title: A4500_021424

description: Library name: A4500_021424

value: Monoclonal ANTI-FLAG M2 antibody, produced in mouse (Sigma-Aldrich, cat. number:F1804)

value: constitutive expression, 16 h, 37°C


title: camta1 moderate stress replicate 1

status: Public on Jul 23 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

description: Library name: camta1_D_1

library_source: transcriptomic

data_processing:
Raw data were first checked with Fastqc and then mapped to TARI10 with STAR. The gene expression profiles were quantified with HOMER.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values file

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Leaves

extract_protocol:
Col-0 and camta1 mutants (SALK_008187.38.30.x) were grown on plates for 14 days. Seedlings of the same developmental stage were then trasfered to control plates and moderate low water plates (50% water content). after 14 days on stress plates, plants were transfered to control plates with increased water availability, and whole rosettes (n= 3 – 4) were sampled and frozen. Treatments: Well-watered, moderate stress, recovery 15 mins, well-watered (controlled for plant transfer and watering and collected after 15 mins).
The library was prepared using illumina mRNA prep kit following manufacturer's protocols.

tag: tissue

value: Leaves

tag: cell type

value: bulk

tag: genotype

tag: treatment

value: Moderate osmotic stress (low-water plates, with 50% water content based on method describes in Gonzalez et al., 2023)


title: camta1 well-watered replicate 3

description: Library name: camta1_W_3

value: Well-watered (Control plates, with 100% water content)


title: camta1 well-watered replicate 4

description: Library name: camta1_W_4


title: camta1 well-watered replicate 2

description: Library name: camta1_W_2


title: camta1 well-watered replicate 1

description: Library name: camta1_W_1


title: Col stress recovery 15 minutes replicate 3

description: Library name: Col_R15_3

value: Col-0 (WT)

value: Recovery from moderate osmotic stress (collected 15 minutes after trasfer to control plates)


title: Col well-watered 15 minutes replicate 3

description: Library name: Col_W15_3

value: Well-watered (Control plates, with 100% water content, collected 15 minutes after transfer to new control plates with additional water)


title: Col well-watered 15 minutes replicate 1

description: Library name: Col_W15_1


title: Col stress recovery 15 minutes replicate 2

description: Library name: Col_R15_2


title: Col well-watered 15 minutes replicate 2

description: Library name: Col_W15_2


title: Col moderate stress replicate 3

description: Library name: Col_D_3


title: Col moderate stress replicate 2

description: Library name: Col_D_2


title: timecourse_drought_day5, snRNAseq

description: HT-v3.1 10x Genomics

library_source: transcriptomic single cell

data_processing:
For the snRNA-seq libraries, CellRanger (v.6.0.1) was used to perform sample-demultiplexing, barcode processing and single-nuclei gene-UMI counting.
An expression matrix was obtained for each experiment by aligning to the A. thaliana genome (TAIR 10) using CellRanger with default parameters.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Arabidopsis

source_name: Whole rosette

extract_protocol:
Seedlings were transferred to vermiculite pots two weeks after germination in trays, 6 seedlings per pot. Vermiculite was saturated with ¾ LS liquid media before the seedling transfer, 2L media per tray. After two days each tray was watered with 2L ultra-pure water, and this continued for two weeks until the drought treatment started. When plants were 30 days old, each pot was weighed and transferred to a dry tray. The experiment started when each pot reached to 30% SWC. Between 12-18 whole rosettes were collected for each time point * condition sample. We used mortar and pestle to grind the frozen tissue. Powdered tissue was then placed in a nuclei extraction buffer [NEB; 500ul 1M TRIS pH=7.4 (Cat# 15567027, Thermo Fisher Scientific, MA), 150ul 1M MgCl2 (Cat# AM9530G, Fisher Scientific, MA), 100ul 1M NaCl (Cat# AM9760G Fisher Scientific, MA), 50ml nuclease-free water (Cat# AM9937 Thermo Fisher Scientific, MA), 25ul 1M spermine (Cat# 85590-5G, MilliporeSigma, MA), 10ul 1M sperimidine (Cat# S2626-5G, MilliporeSigma, MA), 500ul proteinase inhibitor (PI; Cat# P9599-5ML MilliporeSigma, MA), 250ul BSA (Cat# B2518-100MG, MilliporeSigma, MA), 250ul SUPERase-In ()] and incubated for 10 min. After incubation, tissue was filtered through a 40um filter (Cat# 43-57040-51, pluriSelect, Germany). We then centrifuged at 500 rcf for 5 min at 4°C. Supernatant was aspirated out and nuclei were resuspended with NEB + 500ul 10% Triton (Cat# 93443-100ML, MilliporeSigma, MA) and no PI. We incubated for 15 min, filtered through a 40um filter and spun at 500 rcf for 5 min. We washed until the pallet was clear. In 15 mL tubes, we prepared the density gradient using the Density Buffer [DB; 120 mM Tris-Cl pH=8 (Cat# AM9855G, Fisher Scientific, MA), 150 mM KCl (Cat# AM9640G, Fisher Scientific, MA), 30 mM MgCl2, 35mL H20 per 50mL] and filter sterilized it. We mixed 5 volumes of Optiprep (Cat# D1556-250ML, MilliporeSigma, MA) and the buffer volume to create a 50% stock. We also made a dilutant stock [400 mM Sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-Cl pH 8, 28mL H20 per 50mL] that we filter sterilized.  We created gradient tubes by preparing two 15ml tubes. A 45% solution was made by mixing 9ml 50% solution and 1ml dilutant, and a 15% solution by combining 1.5ml 50% stock and 3.5ml dilutant. To create the gradient tubes for each sample we poured ~2ml 45% solution and ~1.5ml 15% into each 15ml tube. We gently poured 2ml of the nuclei solution at the top of the density gradient and then spun the tubes at 1,500 rcf for 5 min with no breaks. After the spin, we pipette off nuclei and place them into a 15 ml tube with ~ 6mL of NEB (with no triton or PI).  After counting the nuclei, the nuclei suspension was loaded onto microfluidic chips (10X Genomics) with HT-v3.1 chemistry to capture ~20,000 cells/sample. Cells were barcoded with a Chromium X Controller (10X Genomics). mRNA was reverse transcribed and Illumina libraries were constructed for sequencing with reagents from a 3’ Gene Expression HT-v3.1 kit (10X Genomics) according to the manufacturer’s instructions. cDNA and final library quality were assessed using Tape-Station High Sensitivity DNA Chip (Agilent, CA).
HT-v3.1 10x Genomics

value: Whole rosette

tag: age

value: Col - 0

value: Drought Day 0 (37% SWC)


title: Col well-watered replicate 1

description: Library name: Col_W_1


title: timecourse_drought_day4, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought Day 0 (49% SWC)


title: Col well-watered replicate 2

description: Library name: Col_W_2


title: timecourse_drought_day1, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought Day 0 (86% SWC)


title: timecourse_drought_day2, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought Day 0 (73% SWC)


title: timecourse_drought_day3, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought Day 0 (62% SWC)


title: timecourse_drought_day0, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought Day 0 (100% SWC)


title: well-watered_verm_time15_rep1, snRNAseq

description: HT-v3.1 10x Genomics

value: Well-watered


title: recovery_verm_time15_rep1, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought + rehydration 15 mins


title: well-watered_verm_time15_rep2, snRNAseq

description: HT-v3.1 10x Genomics


title: drought_verm_time0_rep1, snRNAseq

description: HT-v3.1 10x Genomics

value: Drought 30% SWC


title: Col well-watered replicate 3

description: Library name: Col_W_3

value: Leaves

value: bulk


title: Col stress recovery 15 minutes replicate 1

description: Library name: Col_R15_1


title: Bulk3_Recovery_25% time 120, rep3

data_processing:
Raw RNA sequencing reads in FASTQ files were quality-tested using FASTQC and the adapters were trimmed using cutadapt.
Resulted reads were aligned to the reference A. thaliana genome (TAIR 10) with HISAT2 and the raw gene expression levels were counted using htseq-count.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Whole Rosette

growth_protocol: Col-0 seeds were sterilized with chlorine fumes generated by mixing 100 ml bleach and 4 ml hydrochloric acid (HCl 1M). Sterilized seeds were sown on 2-strength MS media, stratified at 4 °C for three days, and grown in short-day conditions (8h light: 16h dark) at 22 °C with a light intensity of ~110–130 μmol m−2 s−1. For drought treatments, seedlings were transferred to vermiculite pots two weeks after germination in trays, with 6 seedlings per pot. Vermiculite was saturated with ¾ LS liquid media before the seedling transfer, 2L media per tray. After two days each tray was watered with 2L ultra-pure water, and this continued for two weeks until the drought treatment started. When plants were 30 days old, each pot was weighed and transferred to a dry tray. The pots in the tray were weighed daily, and relative water content was calculated. The experiment started when each pot reached to 30% soil-water content (SWC). Three whole Arabidopsis rosettes per treatment were collected separately as an independent sample. Three samples per treatment were collected alongside a well-watered control at each time point. For sterile stress-on-plates experiments, plates were prepared according to Gonzales et al., 2022. Col-0 seeds were sterilized and seeded on plates. Plates were kept in the dark at 4C for three days. After three days plates were moved to a growth chamber with short-day photoperiod light and 22 °C temperature.

extract_protocol:
Total RNA was extracted from three independent biological replicates of each time-point using RNeasy Plant Mini Kits (Cat#79254, Qiagen, CA). Tape Station checked RNA quantity for quality control.
Library construction was performed using Illumina Stranded mRNA Prep (Cat# 20040534, Illumina, CA).

value: Whole Rosette

tag: cell line

value: LW Plates

value: Recovery_25% time 120


title: Bulk3_Recovery_25% time 120, rep2

treatment_protocol: For drought treatments, seedlings were transferred to vermiculite pots two weeks after germination in trays, with 6 seedlings per pot. Vermiculite was saturated with ¾ LS liquid media before the seedling transfer, 2L media per tray. After two days each tray was watered with 2L ultra-pure water, and this continued for two weeks until the drought treatment started. When plants were 30 days old, each pot was weighed and transferred to a dry tray. The pots in the tray were weighed daily, and relative water content was calculated. The experiment started when each pot reached to 30% soil-water content (SWC).


title: well-watered_verm_time0_rep1, snRNAseq

description: HT-v3.1 10x Genomics


title: Col moderate stress replicate 4

description: Library name: Col_D_4

value: Col-0 (WT)

value: Moderate osmotic stress (low-water plates, with 50% water content based on method describes in Gonzalez et al., 2023)


title: Bulk3_Recovery_25% time 120, rep1


title: well-watered_verm_time0_rep2, snRNAseq

description: HT-v3.1 10x Genomics

value: Whole rosette

value: Col - 0


title: Bulk3_well-watered time 120, rep3

value: well-watered time 120


title: Bulk3_well-watered time 120, rep1


title: Col well-watered replicate 4

description: Library name: Col_W_4

value: Well-watered (Control plates, with 100% water content)


title: recovery_verm_time15_rep2, snRNAseq

description: HT-v3.1 10x Genomics


title: Bulk3_well-watered time 120, rep2


title: Col moderate stress replicate 1

description: Library name: Col_D_1


title: Bulk3_Recovery_25% time 90, rep2

value: Recovery_25% time 90


title: Bulk3_Recovery_25% time 90, rep3


title: Bulk3_Recovery_25% time 90, rep1


title: Bulk3_well-watered time 90, rep3

value: well-watered time 90


title: drought_verm_time0_rep2, snRNAseq

description: HT-v3.1 10x Genomics


title: Bulk3_well-watered time 90, rep1


title: Bulk3_Recovery_25% time 60, rep3

value: Recovery_25% time 60


title: Bulk3_well-watered time 90, rep2


title: Bulk3_Recovery_25% time 60, rep2


title: Bulk3_Recovery_25% time 60, rep1


title: Bulk3_well-watered time 60, rep1

value: well-watered time 60


title: Bulk3_well-watered time 60, rep2


title: Bulk3_well-watered time 60, rep3


title: Bulk3_Recovery_25% time 30, rep2

value: Recovery_25% time 30


title: Bulk3_Recovery_25% time 30, rep3


title: Bulk3_Recovery_25% time 30, rep1


title: Bulk3_well-watered time 30, rep2

value: well-watered time 30


title: Bulk3_well-watered time 30, rep1


title: Bulk3_well-watered time 15, rep2

value: well-watered time 15


title: Bulk3_Recovery_25% time 15, rep1

value: Recovery_25% time 15


title: Bulk3_well-watered time 15, rep1

value: Whole Rosette


title: Bulk3_well-watered time 15, rep3

value: LW Plates


title: Bulk3_Recovery_25% time 15, rep3


title: Bulk3_Stress_25%, rep2


title: Bulk3_Stress_25%, rep3


title: Bulk3_well-watered time 0, rep3

value: well-watered time 0


title: Bulk3_well-watered time 0, rep2


title: Bulk2_recovery_ time 120, rep2

value: recovery_ time 120


title: Bulk2_recovery_ time 120, rep1


title: Bulk3_Stress_25%, rep1


title: Bulk2_Well-watered time 120 mins, rep3

value: Well-watered time 120 mins


title: Bulk2_Recovery_time 60, rep3

value: Recovery_time 60


title: Bulk2_Recovery_time 60, rep2


title: Bulk2_Well-watered time 120 mins, rep1


title: Bulk2_Well-watered time 60 mins, rep1

value: Well-watered time 60 mins


title: Bulk2_Well-watered time 120 mins, rep2


title: Bulk2_Well-watered time 60 mins, rep3


title: Bulk2_Recovery_time 60, rep1


title: Bulk2_Well-watered time 60 mins, rep2


title: Bulk3_well-watered time 30, rep3


title: Bulk2_Recovery_time 30, rep3

value: Recovery_time 30


title: Bulk2_Recovery_time 30, rep1


title: Bulk2_Recovery_time 15, rep3

value: Recovery_time 15


title: Bulk2_Recovery_time 30, rep2


title: Bulk2_Stress_50%, rep2


title: Bulk2_Well-watered time 0, rep3

value: Well-watered time 0


title: Bulk3_Recovery_25% time 15, rep2


title: Bulk2_recovery_ time 120, rep3


title: Bulk2_Stress_50%, rep3


title: Bulk3_well-watered time 0, rep1


title: Bulk2_Well-watered time 0, rep2


title: Bulk2_Well-watered time 0, rep1


title: Bulk1_Well-watered time 6 hours, rep3

value: Vermaculite

value: Well-watered time 6 hours


title: Bulk1Well-watered time 48 hours, rep2

value: Well-watered time 48 hours


title: Bulk1_Well-watered time 6 hours, rep2


title: Bulk1_Well-watered time 6 hours, rep1


title: Bulk1_Well-watered time 4 hours, rep2

value: Well-watered time 4 hours


title: Bulk1_Well-watered time 4 hours, rep3


title: Bulk1_Well-watered time 120 mins, rep1


title: Bulk1_Well-watered time 120 mins, rep2


title: Bulk1_Well-watered time 90 mins, rep3

value: Well-watered time 90 mins


title: Bulk2_Recovery_time 15, rep2


title: Bulk1_Well-watered time 90 mins, rep2


title: Bulk1_Well-watered time 90 mins, rep1


title: Bulk1_Well-watered time 60 mins, rep3


title: Bulk1_Well-watered time 60 mins, rep2


title: Bulk2_Recovery_time 15, rep1


title: Bulk1_Well-watered time 30 mins, rep3

value: Well-watered time 30 mins


title: Bulk1_Well-watered time 60 mins, rep1


title: Bulk1_Well-watered time 30 mins, rep2


title: Bulk1_Well-watered time 15 mins, rep2

value: Well-watered time 15 mins


title: Bulk2_Stress_50%, rep1

value: Whole Rosette


title: Bulk1_Well-watered time 4 hours, rep1


title: Bulk1_Well-watered time 0, rep2


title: Bulk1_Well-watered time 15 mins, rep3


title: Bulk1_Drought 30% SWC + Recovery 48 hours, rep3

value: Drought 30% SWC + Recovery 48 hours


title: Bulk1Well-watered time 48 hours, rep3


title: Bulk1_Well-watered time 15 mins, rep1


title: Bulk1Well-watered time 48 hours, rep1


title: Bulk1_Drought 30% SWC + Recovery 48 hours, rep2


title: Bulk1_Drought 30% SWC + Recovery 48 hours, rep1


title: Bulk1_Well-watered time 120 mins, rep3


title: Bulk1_Drought 30% SWC + Recovery 6 hours, rep2

value: Drought 30% SWC + Recovery 6 hours


title: Bulk1_Well-watered time 0, rep1


title: Bulk1_Well-watered time 0, rep3


title: Bulk1_Drought 30% SWC + Recovery 6 hours, rep3


title: Bulk1_Drought 30% SWC + Recovery 4 hours, rep1

value: Drought 30% SWC + Recovery 4 hours


title: Bulk1_Drought 30% SWC + Recovery 6 hours, rep1


title: Bulk1_Drought 30% SWC + Recovery 120 mins, rep1

value: Drought 30% SWC + Recovery 120 mins


title: Bulk1_Drought 30% SWC + Recovery 4 hours, rep3


title: Bulk1_Drought 30% SWC + Recovery 60 mins, rep3

value: Drought 30% SWC + Recovery 60 mins


title: Bulk1_Drought 30% SWC + Recovery 4 hours, rep2


title: Bulk1_Drought 30% SWC + Recovery 60 mins, rep2


title: Bulk1_Drought 30% SWC + Recovery 120 mins, rep2


title: Bulk1_Drought 30% SWC + Recovery 120 mins, rep3


title: Bulk1_Well-watered time 30 mins, rep1


title: Bulk1_Drought 30% SWC + Recovery 60 mins, rep1


title: Bulk1_Drought 30% SWC + Recovery 30 mins, rep3

value: Drought 30% SWC + Recovery 30 mins


title: Bulk1_Drought 30% SWC + Recovery 90 mins, rep1

value: Drought 30% SWC + Recovery 90 mins


title: Bulk1_Drought 30% SWC + Recovery 90 mins, rep3


title: Bulk1_Drought 30% SWC + Recovery 30 mins, rep2


title: Bulk1_Drought 30% SWC + Recovery 15 mins, rep3

value: Drought 30% SWC + Recovery 15 mins


title: Bulk1_Drought 30% SWC + Recovery 30 mins, rep1


title: Bulk1_Drought 30% SWC + Recovery 15 mins , rep1


title: Bulk1_Drought 30% SWC time 0, rep2

value: Drought 30% SWC (time 0)


title: Bulk1_Drought 30% SWC time 0, rep3

value: Vermaculite


title: Bulk1_Drought 30% SWC + Recovery 15 mins, rep2


title: Colon tissue W11

status: Public on Jul 21 2025

city: Shanghai

first: Lu

last: Chen

state: Xuhui

address: Fudan University, Shanghai

department: Shanghai Cancer Center

country: China

institute: Fudan University

description:
Library name: Sample5
Column names in processed data.xlsx:  W11-TPM

data_processing:
Raw reads were quality-checked using FastQC.
Clean reads with Q20 and Q30 were retained and aligned to the mouse reference genome (GRCm39/mm39) using HISAT2 (v2.2.1).
Gene-level expression was quantified using FeatureCounts.
Expression values were normalized to TPM and log2(TPM + 1) for downstream analyses.
Assembly: GRCm38 (mm38)
Supplementary files format and content: Processed data includes a TPM expression matrix in .xlsx format. Rows correspond to genes and columns to samples. Expression units are log2(TPM + 1).

organism: Mus musculus

source_name: Colon

growth_protocol: Mice were maintained under SPF conditions with ad libitum access to food and water. No specific growth manipulation was applied.

extract_protocol:
Approximately 40 mg of colon tissue was homogenized in TRIzol Reagent following the manufacturer's protocol. Total RNA was extracted and purified for downstream analysis.
RNA libraries were prepared using the standard Illumina TruSeq RNA Sample Preparation Kit protocol. Library quality was assessed using Agilent Bioanalyzer 2100.

treatment_protocol: Mice were treated with AOM/DSS to induce colitis-associated cancer. Samples were collected at W0 (Control), W2, W5, W8, and W11 post-induction to capture different disease stages.

value: Colon

value: Intestinal epithelial cells

value: WT

value: AOM/DSS, Week 11

tag: batch

tag: time

value: Week 11


title: Bulk1_Drought 30% SWC time 0, rep1


title: Colon tissue W8

description:
Library name: Sample4
Column names in processed data.xlsx:  W8-TPM

value: AOM/DSS, Week 8

value: Week 8


title: Colon tissue W5

description:
Library name: Sample3
Column names in processed data.xlsx:  W5-TPM

value: AOM/DSS, Week 5

value: Week 5


title: H4K12ac CUT&RUN, Control RNAi, IgG antibody for CUT&RUN, Replicate 1

status: Public on Jul 16 2025

city: Planegg-Martinsried

first: Zivkos

last: Apostolou

address: Großhaderner Strasse 9

country: Germany

institute: Biomedical Center Munich, LMU

description: Library name: H4K12ac-CUT_RUN_Ctrl-RNAi_IgG_Rep1

library_source: genomic

data_processing:
Raw reads from FASTQ files were first trimmed to remove sequencing adaptors using cutadapt (v1.16).
Trimmed reads were then aligned to the Drosophila melanogaster reference genome (Ensembl BDGP6.46) using Bowtie2, followed by processing with SAMtools (v1.9) to filter alignments with a mapping quality of at least 2 (-q 2), and BEDTools (v2.28.0).
BigWig files were generated using bamCompare (deepTools v3.5.0), normalizing each CUT&RUN sample to its corresponding IgG control (for H2A.V and H2A.Vac) or pre-immune serum (for Tip60), while also adjusting for sequencing depth. ChIP-seq samples were normalized to its corresponding input control, while also adjusting for sequencing length.
For each condition, biological replicates were averaged according to the number of mapped reads using bigwigAverage (deepTools v3.5.6).
Peak calling for Tip60 was performed independently in each replicate with MACS2 (v2.1.2) using the parameters: --qvalue 0.05 --fe-cutoff 2, and only peaks present in all three replicates were retained.
Assembly: Drosophila melanogaster reference genome (Ensembl BDGP6.46)
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Drosophila embryonic Kc167 and S2 cells were obtained from Drosophila Genomic Resource Center. Cells were cultured at 26°C in Schneider’s Drosophila Medium (Thermo-Fischer, Cat. No. 21720024) supplemented with 10% FBS (Capricorn, Cat. No. FBS-12A) and 1% Penicillin-Streptomycin solution (PenStrep; Sigma-Aldrich, Cat. No. P-4333).

extract_protocol:
CUT&RUN was performed as previously described (Meers M.P. et.al., 2019. DOI: 10.7554/eLife.46314). Briefly, Concanavalin-A magnetic beads (10 μl of slurry/reaction) were pre-activated by washing 2 times with Binding Buffer (BB: 20 mM Hepes pH 7.5 (NaOH), 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 106 Kc167 cells per condition were bound to the beads, and washed twice with Wash Buffer (WB: 20 mM Hepes pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 1x cOmplete EDTA-free Protease inhibitor). Cells were permeabilized using 150 μl of Antibody Buffer (AB: 20 mM Hepes, pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 2 mM EDTA, 0.5 mM Na-butyrate). Antibodies were mixed into AB at the indicated dilutions. Samples were put on a nutator at RT for 2 hours, and washed twice with Dig-Wash Buffer (Dig-WB: 20 mM Hepes, pH 7.5 (NaOH), 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 1x cOmplete EDTA-free Protease inhibitor). pAG/MNase protein (700 ng/ml) was mixed into 150 μl of Dig-WB and samples were placed on a nutator at 4°C for 1 hour, and then washed twice with Dig-WB. Chromatin digestion was performed by the addition of 2 mM (f.c.) CaCl2 into 100 μl of Dig-WB and incubated at 4°C for 30 min. The reaction was stopped by adding 100 μl of 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 μg/ml RNase A, 50 μg/ml glycogen) and the chromatin fragments were released from insoluble nuclear chromatin by incubating at 37°C for 30 min. Samples were collected by a quick spin and placed on a magnet stand to concentrate the magnetic beads with bound chromatin fragments. Chromatin was digested with 0.25 mg/ml Proteinase K/ 0.1% SDS, and DNA was purified by phenol/chloroform extraction. DNA concentrations were determined using Qubit (Thermo Fisher).                                    ChIP-seq was performed using 70 million S2 cells fixed with 2.2 ml 10x Fixing Solution (0.1 M NaCl, 50 mM Hepes pH 7.6, 1 mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) for 8 min at RT. Fixation was quenched with 125 mM glycine for 10 min on ice, cells were pelleted (1500 rpm, 10 min, 4°C), and washed twice with 10 ml ice-cold PBS. Nuclei were isolated in 1 ml 0.5% Triton/PBS supplemented with 1x cOmplete EDTA-free protease inhibitors and 2 mM Na-butyrate (rotate 15 min, 4°C), centrifuged (3000 rpm, 10 min), and washed once with PBS. Pellets were resuspended in 1 ml RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.1% SDS, 1% Triton X-100) supplemented with 2 mM CaCl2, 1x cOmplete EDTA-free protease inhibitors, 1 mM PMSF, and 2 mM Na-butyrate. Lysates of 1 ml were digested with 0.6 U MNase (Sigma–Aldrich), was resuspended in EX-50 (50 mM KCl, 10 mM HEPES, pH 7.6, 1.5 mM MgCl2, 0.5 mM EGTA, 10% glycerol) at 0.6 U/μl, at 37°C for 35 min and stopped with 22 μl 0.5 M EGTA on ice. Chromatin was mildly sheared with a Covaris AFA S220 (50 W peak power, 200 cycles/burst, 20% duty factor, 8 min, 4°C), centrifuged (16,000 g, 20 min, 4°C), and supernatant was pre-cleared with 10 μl Protein A+G beads per 100 μl chromatin (1 h, 4°C). Beads were removed (3000 rpm, 3 min), and 50 μl input was collected. For IP, 200 μl chromatin were diluted to 500 μl in RIPA, incubated overnight at 4°C with antibody or IgG control, and captured with 40 μl Protein A+G beads (3 h, 4°C). Beads were washed 5× with 1 ml RIPA, resuspended in 100 μl TE (10 mM Tris pH 8.0, 1 mM EDTA), and inputs adjusted to equal volume. Decrosslinking was performed with RNase A (50 μg/ml, 30 min, 37°C), followed by Proteinase K (0.5 mg/ml) and SDS (0.6%) at 68°C for 2 h. DNA was purified using AMPure XP beads. To 100 μl sample, 200 μl beads (1:1 dilution) were added, mixed by pipetting, and incubated 5 min at RT. Tubes were placed on a magnetic stand for ≥2 min, supernatant removed, and beads washed twice with 200 μl 80% ethanol. After a brief spin, residual ethanol was removed on the magnetic stand and beads were air-dried for 2 min. DNA was eluted in 30 μl TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) by pipetting, incubated 2 min at RT, and collected after 1 min on the magnetic stand.
For ChIP-seq samples, libraries were prepared using NEB Next Ultra II DNA Library (New England Biolabs) according to the manufacturer's instructions. For CUT&RUN, sequencing libraries were prepared as described (25). All libraries were sequenced on an Illumina NextSeq1000/2000 sequencer at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU). For CUT&RUN about 5x106 paired-end reads were sequenced per sample for each of the biological replicates.

treatment_protocol: Double-stranded RNA (dsRNA) targeting the desired sequences was generated by in vitro transcription using the HiScribe T7 High Yield RNA Synthesis Kit (NEB, Cat. No. E2040S). For CUT&RUN, the cells underwent two consecutive rounds of RNAi. In brief, 6 μg of dsRNA was added to 10⁶ Kc167 cells in 0.5 ml of serum-free medium. Following a 1-hour incubation at 26°C, an equal volume of medium containing 20% fetal bovine serum (FBS) and 2% PenStrep was added, resulting in final concentrations of 10% FBS and 1% PenStrep. Cells were incubated in 12-well plates at 26°C for 3 days. On day 4, cells were split, counted and 0.8×10⁶ RNAi-treated cells of each condition was used for the second round of RNAi.

tag: cut&run /_chip_antibody

value: IgG (Cell Signaling, #2729S)

value: Ctrl-RNAi


title: Bulk1_Drought 30% SWC + Recovery 90 mins, rep2

value: Whole Rosette


title: H4K12ac CUT&RUN, Control RNAi, H4K12ac antibody for CUT&RUN, Replicate 1

description: Library name: H4K12ac-CUT_RUN_Ctrl-RNAi_H4K12ac_Rep1

value: H4K12ac (Sigma-Aldrich, #07-595)


title: H2A.V CUT&RUN, Tip60 RNAi, H2A.V antibody for CUT&RUN, Replicate 1

description: Library name: H2A.V-CUT_RUN_Tip60-RNAi_H2A.V_Rep1

value: H2A.V (Peter B. Becker Lab, SA4871)


title: H2A.V CUT&RUN, Tip60 RNAi, H2A.V antibody for CUT&RUN, Replicate 3

description: Library name: H2A.V-CUT_RUN_Tip60-RNAi_H2A.V_Rep3


title: H2A.V CUT&RUN, Control RNAi, H2A.V antibody for CUT&RUN, Replicate 3

description: Library name: H2A.V-CUT_RUN_Ctrl-RNAi_H2A.V_Rep3


title: H2A.V CUT&RUN, Control RNAi, H2A.V antibody for CUT&RUN, Replicate 2

description: Library name: H2A.V-CUT_RUN_Ctrl-RNAi_H2A.V_Rep2


title: H2A.V CUT&RUN, Control RNAi, H2A.V antibody for CUT&RUN, Replicate 1

description: Library name: H2A.V-CUT_RUN_Ctrl-RNAi_H2A.V_Rep1


title: H2A.V CUT&RUN, Tip60 RNAi, IgG antibody for CUT&RUN, Replicate 1

description: Library name: H2A.V-CUT_RUN_Tip60-RNAi_IgG_Rep1


title: H2A.Vac CUT&RUN, Tip60 RNAi, H2A.Vac antibody for CUT&RUN, Replicate 3

description: Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_H2A.Vac_Rep3

value: H2A.Zac (Cell Signaling, #75336S)


title: Colon tissue W0 (Control)

description:
Library name: Sample1
Column names in processed data.xlsx:  W0-TPM

value: Control, Week 0

value: Week 0


title: H2A.V CUT&RUN, Tip60 RNAi, H2A.V antibody for CUT&RUN, Replicate 2

description: Library name: H2A.V-CUT_RUN_Tip60-RNAi_H2A.V_Rep2


title: H2A.Vac CUT&RUN, Tip60 RNAi, H2A.Vac antibody for CUT&RUN, Replicate 1

description: Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_H2A.Vac_Rep1


title: H2A.Vac CUT&RUN, Control RNAi, H2A.Vac antibody for CUT&RUN, Replicate 3

description: Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_H2A.Vac_Rep3


title: H2A.Vac CUT&RUN, Control RNAi, IgG antibody for CUT&RUN, Replicate 3

description:
Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_IgG_Rep3
Sample H2A.Vac-CUT&RUN_Ctrl-RNAi_IgG_Rep3 was also used as an IgG control for sample H2A.V-CUT&RUN_Ctrl-RNAi_H2A.V_Rep3


title: H2A.Vac CUT&RUN, Tip60 RNAi, IgG antibody for CUT&RUN, Replicate 3

description:
Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_IgG_Rep3
Sample H2A.Vac-CUT&RUN_Tip60-RNAi_IgG_Rep3 was also used as an IgG control for sample H2A.V-CUT&RUN_Tip60-RNAi_H2A.V_Rep3


title: H2A.Vac CUT&RUN, Tip60 RNAi, H2A.Vac antibody for CUT&RUN, Replicate 2

description: Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_H2A.Vac_Rep2


title: H2A.V CUT&RUN, Control RNAi, IgG antibody for CUT&RUN, Replicate 1

description: Library name: H2A.V-CUT_RUN_Ctrl-RNAi_IgG_Rep1


title: H2A.Vac CUT&RUN, Tip60 RNAi, IgG antibody for CUT&RUN, Replicate 2

description: Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_IgG_Rep2


title: H2A.Vac CUT&RUN, Control RNAi, H2A.Vac antibody for CUT&RUN, Replicate 1

description: Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_H2A.Vac_Rep1


title: Tip60 CUT&RUN, Tip60 RNAi, Tip60 antibody for CUT&RUN, Replicate 2

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_Tip60_Rep2

value: Tip60 (this study, SAC390)


title: Tip60 CUT&RUN, Tip60 RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 3

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_PPI_Rep3

value: PPI (this study, GU612)


title: Tip60 CUT&RUN, Tip60 RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 2

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_PPI_Rep2


title: Tip60 CUT&RUN, Tip60 RNAi, Tip60 antibody for CUT&RUN, Replicate 3

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_Tip60_Rep3


title: Tip60 CUT&RUN, Tip60 RNAi, Tip60 antibody for CUT&RUN, Replicate 1

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_Tip60_Rep1


title: H2A.Vac CUT&RUN, Control RNAi, IgG antibody for CUT&RUN, Replicate 1

description:
Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_IgG_Rep1
Sample H2A.Vac-CUT&RUN_Ctrl-RNAi_IgG_Rep1 was also used as an IgG control for sample H2A.V-CUT&RUN_Ctrl-RNAi_H2A.V_Rep2


title: Tip60 CUT&RUN, Control RNAi, Tip60 antibody for CUT&RUN, Replicate 2

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_Tip60_Rep2


title: Tip60 CUT&RUN, Control RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 1

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_PPI_Rep1


title: CosMx Slide 3: Mm Parabrachial Nucleus

status: Public on Jul 06 2025

type: other

city: Philadelphia

first: John

middle: Nicholas

last: Betley

state: Pennsylvania

address: 433 S University Avenue, Lynch Bldg, Rm 321

department: Biology

institute: University of Pennsylvania

description: Spatial Transcriptomics, CosMx

hyb_protocol: Hybridization was performed by incubating the fresh frozen sections with the CosMx SMI probe panel under controlled temperature and humidity conditions. Blocking steps were used to reduce nonspecific binding, and stringent washes were performed to remove unbound probes. After hybridization, iterative cycles of fluorescent readout were conducted, each involving hybridization of readout probes, imaging, and stripping. Post-processing steps included nuclear staining (e.g., DAPI) and optional immunofluorescent staining for protein markers to aid in cell segmentation and contextual analysis.

scan_protocol: Scanning and image acquisition were performed using the NanoString CosMx Spatial Molecular Imager platform, which conducts cyclic fluorescent imaging of transcript barcodes in situ. High-resolution imaging was carried out using automated epifluorescence microscopy integrated into the CosMx instrument, capable of subcellular resolution across large fields of view. The platform captures multiple optical channels per cycle to detect hybridized readout probes corresponding to gene-specific barcodes.

data_processing: Raw spatial transcriptomic data were processed using the NanoString AtoMx Spatial Informatics Platform (SIP) to assign transcripts to segmented cells.  Output files were exported as flat CSVs and integrated into Python for downstream processing using Scanpy and Squidpy.  Vector-based spatial subsetting was performed by looping over manually drawn polygon masks corresponding to the parabrachial nucleus (PBN), isolating cells within each defined region.  Gene expression matrices were normalized, clustered, and visualized using Scanpy’s default pipeline, and annotated .h5ad files were generated.

molecule: other

source_name: formalin paw injection

label_protocol: RNA targets were labeled using the NanoString CosMx Spatial Molecular Imaging (SMI) platform according to manufacturer protocols. Fresh frozen tissue sections were fixed, permeabilized, and hybridized in situ with a multiplexed panel of barcoded probes targeting ~1,000 genes. Each probe contains a target-specific sequence and a readout domain, which is later decoded through sequential rounds of fluorescent imaging. The labeling preserves spatial context and subcellular resolution for each transcript.

extract_protocol: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat

value: Coronal Mouse Brain section ~-5.2mm from Bregma


title: H2A.Vac CUT&RUN, Tip60 RNAi, IgG antibody for CUT&RUN, Replicate 1

description:
Library name: H2A.Vac-CUT_RUN_Tip60-RNAi_IgG_Rep1
Sample H2A.Vac-CUT&RUN_Tip60-RNAi_IgG_Rep1 was also used as an IgG control for sample H2A.V-CUT&RUN_Tip60-RNAi_H2A.V_Rep2


title: Tip60 CUT&RUN, Control RNAi, Tip60 antibody for CUT&RUN, Replicate 3

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_Tip60_Rep3


title: Tip60 CUT&RUN, Tip60 RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 1

description: Library name: Tip60-CUT_RUN_Tip60-RNAi_PPI_Rep1


title: Tip60 CUT&RUN, Control RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 3

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_PPI_Rep3


title: Tip60 CUT&RUN, Control RNAi, Tip60 antibody for CUT&RUN, Replicate 1

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_Tip60_Rep1


title: CosMx Slide 2: Mm Parabrachial Nucleus

description: Spatial Transcriptomics, CosMx


title: Sox2 E14.5 CUT&RUN repeat 2 Treatment

status: Public on Jun 23 2025

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Sox2 E14.5 CUT&RUN repeat 2 Treatment

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by BWA
BAM filtering was performed by samtools and markduplicate by Picard tool
Peaks were called by MACS
BW was generated by bamCoverage
Assembly: mm10
Supplementary files format and content: BW
Library strategy: CUT&RUN

source_name: Retina

extract_protocol:
Freshly dissected E14.5 retinae were lysed for 10 minutes at RT in lysis buffer. Nuclei were then bound to Bio-Mag Plus Concanavalin A coated beads (Cell Signaling #86057-3). After blocking with 2mM EDTA blocking solution for 10 mins at RT, beads were washed and then bound to SOX2 antibody (Active Motif #39844) overnight. The next day, samples were treated with pA-MNase and subjected to digestion with the addition of CaCl2. The digestion reaction was stopped after 30 minutes then samples were treated with RNase for 20 mins at 37°C to release CUT&RUN fragments from beads. Fragments were then purified using phenol-chloroform extraction followed by ethanol precipitation.
Library preparation was then performed with NEBNext Ultra II DNA Library Kits for Illumina (NEB #E7645, E7103) using 10ng of CUT&RUN fragments.

value: Retina

value: SOX2 antibody


title: H2A.Vac CUT&RUN, Control RNAi, H2A.Vac antibody for CUT&RUN, Replicate 2

description: Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_H2A.Vac_Rep2


title: AS

status: Public on May 28 2025

type: genomic

city: New Haven

first: Sung Eun

last: Wang

state: CT

address: 300 Cedar st

institute: Yalde University

hyb_protocol: BS converted DNA was amplified, fragmented, and hybridized to human Infinium MethylationEPIC v2.0 BeadChip using illumina standard protocol

scan_protocol: Array was imaged using array reader (Nextseq 550)

data_processing: Rn beads package in R environment

label: other

organism: Homo sapiens

source_name: skin fibroblasts

label_protocol: standard illumina protocol

extract_protocol: cell free DNA was extracted from fibroblasts using QIAGEN kit

value: skin fibroblasts

value: fibroblasts

tag: disease state

value: Angelman syndrome patiend derived fibroblsts


title: H2A.Vac CUT&RUN, Control RNAi, IgG antibody for CUT&RUN, Replicate 2

description: Library name: H2A.Vac-CUT_RUN_Ctrl-RNAi_IgG_Rep2


title: Sox2 E14.5 CUT&RUN repeat 2 Input

description: Sox2 E14.5 CUT&RUN repeat 2 Input

value: input


title: PWS II

value: Prader-willi syndrome (large deletion type II)


title: PWS UPD

value: uniparental disomy_maternal chr15


title: Ctr-AG03

value: healthy control


title: Sox2 E14.5 CUT&RUN repeat 1 Input

description: Sox2 E14.5 CUT&RUN repeat 1 Input


title: Ctr-CU


title: PWS I

value: Prader-Willi syndrome (large deletion type I)


title: Ctr2


title: LC_08_1

status: Public on May 27 2025

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Former library name: LC_10_1
breast cancer bone metastasis

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: CRGh38
Supplementary files format and content: tab-seperarated values files and matrix files

source_name: Bone

extract_protocol:
Tissues were minced and homogenized in 24-well plates using scalpels and pestles, with 0.5 ml of DMEM. Subsequently, 1 ml of tissue dissociation buffer was added, and the mixture was incubated at 37°C for 45 minutes. The dissociation solution was prepared by dissolving collagenase A (Sigma, 11088793001) in a mixture of 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to achieve a working concentration of 1 mg ml⁻¹. The resulting tissue suspension was filtered through a 70-μm strainer to ensure complete homogenization, and the strainer was rinsed with DMEM to recover any remaining single cells. The flow-through was then centrifuged at 500g for 5 minutes, and the supernatant was carefully decanted. In cases where red blood cells (RBCs) were present, a 1×RBC lysis buffer (1:10 dilution of 10× RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied and incubated at room temperature for 10 minutes. To halt and remove RBC lysis, 20 ml of DMEM was added, and the mixture was centrifuged at 450g for 5 minutes. The supernatant was discarded, and the cell pellet was washed with 10 ml of cold DMEM at 4°C. After another centrifugation at 500g for 5 minutes, the supernatant was removed, and the cells were resuspended in cold PBS (Sigma, D8537) containing 0.04% BSA. Finally, the cell suspension was passed through a 40-μm flowmi cell strainer to ensure uniformity.
Library construction follows CellPlex and TotalSeqC sample multiplexing protocal, for CellPlex multiplexed sample, we used 3' end sequencing protical, while we used 5' end sequencing for TotalSeqC multiplexed samples.

value: Bone


title: LC_07_1

description:
Former library name: LC_09_1
breast cancer bone metastasis


title: CosMx_Mouse_brains

status: Public on Jun 17 2025

type: RNA

city: Utrecht

first: Stefan

last: Prekovic

address: Universiteitsweg 100

department: CMM

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Samples were processed using Nanostring's (Bruker) standard protocol

scan_protocol: Samples were scanned using Nanostring's (Bruker) standard protocol

data_processing:
Data was processed using R. Please see associated code on Github for further information on sample metadata.
Values in the count matrix (Flatfiles) represent number of times a transcript was detected. Values in the post-proseg output count matrix represent rounded counts.

label: Flurorescent probes (red, green, blue, yellow)

source_name: CosMx spatial transcriptomics slide containing TMAs of irradiated and control brains

label_protocol: Sample processing followed NanoString's (Bruker) standard protocol, using the Mouse RNA Neuroscience Panel (1.0) and the Neuroscience Cell Segmentation Kit wit hthe Mouse Neuroscience Supplemental Segmentation kit and Mm CD68

growth_protocol: C57Bl/6NRj male mice were housed with 3-5 animals in clear cages containing wood shavings, food and water ad libitum on a fixed 12:12 h light:dark cycle

extract_protocol: Samples were fixed using 4% formaldehyde/10% formalin, put into paraffin and cut into 5µm thick sections to be processed using Nanostring's (Bruker) standard protocol

treatment_protocol: Animals were irradiated for 3 consecutive days with 10Gy per day at 6 weeks of age and followed up for 30 days, sham-controls were not irradiated but otherwise received the same dose and duration of isoflurane treatment.

value: brain


title: CC_03_1

description: breast cancer bone metastasis


title: Tip60 CUT&RUN, Control RNAi, PPI-Serum (pre-immune serum) for CUT&RUN, Replicate 2

description: Library name: Tip60-CUT_RUN_Ctrl-RNAi_PPI_Rep2

value: Ctrl-RNAi


title: Ctr1


title: BDC_01_2

description:
Former library name: CC_02_2
breast cancer bone metastasis


title: BC_12_1

description:
Library name: BC_12_1
breast cancer bone metastasis


title: Sox2 E14.5 CUT&RUN repeat 1 Treatment

description: Sox2 E14.5 CUT&RUN repeat 1 Treatment


title: PC_01_1

description:
Library name: PC_01_1
breast cancer bone metastasis


title: BC_10_1

description:
Library name: BC_10_1
breast cancer bone metastasis


title: BC_11_1

description:
Library name: BC_11_1
breast cancer bone metastasis


title: TC_02_1

tag: group

value: thyroid cancer bone metastasis


title: TC_01_1


title: Colon tissue W2

description:
Library name: Sample2
Column names in processed data.xlsx:  W2-TPM

value: Colon

value: Intestinal epithelial cells

value: WT

value: AOM, Week 2

value: Week 2


title: LC_04_1

description: Former library name: LC_06_1

value: lung cancer bone metastasis


title: LC_06_1

description: Former library name: LC_08_1


title: LC_05_1

description: Former library name: LC_07_1


title: LC_05_2

description: Former library name: LC_07_2


title: LC_02_1

description: Former library name: LC_04_1


title: LC_03_1

description: Former library name: LC_05_1


title: LC_08_2

description:
Former library name: LC_10_2
breast cancer bone metastasis


title: KC_09_1

description: Former library name: KC_14_1

value: renal cancer bone metastasis


title: KC_10_2

description: Former library name: KC_15_2


title: KC_09_2

description: Former library name: KC_14_2


title: KC_08_2

description: Former library name: KC_13_2


title: KC_08_1

description: Former library name: KC_13_1


title: KC_10_1

description: Former library name: KC_15_1


title: KC_07_1

description: Former library name: KC_12_1


title: KC_06_1

description: Former library name: KC_11_1


title: KC_06_2

description: Former library name: KC_11_2


title: KC_05_1

description: Former library name: KC_10_1


title: KC_05_2

description: Former library name: KC_10_2


title: BDC_01_1

description:
Former library name: CC_02_1
breast cancer bone metastasis


title: KC_04_1

description: Former library name: KC_09_1


title: CC_02_1

description: Former library name: KC_08_1


title: KC_14_1

description: Former library name: KC_07_1


title: KC_13_1

description: Former library name: KC_06_1


title: KC_12_1

description: Former library name: KC_05_1


title: CC_02_2

description: Former library name: KC_08_2


title: KC_11_1

description: Former library name: KC_04_1


title: KC_02_1


title: KC_03_1


title: KC_01_1


title: ctrl_05_1

value: health bone marrow


title: LC_01_1

description: Former library name: LC_03_1


title: ctrl_04_1


title: ctrl_04_2


title: ctrl_03_2


title: EC_01_1

value: esophagus cancer bone metastasis


title: ctrl_03_1


title: BC_09_1

value: breast cancer bone metastasis


title: ctrl_02_2


title: ctrl_02_1


title: CC_01_1

value: colon cancer bone metastasis


title: CC_01_2


title: BC_08_2


title: BC_05_1


title: ctrl_01_2


title: BC_06_1


title: BC_07_1


title: BC_08_1


title: BC_03_1


title: BC_01_1


title: BC_04_1


title: BC_02_1


title: F002_hPSC-CMs_RAMP

status: Public on May 13 2025

city: Lisbon

first: Paulo

last: Caldas

state: Porto Salvo

address: Campus Taguspark

department: SCERG

country: Portugal

institute: Instituto Superior Tecnico

description: No documented disease

data_processing:
Briefly, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or Unique Molecular Identifier (UMI). This UMI was then later used during the deduplication step with “umi_tools dedup --umi-separator=':' -I "mapped_file.bam" --paired”. Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore v0.5.0 (doi: 10.5281/zenodo.5127899, Cutadapt version 1.15, parameters:–paired). Trimmed reads were aligned to the human reference genome in paired-end mode. Alignments were carried out with STAR v2.7.11a. Deduplication was then carried out with UMI-tools v1.1 (see above).
To quantify allelic-specifc expression (ase), gene-level haplotype expression was gnerated using phASER v.0.9.9.4 (Castel et al., 2016). A VCF file storing gene sequence variations was first generated from Exome-Seq. Only reads uniquely mapped and with a base quality ≥10 were used for phasing.
Assembly: GRCh38
Supplementary files format and content: Files labeled as "phaser_out*" contain the output from phASER's allele-specific expression (ASE) analysis. These files display the number of raw read counts per allele, accompanied by additional information about the corresponding variants. The data is organized in a tab-delimited format, with each row representing a gene and columns including chromosome (<chr>), start position (<start>), end position (<end>), and gene ID (<gene_id>). For each gene, counts for allele a (<aCount>), allele b (<bCount>), and total number of reads (<totalCount>) are provided. Additionally, the file indicates the number of variants (<n_variants>) and specifies which variants are present (<variants>).

source_name: human induced pluripotent stem cell-derived cardiomyocytes

extract_protocol:
Total RNA was isolated using NZYol RNA Isolation Reagent (NZYTech)
The library preparation of RNA-AMP-seq was performed using a similar procedure previously employed for IMPLICON (DOI: 10.1093/nar/gkaa567). Briefly, a first PCR amplifies each region per sample in individual reactions: 1ug (2μl) of cDNA is amplified with 2μl of each forward and reverse 10μM primer in 8μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 16μl. cDNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 35 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. Then a second PCR reaction, attached barcoded Illumina adapters to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl of 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Finally, 2ug of each iTAGed sample are pooled together and cleaned-up with 1x AMPure XP beads and eluted in a final volume of 20μl. The library was verified by running 1:30 dilutions on an Agilent bioanalyzer
Amplicon sequencing

treatment_protocol: RNA from hiPSCs and hiPSC-derived cardiomyocytes (hiPSC-CM) was treated with DNaseI (Roche) to remove contaminating DNA according to manufacturer’s instructions. DNaseI-treated RNA (500 ng) was reverse-transcribed using random primers and a High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems) according to the manufacturer’s instructions.


title: ctrl_05_2


title: CD_hiPSC-CMs_RAMP

description: No documented disease

value: human induced pluripotent stem cell-derived cardiomyocytes


title: F002_hiPSCs_RAMP

description: No documented disease

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: CE_hiPSC-CMs_RAMP

description: No documented disease


title: CD_hiPSCs_RAMP

description: No documented disease


title: ASD_hiPSC-CMs_RAMP

description: Angelman syndrome D.


title: ASD_hiPSCs_RAMP

description: Angelman syndrome D.


title: ctrl_01_1

value: Bone


title: 2040cl6_IMP

data_processing:
Standard Illumina base-calling pipeline.
As first step in the processing, the first 8 bp of Read 2 were removed and written into the readID of both reads as an in-line barcode, or UMI (Unique Molecular Identifier). This UMI was then later used during the de-duplication step with "deduplicate bismark --barcode mapped_file.bam
Raw sequence reads were then trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.2 for hybrid mouse tissues, v0.4.4 for human and inbred mouse tissues, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 2.3 for hybrid mouse tissues, v1.9.1 for human and inbred mouse tissues), parameters: --paired). Trimmed reads were aligned to the mouse or human reference genome in paired-end mode. Alignments were carried out with Bismark v0.14.4 for hybrid mouse tissues and v0.18.2 for human and inbred mouse tissues (Krueger and Andrews, 2011). CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor (v0.22.1 for hybrid mouse tissues, v0.18.2 for human and inbred mouse tissues). Deduplication was then carried out with deduplicate_bismark, using the --bacode option to take UMIs into account (see above)). For hybrid mouse strain experiments, the data was aligned to a hybrid genome of Black6/CAST (the genome was prepared with the SNPsplit package (v0.3.4, https://github.com/FelixKrueger/SNPsplit)). Following alignment and deduplication, reads were split allele-specifically with SNPsplit.
Assembly: GRCh38
Supplementary files format and content: The Bismark CpG coverage file is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
Genomic DNA was purified using conventional phenol:chloroform:isoamyl alcohol extraction.
The library preparation of IMPLICON protocol includes 2 PCR reactions. In the first reaction each sample is amplified with each primer pair in individual reactions: 30ng (2μl of 66μl eluted bisulfite treated DNA) of bisulfite treated DNA is amplified with 2μl of each forward and reverse 10μM primer in 8μl of 2x KAPA HiFi Uracil+ ReadyMix in a final volume of 16μl. DNA was amplified using the following conditions: initial denaturation at 95°C for 5min, 35 cycles of 98°C denaturation for 20 seconds, variable annealing temperature for 15 seconds and extension at 72°C for 60 seconds; followed by a final extension at 72°C for 10 minutes. All PCR reactions for each individual sample were pooled together and samples cleaned-up using 1.5x AMPure XP beads and eluted in 20μl H2O. In the second PCR reaction, barcoded Illumina adapters are attached to the pooled PCR samples ensuring that each sample pool receives a unique reverse barcoded adapter. The 20μl PCR pool was amplified using 1μl of 10μM Illlumina PE1.0 primer (same for all samples) and 1μl of 10μM Illumina iTAG primer (distinct for each sample) and 25μl of 2x KAPA HiFi Uracil+ ReadyMix in a 50μl volume reaction using the following conditions: initial denaturation at 98°C for 45 seconds, 5 cycles of 98°C denaturation for 15 seconds, 65°C annealing for 30 seconds and extension at 72°C for 30 seconds; followed by a final extension at 72°C for 5 minutes. Reactions were cleaned-up with 1x AMPure XP beads and eluted in 20μl. Finally, 2ug of each iTAGed sample are pooled together and cleaned-up with 1x AMPure XP beads and eluted in a final volume of 20μl. This final library is then verified by running 1:30 dilutions on Agilent bioanalyser.

treatment_protocol: 1μg of genomic DNA was bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) according to manufacturer’s instructions with column clean-up and eluted in 66μl elution buffer to obtain a final concentration of ~15ng/μl bisulfite converted DNA.


title: 2040Fib_IMP

source_name: human dermal fibroblasts

value: human dermal fibroblasts


title: 2042cl1_IMP


title: 2042Fib_IMP


title: F7cl4_IMP


title: F7cl4_D7_1

description: No documented disease

data_processing:
To quantify gene expression from our sequencing data (paired-ended strand-specific) reads were mapped to the reference genome (GRCh38 assembly; release 37, GRCh38.p13) using STAR (v2.7.8a)
To quantify allelic-specifc expression (ase), gene-level haplotype expression was gnerated using phASER v.0.9.9.4 (Castel et al., 2016). A VCF file storing gene sequence variations was first generated from Exome-Seq. Only reads uniquely mapped and with a base quality ≥10 were used for phasing.
Assembly: GRCh38
Supplementary files format and content: Files labeled as "readcounts_matrix*" store raw read counts for every gene across each sample.
Supplementary files format and content: Files labeled as "phaser_out*" contain the output from phASER's allele-specific expression (ASE) analysis. These files display the number of raw read counts per allele, accompanied by additional information about the corresponding variants. The data is organized in a tab-delimited format, with each row representing a gene and columns including chromosome (<chr>), start position (<start>), end position (<end>), and gene ID (<gene_id>). For each gene, counts for allele a (<aCount>), allele b (<bCount>), and total number of reads (<totalCount>) are provided. Additionally, the file indicates the number of variants (<n_variants>) and specifies which variants are present (<variants>).

source_name: human iPSC-derived ectodermal cells

extract_protocol:
Total RNA was isolated using NZYol RNA Isolation Reagent (NZYTech)
RNA was used for 250–300 bp insert cDNA library following manufacturer's recommendations and libraries were sequenced with NovaSeq 6000 platform using paired-end 150-bp mode.

treatment_protocol: RNA from biological samples was treated with DNaseI (Roche) to remove contaminating DNA according to manufacturer’s instructions.

value: human iPSC-derived ectodermal cells


title: F7cl4_3

description: No documented disease


title: CD_IMP


title: F7cl4_D0_1

description: No documented disease


title: F7cl15_IMP


title: F7cl4_1

description: No documented disease


title: CE_IMP


title: CE_hiPSCs_RAMP

description: No documented disease


title: F7cl15_1

description: No documented disease


title: F7cl15_3

description: No documented disease


title: F7cl15_D7_1

description: No documented disease


title: F7cl15_2

description: No documented disease


title: F002_3

description: No documented disease


title: F7cl4_2

description: No documented disease


title: F002_2

description: No documented disease


title: F002_1

description: No documented disease


title: CE_2

description: No documented disease


title: CD_2

description: No documented disease


title: 2042cl9_IMP


title: CD_1

description: No documented disease


title: CE_1

description: No documented disease


title: ASD_1

description: Angelman Syndrome D.


title: T5_e17_rep 2

status: Public on May 09 2025

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: ST211_23

data_processing:
Datasets were processed using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp. Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3), SenDRT9 plasmid sequence, and the T5 genome (NC_005859.1) using bwa-mem2 (v2.2.1) with default parameters. SAMtools (v1.17) was used to sort and index alignments. Aligned reads were assigned to annotated transcriptome features using featureCounts (v2.0.2) with -s 1 for strandedness. After removing low-abundance transcripts (mean counts < 10), gene expression was quantified by dividing counts by gene length and scaling to one million total counts per sample, resulting in transcripts per million (TPM) expression values.
Assembly: Genome reference sequences can be found in the NCBI database via the accession numbers NC_000913.3 (E. coli MG1655) and NC_005859.1 (phage T5). The SenDRT9 plasmid sequences can be found in Tang et al. (2025) Supplementary Table 6.
Supplementary files format and content: A normalized counts file is provided in CSV format that includes transcripts per million (TPM) expression values for each annotated transcript encoded by the host, plasmid, or phage, separated by sample.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: E. coli MG1655 cells expressing wild-type SenDRT9 were grown in liquid culture until OD600 reached 0.4.

extract_protocol:
Samples were collected after 10 minutes of infection by centrifuging 1 mL of culture at 4,000 x g for 3 min, removing the supernatant, and freezing the pellet in liquid nitrogen. To extract RNA, the pellet was resuspended in 750 µL of TRIzol, incubated at RT for 5 min and mixed with 150 µL chloroform. After incubation at RT for 2 min, samples were centrifuged at 12,000 x g for 15 min at 4 °C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research).
RNA was diluted in NEBuffer 2 and heated at 92 °C for 2 min for fragmentation by alkaline hydrolysis. Samples were then treated with TURBO DNase (Thermo Fisher Scientific), RppH (NEB), and T4 PNK (NEB) to remove DNA and prepare RNA ends for adapter ligation. RNA was purified using the Zymo RNA Clean & Concentrator-5 kit. Adapter ligation, reverse transcription, and indexing PCR were performed using the NEBNext Small RNA Library Prep kit. Libraries were sequenced on an Element AVITI in paired-end mode with 75 cycles per end.

treatment_protocol: Cells were infected with WT phage T5 or the indicated escaper phage (T5.e13 or T5.e17) at an MOI of 5.

tag: strain


title: F7cl15_D0_1

description: No documented disease


title: ASD_2

description: Angelman Syndrome D.


title: CD_3

description: No documented disease


title: T5_e17_rep 3

description: Library name: ST211_24


title: ASD_3

description: Angelman Syndrome D.


title: T5_e17_rep 1

description: Library name: ST211_22


title: CE_3

description: No documented disease


title: T5_e13_rep 1

description: Library name: ST211_19


title: T5_e13_rep 2

description: Library name: ST211_20


title: T5_WT_rep2

description: Library name: ST211_14


title: T5_WT_rep3

description: Library name: ST211_15


title: T5_e13_rep 3

description: Library name: ST211_21


title: T5_WT_rep1

description: Library name: ST211_13


title: SenDRT9_Y496F_Y498F_T5_RIP

description: Library name: RZ45_06_R

data_processing:
RIP-seq and corresponding input datasets were processed using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp. Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequence, as well as the T5 genome (NC_005859.1) for +/- infection experiments, using bwa-mem2 (v2.2.1) with default parameters. SAMtools (v1.17) was used to sort and index alignments. Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Assembly: Genome reference sequences can be found in the NCBI database via the accession numbers NC_000913.3 (E. coli MG1655) and NC_005859.1 (phage T5). Plasmid reference sequences can be found in Tang et al. (2025) Supplementary Table 6.
Supplementary files format and content: bigWig (.bw) files represent normalized read coverage files, separated by strand.

growth_protocol: E. coli K-12 strain MG1655 (sSL0810) cells were transformed with plasmids encoding N-terminally 3xFLAG-tagged DRT9 systems or the indicated RT or ncRNA mutants. Individual colonies were inoculated in 20 mL liquid LB and grown at 37 °C to OD600 of 0.3-0.4.

extract_protocol:
Cells were collected by centrifugation at 4,000 x g for 10 min at 4 °C and then washed with 5 mL of cold TBS (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM NaCl). Cells were centrifuged again at 4,000 x g for 5 min at 4 °C. Pellets were washed with 1 mL of cold TBS and centrifuged at 10,000 x g for 5 min at 4 °C. After supernatants were removed, pellets were flash-frozen in liquid nitrogen and stored at –80 °C. To prepare antibody–bead complexes for immunoprecipitation, Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 mL IP Lysis Buffer (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 mL IP Lysis Buffer, combined with anti-FLAG antibody (Sigma-Aldrich, F3165), and rotated for > 3 hours at 4 °C. 60 µL of beads and 20 µL of antibody mix were prepared per sample. Antibody-bead complexes were washed 2× to remove unbound antibodies and resuspended in IP Lysis Buffer to a final volume of 60 µL per sample. Flash-frozen pellets were thawed on ice and resuspended in 1.2 mL IP Lysis Buffer supplemented with 1× Complete Protease Inhibitor Cocktail (Roche) and 0.1 U µL−1 SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). Cells were lysed by sonication and lysates were cleared by centrifugation at 21,000 x g for 15 min at 4 °C. Supernatants were transferred to new tubes and two 10 µL aliquots of each sample (one for RIP-seq and one for cDIP-seq) were set aside and stored at –80 °C as “input” controls. The remainder of each sample was combined with 60 μL of antibody-bead complex and rotated overnight at 4 °C. The next day, each sample was washed 3× with 1 mL ice-cold IP Wash Buffer (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM KCl, 1 mM MgCl2). During the final wash, each sample was split into two 500 µL volumes for downstream RIP or cDIP processing. RIP elution was performed by removing supernatants and resuspending beads in 750 µL TRIzol (Thermo Fisher Scientific). After 5 min incubation at RT, supernatants containing eluted RNA were transferred to new tubes. Samples were then mixed with 150 μL chloroform, incubated at RT for 2 min, and centrifuged at 12,000 x g for 15 min at 4 °C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research). RNA from input samples was isolated in the same manner using TRIzol and column purification.
For RIP-seq library preparation, RNA was diluted in NEBuffer 2 and heated at 92 °C for 2 min for fragmentation by alkaline hydrolysis. Samples were then treated with TURBO DNase (Thermo Fisher Scientific), RppH (NEB), and T4 PNK (NEB) to remove DNA and prepare RNA ends for adapter ligation. RNA was purified using the Zymo RNA Clean & Concentrator-5 kit. Adapter ligation, reverse transcription, and indexing PCR were performed using the NEBNext Small RNA Library Prep kit. Libraries were sequenced on an Element AVITI in paired-end mode with 75 or 150 cycles per end.

treatment_protocol: For phage infection, phage T5 was added to cultures at a multiplicity of infection (MOI) of 5. Cultures were further incubated at 37 °C with shaking for 45 min before harvesting.

tag: rip antibody

value: Monoclonal ANTI-FLAG M2 antibody (Sigma-Aldrich, cat. number:F1804)


title: SenDRT9_Y498F_T5_RIP

description: Library name: RZ45_05_R


title: SenDRT9_Y496F_T5_RIP

description: Library name: RZ45_04_R


title: SenDRT9_WT_T5_input

description: Library name: RZ45_02i_R


title: SenDRT9_Y496F_Y498F_T5_input

description: Library name: RZ45_06i_R


title: PsaDRT9_WT_T5_input

description: Library name: ST155_09i_R


title: SenDRT9_Y496F_T5_input

description: Library name: RZ45_04i_R


title: SenDRT9_U4G4_uninfected_RIP

description: Library name: ST206_17_R


title: SenDRT9_U4A4_uninfected_RIP

description: Library name: ST206_18_R


title: PsaDRT9_MUT_T5_input

description: Library name: ST155_10i_R


title: SenDRT9_U4C4_uninfected_RIP

description: Library name: ST206_16_R


title: SenDRT9_Y498F_T5_input

description: Library name: RZ45_05i_R


title: SenDRT9_U123A_uninfected_RIP

description: Library name: ST206_15_R


title: SenDRT9_C122G_uninfected_RIP

description: Library name: ST206_14_R


title: SenDRT9_A121U_uninfected_RIP

description: Library name: ST206_13_R


title: PsaDRT9_WT_T5_RIP

description: Library name: ST155_09_R


title: SenDRT9_MUT_T5_rep1_RIP

description: Library name: ST206_10_R


title: SenDRT9_MUT_T5_rep2_RIP

description: Library name: ST206_11_R


title: SenDRT9_WT_T5_rep2_RIP

description: Library name: ST206_08_R


title: SenDRT9_WT_T5_rep3_RIP

description: Library name: ST206_09_R


title: SenDRT9_MUT_uninfected_rep3_RIP

description: Library name: ST206_06_R


title: SenDRT9_MUT_uninfected_rep2_RIP

description: Library name: ST206_05_R


title: SenDRT9_WT_uninfected_rep2_RIP

description: Library name: ST206_02_R


title: SenDRT9_WT_uninfected_rep1_RIP

description: Library name: ST206_01_R


title: SenDRT9_U4A4_uninfected_input

description: Library name: ST206_18i_R


title: SenDRT9_WT_T5_rep1_RIP

description: Library name: ST206_07_R


title: SenDRT9_WT_uninfected_rep3_RIP

description: Library name: ST206_03_R


title: PsaDRT9_MUT_T5_RIP

description: Library name: ST155_10_R


title: SenDRT9_U4G4_uninfected_input

description: Library name: ST206_17i_R


title: SenDRT9_U123A_uninfected_input

description: Library name: ST206_15i_R


title: SenDRT9_C122G_uninfected_input

description: Library name: ST206_14i_R


title: SenDRT9_MUT_T5_rep3_RIP

description: Library name: ST206_12_R


title: SenDRT9_A121U_uninfected_input

description: Library name: ST206_13i_R


title: SenDRT9_WT_T5_rep3_input

description: Library name: ST206_09i_R


title: SenDRT9_MUT_T5_rep2_input

description: Library name: ST206_11i_R


title: SenDRT9_WT_T5_rep2_input

description: Library name: ST206_08i_R


title: SenDRT9_MUT_T5_rep3_input

description: Library name: ST206_12i_R


title: SenDRT9_MUT_uninfected_rep3_input

description: Library name: ST206_06i_R


title: SenDRT9_WT_T5_rep1_input

description: Library name: ST206_07i_R


title: SenDRT9_MUT_uninfected_rep1_RIP

description: Library name: ST206_04_R


title: SenDRT9_MUT_uninfected_rep1_input

description: Library name: ST206_04i_R


title: SenDRT9_WT_uninfected_rep3_input

description: Library name: ST206_03i_R


title: SenDRT9_WT_uninfected_rep2_input

description: Library name: ST206_02i_R


title: SenDRT9_WT_uninfected_rep1_input

description: Library name: ST206_01i_R


title: SenDRT9_MUT_T5_rep1_input

description: Library name: ST206_10i_R


title: PsaDRT9_MUT_T5_cDIP

description: Library name: ST155_10_D

library_source: other

data_processing:
cDIP-seq and corresponding input datasets were processed using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp. Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequence, as well as the T5 genome (NC_005859.1) for +/- infection experiments, using bwa-mem2 (v2.2.1) with default parameters. SAMtools (v1.17) was used to sort and index alignments. Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Assembly: Genome reference sequences can be found in the NCBI database via the accession numbers NC_000913.3 (E. coli MG1655) and NC_005859.1 (phage T5). Plasmid reference sequences can be found in Tang et al. (2025) Supplementary Table 6.
Supplementary files format and content: bigWig (.bw) files represent normalized read coverage files, separated by strand.

growth_protocol: E. coli K-12 strain MG1655 (sSL0810) cells were transformed with plasmids encoding N-terminally 3xFLAG-tagged DRT9 systems with a WT or mutant (YAAA) RT active site. Individual colonies for each replicate experiment were inoculated in 20 mL liquid LB and grown at 37 °C to OD600 of 0.3-0.4.

extract_protocol:
Cells were collected by centrifugation at 4,000 x g for 10 min at 4 °C and then washed with 5 mL of cold TBS (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM NaCl). Cells were centrifuged again at 4,000 x g for 5 min at 4 °C. Pellets were washed with 1 mL of cold TBS and centrifuged at 10,000 x g for 5 min at 4 °C. After supernatants were removed, pellets were flash-frozen in liquid nitrogen and stored at –80 °C. To prepare antibody–bead complexes for immunoprecipitation, Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 mL IP Lysis Buffer (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 mL IP Lysis Buffer, combined with anti-FLAG antibody (Sigma-Aldrich, F3165), and rotated for > 3 hours at 4 °C. 60 µL of beads and 20 µL of antibody mix were prepared per sample. Antibody-bead complexes were washed 2× to remove unbound antibodies and resuspended in IP Lysis Buffer to a final volume of 60 µL per sample. Flash-frozen pellets were thawed on ice and resuspended in 1.2 mL IP Lysis Buffer supplemented with 1× Complete Protease Inhibitor Cocktail (Roche) and 0.1 U µL−1 SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). Cells were lysed by sonication and lysates were cleared by centrifugation at 21,000 x g for 15 min at 4 °C. Supernatants were transferred to new tubes and two 10 µL aliquots of each sample (one for RIP-seq and one for cDIP-seq) were set aside and stored at –80 °C as “input” controls. The remainder of each sample was combined with 60 μL of antibody-bead complex and rotated overnight at 4 °C. The next day, each sample was washed 3× with 1 mL ice-cold IP Wash Buffer (20 mM Tris-HCl pH 7.5 at 25 °C, 150 mM KCl, 1 mM MgCl2). During the final wash, each sample was split into two 500 µL volumes for downstream RIP or cDIP processing. cDIP elution was performed by removing supernatants, resuspending beads in 90 µL IP Wash Buffer, and treating samples with 5 µg RNase A (Thermo Fisher Scientific) and 25 µg Proteinase K (Thermo Fisher Scientific). Supernatants containing eluted DNA were transferred to new tubes. DNA was isolated using the Monarch Spin PCR and DNA Cleanup kit (NEB), following the Oligonucleotide Cleanup protocol. Input samples were also treated with RNase A and Proteinase K prior to DNA isolation by column purification.
For cDIP-seq library preparation, samples were heated at 95 °C for 2 min and then immediately placed on ice to denature DNA. Adapter ligation and conversion of ssDNA to dsDNA were performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (IDT). Indexing PCR was performed using NEBNext Ultra II Q5 Master Mix. Libraries were sequenced on an Element AVITI in paired-end mode with 75 or 150 cycles per end.

tag: cdip antibody


title: PsaDRT9_MUT_T5_input

description: Library name: ST155_10i_D


title: PsaDRT9_WT_T5_cDIP

description: Library name: ST155_09_D


title: SenDRT9_MUT_uninfected_rep2_input

description: Library name: ST206_05i_R


title: SenDRT9_MUT_T5_rep3_cDIP

description: Library name: ST206_12_D


title: SenDRT9_U4C4_uninfected_input

description: Library name: ST206_16i_R


title: SenDRT9_MUT_T5_rep1_cDIP

description: Library name: ST206_10_D


title: PsaDRT9_WT_T5_input

description: Library name: ST155_09i_D


title: SenDRT9_WT_T5_rep2_cDIP

description: Library name: ST206_8_D


title: SenDRT9_MUT_T5_rep2_cDIP

description: Library name: ST206_11_D


title: SenDRT9_WT_T5_rep3_cDIP

description: Library name: ST206_9_D


title: SenDRT9_WT_T5_rep1_cDIP

description: Library name: ST206_7_D


title: SenDRT9_MUT_uninfected_rep3_cDIP

description: Library name: ST206_6_D


title: SenDRT9_MUT_uninfected_rep2_cDIP

description: Library name: ST206_5_D


title: SenDRT9_WT_uninfected_rep3_cDIP

description: Library name: ST206_3_D


title: SenDRT9_MUT_uninfected_rep1_cDIP

description: Library name: ST206_4_D


title: SenDRT9_MUT_T5_rep2_input

description: Library name: ST206_11i_D


title: SenDRT9_WT_uninfected_rep2_cDIP

description: Library name: ST206_2_D


title: SenDRT9_MUT_T5_rep1_input

description: Library name: ST206_10i_D


title: SenDRT9_MUT_T5_rep3_input

description: Library name: ST206_12i_D


title: SenDRT9_WT_T5_rep2_input

description: Library name: ST206_8i_D


title: SenDRT9_WT_T5_rep3_input

description: Library name: ST206_9i_D


title: SenDRT9_MUT_uninfected_rep2_input

description: Library name: ST206_5i_D


title: SenDRT9_MUT_uninfected_rep1_input

description: Library name: ST206_4i_D


title: SenDRT9_WT_T5_rep1_input

description: Library name: ST206_7i_D


title: SenDRT9_MUT_uninfected_rep3_input

description: Library name: ST206_6i_D


title: SenDRT9_WT_T5_RIP

description: Library name: RZ45_02_R


title: SenDRT9_WT_uninfected_rep3_input

description: Library name: ST206_3i_D


title: 8035073981-G, Exercise Response (Pre), ATAC, bio rep 2

status: Public on May 05 2025

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Cell Ranger ARC 1.0.0 pipeline was run on the samples following 10x Genomics guidelines. Seurat v4 and Signac v1 were used to perform data processing and analysis.
Assembly: hg38
Supplementary files format and content: rds file contains the integrated data of all samples.
Supplementary files format and content: snATACseq fragments and fragments tabix index files.

source_name: PBMC

extract_protocol:
Frozen human skeletal muscle samples were pulverized and the powder used for nuclei isolation. Briefly, and all on ice, RNAse inhibitor (NEB cat# MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from StemCell cat# 07820), 35% OptiPrep and 30% OptiPrep right before isolation. Each sample was homogenized in a Dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 17,792xg; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei dilution buffer for sn multiome (10x Genomics) and counted (Cellometer).
Sn multiome was performed following the Chromium Single Cell Multiome ATAC and Gene Expression Reagent Kits V1 User Guide (10x Genomics, Pleasanton, CA). Nuclei were counted (Countess counter), transposition was performed in 10 ul at 37C for 60min targeting up to 10,000 nuclei, before loading of the Chromium Chip J (PN-2000264) for GEM generation and barcoding. Following post-GEM cleanup, libraries were pre-amplified by PCR, after which the sample was split into three parts: one part for generating the snRNAseq library, one part for the snATACseq library, and the rest was kept at -20C. SnATAC and snRNA libraries were indexed for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262, and Chromium i7 Sample Index TT, Set A kit PN-3000431 respectively).
Single Cell Multiome ATAC and Gene Expression

value: PBMC

tag: Sex

value: Male

value: Exercise Response

value: Pre


title: SenDRT9_WT_uninfected_rep2_input

description: Library name: ST206_2i_D


title: SenDRT9_WT_uninfected_rep1_input

description: Library name: ST206_1i_D


title: 8035073981-G, Exercise Response (Pre), ATAC, bio rep 1


title: 8035073790-E, Exercise Response (Post), ATAC, bio rep 2

value: Female

value: Post


title: 8035073962-G, Exercise Response (Post), ATAC, bio rep 1


title: 8035073722-I, Exercise Response (Post), ATAC


title: 8035073800-E, Exercise Response (Pre), ATAC, bio rep 1


title: 8035073603-L, Circadian control (Post), ATAC, bio rep 2

value: Circadian control


title: 8035074016-I, Exercise Response (Pre), ATAC


title: 8035073800-E, Exercise Response (Pre), ATAC, bio rep 2


title: 8035073603-L, Circadian control (Post), ATAC, bio rep 1


title: 8035073530-L, Circadian control (Pre), ATAC, bio rep 2


title: 8035074040-J, Exercise Response (Pre), ATAC


title: 8035073605-N, Circadian control (Post), ATAC, bio rep 2


title: 8035073276-N, Circadian control (Pre), ATAC, bio rep 1


title: 8035073524-J, Exercise Response (Post), ATAC


title: 8035073605-N, Circadian control (Post), ATAC, bio rep 1


title: SenDRT9_WT_uninfected_rep1_cDIP

description: Library name: ST206_1_D


title: Uterus, VC or E2 treatment, 72h

status: Public on May 01 2025

city: New Orleans

first: Binghao

last: Zou

address: 1430 Tulane Ave

institute: Tulane University

description: The processed, normalized matrix is provided as processed data

hyb_protocol: The NanoString CosMx Spatial Molecular Imager employs a pre-designed 1000-plex gene panel and cyclic fluorescent in situ hybridization directly on FFPE tissue sections. Rather than generating sequencing libraries, target transcripts were detected in situ and captured as spatially resolved digital gene expression data, which were subsequently processed through normalization and clustering pipelines for analysis.

scan_protocol: Slides with FFPE uterine tissue section was scanned using the NanoString CosMx Spatial Molecular Imager.

data_processing: The raw spatial transcriptomic data were first filtered to remove cells with fewer than 10 detected genes and genes present in fewer than three cells. The resulting dataset was then normalized using the SCTransform method to account for technical variability. Following normalization, principal component analysis (PCA) was applied to reduce dimensionality, with the top 30 principal components used to construct a nearest-neighbor graph for clustering. Finally, cell clusters were identified using Seurat’s FindNeighbors and FindClusters functions, and the clusters were visualized with Uniform Manifold Approximation and Projection (UMAP) for downstream analysis.

source_name: mouse uterus

extract_protocol: Uterine tissues were formalin-fixed, paraffin-embedded, and sectioned at 4 µm before undergoing deparaffinization and rehydration. Tissue sections were processed on the NanoString CosMx Spatial Molecular Imager, where a 1000-plex gene panel was hybridized via cyclic fluorescent in situ hybridization, supplemented with morphological marker staining (B2M/CD298, PanCK, CD45, CD3, and DAPI).

treatment_protocol: Female mice were first ovariectomized to remove endogenous estrogen influences, then allowed to recover. They were subsequently treated with a subcutaneous injection of estradiol (E2) for 72 hours, while control groups received a vehicle treatment.


title: 8035073530-L, Circadian control (Pre), ATAC, bio rep 1


title: 8035073962-G, Exercise Response (Post), ATAC, bio rep 2


title: 8035073276-N, Circadian control (Pre), ATAC, bio rep 2


title: 8035073790-E, Exercise Response (Post), ATAC, bio rep 1


title: SUB-ProS_Glut.9mo

status: Public on Apr 30 2025

description:
Library name: sample 101
read length: 151

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Supplementary files format and content: tab-delimited files (CONTACT files) describing the raw contact number between two genome regions . Columns are: 1. Strand1 (0 for forward, anything else for reverse), 2. Chromosome1, 3. Position1, 4. restriction site fragments, 5. Strand2 (0 for forward, anything else for reverse), 6.  Chromosome2, 7. Position2, 8. restriction site fragments, 9. the score imputed to this read
Library strategy: snm3C-seq

source_name: brain

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: brain

value: female


title: Vip_Gaba.9mo

description:
Library name: sample 107
read length: 151


title: Sst_Gaba.9mo

description:
Library name: sample 104
read length: 151


title: Vip_Gaba.18mo

description:
Library name: sample 105
read length: 151


title: SUB-ProS_Glut.18mo

description:
Library name: sample 99
read length: 151


title: Sst_Gaba.8wk

description:
Library name: sample 103
read length: 151


title: Sst_Gaba.18mo

description:
Library name: sample 102
read length: 151


title: SUB-ProS_Glut.8wk

description:
Library name: sample 100
read length: 151


title: STR_Gaba.8wk

description:
Library name: sample 97
read length: 151


title: STR_D1_Sema5a_Gaba.8wk

description:
Library name: sample 91
read length: 151


title: STR_Gaba.18mo

description:
Library name: sample 96
read length: 151


title: STR_D2_Gaba.18mo

description:
Library name: sample 93
read length: 151


title: Pvalb_Gaba.9mo

description:
Library name: sample 83
read length: 151


title: STR_D1_Sema5a_Gaba.18mo

description:
Library name: sample 90
read length: 151


title: Pvalb_Gaba.8wk

description:
Library name: sample 82
read length: 151


title: Pvalb_Gaba.18mo

description:
Library name: sample 81
read length: 151


title: PB_Evx2_Glut.8wk

description:
Library name: sample 79
read length: 151


title: PB_Evx2_Glut.18mo

description:
Library name: sample 78
read length: 151


title: STR_D1_Gaba.18mo

description:
Library name: sample 87
read length: 151


title: Vip_Gaba.8wk

description:
Library name: sample 106
read length: 151


title: PAG-PPN_Pax5_Sox21_Gaba.18mo

description:
Library name: sample 72
read length: 151


title: STR-PAL_Chst9_Gaba.9mo

description:
Library name: sample 86
read length: 151


title: STR-PAL_Chst9_Gaba.8wk

description:
Library name: sample 85
read length: 151


title: STR-PAL_Chst9_Gaba.18mo

description:
Library name: sample 84
read length: 151


title: STR_D2_Gaba.8wk

description:
Library name: sample 94
read length: 151


title: Oligo_NN.18mo

description:
Library name: sample 69
read length: 151


title: PB_Evx2_Glut.9mo

description:
Library name: sample 80
read length: 151


title: STR_Gaba.9mo

description:
Library name: sample 98
read length: 151


title: PAG_Glut.9mo

description:
Library name: sample 77
read length: 151


title: PAG_Glut.8wk

description:
Library name: sample 76
read length: 151


title: STR_D2_Gaba.9mo

description:
Library name: sample 95
read length: 151


title: OPC_NN.18mo

description:
Library name: sample 66
read length: 151


title: STR_D1_Sema5a_Gaba.9mo

description:
Library name: sample 92
read length: 151


title: Oligo_NN.9mo

description:
Library name: sample 71
read length: 151


title: MEA-COA_Glut.8wk

description:
Library name: sample 61
read length: 151


title: STR_D1_Gaba.8wk

description:
Library name: sample 88
read length: 151


title: STR_D1_Gaba.9mo

description:
Library name: sample 89
read length: 151


title: Oligo_NN.8wk

description:
Library name: sample 70
read length: 151


title: Sample tag library associated with Mouse tumor PHIL, NAT WT and disseminated tumor PHIL and WT CD45 pos, ST, scRNAseq

status: Public on Apr 24 2025

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description:
Library name: Disseminated_Mm_ST
Disseminated_Mm_Expression_Data.st.txt
feature_README.txt

data_processing:
Demultiplexing of BCL files with Bcl2fastq (v2.20.0433, Illumina)
Count matrix generation using the BD Rhapsody™ WTA analysis pipeline (v1.12.1) on the SevenBridges Genomics platform
Assembly: STAR index generation using STAR (v2.5.2b) with gene code GRCm38 v25
Supplementary files format and content: st.txt files: text file showing the input data for the WTA Analysis pipeline at the beginning of the file. Followed by a matrix (first column: “Cell_index”, cell IDs; second column: “Bioproduct”, Gene Symbols; third column: “RSEC_Reads”, Number of UMI reads per cell ID and bioproduct; forth column: “Raw_Molecules”, Reads with the same cell ID, same UMI sequence and same bioproduct collapsed into single molecules; fifth column: “RSEC_Adjusted_Molecules”, Number of molecules detected after RSEC molecular identifier adjustment algorithm, this is the counts used for downstream analysis;
Supplementary files format and content: feature_README.txt: text file that contains the sample tag information

source_name: Disseminated tumor

extract_protocol:
BD Rhapsody Express Single-Cell Analysis System (BD Bioscience)
mRNA Whole Transcriptome Analysis (WTA) and Sample Tag (ST) Library Preparation Protocol (BD Biosciences)

treatment_protocol: Cell hasing unsing BD Rhapsody Mouse Single-Cell Multiplexing kit

value: Disseminated tumor

tag: cell line_injected

value: AKPS organoids (Apc-LOF, p53-LOF, Kras-GOF, Smad4-LOF)

tag: cellular enrichment

tag: bd rhapsody_capture_bead_version

tag: sample tag_(cell_hashing)_version

value: Single-Cell Multiplex Kit - Mouse

tag: library type

value: Sample tag (ST)


title: Mouse tumor PHIL, NAT WT and disseminated tumor PHIL and WT CD45 pos, scRNAseq

description:
Library name: Disseminated_Mm_WTA
Disseminated_Mm_Expression_Data.st.txt
feature_README.txt

tag: tissue

value: Whole transcriptome (WTA)


title: OPC_NN.8wk

description:
Library name: sample 67
read length: 151

tag: cell type


title: OPC_NN.9mo

description:
Library name: sample 68
read length: 151


title: Microglia_NN.9mo

description:
Library name: sample 65
read length: 151


title: Term Infant 2

status: Public on Apr 14 2025

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

data_processing:
Reads with read quality less than 30 were filtered out and CellRanger Count v7.1.0 (10x Genomics) was used to align reads onto the GRCh38 reference genome. The ambient RNA was removed from the CellRanger count matrix h5 file outputs using CellBender v0.2.1. The scRNAseq data was analyzed using Seurat (v4.4.0) in R (v4.3.2). The quality control of the ambient RNA corrected cells filtered out cells with >10 % mitochondrial mRNA mapped UMIs, <500 identified genes, and >7000 identified genes. The data was normalized using SCTransform (v0.4.1) with the glmGamPoi (v1.14.0).
Assembly: GRCh38
Supplementary files format and content: .h5 file of counts after ambient RNA removal by cellbender, and two csv.gz files containing compiled cell counts and annotations.

source_name: Lung tissue

extract_protocol:
Human lung tissue from infants who died with BPD, BPD+PH, and term infant controls were digested in an enzymatic cocktail [collagenase I/dispase II (1 μg/ml) tissue or Miltenyi Multi-Tissue Dissociation Kit] using a gentleMACS Octo Dissociator. Tissue lysates were serially filtered through sterile gauze, 100- and 40-μm sterile filters (Fischer). Single-cell suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a and CD45).
CD45− and C45+ populations were mixed 2:1 and were used as input for generation of scRNA-seq libraries using the 10x Chromium platform 3' or 5′ library preparation kits (10x Genomics) following the manufacturer's recommendations and targeting 10,000-20,000 cells per sample.

value: Lung tissue


title: PAG_Glut.18mo

description:
Library name: sample 75
read length: 151


title: Term Infant 1


title: MEA-COA_Glut.9mo

description:
Library name: sample 62
read length: 151


title: BPD + PH 2


title: BPD 2


title: PAG-PPN_Pax5_Sox21_Gaba.9mo

description:
Library name: sample 74
read length: 151


title: Microglia_NN.18mo

description:
Library name: sample 63
read length: 151


title: Microglia_NN.8wk

description:
Library name: sample 64
read length: 151


title: PAG-PPN_Pax5_Sox21_Gaba.8wk

description:
Library name: sample 73
read length: 151


title: MEA-COA_Glut.18mo

description:
Library name: sample 60
read length: 151


title: 5VP5M

status: Public on Mar 31 2025

city: Baltimore

first: Seth

middle: A

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Spatial transcriptomics experiments were performed with the CosMx Spatial Molecular Imager (NanoString, Seattle, WA), using the 1,000-gene Mouse Neuroscience Panel. Floating sections were placed on a microscope slide, processed, and imaged following manufacturer’s instructions.

scan_protocol: Initial image processing, including cell segmentation and read counting, were performed with AtoMx (NanoString).

data_processing: Cell clustering was performed with Seurat using 49 principal components -- excluding the first principal component, which was strongly correlated with the number of UMIs – and Louvain clustering at a manually-determined resolution of 1.0. Clusters were annotated to known cell types by comparison to cell type markers from snRNA-seq. Of 131,548 cells called by AtoMx, 11,663 were excluded as likely doublets in clusters with mixed markers, and downstream analyses were performed with the remaining 119,885 high-quality cells. Spiny projection neurons were sub-clustered with Seurat (5 principal components, resolution = 0.5) to evaluate their spatial distribution within the striatum. Cell type-specificity of DEGs (from snRNA-seq) was examined by plotting their expression on UMAPs, violin plots, and spatial expression plots. Cell type-specificity for modules by scoring their expression in each cell using the AddModuleScore() function from Seurat.

source_name: Whole Brain

extract_protocol: The forebrain of an 8-week old, male mouse was formalin-fixed, coronally cut into 5 mm slices and placed in cassettes for paraffin-embedding. These formalin-fixed paraffin embedded (FFPE) blocks were sectioned on the microtome, where 5 µm FFPE scrolls were cut, then transferred to a RNAse-free molecular grade water bath

tag: line

tag: region

value: forebrain

tag: oreintation

value: coronal

tag: age

value: 8 week old


title: Sample tag library associate with Mouse colon no tumor WT and PHIL CD45 pos, ST, scRNAseq

description:
Library name: Colon_Mm_no_tumor_ST
Colon_Mm_no_tumor_Expression_Data.st.txt
feature_README.txt

value: Colon

value: enhanced beads


title: KrTB-72

status: Public on Mar 19 2025

city: New York City

first: Jorge

last: Baquero

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

description: Library name: Sample 11

data_processing:
Illumina bcl2fastq2 v2.20 was employed for basecalling.
The sequenced reads underwent trimming to eliminate low-quality bases and adapter sequences using cutadapt. Subsequently, these reads were mapped to the mouse GRCm38 reference genome using STAR v2.5.2b.
The extraction of raw read counts was accomplished through HTSeq-count v0.11.2.
Differential expression analysis was conducted using the DESeq2 v1.6.3 package.
We employed the limma package v3.22.7 to remove batch effects from processing samples from different batches.
Assembly: Mouse GRCm38
Supplementary files format and content: Excel file including gene name and log2fold changes (KrTB-D vs. KrTB and KrTB-DN vs. KrTB-N) for each gene

source_name: Tongue epithelia tissue

extract_protocol:
Qiagen's RNEasy Micro kit (Cat # 74004)
The preparation of RNA libraries utilized the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA), following the protocols provided by the manufacturer. The libraries were sequenced with pair-end 51bp reads on the NovaSeq6000 sequencer.

treatment_protocol: Water, water+doxycycline (2 mg/ml), water+4NQO (50 μg/ml), and water+doxycycline+4NQO (2 mg/ml and 50 μg/ml)

value: Tongue epithelia tissue

tag: treatment

value: KrTB-N


title: Hepatocytes (isolated) WT Rep3

status: Public on Apr 29 2025

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
Library name: L146573
SmartSeq-2

data_processing:
alignment of reads and and read counting was done using STAR
TPM were calculated from raw counts using a custom R script
Assembly: GRCm39.109
Supplementary files format and content: tsv file with raw count and TPM values

source_name: Liver

growth_protocol: Periportal assembloids are produced by rocking 1000 dissociated cholangiocytes, 250 or 2500 portal mesenchymal cells and 10 hepatocyte organoids for up to 24hrs in low attachment plate on a shaker (0.5ml of media) and then seeded in matrigel for the following 7 or 18 days (2.5 weeks, long term). HepOrg are grown by plating primary hepatocytes in HM-Wnt media, and then if indicated - switching HepOrg at passage 2 to MM media.

extract_protocol:
Collected in PicoPure Extraction buffer and processed according to PicoPure RNA isolation protocol manufacturer's instructions (ThermoFisher, #KIT0204); RNA eluted in H2O
Illumina Nextera according to manufacturer's instructions.

treatment_protocol: Grown in the MM media for 7days, 14 days or 18 (long term, LT) days; MM media was first described in Cordero-Espinoza et al., 2021, and consists of AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165), supplemented with WNT CM (30%) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503). HM-Wnt hepatocyte organoid media is described in this study as the previously published media (Hu et al., 2018) supplemented with 30% Wnt conditioned medium. The full composition contains  AdDMEM/F12 (ThermoFisher, 12634010) medium containing 1% HEPES (ThermoFisher, #15630-056), 1% Penicillin/Streptomycin (ThermoFisher, #15140-122), Glutamax (ThermoFisher, #35050-068), 1x B27 (Invitrogen, #17504-044) and 1.25 mM N-acetylcysteine (Merck/Sigma, #A9165) –referred to as Basal medium–, which was further supplemented with 10 nM gastrin (Merck/Sigma, #G9145), 50 ng/mL mEGF (ThermoFisher, #PMG8043), 15% RSPO1 conditioned medium (homemade), 100 ng/mL FGF10 (Peprotech, #100-2), 50 ng/mL FGF7 (Peprotech, #100-19-50), 10 mM nicotinamide (Merck/Sigma, #N0636), 25 ng/mL HGF (Peprotech, #100-39),  3 μM CHIR9902 (Tocris, #4423),  1 μM A83-01 (Tocris, #2939) and 10 µM ROCK inhibitor (Ri) (Y-27632, Merck/Sigma, #Y0503), 30% WNT3a conditioned medium (WntCM) (homemade).

value: Liver

tag: cell line

value: Primary

value: hepatocytes

tag: mouse background

tag: genotype

tag: time of_culture

value: freshly isolated


title: Mouse tumor AKPS WT CD45 pos, scRNAseq

description:
Library name: Tumor_Mm_WTA
Tumor_Mm_Expression_Data.st.txt

source_name: Tumor

value: Tumor

tag: strain