lysate baseline


title: TNBC8

value: Primary Breast cancer

value: Female

value: ER-negative, PR-negative, HER2-negative


title: sTFE_INPUT

description: Library name: sTFE_INPUT

source_name: sTFE

value: sTFE


title: cm_ipsc_1_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_1_3_MKDL250010856-1A_22YHCGLT4_L3


title: Young-Tension-TGFb-ATAC-seq_Replicate2

description: Library name: YRT2

value: primary dermal fibroblast

value: young:10 years old


title: cm_ipsc_2_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_2_3_MKDL250010856-1A_22YHCGLT4_L3


title: Old-Tension-TGFb-ATAC-seq_Replicate2

description: Library name: ORT2


title: iPSC cardiodiff lysate control rep1

description:
Library name: cm_ipsc_Lysate_1_MKDL250010856-1A_22YHCGLT4_L3
iPSC lysate control for cardiomyocyte differentiation, replicate 1


title: cm_ipsc_2_1_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_2_1_MKDL250010856-1A_22YHCGLT4_L3


title: cm_ipsc_1_1_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_1_1_MKDL250010856-1A_22YHCGLT4_L3


title: cm_ipsc_1_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_1_2_MKDL250010856-1A_22YHCGLT4_L3


title: cm_ipsc_0_1_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_0_1_MKDL250010856-1A_22YHCGLT4_L3


title: cm_cm_lysate_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_cm_lysate_3_MKDL250010856-1A_22YHCGLT4_L3

value: CM lysate baseline


title: cm_9_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 9 rep 3

description: Library name: cm_9_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=9; time=9; replicate=3


title: cm_cm_lysate_1_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_cm_lysate_1_MKDL250010856-1A_22YHCGLT4_L3


title: cm_ipsc_Lysate_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_Lysate_2_MKDL250010856-1A_22YHCGLT4_L3


title: cm_9_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 9 rep 2

description: Library name: cm_9_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=9; time=9; replicate=2


title: cm_cm_lysate_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_cm_lysate_2_MKDL250010856-1A_22YHCGLT4_L3


title: sTFE_H3K4me3

description: Library name: sTFE_H3K4me3


title: cm_8_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 8 rep 2

description: Library name: cm_8_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=8; time=8; replicate=2


title: cm_9_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 9 rep 1

description: Library name: cm_9_1_MKDL250010856-1A_22YHCGLT4_L3

value: day=9; time=9; replicate=1


title: cm_ipsc_2_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_2_2_MKDL250010856-1A_22YHCGLT4_L3


title: cm_8_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 8 rep 3

description: Library name: cm_8_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=8; time=8; replicate=3


title: cm_6_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 6 rep 3

description: Library name: cm_6_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=6; time=6; replicate=3


title: cm_8_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 8 rep 1

description: Library name: cm_8_1_MKDL250010856-1A_22YHCGLT4_L3

value: not applicable

value: day=8; time=8; replicate=1


title: cm_6_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 6 rep 1

description: Library name: cm_6_1_MKDL250010856-1A_22YHCGLT4_L3

value: iPSC-derived cardiomyocyte differentiation sample

value: Lysate

value: day=6; time=6; replicate=1


title: cm_6_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 6 rep 2

description: Library name: cm_6_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=6; time=6; replicate=2


title: cm_ipsc_0_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_0_2_MKDL250010856-1A_22YHCGLT4_L3

value: iPSC lysate baseline


title: cm_5_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 5 rep 2

description: Library name: cm_5_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=5; time=5; replicate=2


title: cm_7_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 7 rep 3

description: Library name: cm_7_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=7; time=7; replicate=3


title: cm_5_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 5 rep 1

description: Library name: cm_5_1_MKDL250010856-1A_22YHCGLT4_L3

value: day=5; time=5; replicate=1


title: cm_7_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 7 rep 2

description: Library name: cm_7_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=7; time=7; replicate=2


title: cm_4_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 4 rep 3

description: Library name: cm_4_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=4; time=4; replicate=3


title: cm_5_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 5 rep 3

description: Library name: cm_5_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=5; time=5; replicate=3


title: cm_4_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 4 rep 2

description: Library name: cm_4_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=4; time=4; replicate=2


title: cm_ipsc_0_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_ipsc_0_3_MKDL250010856-1A_22YHCGLT4_L3


title: cm_4_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 4 rep 1

description: Library name: cm_4_1_MKDL250010856-1A_22YHCGLT4_L3

value: day=4; time=4; replicate=1


title: cm_7_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 7 rep 1

description: Library name: cm_7_1_MKDL250010856-1A_22YHCGLT4_L3

value: day=7; time=7; replicate=1


title: cm_3_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 3 rep 2

description: Library name: cm_3_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=3; time=3; replicate=2


title: cm_3_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 3 rep 3

description: Library name: cm_3_3_MKDL250010856-1A_22YHCGLT4_L3

value: not applicable

value: day=3; time=3; replicate=3


title: cm_3_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 3 rep 1

description: Library name: cm_3_1_MKDL250010856-1A_22YHCGLT4_L3

value: iPSC-derived cardiomyocyte differentiation sample

value: day=3; time=3; replicate=1


title: cm_2_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 2 rep 1

description: Library name: cm_2_1_MKDL250010856-1A_22YHCGLT4_L3

value: Lysate

value: day=2; time=2; replicate=1


title: cm_2_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 2 rep 3

description: Library name: cm_2_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=2; time=2; replicate=3


title: cm_2_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 2 rep 2

description: Library name: cm_2_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=2; time=2; replicate=2


title: cm_1_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 1 rep 1

description: Library name: cm_1_1_MKDL250010856-1A_22YHCGLT4_L3

value: day=1; time=1; replicate=1


title: cm_1_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 1 rep 2

description: Library name: cm_1_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=1; time=1; replicate=2


title: cm_1_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 1 rep 3

description: Library name: cm_1_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=1; time=1; replicate=3


title: cm_10_2_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_10_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=10; time=10; after end of differentiation experiment


title: cm_0_2_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 0 rep 2

description: Library name: cm_0_2_MKDL250010856-1A_22YHCGLT4_L3

value: day=0; time=0; replicate=2


title: cm_0_3_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 0 rep 3

description: Library name: cm_0_3_MKDL250010856-1A_22YHCGLT4_L3

value: day=0; time=0; replicate=3


title: SN_S5_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag:MCP; replicate=3

description: Library name: SN_S5_3_MKDL250005004-1A_22VVM5LT4_L5

value: immortalized cell line

value: HEK-293T based construct background

value: Supernatant


title: SN_S5_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag:MCP; replicate=2

description: Library name: SN_S5_2_MKDL250005004-1A_22VVM5LT4_L5

value: not applicable


title: SN_S6_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NLuc; replicate=1

description: Library name: SN_S6_1_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NLuc; replicate=1


title: SN_S6_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NLuc; replicate=2

description: Library name: SN_S6_2_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NLuc; replicate=2


title: SN_S5_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag:MCP; replicate=1

description: Library name: SN_S5_1_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S4_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=MMLV-gag WT; replicate=3

description: Library name: SN_S4_3_MKDL250005004-1A_22VVM5LT4_L5


title: cm_0_1_MKDL250010856-1A_22YHCGLT4_L3 | Cardiodiff day 0 rep 1

description: Library name: cm_0_1_MKDL250010856-1A_22YHCGLT4_L3

value: iPSC-derived cardiomyocyte differentiation sample

value: day=0; time=0; replicate=1


title: SN_S3_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=TRACE-seq; replicate=3

description: Library name: SN_S3_3_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S4_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=MMLV-gag WT; replicate=1

description: Library name: SN_S4_1_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S3_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=TRACE-seq; replicate=1

description: Library name: SN_S3_1_MKDL250005004-1A_22VVM5LT4_L5


title: cm_10_1_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_10_1_MKDL250010856-1A_22YHCGLT4_L3

value: Lysate


title: SN_S2_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag WT; replicate=1

description: Library name: SN_S2_1_MKDL250005004-1A_22VVM5LT4_L5


title: cm_10_3_MKDL250010856-1A_22YHCGLT4_L3 | 2025-09-01_Novogene_Cardiodiff

description: Library name: cm_10_3_MKDL250010856-1A_22YHCGLT4_L3


title: SN_S1_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NTVE; replicate=3

description: Library name: SN_S1_3_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NTVE; replicate=3


title: SN_S3_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=TRACE-seq; replicate=2

description: Library name: SN_S3_2_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S4_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=MMLV-gag WT; replicate=2

description: Library name: SN_S4_2_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S2_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag WT; replicate=3

description: Library name: SN_S2_3_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S1_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NTVE; replicate=1

description: Library name: SN_S1_1_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NTVE; replicate=1


title: SN_S1_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NTVE; replicate=2

description: Library name: SN_S1_2_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NTVE; replicate=2


title: SN_S6_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=NLuc; replicate=3

description: Library name: SN_S6_3_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NLuc; replicate=3


title: Pulldown_S4_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=MMLV-gag WT; replicate=3

description: Library name: Pulldown_S4_3_MKDL250005004-1A_22VVM5LT4_L5

value: Pulldown


title: Pulldown_S4_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=MMLV-gag WT; replicate=2

description: Library name: Pulldown_S4_2_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S4_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=MMLV-gag WT; replicate=1

description: Library name: Pulldown_S4_1_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S3_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=TRACE-seq; replicate=3

description: Library name: Pulldown_S3_3_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S3_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=TRACE-seq; replicate=2

description: Library name: Pulldown_S3_2_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S2_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=HIV-gag WT; replicate=1

description: Library name: Pulldown_S2_1_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S3_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=TRACE-seq; replicate=1

description: Library name: Pulldown_S3_1_MKDL250005004-1A_22VVM5LT4_L5


title: SN_S2_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz supernatant; RNA export modality=HIV-gag WT; replicate=2

description: Library name: SN_S2_2_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S2_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=HIV-gag WT; replicate=2

description: Library name: Pulldown_S2_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S6_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NLuc; replicate=2

description: Library name: Lysate_S6_2_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S1_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=NTVE; replicate=3

description: Library name: Pulldown_S1_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S5_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag:MCP; replicate=3

description: Library name: Lysate_S5_3_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S1_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=NTVE; replicate=2

description: Library name: Pulldown_S1_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S5_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag:MCP; replicate=2

description: Library name: Lysate_S5_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S3_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=TRACE-seq; replicate=2

description: Library name: Lysate_S3_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S5_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag:MCP; replicate=1

description: Library name: Lysate_S5_1_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S1_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=NTVE; replicate=1

description: Library name: Pulldown_S1_1_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S3_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=TRACE-seq; replicate=3

description: Library name: Lysate_S3_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S4_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=MMLV-gag WT; replicate=2

description: Library name: Lysate_S4_2_MKDL250005004-1A_22VVM5LT4_L5


title: Pulldown_S2_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz pulldown; RNA export modality=HIV-gag WT; replicate=3

description: Library name: Pulldown_S2_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S4_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=MMLV-gag WT; replicate=1

description: Library name: Lysate_S4_1_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S4_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=MMLV-gag WT; replicate=3

description: Library name: Lysate_S4_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S2_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag WT; replicate=3

description: Library name: Lysate_S2_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S3_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=TRACE-seq; replicate=1

description: Library name: Lysate_S3_1_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S2_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag WT; replicate=2

description: Library name: Lysate_S2_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S1_2_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NTVE; replicate=2

description: Library name: Lysate_S1_2_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S1_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NTVE; replicate=1

description: Library name: Lysate_S1_1_MKDL250005004-1A_22VVM5LT4_L5


title: ISBM-083 + doxycycline rep2

description:
Library name: ISBM_083_DOX_rep2_MKDL250005004-1A_22VVM5LT4_L5
Stable NTVE line ISBM-083, doxycycline induced, replicate 2

value: 500 ng/ml doxycycline


title: ISBM-083 + doxycycline rep3

description:
Library name: ISBM_083_DOX_rep3_MKDL250005004-1A_22VVM5LT4_L5
Stable NTVE line ISBM-083, doxycycline induced, replicate 3


title: Lysate_S6_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NLuc; replicate=3

description: Library name: Lysate_S6_3_MKDL250005004-1A_22VVM5LT4_L5


title: Lysate_S2_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=HIV-gag WT; replicate=1

description: Library name: Lysate_S2_1_MKDL250005004-1A_22VVM5LT4_L5


title: L_ec_9 | Trilineage ectoderm lysate; day 7; clone 9; dox 50 ng/ul

description: Library name: L_ec_9

value: ectoderm

value: Dox=50 ng/ul; day=7; clone=9


title: L_mes_9 | Trilineage mesoderm lysate; day 7; clone 9; dox 50 ng/ul

description: Library name: L_mes_9

value: mesoderm


title: ISBM-083 + doxycycline rep1

description:
Library name: ISBM_083_DOX_rep1_MKDL250005004-1A_22VVM5LT4_L5
Stable NTVE line ISBM-083, doxycycline induced, replicate 1

value: immortalized cell line


title: Lysate_S1_3_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NTVE; replicate=3

description: Library name: Lysate_S1_3_MKDL250005004-1A_22VVM5LT4_L5

value: HEK-293T based construct background


title: L_IPSC_9 | Trilineage ipsc lysate; day 7; clone 16; dox 50 ng/ul

description: Library name: L_IPSC_9

value: not applicable

value: IPSC

value: Dox=50 ng/ul; day=7; clone=16


title: Lysate_S6_1_MKDL250005004-1A_22VVM5LT4_L5 | Elowitz lysate; RNA export modality=NLuc; replicate=1

description: Library name: Lysate_S6_1_MKDL250005004-1A_22VVM5LT4_L5

value: RNA export modality=NLuc; replicate=1


title: L_en_6 | Trilineage endoderm lysate; day 7; clone 6; dox 50 ng/ul

description: Library name: L_en_6

value: endoderm

value: Dox=50 ng/ul; day=7; clone=6


title: L_en_9 | Trilineage endoderm lysate; day 7; clone 9; dox 50 ng/ul

description: Library name: L_en_9

value: Lysate


title: L_IPSC_6 | Trilineage ipsc lysate; day 7; clone 6; dox 50 ng/ul

description: Library name: L_IPSC_6


title: iPSC iPSC lysate clone 16.0 high dox

description:
Library name: L_IPSC_16_dox
iPSC tri-lineage differentiation, iPSC, clone 16.0

value: iPSC

value: Dox=50 ng/ul; day=0; clone=16


title: L_IPSC_wt | Trilineage ipsc lysate; day 7; dox 50 ng/ul

description: Library name: L_IPSC_wt

value: SCTi003-A WT

value: Dox=50 ng/ul; day=7


title: L_ec_16_dox | Trilineage ectoderm lysate; day 7; clone 16; dox 500 ng/ul

description: Library name: L_ec_16_dox

value: Dox=500 ng/ul; day=7; clone=16


title: SN_ec_d4_16_dox | Trilineage ectoderm supernatant; day 4; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d4_16_dox

value: ectoderm

value: Supernatant

value: Dox=500 ng/ul; day=4; clone=16


title: L_mes_wt | Trilineage mesoderm lysate; day 7; dox 50 ng/ul

description: Library name: L_mes_wt

value: mesoderm


title: L_en_wt | Trilineage endoderm lysate; day 7; dox 50 ng/ul

description: Library name: L_en_wt


title: SN_ec_d7_16_dox | Trilineage ectoderm supernatant; day 7; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d7_16_dox


title: SN_ec_d5_16_dox | Trilineage ectoderm supernatant; day 5; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d5_16_dox

value: Dox=500 ng/ul; day=5; clone=16


title: SN_ec_d6_16_dox | Trilineage ectoderm supernatant; day 6; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d6_16_dox

value: not applicable

value: Dox=500 ng/ul; day=6; clone=16


title: SN_ec_d3_16_dox | Trilineage ectoderm supernatant; day 3; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d3_16_dox

value: Dox=500 ng/ul; day=3; clone=16


title: L_ec_6 | Trilineage ectoderm lysate; day 7; clone 6; dox 50 ng/ul

description: Library name: L_ec_6


title: L_mes_6 | Trilineage mesoderm lysate; day 7; clone 6; dox 50 ng/ul

description: Library name: L_mes_6


title: SN_IPSC_6 | Trilineage ipsc supernatant; clone 6; dox 50 ng/ul

description: Library name: SN_IPSC_6

value: IPSC

value: Dox=50 ng/ul; clone=6


title: SN_en_d7_9 | Trilineage endoderm supernatant; day 7; clone 9; dox 50 ng/ul

description: Library name: SN_en_d7_9

value: endoderm

value: Dox=50 ng/ul; day=7; clone=9


title: L_ec_wt | Trilineage ectoderm lysate; day 7; dox 50 ng/ul

description: Library name: L_ec_wt

value: Lysate


title: L_en_16 | Trilineage endoderm lysate; day 7; clone 16; dox 50 ng/ul

description: Library name: L_en_16

value: Dox=50 ng/ul; day=7; clone=16


title: L_IPSC_16 | Trilineage ipsc lysate; day 7; clone 16; dox 50 ng/ul

description: Library name: L_IPSC_16


title: SN_IPSC_16 | Trilineage ipsc supernatant; clone 16; dox 50 ng/ul

description: Library name: SN_IPSC_16

value: Dox=50 ng/ul; clone=16


title: SN_en_d7_16 | Trilineage endoderm supernatant; day 7; clone 16; dox 50 ng/ul

description: Library name: SN_en_d7_16


title: SN_IPSC_9 | Trilineage ipsc supernatant; clone 9; dox 50 ng/ul

description: Library name: SN_IPSC_9

value: Dox=50 ng/ul; clone=9


title: SN_mes_d7_16 | Trilineage mesoderm supernatant; day 7; clone 16; dox 50 ng/ul

description: Library name: SN_mes_d7_16


title: SN_ec_d1_16_dox | Trilineage ectoderm supernatant; day 1; clone 16; dox 500 ng/ul

description: Library name: SN_ec_d1_16_dox

value: Dox=500 ng/ul; day=1; clone=16


title: SN_mes_d7_9 | Trilineage mesoderm supernatant; day 7; clone 9; dox 50 ng/ul

description: Library name: SN_mes_d7_9


title: L_mes_16 | Trilineage mesoderm lysate; day 7; clone 16; dox 50 ng/ul

description: Library name: L_mes_16


title: SN_ec_d7_6 | Trilineage ectoderm supernatant; day 7; clone 6; dox 50 ng/ul

description: Library name: SN_ec_d7_6

value: ectoderm

value: Dox=50 ng/ul; day=7; clone=6


title: SN_mes_d6_16 | Trilineage mesoderm supernatant; day 6; clone 16; dox 50 ng/ul

description: Library name: SN_mes_d6_16

value: Supernatant

value: Dox=50 ng/ul; day=6; clone=16


title: SN_en_d6_16 | Trilineage endoderm supernatant; day 6; clone 16; dox 50 ng/ul

description: Library name: SN_en_d6_16


title: SN_ec_d7_16 | Trilineage ectoderm supernatant; day 7; clone 16; dox 50 ng/ul

description: Library name: SN_ec_d7_16


title: SN_en_d7_6 | Trilineage endoderm supernatant; day 7; clone 6; dox 50 ng/ul

description: Library name: SN_en_d7_6


title: SN_ec_d7_9 | Trilineage ectoderm supernatant; day 7; clone 9; dox 50 ng/ul

description: Library name: SN_ec_d7_9


title: SN_mes_d7_6 | Trilineage mesoderm supernatant; day 7; clone 6; dox 50 ng/ul

description: Library name: SN_mes_d7_6

value: mesoderm


title: SN_en_d6_9 | Trilineage endoderm supernatant; day 6; clone 9; dox 50 ng/ul

description: Library name: SN_en_d6_9

value: not applicable

value: Dox=50 ng/ul; day=6; clone=9


title: SN_ec_d6_16 | Trilineage ectoderm supernatant; day 6; clone 16; dox 50 ng/ul

description: Library name: SN_ec_d6_16


title: iPSC endoderm supernatant day 6.0 clone 6.0

description:
Library name: SN_en_d6_6
iPSC tri-lineage differentiation, endoderm, clone 6.0

value: Dox=50 ng/ul; day=6; clone=6


title: SN_mes_d5_16 | Trilineage mesoderm supernatant; day 5; clone 16; dox 50 ng/ul

description: Library name: SN_mes_d5_16

value: Dox=50 ng/ul; day=5; clone=16


title: SN_en_d5_16 | Trilineage endoderm supernatant; day 5; clone 16; dox 50 ng/ul

description: Library name: SN_en_d5_16


title: SN_mes_d6_9 | Trilineage mesoderm supernatant; day 6; clone 9; dox 50 ng/ul

description: Library name: SN_mes_d6_9


title: SN_ec_d6_9 | Trilineage ectoderm supernatant; day 6; clone 9; dox 50 ng/ul

description: Library name: SN_ec_d6_9


title: SN_ec_d5_16 | Trilineage ectoderm supernatant; day 5; clone 16; dox 50 ng/ul

description: Library name: SN_ec_d5_16


title: L_ec_16 | Trilineage ectoderm lysate; day 7; clone 16; dox 50 ng/ul

description: Library name: L_ec_16


title: SN_mes_d6_6 | Trilineage mesoderm supernatant; day 6; clone 6; dox 50 ng/ul

description: Library name: SN_mes_d6_6


title: SN_mes_d5_9 | Trilineage mesoderm supernatant; day 5; clone 9; dox 50 ng/ul

description: Library name: SN_mes_d5_9

value: Dox=50 ng/ul; day=5; clone=9


title: SN_en_d5_6 | Trilineage endoderm supernatant; day 5; clone 6; dox 50 ng/ul

description: Library name: SN_en_d5_6

value: endoderm

value: Dox=50 ng/ul; day=5; clone=6


title: SN_ec_d5_6 | Trilineage ectoderm supernatant; day 5; clone 6; dox 50 ng/ul

description: Library name: SN_ec_d5_6


title: SN_en_d2_6 | Trilineage endoderm supernatant; day 2; clone 6; dox 50 ng/ul

description: Library name: SN_en_d2_6

value: Dox=50 ng/ul; day=2; clone=6


title: SN_ec_d1_16 | Trilineage ectoderm supernatant; day 1; clone 16; dox 50 ng/ul

description: Library name: SN_ec_d1_16

value: Dox=50 ng/ul; day=1; clone=16


title: SN_en_d2_16 | Trilineage endoderm supernatant; day 2; clone 16; dox 50 ng/ul

description: Library name: SN_en_d2_16

value: Dox=50 ng/ul; day=2; clone=16


title: SN_ec_d2_16 | Trilineage ectoderm supernatant; day 2; clone 16; dox 50 ng/ul

description: Library name: SN_ec_d2_16


title: SN_ec_d5_9 | Trilineage ectoderm supernatant; day 5; clone 9; dox 50 ng/ul

description: Library name: SN_ec_d5_9


title: SN_mes_d2_16 | Trilineage mesoderm supernatant; day 2; clone 16; dox 50 ng/ul

description: Library name: SN_mes_d2_16


title: SN_mes_d2_9 | Trilineage mesoderm supernatant; day 2; clone 9; dox 50 ng/ul

description: Library name: SN_mes_d2_9

value: Dox=50 ng/ul; day=2; clone=9


title: SN_en_d1_16 | Trilineage endoderm supernatant; day 1; clone 16; dox 50 ng/ul

description: Library name: SN_en_d1_16


title: SN_mes_d1_16 | Trilineage mesoderm supernatant; day 1; clone 16; dox 50 ng/ul

description: Library name: SN_mes_d1_16


title: SN_ec_d1_9 | Trilineage ectoderm supernatant; day 1; clone 9; dox 50 ng/ul

description: Library name: SN_ec_d1_9

value: Dox=50 ng/ul; day=1; clone=9


title: SN_mes_d5_6 | Trilineage mesoderm supernatant; day 5; clone 6; dox 50 ng/ul

description: Library name: SN_mes_d5_6


title: SN_mes_d1_9 | Trilineage mesoderm supernatant; day 1; clone 9; dox 50 ng/ul

description: Library name: SN_mes_d1_9


title: SN_en_d2_9 | Trilineage endoderm supernatant; day 2; clone 9; dox 50 ng/ul

description: Library name: SN_en_d2_9


title: SN_mes_d2_6 | Trilineage mesoderm supernatant; day 2; clone 6; dox 50 ng/ul

description: Library name: SN_mes_d2_6


title: 25L008111 | 48h post-tx, HEK wt, L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008111

value: immortalized cell line

value: Lysate

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)


title: SN_ec_d2_6 | Trilineage ectoderm supernatant; day 2; clone 6; dox 50 ng/ul

description: Library name: SN_ec_d2_6

value: ectoderm

value: Supernatant


title: SN_mes_d1_6 | Trilineage mesoderm supernatant; day 1; clone 6; dox 50 ng/ul

description: Library name: SN_mes_d1_6

value: not applicable

value: mesoderm

value: Dox=50 ng/ul; day=1; clone=6


title: SN_en_d5_9 | Trilineage endoderm supernatant; day 5; clone 9; dox 50 ng/ul

description: Library name: SN_en_d5_9


title: SN_ec_d2_9 | Trilineage ectoderm supernatant; day 2; clone 9; dox 50 ng/ul

description: Library name: SN_ec_d2_9


title: 25L008107 | 48h post-tx, HEK wt, L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008107


title: SN_ec_d1_6 | Trilineage ectoderm supernatant; day 1; clone 6; dox 50 ng/ul

description: Library name: SN_ec_d1_6


title: SN_en_d1_9 | Trilineage endoderm supernatant; day 1; clone 9; dox 50 ng/ul

description: Library name: SN_en_d1_9


title: 25L008106 | 48h post-tx, HEK wt, GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM

description: Library name: 25L008106

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM


title: 25L008110 | 48h post-tx, HEK wt, GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM

description: Library name: 25L008110


title: SN_en_d1_6 | Trilineage endoderm supernatant; day 1; clone 6; dox 50 ng/ul

description: Library name: SN_en_d1_6


title: 25L008104 | 48h post-tx, HEK wt, GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM

description: Library name: 25L008104


title: 25L008103 | 48h post-tx, HEK wt, L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008103


title: 25L008105 | 48h post-tx, HEK wt, L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008105


title: 25L008102 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008102

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L1083_pPGK_NLuc-PEST-bpA


title: 25L008100 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008100


title: 25L008101 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008101


title: 25L008098 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008098

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA


title: 25L008099 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008099


title: 25L008093 | 48h post-tx, HEK wt, GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM

description: Library name: 25L008093


title: 25L008094 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008094

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L687_pPGK2_mGag-L21S_(codon_optimized)


title: 25L008090 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008090

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM


title: 25L008092 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008092


title: 25L008088 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008088

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)


title: 25L008091 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008091


title: 25L008085 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008085


title: 25L008087 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008087


title: 25L008082 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008082


title: 25L008084 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008084


title: 25L008095 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008095


title: 25L008081 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008081


title: P60_BRAINSTEM_PLANE_REP3

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description:
Library name: Visium_389-C1
Fresh frozen spatial transcriptomics

data_processing:
Gene expression matrices were generated using SpaceRanger v2.1.0 (10x Genomics) using the GRCm39-2024-A as the reference genome.
For each slice processed with 10x Visium, we used the data included in the “outs” of the SpaceRanger analysis; the raw count matrix (raw_feature_bc_matrix.h5), tissue image (tissue_hires_image.png) and spatial information (tissue_positions.csv and scalefactors_json.json) were used as inputs for analysis.
Assembly: GRCm39-2024-A
Supplementary files format and content: tissue_positions.csv = list of spatial barcodes and coordinates specifying spots
Supplementary files format and content: tissue_lowres_image.png = low res image of tissue
Supplementary files format and content: tissue_hires_image.png = high res image of tissue
Supplementary files format and content: spatial_enrichment.csv = File in CSV format that contains table of Moran's I values for each feature.
Supplementary files format and content: scalefactors_json.json = scalefactor in json format
Supplementary files format and content: raw_feature_bc_matrix.h5 = raw matrix containg barcodes, features and counts om h5 format
Supplementary files format and content: filtered_feature_bc_matrix.h5 = filtered matrix containg barcodes, features and counts om h5 format
Supplementary files format and content: detected_tissue_image.jpg = image of tissue and spots
Supplementary files format and content: aligned_fiducials.jpg = aligned fiducial of the tissue image
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: Brain

growth_protocol: We used brains of male C57BL/6J mice on postnatal day 5, 7, 9, 12, 21, and 60.

extract_protocol:
The brains were simultaneously embedded in OCT compound and frozen for cryo-sectioning at a thickness of 10μm. The tissue preparation followed the protocol provided by the company 10X Genomics more specifically using the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Reagent Kits (catalog numbers 1000193 and 1000187). Brain sections were done on 3 different planes (anterior, thalamic and brainstem planes). The brain sections were thus placed on TO and GEX slides, and then stored at -80°C until further processing. The TO and GEX slides were then fixed in methanol and stained with hematoxylin and eosin (H&E). This helped with tissue morphology visualization using an automated slide scanner (Zeiss Axioscan.Z1). Tissue permeabilization time was optimized using the TO slides, and 30 minutes was selected as the ideal duration. The GEX slides were incubated with reverse transcription reagents (RT) and then followed a cDNA amplification of 15 cycles.
The library construction was performed according to the manufacturer’s protocol. This included steps of cDNA fragmentation, end repair, A-tailing, adaptor ligation, and sample indexing and amplification. A Bioanalyzer (Agilent) assessed the quality control of the constructed libraries. Finally, the Illumina NovaSeq S4 platform by Genome Quebec performed the sequencing. Genome Quebec also completed the base calling, demultiplexing, and FastQ file generation.

value: Brain

tag: brain region

value: BRAINSTEM PLANE

value: male


title: SN_ec_d6_6 | Trilineage ectoderm supernatant; day 6; clone 6; dox 50 ng/ul

description: Library name: SN_ec_d6_6

value: Dox=50 ng/ul; day=6; clone=6


title: 25L008097 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008097

value: immortalized cell line

value: Lysate


title: 25L008089 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008089


title: 25L008083 | 48h post-tx, HEK wt, L1083_pPGK_NLuc-PEST-bpA

description: Library name: 25L008083


title: 25L008086 | 48h post-tx, HEK wt, L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008086

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with L1716_pPGK2_Gag(no-myrist_L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)


title: P9_ANTERIOR_PLANE_REP3

description:
Library name: Visium_389-D1
Fresh frozen spatial transcriptomics

value: ANTERIOR PLANE


title: P60_ANTERIOR_PLANE_REP3

description:
Library name: Visium_389-A1
Fresh frozen spatial transcriptomics


title: P60_THALAMIC_PLANE_REP2

description:
Library name: Visium_389-B1
Fresh frozen spatial transcriptomics

value: THALAMIC PLANE


title: 25L008080 | 48h post-tx, HEK wt, L1691.1_pPGK2_minigag-L21S(ZF1(C_S)-ZF2)_HiBit-PABP-bGH-pA

description: Library name: 25L008080

value: not applicable

value: Supernatant


title: 25L008078 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008078


title: 25L008077 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008077


title: P12_THALAMIC_PLANE_REP3

description:
Library name: Visium_323-D1
Fresh frozen spatial transcriptomics


title: P12_BRAINSTEM_PLANE_REP3

description:
Library name: Visium_323-C1
Fresh frozen spatial transcriptomics


title: 25L008079 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008079


title: 25L008096 | 48h post-tx, HEK wt, L687_pPGK2_mGag-L21S_(codon_optimized)

description: Library name: 25L008096


title: 25L008075 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008075


title: P7_THALAMIC_PLANE_REP2

description:
Library name: Visium_323-B1
Fresh frozen spatial transcriptomics


title: 25L008076 | 48h post-tx, HEK wt, GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM

description: Library name: 25L008076

value: sampled 48h post transfection, 24h post media change, 10%FCS DMEM with PS Pip Cip GM, HEK wt, transfected with GA2469_pPGK2_mGag-L21S_(codon_optimized)_NC-sPAM


title: P7_ANTERIOR_PLANE_REP3

description:
Library name: Visium_323-A1
Fresh frozen spatial transcriptomics


title: 25L008072 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008072


title: P5_BRAINSTEM_PLANE_REP3

description:
Library name: Visium_303-C1
Fresh frozen spatial transcriptomics


title: P5_ANTERIOR_PLANE_REP3

description:
Library name: Visium_303-B1
Fresh frozen spatial transcriptomics


title: 25L008074 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008074


title: P21_BRAINSTEM_PLANE_REP2

description:
Library name: Slide-5_V14S03-315C1
Fresh frozen spatial transcriptomics


title: 25L008070 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008070


title: HEK-293T technical control, replicate 4

description:
Library name: 25L000352
Technical control; library prep conditions: RT19c, Tn5(8min), PCR(19c)

value: HEK-293T based construct background


title: HEK-293T technical control, replicate 2

description:
Library name: 25L000350
Technical control; library prep conditions: RT19c, Tn5(8min), PCR(19c)


title: 25L008071 | 48h post-tx, HEK wt, L1593_pPGK2_Gag(L21S+ZF)-GCN4-HiBit-PABP(RRM1-2_M161A)

description: Library name: 25L008071


title: P21_ANTERIOR_PLANE_REP1

description:
Library name: Slide-5_V14S03-315D1
Fresh frozen spatial transcriptomics


title: HEK-293T technical control, replicate 3

description:
Library name: 25L000351
Technical control; library prep conditions: RT19c, Tn5(8min), PCR(19c)


title: P21_ANTERIOR_PLANE_REP2

description:
Library name: Slide-5_V14S03-315A1
Fresh frozen spatial transcriptomics


title: P5_THALAMIC_PLANE_REP3

description:
Library name: Visium_303-D1
Fresh frozen spatial transcriptomics


title: HEK-293T technical control, replicate 1

description:
Library name: 25L000349
Technical control; library prep conditions: RT19c, Tn5(8min), PCR(19c)


title: 25L008073 | 48h post-tx, HEK wt, GA2468_pPGK2_mGag-L21S_(codon_optimized)_sPAM

description: Library name: 25L008073


title: P21_BRAINSTEM_PLANE_REP1

description:
Library name: Slide-4_V14B09-293B1
Fresh frozen spatial transcriptomics


title: P7_BRAINSTEM_PLANE_REP2

description:
Library name: Slide-4_V14B09-293D1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-17 lysate, +dox, replicate 3

description: Library name: 25L000348

value: doxycycline 500ng/ul


title: HEK-293T ISBM-17 lysate, +dox, replicate 1

description: Library name: 25L000346


title: HEK-293T ISBM-17 lysate, +dox, replicate 2

description: Library name: 25L000347


title: P12_ANTERIOR_PLANE_REP3

description:
Library name: Visium_303-A1
Fresh frozen spatial transcriptomics


title: P5_ANTERIOR_PLANE_REP2

description:
Library name: Slide-3_V14B09-295B1
Fresh frozen spatial transcriptomics


title: P21_THALAMIC_PLANE_REP1

description:
Library name: Slide-4_V14B09-293A1
Fresh frozen spatial transcriptomics


title: P21_THALAMIC_PLANE_REP2

description:
Library name: Slide-5_V14S03-315B1
Fresh frozen spatial transcriptomics


title: P60_BRAINSTEM_PLANE_REP2

description:
Library name: Slide-3_V14B09-295C1
Fresh frozen spatial transcriptomics


title: P5_BRAINSTEM_PLANE_REP2

description:
Library name: Slide-3_V14B09-295A1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-17 lysate, no dox, replicate 3

description: Library name: 25L000345

value: no doxycycline


title: HEK-293T ISBM-17 lysate, no dox, replicate 1

description: Library name: 25L000343


title: P60_ANTERIOR_PLANE_REP1

description:
Library name: Slide-2_V14B09-294D1
Fresh frozen spatial transcriptomics


title: P60_THALAMIC_PLANE_REP1

description:
Library name: Slide-2_V14B09-294C1
Fresh frozen spatial transcriptomics


title: HEK-293T WT lysate, +dox, replicate 1

description: Library name: 25L000340

value: HEK-293T WT


title: P60_ANTERIOR_PLANE_REP2

description:
Library name: Slide-2_V14B09-294A1
Fresh frozen spatial transcriptomics


title: HEK-293T WT lysate, no dox, replicate 1

description: Library name: 25L000337


title: HEK-293T WT lysate, +dox, replicate 3

description: Library name: 25L000342


title: HEK-293T WT lysate, +dox, replicate 2

description: Library name: 25L000341


title: P60_BRAINSTEM_PLANE_REP1

description:
Library name: Slide-2_V14B09-294B1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-83 lysate, +dox, replicate 2

description: Library name: 25L000335


title: HEK-293T ISBM-83 lysate, +dox, replicate 1

description: Library name: 25L000334


title: P12_THALAMIC_PLANE_REP2

description:
Library name: Slide-1_V14B09-296C1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-83 lysate, no dox, replicate 3

description: Library name: 25L000333


title: HEK-293T WT lysate, no dox, replicate 2

description: Library name: 25L000338


title: P12_BRAINSTEM_PLANE_REP2

description:
Library name: Slide-1_V14B09-296B1
Fresh frozen spatial transcriptomics


title: P9_BRAINSTEM_PLANE_REP2

description:
Library name: DubracV12N30-034D1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-83 lysate, +dox, replicate 3

description: Library name: 25L000336


title: P9_THALAMIC_PLANE_REP2

description:
Library name: DubracV12N30-034C1
Fresh frozen spatial transcriptomics


title: P9_ANTERIOR_PLANE_REP2

description:
Library name: Slide-1_V14B09-296A1
Fresh frozen spatial transcriptomics


title: P7_ANTERIOR_PLANE_REP2

description:
Library name: DubracV12N30-034B1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-83 lysate, no dox, replicate 1

description: Library name: 25L000331


title: HEK-293T ISBM-17 lysate, no dox, replicate 2

description: Library name: 25L000344


title: P5_THALAMIC_PLANE_REP2

description:
Library name: DubracV12D05-338D1
Fresh frozen spatial transcriptomics


title: P7_BRAINSTEM_PLANE_REP1

description:
Library name: DubracV12N30-034A1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-64 lysate, +dox, replicate 2

description: Library name: 25L000329


title: HEK-293T ISBM-64 lysate, +dox, replicate 1

description: Library name: 25L000328


title: P9_BRAINSTEM_PLANE_REP1

description:
Library name: DubracV12D05-338A1
Fresh frozen spatial transcriptomics


title: P12_ANTERIOR_PLANE_REP2

description:
Library name: Slide-1_V14B09-296D1
Fresh frozen spatial transcriptomics


title: P12_BRAINSTEM_PLANE_REP1

description:
Library name: DubracV12D05-338B1
Fresh frozen spatial transcriptomics


title: P5_BRAINSTEM_PLANE_REP1

description:
Library name: DubracV12D05-338C1
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-64 lysate, no dox, replicate 2

description: Library name: 25L000326


title: P9_ANTERIOR_PLANE_REP1

description:
Library name: Dubrac_Math_8_V12U06_090_D1_P9_Rostral
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-64 lysate, no dox, replicate 3

description: Library name: 25L000327


title: P9_THALAMIC_PLANE_REP1

description:
Library name: Dubrac_Math_7_V12U06_090_C1_P9_Caudal
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-64 lysate, +dox, replicate 3

description: Library name: 25L000330


title: HEK-293T ISBM-83 lysate, no dox, replicate 2

description: Library name: 25L000332


title: P12_ANTERIOR_PLANE_REP1

description:
Library name: Dubrac_Math_6_V12U06_090_B1_P12_Rostral
Fresh frozen spatial transcriptomics


title: 25L000323 | water control

description:
Library name: 25L000323
Water control

value: water control


title: P7_ANTERIOR_PLANE_REP1

description:
Library name: Dubrac_Math_4_V12U06_016_D1_P7_Rostral
Fresh frozen spatial transcriptomics

value: Brain


title: 25L000322 | N2A control

description:
Library name: 25L000322
Neuro-2a control for rapamycin time course

value: WT (Neuro-2a)

value: N2A control


title: 25L000324 | noTn5 control

description: Library name: 25L000324

value: noTn5 control


title: 25L000321 | lysate 15 noRT control

description:
Library name: 25L000321
No RT control for rapamycin time course

value: immortalized cell line

value: rapamycin, no RT control


title: 25L000320 | rapamycin lysate 15 (20:30)

description:
Library name: 25L000320
Rapamycin time course, Rapamycin, Zeitpunkt 20:30, RT19c, Tn5(8min), PCR(19c)

value: Lysate

value: rapamycin, timepoint 20:30


title: Myeloid, IL18m-day1, BD_SMK

city: Hangzhou

first: Ting

last: Zhou

state: Zhejiang

address: No. 600 Dunyu Road, Xihu District

department: Immunology and Microbiology

institute: Westlake University

description:
Library name: Sample 7_SMK
BD Rhapsody Sample Multiplexing Kit (SMK) Library

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.2.0 for scRNA-seq. The demultiplexing, barcoded processing, gene counting and aggregation were made using the spaceranger software v3.0.0 for spatial transcriptomics.
Assembly: GRCm39
Supplementary files format and content: cells-genes matrix

molecule: protein

source_name: spleen; bone marrow

extract_protocol:
Microfluidic chips(10x Genomics) and magnetic bead methods (BD Rhapsody)
The erythroid sequencing was processed using the 10x Genomics protocol, whereas the myeloid component was conducted according to the BD Rhapsody Single-Cell Whole Transcriptome (WTA) and Sample Multiplexing Kit (SMK) Library Construction Guide.

value: spleen; bone marrow

tag: library type

value: SMK

tag: smk


title: P5_THALAMIC_PLANE_REP1

description:
Library name: Dubrac_Math_1_V12U06_016_A1_P5_Caudal
Fresh frozen spatial transcriptomics

value: THALAMIC PLANE

value: male


title: P5_ANTERIOR_PLANE_REP1

description:
Library name: Dubrac_Math_2_V12U06_016_B1_P5_Rostral
Fresh frozen spatial transcriptomics

value: ANTERIOR PLANE


title: P7_THALAMIC_PLANE_REP1

description:
Library name: Dubrac_Math_3_V12U06_016_C1_P7_Caudal
Fresh frozen spatial transcriptomics


title: HEK-293T ISBM-64 lysate, no dox, replicate 1

description: Library name: 25L000325

value: not applicable


title: Chimpanzee, Putamen, rep 5

city: Dallas

first: Jane

middle: E

last: Johnson

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: Library name: Chimp_put_5

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v6.0.0)
Gene annotation files of non-human primates were generated using Liftoff tool (v1) using the human gene annotation file as reference. Then the genome files were generated using "CellRanger mkref" using the genome fasta files given below with the newly generated gene anniotation files for these species.
The “mkfastq” command was used to generate FASTQ files and the "CellRanger count" command was used to generate raw gene-cell expression matrices.
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Data were filtered, normalized, integrated, clustered, annotated, and visualized using a Seurat v3 pipeline
Assembly: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10), Marmoset: calJac3, Bat:GCF_004126475.2_mPhyDis1.pri.v3, Mouse: mm10, Ferret: GCF_011764305.1_ASM1176430v1.1
Supplementary files format and content: barcodes.tsv.gz' contains cell barcodes, 'features.tsv.gz' containts gene symbols, 'matrix.mtx.gz' contains raw counts. 'meta.tsv.gz' contains the meta data.
Supplementary files format and content: In addition to raw data generated in-house, publicly available raw data for mouse and ferrets from publications were used to process the data for this project. Processed data is also included with this dataset.

molecule: nuclear RNA

organism: Pan troglodytes

source_name: Putamen

extract_protocol:
Nuclei for snRNA-seq were isolated from bat putamen and caudate brain tissue. Briefly, the tissue was homogenized in 500 µL of ice-cold Nuclei EZ lysis buffer (EZ PREP NUC-101, Sigma) using a pre-chilled glass Dounce homogenizer. Debris was removed via density gradient centrifugation using Nuclei PURE 2 M sucrose cushion solution and Nuclei PURE sucrose cushion buffer (Nuclei PURE prep isolation kit, no. NUC201-1KT, Sigma Aldrich). These two solutions were mixed in a 9:1 ratio, and 500 µL of the sucrose solution was added to a 2-ml Eppendorf tube. The homogenized nuclei suspension was mixed with 900 µL of sucrose cushion solution by pipetting 10 times, resulting in a 1,400 µL volume, which was carefully layered over the sucrose buffer without mixing. The samples were centrifuged at 13,000 x g for 45 min at 4 °C, and all but 100 µL of supernatant was discarded. Nuclei were resuspended in 300 µL of nucleus suspension buffer (NSB), consisting of 1× PBS, 2% BSA (no. AM2618, Thermo Fisher Scientific), and 0.4 U µL −1 RNAse inhibitor (no. AM2694, Thermo Fisher Scientific). Samples were then centrifuged at 550 x g for 5 min at 4 °C, and all but 50 µL of supernatant was discarded. The nuclear pellet was resuspended in NSB and filtered through a 40-μm Flowmi cell strainer (Bel-Art Products, #H13680-0040) into a new tube. The nuclei concentration was measured using Hoechst and decreased to 1,000 nuclei per µL with NSB if necessary. Cellular nuclei for snRNA-seq were isolated from the putamen and caudate nuclei of human, chimpanzee, and rhesus macaque tissues. Briefly, the tissue was homogenized in 750 µL of ice-cold NP40 lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Nonidet P40 Substitute, 1 mM DTT, 0.2 U/µL RNAse inhibitor) using a pre-chilled glass Dounce homogenizer. An additional 750 µL of ice-cold NP40 lysis buffer was added, and the mixture was pipette-mixed during a 5-minute incubation on ice. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, resuspended in 1 mL of ice-cold lysis buffer, and incubated on ice for 5 minutes with gentle pipette mixing throughout. The nuclei were then centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. Next, 500 µL of nucleus suspension buffer (NSB) containing 1× PBS, 1% Ultrapure BSA (no. AM2618, Thermo Fisher Scientific), and 0.2 U/µL RNAse inhibitor (no. AM2694, Thermo Fisher Scientific) was added, and the sample was incubated for 5 minutes on ice without mixing. The pellet was resuspended, centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. The nuclei were then resuspended in 500 µL of NSB and filtered through a 70-μm Flowmi cell strainer (no. H13680-0070, Bel-Art) into a 1.5 mL tube.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 (10x Genomics) kit, following the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: sample id

value: female

value: Putamen


title: Her2/Neu lung metastases - replicate 2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
The UMI count matrix was used for downstream analysis with Seurat v3.1.5 R package and popsicleR v0.2.1 R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix file

source_name: Lung

extract_protocol:
Primary tumors and metastasis-containing lungs were finely minced with blades and incubated in dissociation medium 1 (600U/ml collagenase I (ThermoFisher), 400U/ml hyaluronidase (SIGMA), 5U/ml dispase (ThermoFisher), 10µg/ml DNAse (Roche) in DMEM:F12) for 30 min at 37°C. The tissue was then incubated in Haemolytic solution (2 x 3min at 4°C). Tissue pellets were then washed twice in HBSS containing 0.2% EDTA before incubation in dissociation medium 2 (10U/ml dispase and 10µg/ml DNAse in HBSS without Ca2+/Mg2+) at 37°C until complete dissociation of tissue clumps to single cells. Cell suspensions were then washed in HBSS with 0.1% BSA, filtered through a 40µm cell strainer, counted and diluted to ~106 cells/ml.
Cell suspensions were processed with the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and Chip G in a Chromium Controller (10X Genomics) targeting 20,000 cells, following manufacturer’s instructions. Sequencing of single-indexed libraries was performed on Illumina HiSeq or NovaSeq platforms (2x150bp; 40 to 50 thousand reads per cell).

value: Lung

value: MMTV-Neu (FVB)


title: P12_THALAMIC_PLANE_REP1

description:
Library name: Dubrac_Math_5_V12U06_090_A1_P12_Caudal
Fresh frozen spatial transcriptomics

value: Brain


title: Chimpanzee, Putamen, rep 3

description: Library name: Chimp_put_3


title: 25L000317 | rapamycin lysate 12 (17:30)

description:
Library name: 25L000317
Rapamycin time course, Rapamycin, Zeitpunkt 17:30, RT19c, Tn5(8min), PCR(19c)

value: rapamycin, timepoint 17:30


title: Myeloid, IL18m-day1, BD_WTA

description:
Library name: Sample 7_WTA
BD Rhapsody Single-Cell Whole Transcriptome (WTA)

value: mRNA


title: 25L000318 | rapamycin lysate 13 (20:30)

description:
Library name: 25L000318
Rapamycin time course, Rapamycin, Zeitpunkt 20:30, RT19c, Tn5(8min), PCR(19c)

value: immortalized cell line


title: Chimpanzee, Putamen, rep 4

description: Library name: Chimp_put_4


title: Chimpanzee, Putamen, rep 2

description: Library name: Chimp_put_2


title: Chimpanzee, Putamen, rep 1

description: Library name: Chimp_put_1


title: 25L000316 | rapamycin lysate 11 (17:30)

description:
Library name: 25L000316
Rapamycin time course, Rapamycin, Zeitpunkt 17:30, RT19c, Tn5(8min), PCR(19c)


title: Chimpanzee, Putamen, rep 6

description: Library name: Chimp_put_6


title: Chimpanzee, Caudate Nucleus, rep 2

description: Library name: Chimp_caud_2

source_name: Caudate Nucleus

value: Caudate Nucleus


title: Chimpanzee, Caudate Nucleus, rep 3

description: Library name: Chimp_caud_3


title: Chimpanzee, Caudate Nucleus, rep 1

description: Library name: Chimp_caud_1


title: WT RNA-Seq (HCT116), rep03

first: Philipp

last: Schneider

state: Massachusetts

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description:
Library name: RNA_WT_03
WT.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv

data_processing:
The raw reads were initially trimmed using Trimmomatic with the empirically determined parameters “HEADCROP:0 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the sequencing data was performed with FastQC and MultiQC. Subsequently, the trimmed reads were aligned to the ribosomal DNA references, retrieved from NCBI with bowtie2 using the -N 1 option to allow single mismatches in the alignment. Reads identified as non-ribosomal were subjected to splicing-aware alignment with the STAR aligner using the settings “--bamRemoveDuplicatesType UniqueIdenticalNotMulti --outMultimapperOrder Random”. For this step, we employed the hg38 genome and RefSeq annotations for introns and exons. Unaligned reads were removed for further processing and a subset of the unaligned reads was used with BLAST to confirm the absence of any contamination. Picard's markDuplicate function was used on the aligned read set to identify duplicate reads. Using the Bedtools' genomecov function, we generated bedgraph files from BAM files with single-base-pair resolution. These files were normalized to 1x genome coverage and converted to bigwigs. In parallel to this, BAM files were processed by featureCounts to determine gene-and-exon-wise coverage in all RNA-Seq samples.
Raw CUT&RUN reads were trimmed with Trimmomatic and empirically determined parameters “HEADCROP:5 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the CUT&RUN sequencing experiment was performed with FastQC and MultiQC. Mitochondrial reads were removed by alignment to the mitochondrial DNA sequence reference from the hg38 genome using Bowtie2. The remaining non-mitochondrial reads were further aligned to the human genome hg38 using Bowtie 2, allowing for single-base mismatches (parameter -N 1). Poor alignments in the produced BAM alignment file, as determined by score fields AS, YS and MAPQ, multi-aligners, as determined by fields AS and XS, large fragments (TLEN>3500) and flagged singletons were subsequently filtered out with samtools. Replicate marking and removal were accomplished using Picard’s MarkDuplicates. Sample- and antibody-specific CUT&RUN peaks were called with macs3, employing multiple replicates for each experiment and using respective IgG CUT&RUNs as controls with a q-value of 0.01 (-q 0.01). For normalizing CUT&RUN tracks, a "background-interval-set" was generated using the complement of a union peak set derived from all samples and antibodies, extending each peak interval by 10 kbp. Bedgraph files, prepared for each sample with BedTools genomecov, were normalized to a standard 1x coverage on the background intervals.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig files are normalized to 1x background genome coverage

growth_protocol: We grew wild-type and PHC2 L307R HCT116 cells in 6-well plates. The day before harvesting the cells, we plated 2.5×10⁵ cells per well. Cells were harvested by adding 0.5 ml of TRI Reagent (Molecular Research Center, TR118) and transferred to a 1.5 ml tube. Then 0.1 ml of chloroform was added to the tube and vigorously mixed. Afterwards, the sample was incubated at room temperature for 3 minutes and centrifuged at 16,000 RCF for 15 minutes at 4°C. We then carefully transferred the upper aqueous phase to a new tube and added 1 volume of 100% ethanol to 1 volume of sample (1:1 ratio). Then, the RNA was purified using the RNA clean & concentrator kit (Zymo Research, R1016) following the manufacturer’s manual. To remove the DNA we performed the “In-column DNase treatment” and used 5 units of TURBO DNAase (Thermo Fisher Scientific, AM2238) as described in the appendix of the manufacturer manual. The quality and concentration was accessed by nanodrop and Agilent Tapestation. Subsequently, the RNA library was prepared using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, R3000) following the manufacturer’s manual exactly. We started out with 250 ng of RNA. For the final library amplification we ran 12 PCR cycles. Afterwards library quality was assessed using the Agilent Tapestation. The library concentrations were measured using the NEBNext Library Quant Kit for Illumina (New England Biolabs, E7630L) following the manufacturer’s manual exactly. For PHC2 KO and PHC2 KO with PHC2 overexpression through lentivirus, the NEBnext PolyA mRNA magnetic isolation module (New England Biolabs, E7490L) was used instead of the Zymo-Seq RiboFree Total RNA Library Kit.

extract_protocol:
We followed the CUT&RUN protocol from Skene et al. with some minor modifications. First, Concanavalin A (Polysciences, 86057-10) beads were prepared by taking 20 µl per sample and washing the beads three times with 1 ml of Bead Activation Buffer (20 mM HEPES with pH 7.9, 10 mM KCl, 1 mM CaCl₂ 1 mM MnCl₂), incubating for ~15 minutes on a rotator each time. After washing, tubes were placed on a magnetic stand, supernatant was removed, and beads were resuspended in 200 µl Bead Activation Buffer. For each CUT&RUN sample, 1×10⁶ cells were harvested by trypsinization, quenched, and counted. Then cells were spun down at 500 RCF for 5 minutes and washed with 10 ml of PBS with pH 7.4. Then, we resuspend cells in 0.5% formaldehyde in PBS with pH 7.4. Cells were fixed for 5 minutes, then quenched with 1:1 volume of 1 M Tris pH 8.0 for 10 minutes at room temperature. Afterwards, we washed cells twice with 5 ml PBS with pH 7.4 in 15 ml Falcon tubes by spinning at 500 ×g for 3 minutes. Then cells were resuspended in 100 µl of PBS per library. Afterwards, we added 100 µl Wash Buffer (20 mM HEPES with pH 7.5, 150 mM NaCl, 2 mM EDTA with pH 8.0, 0.5% BSA, 0.1% Triton, Protease Inhibitor Tablet Roche cOmplete EDTA-free) and 40 µl of washed ConA beads. This mixture was incubated for 10 minutes on a rotator to bind cells to beads. Then, samples were spun at 50 RCF for 1 minute, moved to a magnetic stand, and cleared for 1 minute. Afterwards, the supernatant was removed and beads were resuspended in 100 µl Wash Buffer and transferred to PCR strip tubes. We then prepared the corresponding antibody solutions (all antibodies were used at 1:400) in 150 µl Wash Buffer. PCR tubes with beads were moved to a magnetic stand, incubated for 1 minute, and then the supernatant was removed. We then added the antibody solution and resuspended the beads. Finally, the tubes were placed on a nutator overnight at 4°C. The next day, the samples were washed twice with 100 µl Wash Buffer. After removing the Wash Buffer, we added 50 µl of proteinA MNase at 700 ng/ml final in Wash Buffer and incubated for 1 hour at room temperature. Then, the beads were washed three times with 100 µl Wash Buffer. Afterwards, the samples were chilled on ice. We then added 100 µl of ice cold Wash Buffer with 10 mM CaCl₂ to each sample and digested for 1 hour at 4°C. During the incubation, we prepared RNase-containing 2× STOP buffer by mixing 4 µl of 100 mg/ml RNase A with 3996 µl 2× STOP buffer (340 mM NaCl, 20 mM EDTA with pH 8.0, 4 mM EGTA with pH 8.0). After the 1 hour incubation, we added 100 µl of STOP/RNase buffer per sample and incubated at 37°C for 15 minutes. Then, samples were placed on the magnet, allowed to clear for 1 minute, and then the supernatant was transferred to new tubes. We then added 2 µl of 10% SDS and 2 µl of 19 mg/mL proteinase K to each tube and mixed gently. With this, reverse crosslink was performed at 50°C overnight. The next day, we performed the DNA Clean-Up using Ampure XP beads (Beckman Coulter, A63881) at 0.9x beads to sample ratio (e.g. 180 µl of beads with 200 µl of DNA sample). Beads and samples were mixed and incubated at room temperature for 10 minutes. Afterwards, we moved the tubes to the magnet, discarded the supernatant, and washed with 200 µl of freshly prepared 90% ethanol without resuspending. This wash was repeated and then the beads were allowed to air dry just until no visible liquid remained. We then removed the tubes from the magnet, added 52 µl of 0.1× TE, resuspended beads by pipetting, and incubated for 2 minutes at room temperature. Then, the tubes were returned to the magnet and we transferred 50 µl of supernatant to new PCR tubes.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®,New England Biolabs, E7645S

value: wild type


title: Her2/Neu primary tumor - replicate 1

description: 10x Genomics

source_name: Mammary gland

value: Mammary gland


title: Her2/Neu primary tumor - replicate 2

description: 10x Genomics


title: PyMT lung metastases - replicate 2

description: 10x Genomics

value: MMTV-PyMT (FVB)


title: WT RNA-Seq (HCT116), rep02

description:
Library name: RNA_WT_02
WT.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv


title: WT RNA-Seq (HCT116), rep01

description:
Library name: RNA_WT_01
WT.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv


title: 25L000313 | rapamycin lysate 8 (14:30)

description:
Library name: 25L000313
Rapamycin time course, Rapamycin, Zeitpunkt 14:30, RT19c, Tn5(8min), PCR(19c)

value: Lysate

value: rapamycin, timepoint 14:30


title: Chimpanzee, Caudate Nucleus, rep 4

description: Library name: Chimp_caud_4

value: male


title: PyMT lung metastases - replicate 1

description: 10x Genomics


title: WT treated with BRM014 RNA-Seq (HCT116), rep02

description:
Library name: RNA_BRM014_02
BRM014.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv


title: WT treated with BRM014 RNA-Seq (HCT116), rep03

description:
Library name: RNA_BRM014_03
BRM014.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv


title: 25L000315 | rapamycin lysate 10 (17:30)

description:
Library name: 25L000315
Rapamycin time course, Rapamycin, Zeitpunkt 17:30, RT19c, Tn5(8min), PCR(19c)


title: 25L000312 | rapamycin lysate 7 (14:30)

description:
Library name: 25L000312
Rapamycin time course, Rapamycin, Zeitpunkt 14:30, RT19c, Tn5(8min), PCR(19c)


title: WT treated with BRM014 RNA-Seq (HCT116), rep01

description:
Library name: RNA_BRM014_01
BRM014.bw
featureCounts.counts.sn.rev.exons.tsv
featureCounts.counts.sn.rev.genes.tsv


title: 25L000311 | rapamycin lysate 6 (11:45)

description:
Library name: 25L000311
Rapamycin time course, Rapamycin, Zeitpunkt 11:45, RT19c, Tn5(8min), PCR(19c)

value: rapamycin, timepoint 11:45


title: 25L000314 | rapamycin lysate 9 (14:30)

description:
Library name: 25L000314
Rapamycin time course, Rapamycin, Zeitpunkt 14:30, RT19c, Tn5(8min), PCR(19c)

value: not applicable


title: 25L000309 | rapamycin lysate 4 (11:45)

description:
Library name: 25L000309
Rapamycin time course, Rapamycin, Zeitpunkt 11:45, RT19c, Tn5(8min), PCR(19c)


title: PyMT primary tumor - replicate 2

description: 10x Genomics


title: PyMT primary tumor - replicate 1

description: 10x Genomics


title: WT SMARCC1 CUT&RUN (HCT116), rep01

description:
Library name: CR_WT_SMARCC1_01
WT_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed


title: 25L000310 | rapamycin lysate 5 (11:45)

description:
Library name: 25L000310
Rapamycin time course, Rapamycin, Zeitpunkt 11:45, RT19c, Tn5(8min), PCR(19c)


title: WT PHC3 CUT&RUN (HCT116), rep03

description:
Library name: CR_WT_PHC3_03
WT_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: Her2/Neu lung metastases - replicate 1

description: 10x Genomics


title: WT SMARCC1 CUT&RUN (HCT116), rep02

description:
Library name: CR_WT_SMARCC1_02
WT_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed


title: 25L000308 | rapamycin lysate 3 (9:00)

description:
Library name: 25L000308
Rapamycin time course, Rapamycin, Zeitpunkt 9:00, RT19c, Tn5(8min), PCR(19c)

value: rapamycin, timepoint 9:00


title: Rhesus Macaque, Putamen, rep 7

description: Library name: Macaque_put_7

organism: Macaca mulatta

value: female

value: Putamen


title: WT PHC3 CUT&RUN (HCT116), rep01

description:
Library name: CR_WT_PHC3_01
WT_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: WT PHC2 CUT&RUN (HCT116), rep03

description:
Library name: CR_WT_PHC2_03
WT_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: WT SMARCC1 CUT&RUN (HCT116), rep03

description:
Library name: CR_WT_SMARCC1_03
WT_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed


title: WT PHC2 CUT&RUN (HCT116), rep02

description:
Library name: CR_WT_PHC2_02
WT_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: 25L000307 | rapamycin lysate 2 (9:00)

description:
Library name: 25L000307
Rapamycin time course, Rapamycin, Zeitpunkt 9:00, RT19c, Tn5(8min), PCR(19c)


title: Rhesus Macaque, Putamen, rep 6

description: Library name: Macaque_put_6


title: WT PHC2 CUT&RUN (HCT116), rep01

description:
Library name: CR_WT_PHC2_01
WT_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: WT IgG CUT&RUN (HCT116), rep03

description:
Library name: CR_WT_IgG_03
WT_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: Rhesus Macaque, Putamen, rep 4

description: Library name: Macaque_put_4


title: 25L000306 | rapamycin lysate 1 (9:00)

description:
Library name: 25L000306
Rapamycin time course, Rapamycin, Zeitpunkt 9:00, RT19c, Tn5(8min), PCR(19c)


title: WT IgG CUT&RUN (HCT116), rep01

description:
Library name: CR_WT_IgG_01
WT_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: Rhesus Macaque, Putamen, rep 5

description: Library name: Macaque_put_5


title: WT IgG CUT&RUN (HCT116), rep02

description:
Library name: CR_WT_IgG_02
WT_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: WT PHC3 CUT&RUN (HCT116), rep02

description:
Library name: CR_WT_PHC3_02
WT_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: WT EED CUT&RUN (HCT116), rep03

description:
Library name: CR_WT_EED_03
WT_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: WT EED CUT&RUN (HCT116), rep02

description:
Library name: CR_WT_EED_02
WT_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: WT EED CUT&RUN (HCT116), rep01

description:
Library name: CR_WT_EED_01
WT_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: 25L000319 | rapamycin lysate 14 (20:30)

description:
Library name: 25L000319
Rapamycin time course, Rapamycin, Zeitpunkt 20:30, RT19c, Tn5(8min), PCR(19c)

value: rapamycin, timepoint 20:30


title: Rhesus Macaque, Putamen, rep 3

description: Library name: Macaque_put_3


title: Total RNA HEK-293T lysate, HIV-gag:MCP, replicate 2

description: Library name: 24L014714

value: HEK-293T background

value: RNA export modality=HIV-gag:MCP; replicate=2


title: Rhesus Macaque, Putamen, rep 1

description: Library name: Macaque_put_1


title: Rhesus Macaque, Putamen, rep 2

description: Library name: Macaque_put_2


title: PHC2 KO with PHC2 lentivirus overexpression PHC3 CUT&RUN (HCT116), rep02

description:
Library name: CR_Lenti_PHC3_02
Lenti_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed

value: PHC2 KO


title: Rhesus Macaque, Caudate Nucleus, rep 4

description: Library name: Macaque_caud_4


title: PHC2 KO with PHC2 lentivirus overexpression PHC3 CUT&RUN (HCT116), rep03

description:
Library name: CR_Lenti_PHC3_03
Lenti_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116), rep03

description:
Library name: CR_Lenti_PHC2_03
Lenti_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: PHC2 KO with PHC2 lentivirus overexpression PHC3 CUT&RUN (HCT116), rep01

description:
Library name: CR_Lenti_PHC3_01
Lenti_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: Total RNA HEK-293T lysate, HIV-gag WT, replicate 3

description: Library name: 24L014712

value: immortalized cell line

value: RNA export modality=HIV-gag WT; replicate=3


title: Total RNA HEK-293T lysate, HIV-gag WT, replicate 2

description: Library name: 24L014711

value: RNA export modality=HIV-gag WT; replicate=2


title: Total RNA HEK-293T lysate, HIV-gag:MCP, replicate 3

description: Library name: 24L014715

value: RNA export modality=HIV-gag:MCP; replicate=3


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116), rep02

description:
Library name: CR_Lenti_PHC2_02
Lenti_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: Rhesus Macaque, Caudate Nucleus, rep 2

description: Library name: Macaque_caud_2

value: Caudate Nucleus


title: Rhesus Macaque, Caudate Nucleus, rep 3

description: Library name: Macaque_caud_3


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116), rep01

description:
Library name: CR_Lenti_PHC2_01
Lenti_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: Total RNA HEK-293T lysate, HIV-gag WT, replicate 1

description: Library name: 24L014710

value: Lysate

value: RNA export modality=HIV-gag WT; replicate=1


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116), rep02

description:
Library name: CR_Lenti_IgG_02
Lenti_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: Total RNA HEK-293T lysate, HIV-gag:MCP, replicate 1

description: Library name: 24L014713

value: RNA export modality=HIV-gag:MCP; replicate=1


title: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep3

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep3

data_processing:
Raw FASTQ files were preprocessed using Trim Galore with default settings to remove adapter sequences and low-quality bases. Trimmed reads were aligned using STAR in two-pass mode to improve splice junction detection. Transcript-level quantification was performed using Salmon with strand-specific settings, using the aligned BAM files as input.   Aligned BAM files were sorted and indexed using samtools75, and splice junction files from STAR were used as input for rMATS to identify differential alternative splicing events between control and anisomycin-treated samples. rMATS was run in paired-end mode for Arabidopsis and human samples and in single-end mode for mouse samples, with strand-specific orientation and the variable read length option enabled.
Assembly: For Arabidopsis, alignments were performed against a genome index generated using the TAIR10 primary assembly and the Ensembl Plants Release 56 GTF annotation. For human RKO, reads were aligned to the GRCh38 primary assembly using the GENCODE v45 annotation. For mouse, reads were aligned to the GRCm39 primary assembly using the Ensembl Release 112 annotation.
Supplementary files format and content: Bigwigs , normalised Bins per million  obtained from deeptools bamCoverage function with binsize set to 5 (similar to Transcripts per million)

source_name: RKO cell lines

extract_protocol:
Cytosolic and nuclear fractions from Arabidopsis and human RKO cells were homogenized and stored in TRIzol at −80 °C until further processing. RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research) according to the manufacturer’s instructions. Neuronal cell samples stored in 300 µL of DNA/RNA Shield were also kept at −80 °C until use. RNA from total cells of these samples was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research), following the recommended protocol. DNase I (NEB) treatment was performed during RNA isolation.
Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads (NEBNext Poly(A) mRNA Magnetic Isolation Module), followed by strand-specific library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. All steps, including mRNA capture, first- and second-strand synthesis, end repair, adaptor ligation, and library amplification, were performed according to the manufacturer’s instructions. Library quality and fragment size distribution were assessed using an Agilent Fragment Analyzer.

value: RKO cell lines

value: ufm1 KO

value: DMSO


title: Rhesus Macaque, Caudate Nucleus, rep 1

description: Library name: Macaque_caud_1

value: male


title: PHC2 KO with PHC2 lentivirus overexpression EED CUT&RUN (HCT116), rep03

description:
Library name: CR_Lenti_EED_03
Lenti_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: PHC2 KO with PHC2 lentivirus overexpression EED CUT&RUN (HCT116), rep01

description:
Library name: CR_Lenti_EED_01
Lenti_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: PHC2 KO with PHC2 lentivirus overexpression EED CUT&RUN (HCT116), rep02

description:
Library name: CR_Lenti_EED_02
Lenti_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: PHC2 KO PHC3 CUT&RUN (HCT116), rep03

description:
Library name: CR_KO_PHC3_03
KO_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: PHC2 KO PHC3 CUT&RUN (HCT116), rep02

description:
Library name: CR_KO_PHC3_02
KO_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep1

description: Library name: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep1


title: PHC2 KO PHC3 CUT&RUN (HCT116), rep01

description:
Library name: CR_KO_PHC3_01
KO_PHC3.bw
featureCounts_peak_coverage_PHC3.tsv
PHC3_merged_peaks.bed


title: PHC2 KO PHC2 CUT&RUN (HCT116), rep03

description:
Library name: CR_KO_PHC2_03
KO_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed