title: pair3, intra, 100% CICI, rep1

description: Library name: pair3_100_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::612715_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx


title: IL12B-3_S9

status: Public on Jan 23 2026

type: SRA

city: New Haven

first: Chuanpeng

last: Dong

state: CT

address: 850 West Campus Dr

department: Genetics

country: USA

institute: Yale University School of Medicine

description: Bulk RNA-seq

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the mouse genome reference version gencode.vM32 by STAR 2.7.10b. Reads mapped to each gene were counted using --quantMode GeneCounts in STAR.
Assembly: gencode.vM32
Supplementary files format and content: tab-delimited text files include read counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: E0771 cells

extract_protocol:
RNA was  extracted by TRIZOL.
The RNA sequencing library was prepared using the NEBNext rRNA Depletion Kit v2 and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

tag: cell type

value: E0771 cells

tag: treatment


title: β-cat4A 4hr replicate 1

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

description:
Library name: Mut_m20
B-cat4A Veh

data_processing:
Filtering using Xenome
Alignment using STAR
Quantification using RSEM
Assembly: hg38
Supplementary files format and content: Quantification using RSEM

molecule: polyA RNA

organism: Homo sapiens

source_name: Pancreas

growth_protocol: Orthopic tumour model

extract_protocol: Illumina stranded

treatment_protocol: ETC-159 bid

tag: tissue

value: Pancreas

tag: cell line

value: HPAF-II

value: Cancer

tag: genotype

tag: timepoint

tag: batch


title: β-cat4A 4hr replicate 4

description:
Library name: Mut_m8
B-cat4A Veh


title: IL12B-2_S8

description: Bulk RNA-seq


title: SCN_L_CT22_1

city: Bethesda

first: Samer

last: Hattar

state: MD

address: 9000 Rockville Pike

department: National Institute of Mental Health

institute: National Institutes of Health

description:
Library name: S05
10X Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment, aggregation, barcode processing, and gene expression matrix generation were completed with CellRanger 6.0.0 software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Anterior hypothalamus

extract_protocol:
Tissues were pooled from three mice per CT. Nuclei extractions were performed by detergent-mechanical cell lysis followed by homogenization and sucrose density gradient as described in Matson et al., 2018.
Libraries were generated with the 3′ single-cell gene expression solution V3 (10X Genomics) according to manufacturer’s instructions.

treatment_protocol: Mice housed under 12L:12D cycles were kept in darkness for one day prior to tissue collection to prevent any effects from prior light exposure. A light pulse was then applied for 15 minutes either at circadian time 6 (CT6), or CT14, or CT22. Hypothalamus tissue containing the SCN was collected 45 minutes after exposure.

value: Anterior hypothalamus

value: L

tag: ct time


title: 4II-1_S13

description: Bulk RNA-seq


title: β-cat4A 4hr replicate 3

description:
Library name: Mut_m7
B-cat4A Veh


title: SCN_L_CT6_1

description:
Library name: S01
10X Genomics


title: SCN_L_CT14_2

description:
Library name: S04
10X Genomics


title: β-cat4A 4hr replicate 2

description:
Library name: Mut_m6
B-cat4A Veh


title: SCN_L_CT14_1

description:
Library name: S03
10X Genomics


title: 4II-2_S14

description: Bulk RNA-seq


title: KPO2-rep4

city: Gothenburg

first: Volkan

last: Sayin

address: Medicinaregatan 1F

department: Department of Surgery

country: Sweden

institute: University of Gothenburg

data_processing:
Indexing of the ENSEMBL GRCm39 reference genome as well as alignment of sequencing reads was performed using STAR version 2.7.9a
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalised counts for each sample

source_name: primary lung tumor

extract_protocol:
RNA was extracted using RNeasy Plus Mini kit (Qiagen)
RNA libraries were prepared with the Nextera XT DNA library preparation kit and Nextera XT index kit v2 (Illumina), according to the manufacturer’s recommendations

value: primary lung tumor

value: KP-O

value: epithelial cells

value: KrasG12D; p53 fl/fl


title: SCN_L_CT6_2

description:
Library name: S02
10X Genomics


title: pair3, intra, 50% CICI, rep1

city: State College

first: Yi

last: Li

state: PA

address: 406 SOUTH FREAR, UNIVERSITY PARK

institute: Penn State University

description: Library name: pair3_50_rep1

library_source: genomic

data_processing:
Next generation sequencing was performed on NextSeq 2000, and 100 million of  50 bp paired-end reads were generated for each replicate. Hi-C data analysis was performed with HiC-pro (version 3.1.0), cooler(version 0.10.0), cooltools (version 0.7.0) and HiCExplorer (version 3.7.2).
Assembly: sacCer3
Supplementary files format and content: cool files

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: strain

growth_protocol: Yeast strains were grown in 200 mL SCD-Met medium until OD660 reached 0.3.

extract_protocol:
Standard method was used to perform Hi-C and extract DNA.
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: To arrest cells in the G1 phase, 80 µM alpha-factor (Zymo, Y1001) was added to the culture for a total of 2.5 hours. During the final hour of this incubation, 1 ng/µL rapamycin was added to induce CICI. DMSO was added in the control group instead. After 1 hour of rapamycin treatment, cells were harvested for imaging analysis and Hi-C measurement.

value: strain

value: 50% CICI cell + 50% DMSO cell


title: pair3, intra, 10% CICI, rep1

description: Library name: pair3_10_rep1

value: 10% CICI  cell + 90% DMSO cell


title: pair4, intra, 20% CICI, rep1

description: Library name: pair4_20_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::966177_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx

value: 20% CICI cell + 80% DMSO cell


title: pair3, intra, 0% CICI, rep1

description: Library name: pair3_0_rep1

value: 0% CICI  cell + 100% DMSO cell


title: IL12B-1_S7

description: Bulk RNA-seq


title: β-cat4A Veh replicate 3

description:
Library name: Mut_m2
B-cat4A Veh

value: Vehicle


title: KPO2-rep3


title: 41BBL-1_S10

description: Bulk RNA-seq

value: E0771 cells


title: β-cat4A Veh replicate 5

description:
Library name: Mut_m5
B-cat4A Veh

value: Pancreas


title: pair4, intra, 0% CICI, rep1

description: Library name: pair4_0_rep1


title: 41BBL-3_S12

description: Bulk RNA-seq


title: 41BBL-2_S11

description: Bulk RNA-seq


title: 4II-3_S15

description: Bulk RNA-seq


title: β-cat4A Veh replicate 2

description:
Library name: Mut_m1
B-cat4A Veh

value: HPAF-II


title: β-cat4A Veh replicate 4

description:
Library name: Mut_m3
B-cat4A Veh

value: Cancer


title: pair3, intra, 20% CICI, rep1

description: Library name: pair3_20_rep1

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::612715_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx


title: DNA_lib_3

city: guangzhou

first: wang

last: xing

address: No. 382, Outer Ring East Road, Guangzhou University Town, Panyu District

country: China

institute: South China University of Technology

description: Library name: Sample6

data_processing:
Raw sequencing reads were demultiplexed and quality filtered according to standard Illumina procedures. Sequencing libraries consisted of PCR-amplified barcode-containing fragments; therefore, barcode sequences were directly counted by matching reads to the reference barcode list. Barcode read counts from RNA-derived libraries were used to quantify promoter-driven transcriptional output, while barcode read counts from DNA-derived libraries were used to assess construct abundance in the input library. RNA and DNA barcode counts were independently normalized by library size, and promoter strength was calculated as the ratio of normalized RNA to DNA barcode counts. Promoter activity values were averaged across three independent biological replicates.
Assembly: ASM98243v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Seq denotes the sequence, "Length" denotes sequence length, and "Seq_Num" denotes read counts.

organism: Escherichia coli DH5[alpha]

growth_protocol: Escherichia coli DH5[alpha] cells carrying the pooled barcoded promoter plasmid library were cultured in LB medium supplemented with 50 µg/mL kanamycin at 37 C with shaking at 200 rpm. After overnight growth on selective plates, approximately 20,000 monoclonal colonies were pooled and inoculated into liquid LB medium at a 1:1000 dilution. Cultures were grown for 4 h under the same conditions prior to sample collection.

extract_protocol:
Cells were harvested from the pooled cultures at a defined time point. Total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit according to the manufacturer’s instructions. In parallel, plasmid DNA was extracted from the same cultures to assess construct abundance in the library.
For RNA-derived samples, total RNA was reverse transcribed into cDNA using the HiScript IV 1st Strand cDNA Synthesis Kit. Barcode-containing regions were selectively amplified by PCR using the primers Test-bar-F/R. For DNA-derived samples, barcode regions were directly amplified from plasmid DNA using the same primer pair. Sequencing libraries were constructed from the amplified products following standard Illumina protocols.

tag: strain

value: WT


title: KPO2-rep2

value: primary lung tumor


title: WT 56hr replicate 3

description:
Library name: WT_m20
WT 56hr


title: β-cat4A Veh replicate 1

description:
Library name: Mut_m17
B-cat4A Veh


title: DNA_lib_2

description: Library name: Sample5


title: KPO1-rep3

value: KP-O


title: KPO1-rep4

value: epithelial cells


title: DNA_lib_1

description: Library name: Sample4


title: RNA_pool_3

description: Library name: Sample3


title: WT 56hr replicate 2

description:
Library name: WT_m18
WT 56hr


title: WT 16hr replicate 3

description:
Library name: WT_m19
WT 16hr


title: Ovaries_flamdeltaprom/WT_3

city: CLERMONT FERRAND

first: Stephanie

last: MAUPETIT MEHOUAS

address: Faculté de Médecine, 28 place Henri DUNANT

country: France

institute: CNRS UMR6293, INSERM U1103 - l’Université Clermont Auvergne (UCA)

description:
Library name: flamWT_3
flam3

data_processing:
Made by BGI : the raw reads were filtered. Data filtering includes removing adapter sequences, contamination and low-quality reads from raw reads.
Alignment against Drosophila melanogaster genome release 6.48 and against Drosophila melanogaster consensus TE (https://github.com/bergmanlab/transposons) using STAR Aligner (v2.7.8a)
raw count using featureCounts v2.0.1
DESeq2_1.30.1 analysis
Assembly: Drosophila melanogaster genome release 6.48 and consensus TE (https://github.com/bergmanlab/transposons)
Supplementary files format and content: count_TJsKD.txt
Supplementary files format and content: count_FDP.txt

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: ovaries are extracted from flies aged from 3-6 days old.

extract_protocol:
total RNA was extracted on ovaries using TRIzol (invitrogen)
DNBSEQ Eukaryotic Strand-specific mRNA library

value: ovaries

value: flamDeltaProm/FM7 ; +/+ ; +/+


title: KPO1-rep2

value: KrasG12D; p53 fl/fl


title: Ovaries_flamdeltaprom/flamdeltaprom_2

description:
Library name: flamDP_2
deltaF2

value: flamDeltaProm/flamDeltaProm ; +/+ ; +/+


title: Ovaries_flamdeltaprom/flamdeltaprom_3

description:
Library name: flamDP_3
deltaF3


title: Ovaries_flamdeltaprom/WT_2

description:
Library name: flamWT_2
flam2


title: WT 56hr replicate 1

description:
Library name: WT_m16
WT 56hr


title: Ovaries_flamdeltaprom/WT_1

description:
Library name: flamWT_1
flam1


title: KPO1-rep1


title: KPO2-rep1


title: RNA_pool_2

description: Library name: Sample2


title: Ovaries_flamdeltaprom/flamdeltaprom_1

description:
Library name: flamDP_1
deltaF1


title: RNA_pool_1

description: Library name: Sample1


title: KPY2-rep3

value: KP-Y


title: E16.5 Mouse Cochlea, SCR240, Ebf1-cKO, ATAC

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
Library name: E16_EbfKO_ATAC
S240_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
CellRanger arc count (2.0) was used to align sequencing reads to the mm10 genome and define ATAC peaks. The aligned data was loaded into R and further analyzed using the Signac (v1.14.0; Stuart et al., 2021) and Seurat (v5.2.1; Hao et al., 2024) packages. Ebf1-cKO and control samples from the same timepoint were combined and analyzed together. To ensure consistent peak definitions, overlapping or adjacent genomic intervals between the two conditions were merged into a single peak, and the peak expression matrix was calculated using the new merged peak set in Signac using ‘FeatureMatrix’ and stored in the ATAC assay.
Assembly: mm10
Supplementary files format and content: Gene and peak expression matrices generated from cellranger arc count are supplied for each age and condition as filtered_feature_bc_matrix.h5 files.
Supplementary files format and content: Additionally, the ATAC fragment files generated from cellranger arc count are supplied as atac_fragments.tsv.gz files

source_name: Cochlea

extract_protocol:
After collecting E14.5 or E16.5 embryos from Ebf1fl/fl females timed-mated with Slc26a9P2A-Cre Ebf1fl/fl males, tail snips were gathered for Slc26a9P2A-Cre qPCR genotyping, and the temporal bones were removed. The cochlear ducts were then dissected in 1% 1 M HEPES diluted in HBSS and pooled according to genotype in cryogenic tubes. Next, the saline solution was removed, and the cochlear ducts were snap frozen and stored in liquid nitrogen. Once E14.5 and E16.5 samples with at least six Slc26a9P2A-Cre Ebf1fl/fl and six Ebf1fl/fl cochlear ducts had been obtained, the samples were thawed on ice, and the nuclei were isolated using a modified version of the protocol for the Chromium Nuclei Isolation Kit (10x Genomics 1000493) that omitted steps involving vortexing or use of a pestle or column. Briefly, the samples were lysed and then filtered using tubes with cell strainer caps (FALCON 352235) before being spun down at 500 RCF for 3 min at 4°C. The nuclei pellets were then washed, centrifuged at 500 RCF for 10 min at 4°C, and resuspended. Following nuclei isolation and purification, samples were centrifuged at 300 RCF for 5 min at 4°C and resuspended in HBSS to reach a concentration of 5000 cells/µL.
Library construction was done with a 9,000 targeted nuclei recovery using the Chromium Next Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics 10000285) following the manufacturer’s protocol. Briefly, nuclei were encapsulated in a gel matrix and uniquely barcoded using the 10x Chromium Controller (Chip J, 10x Genomics 1000230). Libraries were then sequenced using Illumina NovaSeq.

value: Cochlea

tag: developmental stage


title: WT 16hr replicate 2

description:
Library name: WT_m12
WT 16hr


title: WT 16hr replicate 1

description:
Library name: WT_m11
WT 16hr


title: KPY2-rep4


title: Sham 2 h_rep3

city: Changsha

first: Wei

last: Jiang

state: Hunan

address: Lushan Road (S), Yuelu District,Changsha, Hunan Province

department: College of Biology

institute: Hunan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8

source_name: Hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three replicate were cerebral ischemic treated for 2 h.

value: Hippocampus

value: Sham operation


title: KPY2-rep2


title: Primary Adar1f/f/Cre-ER HSCs, Vehicle, culture activation for 4 days

city: Wuhan

first: Yue

last: Xi

state: Hubei

address: 81 St

department: College of life sciences

institute: Wuhan University

description: Library name: Vehicle

data_processing:
Illumina ® TruSeq ® Stranded Total RNA Sample Preparation kits
Illumina Real Time Analysis software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome
RNA-seq analysis was performed using Illumina Real Time Analysis software, STAR, and Cufflinks.
Assembly: GRCm38
Supplementary files format and content: the processed data file includes gene names, FPKM values, log2FC, and p values for each sample
Supplementary files format and content: Excel

source_name: liver

growth_protocol: DMEM with 10% FBS

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit
Libraries were prepared according to Illumina's instructions

value: liver

value: primary hepatic stellate cell

value: nonparenchymal cell

value: vehicle


title: Sham 2 h_rep2


title: Primary Adar1f/f/Cre-ER HSCs, 4-OHT, culture activation for 4 days

description: Library name: 4-OHT

value: 100 nM 4-OHT


title: E16.5 Mouse Cochlea, SCR240, Ebf1-cKO, RNA

description:
Library name: E16_EbfKO_RNA
S240_filtered_feature_bc_matrix.h5


title: WT 4hrs replicate 3

description:
Library name: WT_m9
WT 4hrs

value: Pancreas

value: HPAF-II

value: Cancer

value: WT


title: E16.5 Mouse Cochlea, SCR239, Control, ATAC

description:
Library name: E16_Control_ATAC
S239_filtered_feature_bc_matrix.h5

value: Control


title: KPY2-rep1

value: primary lung tumor

value: epithelial cells


title: KPY1-rep3

value: KrasG12D; p53 fl/fl


title: WT Veh replicate 3

description:
Library name: WT_m5
WT Veh

value: Vehicle


title: Sham 2 h_rep1


title: WT 4hrs replicate 1

description:
Library name: WT_m2
WT 4hrs


title: Cerebral Ischemia 2 h_rep3

value: focal middle cerebral artery occlusion (MCAO)


title: E16.5 Mouse Cochlea, SCR239, Control, RNA

description:
Library name: E16_Control_RNA
S239_filtered_feature_bc_matrix.h5

value: Cochlea


title: E14.5 Mouse Cochlea, SCR238, Ebf1-cKO, RNA

description:
Library name: E14_EbfKO_RNA
S238_filtered_feature_bc_matrix.h5


title: E14.5 Mouse Cochlea, SCR237, Control, ATAC

description:
Library name: E14_Control_ATAC
S237_filtered_feature_bc_matrix.h5


title: pair4, intra, 10% CICI, rep1

description: Library name: pair4_10_rep1

value: strain

value: MATa, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-FKBP12-REV1pr-TetR-FRB, Chr15::433546_LacO, Chr15::966177_TetO, MYO1-CFP-KanMx, NUP49-CFP-KanMx

value: 10% CICI  cell + 90% DMSO cell


title: WT Veh replicate 1

description:
Library name: WT_m1
WT Veh


title: Cerebral Ischemia 2 h_rep2

value: Hippocampus


title: KPY1-rep2

value: KP-Y


title: E14.5 Mouse Cochlea, SCR237, Control, RNA

description:
Library name: E14_Control_RNA
S237_filtered_feature_bc_matrix.h5


title: TapeLift_128_49_2_Tapes

status: Public on Jan 22 2026

type: genomic

city: Heidelberg

first: Oliver

last: Gilliam

address: Im Neuenheimer Feld

country: Germany

institute: German Cancer Research Center

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe package in R environment v4.4.1

label: Cy3 and Cy5

source_name: Epidermis

label_protocol: Standard Illumina Protocol

extract_protocol: For gDNA extraction, 2.5 mL of lysis buffer (10 mM TRIS-HCl, pH 8.0; 5 mM EDTA; 100 mM NaCl; 1% SDS (w/v); 100 µg/mL Proteinase K; 40 µg/mL RNAse A) were added to the 50-mL Falcon tube containing the four adhesive strips, ensuring complete submersion. The tube was then sealed with Parafilm and incubated overnight at 37°C. The following morning, the lysate was transferred to a 15-mL Falcon tube, excluding the strips, and supplemented with 1.25 mL of 5 M sodium chloride solution. After vigorous mixing, the solution was aliquoted into three 1.5-mL Eppendorf tubes and centrifuged at room temperature and maximum speed for 8 minutes. The clear supernatants were pooled into a fresh 15-mL Falcon tube, while the precipitates were discarded. In cases where residual debris remained post-centrifugation, an additional centrifugation step was performed until a debris-free supernatant was obtained.  Subsequently, 4 µL of GlycoBlue Co-precipitant (Thermo) were added to the pooled supernatant, followed by brief vortexing. The solution was further mixed with 2.8 mL of isopropanol by inversion (10–15 repetitions) and incubated at -80°C for 10 minutes. The entire volume was then divided into four 1.5-mL Eppendorf tubes and centrifuged at 4°C and maximum speed for 10 minutes, resulting in the formation of small, visible gDNA pellets. The supernatants were carefully removed, and 50 µL of 70% ethanol were added to each tube to wash the precipitated material. The four pellets were detached and pooled into a single Eppendorf tube using the ethanol, followed by centrifugation at 4°C and maximum speed for 5 minutes. After discarding the supernatant, the pellet was air-dried for a few minutes to ensure the complete evaporation of residual alcohol. Finally, the dried gDNA pellet was resuspended in 40 µL of ddH₂O.

tag: Sex

value: F

value: Epidermis

tag: age


title: WT Veh replicate 2

description:
Library name: WT_m4
WT Veh

value: Pancreas

value: HPAF-II


title: KPY1-rep4


title: TapeLift_127_25_2_Tapes


title: TapeLift_129_28_2_Tapes

value: M


title: Cerebral Ischemia 2 h_rep1


title: KPY1-rep1


title: TapeLift_121_53_Validation


title: TapeLift_126_55_1_Tape


title: TapeLift_123_64_Validation


title: TapeLift_120_51_Validation


title: E14.5 Mouse Cochlea, SCR238, Ebf1-cKO, ATAC

description:
Library name: E14_EbfKO_ATAC
S238_filtered_feature_bc_matrix.h5


title: TapeLift_122_63_Validation


title: TapeLift_118_51_Validation


title: TapeLift_119_50_Validation


title: TapeLift_116_49_Validation


title: TapeLift_114_47_Validation


title: TapeLift_113_48_Validation


title: TapeLift_124_64_Validation


title: TapeLift_115_48_Validation


title: TapeLift_108_21_Validation


title: TapeLift_105_60

type: other

data_processing:
SeSAMe package in R environment v4.4.1
Average Beta

label: Cy3 and Cy57

molecule: other

value: Male


title: TapeLift_125_28_1_Tape


title: TapeLift_106_29_Validation


title: TapeLift_104_82

label: Cy3 and Cy56


title: TapeLift_107_28_Validation


title: TapeLift_102_54

label: Cy3 and Cy54

value: Female


title: TapeLift_109_26_Validation


title: TapeLift_101_26

label: Cy3 and Cy53


title: TapeLift_100_70

label: Cy3 and Cy52


title: TapeLift_117_56_Validation


title: TapeLift_94_21


title: TapeLift_111_31_Validation


title: TapeLift_103_81

label: Cy3 and Cy55


title: TapeLift_110_37_Validation


title: TapeLift_97_29


title: TapeLift_93_23


title: TapeLift_96_27


title: TapeLift_98_26


title: TapeLift_89_39


title: TapeLift_112_35_Validation


title: TapeLift_92_21


title: TapeLift_91_23


title: TapeLift_88_82


title: TapeLift_95_23


title: TapeLift_82_72


title: TapeLift_87_21


title: TapeLift_85_39


title: TapeLift_76_64


title: TapeLift_78_46


title: TapeLift_75_63


title: TapeLift_70_31


title: TapeLift_71_30


title: TapeLift_69_39


title: WT 4hrs replicate 2

description:
Library name: WT_m3
WT 4hrs

value: Cancer

value: WT


title: TapeLift_66_52


title: TapeLift_79_58


title: TapeLift_86_64


title: TapeLift_61_32


title: TapeLift_59_58


title: TapeLift_80_36


title: TapeLift_83_58


title: TapeLift_73_36


title: TapeLift_77_47


title: TapeLift_56_85


title: TapeLift_72_71


title: TapeLift_65_64


title: TapeLift_63_30


title: TapeLift_67_76


title: TapeLift_84_54


title: TapeLift_48_23


title: WT7_wt_low, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 15 μg/L

city: Buffalo

first: Charikleia

last: Karageorgiou

state: NY

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

description:
Library name: WT7
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

data_processing:
Mutltiple tools (FastQC, MultiQC, cutadapt, Bowtie2, samtools, featureCounts, DESeq2)
Sequence reads were assessed with FastQC and MultiQC
RNA-seq reads were mapped to Kluyveromyces lactis CBS 2359 reference (Klac_CBS2359_s29) using bowtie2
RNA-seq reads were quantified using featureCounts
The differential expression analysis was carried out using DESeq2
Assembly: Kluyveromyces lactis CBS 2359; GenBank assembly accession GCA_000002495.2 (Klac_CBS2359_s29).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include Deseq2 normalized values for each Sample

organism: Kluyveromyces lactis

source_name: LRY2992 (MATa SIR2 hmldelta hmrdelta)

growth_protocol: Kluyveromyces lactis strains LRY2992 (WT, MATa SIR2 hmlΔ hmrΔ) and LRY2993 (sir2Δ, MATα sir2Δ hmlΔ hmrΔ) were streaked on YPD, then inoculated into 10 mL YM minimal medium (yeast nitrogen base lacking niacin + 5 g/L (NH₄)₂SO₄ + 20 g/L glucose) supplemented with 400 µg/L nicotinic acid and grown overnight at 30 °C. Overnight cultures were diluted to OD₆₀₀ ≈ 0.3 in the same medium containing the indicated nicotinic-acid concentration (15, 45, 135 or 400 µg L⁻¹) and incubated 4 h (OD₆₀₀ ≈ 1.0) before harvest.

extract_protocol:
Ten OD₆₀₀ units of log-phase cells were washed in 500μl AE buffer (50mM NaoAc, ph=5.3; 10mM EDTA) and stored at -80°C. Frozen pellets were resuspended in 500μl AE/SDS buffer (10 parts AE: 1 part 10% SDS) and an equal amount of phenol-equilibrated with citrate (pH 4.5), vortexed and incubated at 65 °C for 4 min as per Schmitt et al., 1990. A second extraction with phenol/chloroform was followed by ethanol precipitation. Residual DNA was removed with DNase I (NEB M0303S).
Poly(A)⁺ RNA selection and library preparation were completed by Azenta sequencing services. Paired-end 150 bp reads were generated on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: Intracellular NAD⁺ was modulated solely by the precursor concentration. No other treatments were applied. WT and sir2Δ strains were grown in parallel at each nicotinic-acid level to separate genotype from metabolic effects.

value: LRY2992 (MATa SIR2 hmldelta hmrdelta)

value: yeast cells

value: nicotinic acid 15 μg/L


title: WT6_wt_lmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: WT6
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 45 μg/L


title: TapeLift_62_78


title: WT8_wt_low, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: WT8
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: WT5_wt_lmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: WT5
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: TapeLift_46_61


title: TapeLift_68_36


title: TapeLift_58_53


title: TapeLift_44_35


title: TapeLift_74_26


title: RESUB_WT1R_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: RESUB-WT1R
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 400 μg/L


title: WT2_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: WT2
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: TapeLift_52_59


title: WT4_wt_hmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: WT4
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: nicotinic acid 135 μg/L


title: TapeLift_60_66


title: compound 20_4_2

first: hongxuan

last: cao

address: 152 Luoyu Road, Hongshan District

institute: Central China Normal University

description:
Library name: Sample 5
column name in All_Samples_FPKM.txt: CHX45-2_FPKM

data_processing:
1.Genome mapping using hisat2 verion 2.1.0 with parameter --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000 -x ref.genome.fa -1 sample_1.fq.gz -2 sample_2.fq.gz.
2.Transcript assembly using stringTie version 1.3.3 with parameter sample.bam -G ref.gtf -o stringtie.gtf -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8.
3. Merge all sample’s gtf using cuffmerge in cufflinks version 2.2.1 and Compare with reference annotation information to select new transcripts using cuffcompare in cufflinks version 2.2.1.
4.Predict the protein coding potential of new transcripts using CPC version 0.9-r2 with Default parameters.
5. Calculate the expression levels of genes and transcripts using stringTie verison 1.3.3 .
Assembly: GCA 000182965.3
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Candida albicans

source_name: C. albicans SC5314 cells

extract_protocol:
RNA was extracted using a RiboPure-Yeast kit (Ambion) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: C. albicans SC5314 cells

value: Wild-type

value: treated with 4 μM compound 20

value: 3 hours


title: compound 20_4_3

description:
Library name: Sample 6
column name in All_Samples_FPKM.txt: CHX45-3_FPKM


title: TapeLift_40_30

value: Epidermis


title: compound 20_4_1

description:
Library name: Sample 4
column name in All_Samples_FPKM.txt: CHX45-1_FPKM


title: TapeLift_55_38


title: contr_3

description:
Library name: Sample 3
column name in All_Samples_FPKM.txt: DMSO-1_FPKM

value: without drug treatment


title: TapeLift_39_56


title: TapeLift_54_85


title: TapeLift_51_18


title: TapeLift_53_60


title: TapeLift_49_63


title: KS25_II559_3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: 13712-KS-9

data_processing:
Raw FASTQs were processed thrgouh the nf-core RNA-seq pipeline
Assembly: GRCh38
Supplementary files format and content: Gene quantification from RSEM STAR

source_name: human

growth_protocol: Fibroblasts were maintained in Dulbecco’s Modified Eagle Medium (DMEM, high glucose) supplemented with 10% fetal bovine serum and cultured at 37 °C in a humidified 5% CO₂ incubator

extract_protocol:
Total RNA was extracted using the Zymo Research RNA isolation kit
Poly(A)-enriched, stranded mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit, quantified, pooled equimolarly, and sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150-bp reads

treatment_protocol: Human fibroblasts at early confluence were serum-starved in 0.5% FBS for 12 hours, pre-treated with the NNMT inhibitor II559 for 12 hours, and then stimulated with TGFβ1 for an additional 72 hours.

value: human

value: fibroblast

value: All batch are same


title: TapeLift_50_47

value: Female


title: KS25_II559_2

description: Library name: 13712-KS-8


title: TapeLift_47_62

value: Male


title: DEL7_del_low, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: DEL7
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

source_name: LRY2993 (MATalpha sir2delta hmldelta hmrdelta)


title: KS25_II559_1

description: Library name: 13712-KS-7


title: TapeLift_34_80


title: DEL5_del_lmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: DEL5
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: LRY2993 (MATalpha sir2delta hmldelta hmrdelta)


title: DEL6_del_lmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 45 μg/L

description:
Library name: DEL6
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: yeast cells


title: TapeLift_33_27


title: KS25_CTR_3

description: Library name: 13712-KS-3

value: Control


title: TapeLift_43_63


title: TapeLift_42_61


title: WT3_wt_hmid, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: WT3
LRY2992 (MATa SIR2 hmlΔ hmrΔ)

value: LRY2992 (MATa SIR2 hmldelta hmrdelta)


title: TapeLift_41_55


title: RESUB_DEL8_del_low, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 15 μg/L

description:
Library name: RESUB-DEL8
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: nicotinic acid 15 μg/L


title: contr_2

description:
Library name: Sample 2
column name in All_Samples_FPKM.txt: DMSO-1_FPKM


title: DEL2_del_high, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: DEL2
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: nicotinic acid 400 μg/L


title: TC32-FLI1-MMA-100nM-18hr-biolrep2

first: Patrick

middle: J

last: Grohar

address: 1600 Huron Pkwy

institute: University of Michigan Medical School

description: Library name: 182G

data_processing:
Sequence quality by FASTQc
Trimmed with Trim Galore v6.6
aligned, peaks called with Macs2 v 2.2.4
FRIP using bedtools
Assembly: HG38
Supplementary files format and content: FASTqc
Library strategy: CUT&Tag

source_name: Cell line

growth_protocol: RPMI with 10% FBS and P/S

extract_protocol:
Purified on column
Tagmented as part of Cut&Tag protocol

treatment_protocol: Plate, recover overnight, apply drug for described times

value: Cell line

value: Ewing sarcoma

value: WT

tag: cut&tag antibody

value: Mithramycin 100nM 18hr


title: contr_1

description:
Library name: Sample 1
column name in All_Samples_FPKM.txt: DMSO-1_FPKM

value: C. albicans SC5314 cells

value: Wild-type

value: 3 hours


title: TapeLift_30_48

value: Epidermis


title: TC32-FLI1-Solvent-18hr-biolrep1

description: Library name: 182E

value: Solvent (PBS)


title: TC32-FLI1-MMA-100nM-18hr-biolrep1

description: Library name: 182F


title: TapeLift_29_34

value: Female


title: DEL1_del_high, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: DEL1
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: RESUB_WT1_wt_high, LRY2992 (MATa SIR2 hmlΔ hmrΔ), nicotinic acid 400 μg/L

description:
Library name: RESUB-WT1
LRY2992 (MATa SIR2 hmlΔ hmrΔ)


title: KS25_CTR_1

description: Library name: 13712-KS-1

value: human

value: fibroblast

value: All batch are same


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 3

city: Berkeley

first: Britt

middle: Aspen

last: Glaunsinger

state: CA

address: 565 Li Ka Shing Center

department: Department of Plant and Microbial Biology

institute: University of California, Berkeley

description:
Library name: BGXM003L
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

data_processing:
Reads were trimmed with Trimmomatic v0.39
Trimmed reads were aligned to a concatenated human (hg38) and yeast (SacCer3) genome with bowtie 2 v2.5.2
The BAM files were then deduplicated with UMI_tools v1.1.5
The spike-in normalization factors were calculated by counting reads mapped to yeast genome using Samtools idxstats(Li et al., 2009), followed by conversion to scaling factors that are proportional to the reciprocal to the spike-in read counts.
Alternatively, the normalization factors were calculated according to Greenlist method by de Mello et al (de Mello et al. 2024), using Deeptools multibamSummary functions to quantify reads in the greenlist regions provided and to calculate scaling factors.
BigWig files were generated with Deeptools bamCoverage function, using scaling factors generated above. BigWig files of biological replicates were averaged using Deeptools bigwigAverage function. For both operations, bin sizes were set to 20bp. Differential binding analysis was performed with DiffBind v3.12.0.
Assembly: hg38, SacCer3
Supplementary files format and content: Scaled BigWig files by Deeptools
Library strategy: CUT&Run

growth_protocol: A549 WT and RNase L-KO cells were maintained in DMEM supplemented with 10% FBS in humidified incubator with 5% CO2 at 37°C

extract_protocol:
CUT&RUN was done according to previous reports (Miura and Chen, 2020; Morgens et al., 2025) with modifications. Briefly, 250,000 A549 WT or RNase L KO cells per well were seeded on a 12-well plate and cultured overnight before transfection. Then cells were then transfected with RNAiMAX alone or with 0.76 μg/ml poly(I:C) for 4 hours The cells were permeabilize on plate with 500μL Perm buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma, S2626), 0.1% Triton X-100 (Sigma, X100), and proteinase inhibitor (Roche, 04693132001)) for 15 minutes at room temperature. The cells were washed again with Perm buffer then incubated with either anti-Rpb1 S5P CTD (4H8, Cell Signaling, cat #2629) at 1: 50 dilution, equal mass of mouse normal IgG (Santa Cruz, cat # sc-2025), or anti-Rpb1 S2P CTD (clone E1Z3G, Cell Signaling, cat # 13499) at 1: 50 dilution, in 200μL Perm buffer for 1 hour at room temperature. The cells were then washed twice with Perm buffer and incubated with pAG-MNase (Cell Signaling, cat #40366) at 1:33 dilution in 200μL Perm buffer for 1 hour at room temperature.  The cells were then washed twice with Perm buffer and chill on ice. Then 225 μL ice-cold Perm buffer containing 5 mM CaCl2 was dispensed per well, and the plate was incubated in a refrigerator at 4°C for 30 min for targeted digestion. The reaction was halted by adding 75 μL 4× STOP solution (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 100 μg/ml RNase A (Invitrogen, cat # 12091021) and 0.1% Triton X-100, spiked with yeast genomic DNA (Cell Signaling, cat #40366) at 10pg per sample for 4H8 and IgG, 30pg per sample for E1Z3G). The plate was then incubated at 37°C for 30min to facilitate fragment release. The supernatant was collected and then 3μL 20% SDS solution and 3.75μL 20mg/ml proteinase K solution was added. The mixture was then incubated at 50°C for 1 hour. The DNA was extracted with phenol:chloroform.
The sequencing library was constructed with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, cat # E7645L) following a previous report (Liu et al., 2018a) with modifications. Briefly, equal volume of purified DNA fragments was used. End prep was performed at 20°C for 30 min and then 50°C for 60min to prevent short fragment melting. Fragments were then ligated to adaptors from NEBNext® Multiplex Oligos for Illumina® (Unique Dual Index UMI Adaptors DNA Set 1, NEB, cat # E7395S) and cleaned up twice with 1.1X Ampure XP beads (Beckman Coutler, cat # A63880). The resulting ligated products were then PCR amplified for 10 cycles for 4H8 and E1Z3G, and 14 cycles for IgG samples, respectively. The cycle numbers were determined empirically by qPCR. The amplified libraries were double-sided size selected with 0.6X and 1.1X Ampure XP beads and further cleaned up by 1 round with 1.1X bead for 4H8, E1Z3G, or 3 rounds for IgG samples, to remove adaptor dimers.  The libraries were sequenced on AVITI platform (Element Biosciences) by UC Davis sequencing core.

treatment_protocol: 250,000 A549 WT or RNase L KO cells per well were seeded on a 12-well plate and cultured overnight before transfection. Then cells were then transfected with RNAiMAX alone or with 0.76 μg/ml poly(I:C) for 4 hours.

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells

value: RNase L-KO

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 S2P CTD (E1Z3G)


title: TC32-FLI1-Media-18hr-biolrep1

description: Library name: 182C

value: Media


title: TC32-H3K27Ac-Media-18hr-biolrep1

description: Library name: 182A

value: Cell line


title: KS25_TGF_3

description: Library name: 13712-KS-6


title: TapeLift_26_57


title: TapeLift_38_61


title: TapeLift_36_26

value: Male


title: A549 WT, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 3

description:
Library name: BGXM003J
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: WT


title: KS25_TGF_2

description: Library name: 13712-KS-5


title: TC32-FLI1-MMA-20nM-72hr-biolrep1

description: Library name: 181F

value: Ewing sarcoma

value: Mithramycin 20nM 72hr


title: TC32-FLI1-Media-72hr-biolrep3

description: Library name: 181E


title: KS25_TGF_1

description: Library name: 13712-KS-4


title: A549 WT, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 3

description:
Library name: BGXM003I
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: mock-transfected with RNAiMAX; antibody RPB1 S2P CTD (E1Z3G)


title: KS25_CTR_2

description: Library name: 13712-KS-2

value: Control


title: TapeLift_23_59

value: Epidermis


title: TC32-FLI1-Media-72hr-biolrep1

description: Library name: 181C


title: TapeLift_32_73


title: DEL3_del_hmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: DEL3
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)

value: LRY2993 (MATalpha sir2delta hmldelta hmrdelta)

value: yeast cells

value: nicotinic acid 135 μg/L


title: DEL4_del_hmid, LRY2993 (MATα sir2Δ hmlΔ hmrΔ), nicotinic acid 135 μg/L

description:
Library name: DEL4
LRY2993 (MATα sir2Δ hmlΔ hmrΔ)


title: TC32-IgG-Media-72hr-biolrep1

description: Library name: 181B

value: IgG


title: TapeLift_31_54


title: RPTEC/TERT1 / fHDF/TERT166 co-cultures on LN/PC, replicate 2

city: Stuttgart

first: Florian

last: Büttner

address: Auerbachstraße 112

institute: Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology

description: Library name: PRF_2

data_processing:
Raw RNA-seq data were processed using the nf-core/rnaseq pipeline (version 3.18.0). Transcript expression was quantified by Salmon (version 1.10.3) with gene annotations from gencode (version 46). Genes with a minimum TPM > 1 across at least 2 samples were analysed with the DESeq2 package in R (4.3.1.). Count data were normalized by variance-stabilizing transformation.
Assembly: Gencode (version 46)
Supplementary files format and content: tab-delimited text file includes variance stabilization normalized gene counts for all samples for genes with a minimum TPM > 1 across at least 2 samples

growth_protocol: Immortalized renal epithelial cells RPTEC/TERT1 and immortalized human dermal fibroblasts fHDF/TERT166 were purchased from Evercyte GmbH, Vienna, Austria. RPTEC cells were cultured in a 1:1 mixture of DMEM without glucose and Ham’s F12, resulting in a final concentration of 5 mM glucose, and supplemented with 2 mM GlutaMAX, 5 μg/ml bovine insulin, 5 μg/ml transferrin, 10 ng/ml epidermal growth factor, 36 ng/ml hydrocortisone, 5 ng/ml sodium selenite, 100 U/ml penicillin and 100 μg/ml streptomycin and 0.5% FBS. Fibroblasts were expanded in DMEM/F12 (1:1) with glutamine and 1.2 g/L NaHCO3, supplemented with 10% FBS and 100 μg/ml G418. For co-cultures, RPTEC cell medium was used as previously described. RPTEC were seeded at a density of 140,000 cells/cm2 and fibroblasts at a density of 14,000 cells/cm2. Fibroblasts were seeded 30 minutes prior to seeding of RPTEC to allow for cell attachment. The cells were cultured at 37 °C and 5% CO2, and the medium was renewed every 48 to 72 hours. Experiments were performed 14 days after seeding to allow differentiation of RPTEC.

extract_protocol:
SR, SRF, PR, PRF and F cultures were washed once with DPBS. The LN/FN-silk membranes (SR, SRF) were then scraped off, the LN/PC membranes (PR, PRF) were cut out from the holder with an autoclaved blade and the basolateral fibroblasts (F) were scrapped off from the bottom of the well. Three to eight membranes were pooled and stored in 100 µl RNAlater. The samples were snap-frozen and stored at -80 °C until further processing. Total RNA was isolated using the Zymo Quick-RNA Microprep Kit including DNAse treatment according to the manufacturer’s instructions.
Samples were processed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads and fragmented. Subsequently synthesized cDNA was ligated to the sequencing adapters before amplification by PCR. Clustering and DNA sequencing were performed on a NovaSeqX plus instrument (Illumina) with a final loading concentration of 160 pM DNA at GenomeScan BV, Leiden, The Netherlands.

value: Immortalized renal proximal tubular epithelial cells


title: TapeLift_20_33


title: RPTEC/TERT1 monocultures on LN/PC, replicate 3

description: Library name: PR_3


title: RPTEC/TERT1 monocultures on LN/PC, replicate 1

description: Library name: PR_1


title: RPTEC/TERT1 monocultures on LN/PC, replicate 2

description: Library name: PR_2


title: TC32-FLI1-MMA-20nM-72hr-biolrep2

description: Library name: 181G


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 1

description:
Library name: BGXM003D
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells


title: TC32-FLI1-MMA-100nM-18hr-biolrep3

description: Library name: 182H

value: Mithramycin 100nM 18hr


title: fHDF/TERT166 monocultures, replicate 3

description: Library name: F_3

value: Immortalized foreskin dermal fibroblasts


title: fHDF/TERT166 monocultures, replicate 2

description: Library name: F_2


title: TC32-IgG-Media-18hr-biolrep1

description: Library name: 182B

value: Media


title: TapeLift_19_24

value: Female


title: TC32-FLI1-Media-18hr-biolrep2

description: Library name: 182D

value: Cell line


title: A549 RNaseL-KO, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 3

description:
Library name: BGXM003K
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: RNase L-KO


title: TapeLift_27_56

value: Male


title: A549 RNaseL-KO, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 1

description:
Library name: BGXM003C
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G


title: TapeLift_18_24


title: TapeLift_25_58


title: RPTEC/TERT1 / fHDF/TERT166  co-cultures on LN/FN-silk, replicate 2

description: Library name: SRF_2


title: TC32-FLI1-MMA-20nM-72hr-biolrep3

description: Library name: 181H

value: Ewing sarcoma

value: WT

value: Mithramycin 20nM 72hr


title: TapeLift_16_23

value: Epidermis


title: TC32-FLI1-Media-72hr-biolrep2

description: Library name: 181D


title: TapeLift_24_50


title: RPTEC/TERT1 / fHDF/TERT166  co-cultures on LN/FN-silk, replicate 1

description: Library name: SRF_1


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 2

description:
Library name: BGXM003H
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 S2P CTD (E1Z3G)


title: TapeLift_13_47


title: A549 RNaseL-KO, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 2

description:
Library name: BGXM003G
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: mock-transfected with RNAiMAX; antibody RPB1 S2P CTD (E1Z3G)


title: A549 WT, mock-transfected, IgG control CUT&RUN-seq replicate 2

description:
Library name: BGXM002N
RPB1 S5P occupancy profiling by RPB1 antibody IgG control

data_processing:
Reads were trimmed with Trimmomatic v0.39    Trimmed reads were aligned to a concatenated human (hg38) and yeast (SacCer3) genome with bowtie 2 v2.5.2      The BAM files were then deduplicated with UMI_tools v1.1.5      The spike-in normalization factors were calculated by counting reads mapped to yeast genome using Samtools idxstats(Li et al., 2009), followed by conversion to scaling factors that are proportional to the reciprocal to the spike-in read counts.    Alternatively, the normalization factors were calculated according to Greenlist method by de Mello et al (de Mello et al. 2024), using Deeptools multibamSummary functions to quantify reads in the greenlist regions provided and to calculate scaling factors.      BigWig files were generated with Deeptools bamCoverage function, using scaling factors generated above. BigWig files of biological replicates were averaged using Deeptools bigwigAverage function. For both operations, bin sizes were set to 20bp. Differential binding analysis was performed with DiffBind v3.12.0.
Assembly: hg38, SacCer3
Supplementary files format and content: bw

extract_protocol:
The cells were permeabilize on plate with 500μL Perm buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma, S2626), 0.1% Triton X-100 (Sigma, X100), and proteinase inhibitor (Roche, 04693132001)) for 15 minutes at room temperature. The cells were washed again with Perm buffer then incubated with either anti-Rpb1 S5P CTD (4H8, Cell Signaling, cat #2629) at 1:50 dilution in 200μL Perm buffer or equal mass of mouse normal IgG (Santa Cruz, cat # sc-2025) for 1 hour at room temperature. The cells were then washed twice with Perm buffer and incubated with pAG-MNase (Cell Signaling, cat #40366) at 1:33 dilution in 200μL Perm buffer for 1 hour at room temperature.  The cells were then washed twice with Perm buffer and chill on ice. Then 225 μL ice-cold Perm buffer containing 5 mM CaCl2 was dispensed per well, and the plate was incubated in a refrigerator at 4°C for 30 min for targeted digestion. The reaction was halted by adding 75 μL 4× STOP solution (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 100 μg/ml RNase A (Invitrogen, cat # 12091021) and 0.1% Triton X-100, spiked with yeast genomic DNA (Cell Signaling, cat #40366) at 10pg per sample). The plate was then incubated at 37°C for 30min to facilitate fragment release. The supernatant was collected and then 3μL 20% SDS solution and 3.75μL 20mg/ml proteinase K solution was added. The mixture was then incubated at 50°C for 1 hour. The DNA was extracted with phenol:chloroform.
The sequencing library was constructed with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, cat # E7645L) with modifications. Briefly, equal volume of purified DNA fragments was used. End prep was performed at 20°C for 30 min and then 50°C for 60min to prevent short fragment melting. Fragments were then ligated to adaptors from NEBNext® Multiplex Oligos for Illumina® (Unique Dual Index UMI Adaptors DNA Set 1, NEB, cat # E7395S) and cleaned up twice with 1.1X Ampure XP beads (Beckman Coutler, cat # A63880). The resulting ligated products were then PCR amplified for 10 cycles and 14 cycles for 4H8 and IgG samples, respectively. The cycle numbers were determined empirically by qPCR. The amplified libraries were double-sided size selected with 0.6X and 1.1X Ampure XP beads and further cleaned up by 1 round or 3 rounds with 1.1X bead for 4H8 or IgG samples, respectively, to remove adaptor dimers.

value: mock-transfected with RNAiMAX; antibody IgG control


title: A549 WT, mock-transfected, IgG control CUT&RUN-seq replicate 3

description:
Library name: BGXM002O
RPB1 S5P occupancy profiling by RPB1 antibody IgG control


title: RPTEC/TERT1 monocultures on LN/FN-silk, replicate 2

description: Library name: SR_2


title: RPTEC/TERT1 / fHDF/TERT166 co-cultures on LN/PC, replicate 3

description: Library name: PRF_3


title: RPTEC/TERT1 monocultures on LN/FN-silk, replicate 1

description: Library name: SR_1


title: TC32-H3K27Ac-Media-72hr-biolrep1

description: Library name: 181A


title: TapeLift_21_44


title: CD74 positive cells in H2030-BrM model replicate #3

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description:
Library name: S18-CD74p
SingleRead 85 bases

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (GRCm39) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Assembly: GRCm39/vM26
Supplementary files format and content: tab-delimited text file includes normalized transcripts abundance measured in FPKM values

source_name: H2030-BrM brain metastasis

growth_protocol: B16/F10-BrM iCr tumors or H2030-BrM ic brain metastasais were generated. At endpoint, CD74+/CD74-  CX3CR1+ CD11b+ cells were sorted  from the tumors using CD74-AF647 (BioLegend, 151003), CX3CR1-APC/Fire750 (BioLegend, 149039), CD11b-PerCP-Cy5.5 (eBioscience, 45-0112-82)

extract_protocol:
RNA was harvested using PicoPure RNA isolation Kit (ThermoFisher).
Total RNA samples were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Briefly, an oligo(dT) primed reverse transcription with a template switching reaction was followed by double stranded cDNA production by limited-cycle PCR.  {Non-directional}  sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805) and subsequently analysed on an Illumina instrument (see below) by following manufacturer's protocols.

value: H2030-BrM brain metastasis

value: CD74 positive microglia/macrophages


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 3

description:
Library name: BGXM002L
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 CTD (4H8)


title: CD74 positive cells in H2030-BrM model replicate #4

description:
Library name: S9-CD74p
SingleRead 85 bases


title: TapeLift_22_50


title: SHP-77 Lurbi 3

city: Indianapolis

first: Misty

last: Shields

state: IN

address: 980 W. Walnut St

institute: Indiana University

description: Library name: Sample 24

data_processing:
The sequence data were mapped to the human reference genome hg38 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.4.17).
Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -Q 10”. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR (v.4.2.0).
False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Lung cancer cells

growth_protocol: All cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Qiagen RNeasy Plus MiniKit
100 nanograms of total RNA was used for library preparation with the llumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit

value: Lung cancer cells

value: SHP-77 Lurbi 3


title: A549 WT, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 2

description:
Library name: BGXM003F
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G


title: TapeLift_11_44


title: CD74 positive cells in H2030-BrM model replicate #2

description:
Library name: S17-CD74p
SingleRead 85 bases


title: SHP-77 Lurbi 2

description: Library name: Sample 23

value: SHP-77 Lurbi 2


title: SHP-77 Lurbi 1

description: Library name: Sample 22

value: SHP-77 Lurbi 1


title: A549 WT, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 2

description:
Library name: BGXM003E
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G


title: A549 WT, mock-transfected, IgG control CUT&RUN-seq replicate 1

description:
Library name: BGXM002M
RPB1 S5P occupancy profiling by RPB1 antibody IgG control


title: CD74 negative cells in H2030-BrM model replicate #4

description:
Library name: S9-CD74m
SingleRead 85 bases

value: CD74 negative microglia/macrophages


title: TapeLift_8_48

value: Female


title: RPTEC/TERT1 / fHDF/TERT166 co-cultures on LN/PC, replicate 1

description: Library name: PRF_1

value: Immortalized renal proximal tubular epithelial cells


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 2

description:
Library name: BGXM002H
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: RNase L-KO


title: A549 WT, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 3

description:
Library name: BGXM002I
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: WT

value: mock-transfected with RNAiMAX; antibody RPB1 CTD (4H8)


title: CD74 negative cells in H2030-BrM model replicate #3

description:
Library name: S18-CD74m
SingleRead 85 bases


title: fHDF/TERT166 monocultures, replicate 1

description: Library name: F_1

value: Immortalized foreskin dermal fibroblasts


title: SHP-77 DMSO 2

description: Library name: Sample 20

value: SHP-77 DMSO 2


title: A549 WT, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 3

description:
Library name: BGXM002J
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8


title: DKO 3 (Gli1-CreER;Arid1afl/fl;Arid1bfl/fl)_RNA-seq

city: Los Angeles

first: Mingyi

last: Zhang

address: 2250 Alcazar Street, CSA103, HSC

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

description: Library name: S31_DKO

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
Upper quartile was used to normalize the data and differential expression was calculated by selecting transcripts that changed with FDR<0.1
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample

source_name: incisor mesenchyme

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Freshly collected proximal mouse incisor from Gli1-CreER;Arid1afl/fl;Arid1bfl/fl mice were collected at 4 days post-tamoxifen induction for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
cDNA library preparation and sequencing were performed at the Molecular Genomics Core at the University of Southern California.

treatment_protocol: 20ml/ml concentrated tamxifen was administered to mice via intraperitoneal injection at a dosage of 1.5mg/10g body weight

value: incisor mesenchyme

value: Tamoxifen induction


title: A549 WT, transfected with poly(I:C), RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 1

description:
Library name: BGXM003B
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 S2P CTD (E1Z3G)


title: A549 RNaseL-KO, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 2

description:
Library name: BGXM002G
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells


title: A549 WT, mock-transfected, RPB1 S2P CTD (E1Z3G) CUT&RUN-seq replicate 1

description:
Library name: BGXM003A
RPB1 S2P occupancy profiling by RPB1 antibody clone E1Z3G

value: mock-transfected with RNAiMAX; antibody RPB1 S2P CTD (E1Z3G)


title: DKO 2 (Gli1-CreER;Arid1afl/fl;Arid1bfl/fl)_RNA-seq

description: Library name: S20_DKO


title: DKO 1 (Gli1-CreER;Arid1afl/fl;Arid1bfl/fl)_RNA-seq

description: Library name: S19_DKO


title: TapeLift_15_56

value: Male

value: Epidermis


title: TapeLift_6_53


title: H82 Lurbi 3

description: Library name: Sample 18

value: Lung cancer cells

value: H82 Lurbi 3


title: RPTEC/TERT1 monocultures on LN/FN-silk, replicate 3

description: Library name: SR_3


title: CD74 negative cells in H2030-BrM model replicate #1

description:
Library name: S16-CD74m
SingleRead 85 bases

value: H2030-BrM brain metastasis

value: CD74 negative microglia/macrophages


title: TapeLift_5_27


title: RPTEC/TERT1 / fHDF/TERT166  co-cultures on LN/FN-silk, replicate 3

description: Library name: SRF_3

value: Immortalized renal proximal tubular epithelial cells


title: CD74 positive cells in B16/F10-BrM model replicate #4

description:
Library name: S14-CD74p
SingleRead 85 bases

source_name: B16/F10-BrM brain metastasis

value: B16/F10-BrM brain metastasis

value: CD74 positive microglia/macrophages


title: A549 WT, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 2

description:
Library name: BGXM002E
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: WT

value: mock-transfected with RNAiMAX; antibody RPB1 CTD (4H8)


title: TapeLift_4_27


title: H82 Lurbi 1

description: Library name: Sample 16

value: H82 Lurbi 1


title: TapeLift_12_46

value: Female


title: H82 Lurbi 2

description: Library name: Sample 17

value: H82 Lurbi 2


title: A549 RNaseL-KO, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 1

description:
Library name: BGXM002D
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: RNase L-KO

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 CTD (4H8)


title: TapeLift_14_82


title: TapeLift_2_30


title: A549 RNaseL-KO, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 3

description:
Library name: BGXM002K
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells


title: CD74 positive cells in B16/F10-BrM model replicate #1

description:
Library name: S11-CD74p
SingleRead 85 bases


title: H82 DMSO 2

description: Library name: Sample 14

value: H82 DMSO 2


title: TapeLift_10_40

value: Epidermis


title: CD74 positive cells in H2030-BrM model replicate #1

description:
Library name: S16-CD74p
SingleRead 85 bases


title: TapeLift_9_27


title: A549 WT, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 1

description:
Library name: BGXM002B
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8


title: A549 WT, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 1

description:
Library name: BGXM002A
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8


title: TapeLift_3_35


title: CD74 negative cells in H2030-BrM model replicate #2

description:
Library name: S17-CD74m
SingleRead 85 bases


title: H82 DMSO 3

description: Library name: Sample 15

value: Lung cancer cells

value: H82 DMSO 3


title: TapeLift_7_28

value: Male


title: CD74 negative cells in B16/F10-BrM model replicate #3

description:
Library name: S13-CD74m
SingleRead 85 bases

value: CD74 negative microglia/macrophages


title: CD74 negative cells in B16/F10-BrM model replicate #2

description:
Library name: S12-CD74m
SingleRead 85 bases


title: SHP-77 DMSO 1

description: Library name: Sample 19

value: SHP-77 DMSO 1


title: NP treated PT

first: Lonnie

last: Shea

institute: University of Michigan- Ann Arbor

description:
Library name: 10577-KG-5
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

data_processing:
This pool was subjected to 28x151bp of sequencing according to the manufacturer’s protocol (Illumina NovaSeqXPlus). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. Cell Ranger (v8.8.0) was used to align reads to mouse reference GRCm38 (mm10-2020-A).
per-sample-out .bam files were converted to fastq using Cell Ranger (v9.0.1) bamtofastq: bamtofastq --reads-per-fastq=500000000000 <input file> <output file>
Assembly: GRCm38 (mm10-2020-A)
Supplementary files format and content: tab-separated values files and matrix files

source_name: Primary tumor

growth_protocol: 4T1-tdTomato-luc2 purchased from Perkin Elmer were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Avantor) at 37°C and 5% CO2. 4T1 cells were authenticated by short tandem repeat profiling (ATCC). 4T1 cells were enzymatically detached using 0.25% trypsin-EDTA (Gibco) and resuspended in Dulbecco’s phosphate buffer saline (DPBS, Gibco) at a density of 2e6 cells/mL for inoculation. Eight-week-old, female BALB/c mice (Jackson strain #000651) were orthotopically inoculated with 50 μL of cell suspension in their fourth right mammary fat pad.

extract_protocol:
Lungs were explanted and mechanically minced with scalpels and enzymatically digested with TM liberase (Roche) and 150 U/mL DNase I (Sigma) for 30 minutes at 37°C. Digested lungs were then passed through 70 μm cell strainers (Corning) and washed with DPBS supplemented with 0.5% bovine serum albumin and 2mM EDTA (MACS buffer). Lungs were then processed with ACK buffer (Gibco) for 5 minutes at room temperature to lyse erythrocytes and quenched with MACS buffer. The resulting single cell suspensions were resuspended at a concentration of 1e6 cells/100 μL for flow cytometry sorting. Cells were then prepared for flow-assisted cell sorting by staining with AF488-CD45 (Biolegend) and sorted into CD45+NP+, CD45+NP-, and CD45- populations on the Bigfoot Cell Sorter (Invitrogen). Primary tumors were excised, mechanically minced with scalpels and enzymatically digested using the tumor dissociation kit (TDK, Miltenyi), incubated for 30 min at 37°C. Digested PTs were then passed through 70 μm cell strainers (Corning) and washed with DPBS supplemented with 0.5% bovine serum albumin and 2mM EDTA (MACS buffer). PTs were then processed with ACK buffer (Gibco) for 5 minutes at room temperature to lyse erythrocytes and quenched with MACS buffer. Single cell suspesions of lung and PT were treated with Chromium Fix RNA Profiling kit according to manufacturers instructions.
Chromium Fix RNA Profiling (10x Genomics) using the Chromium Mouse Transcriptome Probe Set v1.0.1.

treatment_protocol: Mice were treated intravenously with saline (control) or 1mg of NPs every three days starting at D1 post-inocluation (D1, 4, 7, 10, 13 NP treatments).

value: Primary tumor

value: 8-10 weeks

value: female

value: BALB/c

value: NP

tag: disease model

value: 4T1 triple negative breast cancer


title: SHP-77 DMSO 3

description: Library name: Sample 21

value: SHP-77 DMSO 3


title: H209 Lurbi 1

description: Library name: Sample 10

value: H209 Lurbi 1


title: H209 DMSO 2

description: Library name: Sample 8

value: H209 DMSO 2


title: A549 WT, transfected with poly(I:C), RPB1 CTD (4H8) CUT&RUN-seq replicate 2

description:
Library name: BGXM002F
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: Adenocarcinomic Human Alveolar Basal Epithelial Cells

value: WT

value: transfected with 0.76 μg/ml poly(I:C); antibody RPB1 CTD (4H8)


title: NP treated lung, sorted NP-CD45+

description:
Library name: 10577-KG-2
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

source_name: Lung

value: Lung


title: CD74 positive cells in B16/F10-BrM model replicate #2

description:
Library name: S12-CD74p
SingleRead 85 bases

value: B16/F10-BrM brain metastasis

value: CD74 positive microglia/macrophages


title: A549 RNaseL-KO, mock-transfected, RPB1 CTD (4H8) CUT&RUN-seq replicate 1

description:
Library name: BGXM002C
RPB1 S5P occupancy profiling by RPB1 antibody clone 4H8

value: RNase L-KO

value: mock-transfected with RNAiMAX; antibody RPB1 CTD (4H8)


title: 2_LX2_Untreated

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

description: Library name: 2UNTREADTED-Ctrl

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison. Gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The species GO list was used to cluster the set of genes based on their biological process and determine their statistical significance. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components.The top 500 genes, selected by highest row variance, were used to generate the plot.
Assembly: GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: Processed data file_in excel with data with 3 repetitions from Untreated Vs GDF15 Treated conditions

source_name: Liver

growth_protocol: After 24hrs of cells plated either treated with GDF15 recombinant protein at 1ug/ml or untreated. Cells were treated for 24hrs and RNA was exacted for down stream process.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit following manufacturer's instructions (Qiagen, Hilden, Germany).
ERCC RNA Spike-In Mix (Cat: #4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The RNA sample received was quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA,USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Untreated and treated with GDF15 at 1ug/ml for 24hrs

value: Liver

value: Epithelial

value: Untreated


title: TapeLift_1_25

value: Female

value: Epidermis


title: 2_LX2_GDF15 treated

description: Library name: 2TREADTED-24HRS

value: GDF15 treated


title: H82 DMSO 1

description: Library name: Sample 13

value: Lung cancer cells

value: H82 DMSO 1


title: H209 Lurbi 3

description: Library name: Sample 12

value: H209 Lurbi 3


title: CD74 positive cells in B16/F10-BrM model replicate #3

description:
Library name: S13-CD74p
SingleRead 85 bases


city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description:
Library name: Pancreatic live cell of beta cell-ProTracer system
Pancreatic live cell of beta cell-ProTracer system scRNA-seq

data_processing:
For 10x Genomics–based scRNA-seq, raw data were processed using the Cell Ranger software suite with default alignment parameters, incorporating a customized reference built from refdata-gex-GRCm39-2024-A supplemented with the tdT sequence.
Assembly: refdata-gex-GRCm39-2024-A
Supplementary files format and content: Expression matrix
Supplementary files format and content: scRNA_seq.tar:Cellrangeroutput; Beta.cell.expression.matrix.txt:UMI counts matrix

source_name: Pancreatic

extract_protocol:
For 10x Genomics-based scRNA-seq in mice, sorted pancreatic live cell were sorted from Ins2-DreER, Ki67-CrexER, and R26-RSR-LSL-tdT mouse line
For 10x Genomics-based scRNA-seq, libraries were prepared using Single Cell 5’ Library and Gel Bead Kit V3. Sequencing was performed on an Illumina Novaseq Xplus platform to generate 150 bp paired-end reads.

value: Pancreatic

value: Pancreatic live cell

value: beta cell-ProTracer system


title: Sample_YBX1_FB_IGO_16203_B_1

city: New York

first: Yuzhe

last: Shi

address: 1250 First Avenue

department: Immunolgy

institute: Memorial Sloan Kettering Cancer Center

description: Library name: Sample_YBX1_FB_IGO_16203_B_1

data_processing:
Single-cell CITE sequencing data were processed using Seurat v5. Cells were filtered to retain those with 1,300–5,500 detected genes, 3,000–25,000 unique molecular identifiers (UMIs), and a mitochondrial read fraction below 10%. Following filtering, UMI counts were log-normalized and scaled, while regressing out the number of UMIs and mitochondrial read fraction.
Dimensionality reduction was performed using principal component analysis (PCA), with the top 20 principal components retained for constructing a shared nearest neighbor (SNN) graph and generating a uniform manifold approximation and projection (UMAP) embedding. T cell subsets were identified using ProjectTILs.
Differentially expressed genes (DEGs) were identified for each condition relative to the respective control using the FindMarkers function in Seurat. DEGs were filtered based on an adjusted p-value threshold of < 0.05. GSEA was performed using clusterProfiler, ranking genes by log2 fold change and leveraging the Molecular Signatures Database (MSigDB) gene set collection to assess enriched pathways.
Assembly: hg38

source_name: T cell

extract_protocol:
CAR T cells after two rounds of tumor stimulation were counted and assessed for cell viability. 1 million cells per condition were stained in cell staining buffer containing cell hashing antibodies for 30 minutes at 4°C. 3ml cell staining buffer was added and centrifuged at 400g for 5 mins. Repeated wash two more times for a total of three washes. Cells were resuspended in 500 μl of cell staining buffer and slowly filtered through a 40 μM cell strainer. Cell concentration and viability were verified and loaded on the 10X Chromium Next GEM Chip K Kit.
Libraries were prepared according to manufacturer’s protocol (5’V2 kit, 10x Genomics)

value: T cell

value: primary T cell

value: immune cell


title: H209 DMSO 3

description: Library name: Sample 9

value: H209 DMSO 3


title: CD74 negative cells in B16/F10-BrM model replicate #4

description:
Library name: S14-CD74m
SingleRead 85 bases

value: B16/F10-BrM brain metastasis

value: WT

value: CD74 negative microglia/macrophages


title: H187 Lurbi 3

description: Library name: Sample 6

value: H187 Lurbi 3


title: CD45+ Immune Cells in the Mouse Brain – Control of Alzheimer’s Disease (AD)

description:
Library name: Cd45+_immune_cells_in_CTR_AD
10x Genomics

data_processing:
Seven 10x barcoded sequencing libraries were generated using the 10x Single Cell 3' v3 kits (10x Genomics, Inc.). These libraries were sequenced in multiple rounds until each sample achieved a mean depth of 25,000 reads per cell. The mean number of reads per cell was calculated by processing the accumulated raw FASTQ files from each sequencing round with CellRanger Count (10X Genomics Cell Ranger v7.1.0) using default parameters. The sequencing data were aligned to the prebuilt 10x mouse GRCh38 (GENCODE v32/Ensembl 98) scRNA-seq reference genome (mm10-2020-A). This analysis yielded a median of 264 million sequenced reads per sample, with individual sample reads as follows: CTR_BrM: 264,577,836; BrM_VEH: 236,382,953; BrM_IBU: 295,303,588; CTR_MS: 96,922,258; MS: 222,018,909; CTR_AD: 335,324,101; AD: 275,467,604.
Initial assessments of the cancer model samples revealed the presence of metastatic cells of human origin, raising concerns regarding potential contamination with human environmental RNA. To facilitate simultaneous analysis of all samples while addressing human cell and RNA contamination, the raw FASTQ data from the gene expression libraries of all samples were aligned to the human GRCh38 (GENCODE v32/Ensembl 98) and mouse GRCh38 (GENCODE v32/Ensembl 98) 10x prebuilt scRNA-seq reference genome (GRCh38_and_mm10-2020-A). This alignment was processed using CellRanger Count (10X Genomics Cell Ranger v7.1.0) with default parameters.
In total, 12,219 cells were retrieved from CTR_BrM, 9,445 from BrM_VEH, 11,850 from BrM_IBU, 29,818 from CTR_AD, 11,388 from AD, 13,189 from CTR_MS, and 18,849 from MS. Background ambient RNA and barcode-swapped reads were subsequently removed from the count matrix using the Cellbender v0.3.0 Python package (Fleming et al., 2023) (Python v3.7.12 (Van Rossum and Drake, 2009)) with default parameters. This processing yielded a refined count matrix, identifying barcodes corresponding to genuine cells.
After applying Cellbender, the cell counts were adjusted to 10,237 in CTR_BrM, 9,452 in BrM_VEH, 11,383 in BrM_IBU, 12,143 in CTR_AD, 10,262 in AD, 3,665 in CTR_MS, and 8,530 in MS. The removal of doublet artifacts was performed using the Scrublet v0.2.3 Python package (Wolock et al., 2019) (Python v3.7.10 (Van Rossum and Drake, 2009)) with default parameters. Following doublet removal, the final cell counts were 10,159 in CTR_BrM, 9,379 in BrM_VEH, 11,370 in BrM_IBU, 12,143 in CTR_AD, 9,283 in AD, 3,659 in CTR_MS, and 8,528 in MS.
All subsequent single-cell transcriptomic analyses were conducted using R Statistical Software (v4.2.0) with the Seurat v5 (v4.9.9.9059) package (Hao et al., 2021; R: The R Project for Statistical Computing). For quality control, human genes and those expressed in fewer than three cells were excluded. After filtering out human genes, cells with more than 5% mitochondrial content or fewer than 1,500 detected mouse genes were also excluded. This filtering resulted in a total of 43,245 high-quality cells, distributed as follows: 7,360 in CTR_BrM, 5,202 in BrM_VEH, 5,870 in BrM_IBU, 9,108 in CTR_AD, 6,363 in AD, 2,885 in CTR_MS, and 6,457 in MS.
For each sample, UMI count data were normalized using a regularized negative binomial regression approach via SCTransform (sctransform v0.3.5). SCTransform was executed with the parameter vst.flavor set to "v2" to enhance regularization, and the method was set to "glmGamPoi" to fit a generalized linear Gamma-Poisson model, thereby improving the speed of the learning procedure and enhancing computational efficiency. In the subsequent step, mitochondrial content was regressed out in a second non-regularized linear regression.
To ensure that SCTransform residuals were computed for the top variable genes across all samples, the SelectIntegrationFeatures function was utilized to identify the top 3,000 highly variable genes (HVGs). These features were then employed in the PrepSCTIntegration function to recompute residuals for any missing values across the selected HVGs, utilizing stored model parameters. Upon obtaining the residuals for the common HVGs, Principal Component Analysis (PCA) was conducted on the SCT-normalized data of each sample, focusing on the top 3,000 HVGs.
Integration anchors were identified using the FindIntegrationAnchors function, specifying SCT as the normalization method, the top 3,000 HVGs as anchor features, and employing reciprocal PCA (RPCA) for reduction over the top 30 PCA components, with k set to 20 for anchor selection.
The seven datasets were integrated into a single dataset using the IntegrateData function, applying the previously identified anchors, SCT normalization, and the top 30 dimensions for the anchor weighting procedure. To facilitate dimensionality reduction, a new PCA was performed on the integrated dataset, followed by a nonlinear dimensionality reduction using Uniform Manifold Approximation and Projection (UMAP) applied to the 30 most significant PCA dimensions.
A Shared Nearest-Neighbor (SNN) graph was constructed utilizing the FindNeighbors function, based on the 30 most significant principal components (PCs). Cell clusters were subsequently identified through the implementation of the FindClusters function with default parameters.
For differential expression analysis within the integrated object comprising multiple SCT models, the dataset was prepared using the PrepSCTFindMarkers function. Differentially expressed genes between identified clusters were determined via a Wilcoxon rank-sum test, implemented through the Seurat package’s FindAllMarkers function, with default parameters. This analytical approach culminated in the identification of 16 distinct immune subpopulations. Gene expression plots were generated using the FeaturePlot function.
Enrichment scores for the identified gene signatures were computed using the AddModuleScore function with default settings, facilitating a systematic assessment of gene expression patterns across clusters and conditions. The visualizations were enhanced with the "RdBu" gradient color scheme from the RColorBrewer package. To enhance the interpretability of the expression data, the maximum and minimum cutoff values for visualization were adjusted, emphasizing biologically relevant expression ranges.
Assembly: Human GRCh38 (GENCODE v32/Ensembl 98) and mouse GRCh38 (GENCODE v32/Ensembl 98) 10x prebuilt scRNA-seq reference genome (GRCh38_and_mm10-2020-A)
Supplementary files format and content: Single cell Seurat object: Seurat_integrated_immune_populations_in_BrM_AD_MS.rds
Supplementary files format and content: CTR_BrM - Cell barcode: CTR_BrM_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_BrM - Gene name: CTR_BrM_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_BrM - Expression matrix: CTR_BrM_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: BrM_VEH - Cell barcode: BrM_VEH_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: BrM_VEH - Gene name: BrM_VEH_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: BrM_VEH - Expression matrix: BrM_VEH_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: BrM_IBU - Cell barcode: BrM_IBU_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: BrM_IBU - Gene name: BrM_IBU_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: BrM_IBU - Expression matrix: BrM_IBU_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: CTR_AD - Cell barcode: CTR_AD_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_AD - Gene name: CTR_AD_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_AD - Expression matrix: CTR_AD_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: AD - Cell barcode: AD_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: AD - Gene name: AD_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: AD - Expression matrix: AD_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: CTR_MS - Cell barcode: CTR_MS_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: CTR_MS - Gene name: CTR_MS_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: CTR_MS - Expression matrix: CTR_MS_post_cellbender_filtered_matrix.mtx.gz
Supplementary files format and content: MS - Cell barcode: MS_post_cellbender_filtered_barcodes.tsv.gz
Supplementary files format and content: MS - Gene name: MS_post_cellbender_filtered_features.tsv.gz
Supplementary files format and content: MS - Expression matrix: MS_post_cellbender_filtered_matrix.mtx.gz

source_name: Brain

extract_protocol:
CD45+ cells were isolated by FACS
FACS-purified CD45⁺ cells were processed for library preparation using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121), following the manufacturer’s instructions. The protocol included GEM generation, barcoding, GEM-RT clean-up, cDNA amplification, and library construction. The sequencing was conducted on an Illumina NextSeq 550 instrument equipped with v2.5 reagent kits, employing a PairEnd run type of 28 bp R1 and 56 bp R2. Primary data processing, including image analysis, per-cycle basecalling, and quality score assignment, was carried out using Real Time Analysis software (RTA v2, Illumina). Additionally, the conversion of BCL files to FASTQ format was executed with bcl2fastq2 within the Local Run Manager RNAfusion Analysis Module v2 (Illumina).

tag: library name

value: Immune cells

value: No treatment


title: H209 Lurbi 2

description: Library name: Sample 11

value: H209 Lurbi 2


title: BAT, E4BP4-OE5

city: Ribeirão Preto

first: Carlos

middle: H

last: Sponton

state: São Paulo

address: Av. Bandeirantes, 3900

department: Department of Physiology, Ribeirão Preto Medical School, Universidade de São Paulo (FMRP-USP)

country: Brazil

institute: USP

description: Library name: Sample10

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality using Trimmomatic tool
All workflow was using the tool Irna
Assembly: mm10
Supplementary files format and content: normalized counts

source_name: Brown adipose tissue

extract_protocol:
RNA was harvested using Pure Link RNA Mini kit (Invitrogen)
RNA libraries were prepared by Novogene

value: Brown adipose tissue

value: OE

value: HFD 10 weeks


title: Seq-Scope-X-Tonsil

first: Jun Hee

last: Lee

address: 109 Zina Pitcher Pl

description:
Library name: Seq-Scope-X-Tonsil
Seq-Scope-X-Tonsil

library_source: other

data_processing:
Seq-Scope-X transcriptome data were processed using the Seq-Scope pipeline with adjustments for experimentally determined expansion factors, following the NovaScope and NEDA workflows. Processing included generation of spatial barcode maps, alignment to reference genomes, construction of spatial gene expression matrices, and clustering using Seurat v5.  Spatial factor discovery was performed using Latent Dirichlet Allocation, and FICTURE was used to project cell-type factors into raw pixel space. Microscopy images, which lacked fiducial markers, were aligned to transcriptomic data using QGIS and further processed with CellProfiler and Photoshop. Differential expression, clustering, and integration analyses were conducted on hexagonally binned data to enable spatial and functional interpretation.
Other data could be found at Deep Blue Repository at (https://doi.org/10.7302/kj26-7j44)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz Digital Gene Expression Data in Matrix Market Format
Supplementary files format and content: transcripts.sorted.tsv.gz Spatial Digital Expression Spreadsheet
Library strategy: Spatial Transcriptomics

molecule: protein

source_name: tonsil

growth_protocol: Mouse liver, colon, and spleen tissues were collected from 8-week-old male C57BL/6 wild-type mice, and brain tissue was obtained from a 6-month-old male mouse. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Michigan (protocol PRO00011369).  Human tonsil tissue was obtained from the UCLA Pathology Biobank as a discarded surgical specimen from an adult patient with chronic tonsillitis. The sample was fully de-identified prior to acquisition and classified as IRB-exempt under institutional and federal guidelines, with no access to identifiable patient information.

extract_protocol:
Fresh frozen tissues were cryosectioned, mounted on charged slides, fixed with formaldehyde, and permeabilized with methanol. Anchor probes were hybridized in a formamide-containing buffer under humidified conditions. Tissues were then embedded in a polyacrylate-based monomer solution, polymerized, and cleared using digestion buffer with Proteinase K.
Tissue expansion was performed by incubation in diluted SSC, and DAPI staining was used to assess tissue integrity. Expanded gels were trimmed for imaging and alignment, then placed onto Seq-Scope Chips. Probe release and transcript transfer were achieved by heat incubation, followed by standard Seq-Scope library preparation, omitting tissue digestion as tissues were not directly attached to the chip.

treatment_protocol: For spatial proteomic analysis, tissues were permeabilized with methanol, blocked with a BSA-containing solution, and incubated overnight with TotalSeq™-A oligonucleotide-tagged antibody cocktails. After washing and post-fixation, tissues were processed using the same embedding, clearing, and expansion steps as in the transcriptome workflow.  Library preparation was modified to capture antibody-bound DNA oligonucleotides. Following reverse transcription, antibody tag libraries were eluted, purified, amplified by AT-PCR and indexing PCR, size-selected to isolate ~250 bp fragments, and sequenced on an Illumina NovaSeq-X platform.

value: tonsil

value: Tonsilitis


title: Saline treated PT (control)

description:
Library name: 10577-KG-6
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: Primary tumor

value: 8-10 weeks

value: female

value: BALB/c

value: PBS

value: 4T1 triple negative breast cancer


title: CD74 negative cells in B16/F10-BrM model replicate #1

description:
Library name: S11-CD74m
SingleRead 85 bases

value: B16/F10-BrM brain metastasis

value: WT


title: 3_LX2_Untreated

description: Library name: 3UNTREADTED-Ctrl

value: Liver

value: Epithelial

value: Untreated


title: Sample_YBX1_IGO_16203_1

description: Library name: Sample_YBX1_IGO_16203_1

value: T cell

value: primary T cell

value: immune cell


title: NP treated lung, sorted NP+CD45+

description:
Library name: 10577-KG-1
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: Lung

value: NP


title: 3_LX2_GDF15 treated

description: Library name: 3TREADTED-24HRS

value: GDF15 treated


title: CD45+ Immune Cells in the Mouse Brain – H2030 Brain Metastasis (BrM) Treated with Ibudilast

description:
Library name: Cd45+_immune_cells_in_BrM_IBU
10x Genomics

value: Immune cells

value: Ibudilast


title: H187 Lurbi 2

description: Library name: Sample 5

value: Lung cancer cells

value: H187 Lurbi 2


title: 1_LX2_GDF15 treated

description: Library name: 1TREADTED-24HRS


title: NP treated lung, CD45-

description:
Library name: 10577-KG-3
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: 8-10 weeks

value: female

value: BALB/c


title: CD45+ Immune Cells in the Mouse Brain – H2030 Brain Metastasis (BrM)

description:
Library name: Cd45+_immune_cells_in_BrM_VEH
10x Genomics

value: WT

value: Vehicle


title: PBS treated lung (control)

description:
Library name: 10577-KG-4
10x Chromium GEM-X Flex Gene Expression (Fix RNA Profiling)

value: PBS

value: 4T1 triple negative breast cancer


title: H209 DMSO 1

description: Library name: Sample 7

value: H209 DMSO 1


title: H187 DMSO 3

description: Library name: Sample 3

value: H187 DMSO 3


title: CD45+ Immune Cells in the Mouse Brain – Control of Multiple Sclerosis (MS)

description:
Library name: Cd45+_immune_cells_in_CTR_MS
10x Genomics

value: No treatment


title: CD45+ Immune Cells in the Mouse Brain – Multiple Sclerosis (MS)

description:
Library name: Cd45+_immune_cells_in_MS
10x Genomics


title: CD45+ Immune Cells in the Mouse Brain – Alzheimer’s Disease (AD)

description:
Library name: Cd45+_immune_cells_in_AD
10x Genomics


title: 1_LX2_Untreated

description: Library name: 1UNTREADTED-Ctrl

value: Liver

value: Epithelial

value: Untreated


title: No.10-Vessels_01 002

city: Houston

first: Akira

last: Yamamoto

state: Texas

address: One Baylor Plaza

country: Japan

institute: Baylor College of Medicine

description:
Library name: DSP-1001660021516-H-H10
Control_No.10-Vessels_01 002_1.Normal_distal

data_processing:
Raw sequencing data (FASTQ files) were processed using the NanoString GeoMx DSP analysis pipeline to generate DCC files.
Quality control was performed to remove low-quality segments and outlier probes based on sequencing and probe-level QC metrics.
Gene-level counts were generated by collapsing probe counts to target genes.
Counts were normalized using Q3 (75th percentile) normalization and background correction based on negative control probes.
Assembly: GRCh38
Supplementary files format and content: Processed data include NanoString GeoMx DSP DCC files containing gene-level counts for each ROI, and a tab-delimited matrix file containing normalized gene expression values (genes × ROIs).
Library strategy: Spatial transcriptomics

source_name: lung

growth_protocol: Human lung tissue specimens were obtained from explanted lungs at the time of lung transplantation or from pneumonectomy specimens for lung cancer.

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) lung tissue sections using the NanoString GeoMx DSP RNA Whole Transcriptome Atlas protocol according to the manufacturer’s instructions.
Sequencing libraries were prepared using the NanoString GeoMx DSP RNA Whole Transcriptome Atlas (Human) following the manufacturer’s protocol.

treatment_protocol: No experimental treatment was applied to the tissue prior to RNA extraction.

value: lung

value: Vessels

value: wild type


title: No.10-Vessels_01

description:
Library name: DSP-1001660021516-H-H09
Control_No.10-Vessels_01_1.Normal_distal


title: BAT, E4BP4-OE2

description: Library name: Sample7

value: Brown adipose tissue

value: OE

value: HFD 10 weeks


title: H157_W6134

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

description: Library name: H157_W6134

data_processing:
Sequencing was performed on the BGISEQ platform at BGI Tech (Wuhan, China). The FASTQ-formatted sequence data were analyzed by using a standard BWA–Bowtie–Cufflinks workflow. Sequence reads were mapped to GRCh38/hg38 assembly with BWA and Biotie software. The Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression, and analysis of different expression.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H157 cells were cultured in RPMI1640 supplemented with 10% FBS. Cells were grown at 37 °C in 5% CO2 incubators.

extract_protocol:
The extraction steps of total RNA were according to the manufacturer's protocol of the Vazyme Super FastPure Cell RNA Isolation Kit (Vazyme Biotech, Nanjing, China)
Transcriptomic sequencing of RNA-seq libraries were validated through MGISEQ2000 machine (BGI Tech, China).

treatment_protocol: H157 cells were treated with vehicle (DMSO) or W6134 (2.5 μM) for 48 hours.

value: non-small cell lung adenocarcinoma cells


title: BAT, E4BP4-OE1

description: Library name: Sample6


title: BAT, Control5

description: Library name: Sample5

value: Control


title: BAT, E4BP4-OE4

description: Library name: Sample9


title: H187 DMSO 1

description: Library name: Sample 1

value: Lung cancer cells

value: H187 DMSO 1


title: BAT, E4BP4-OE3

description: Library name: Sample8


title: No.10-Ep_02 002

description:
Library name: DSP-1001660021516-H-H06
Control_No.10-Ep_02 002_1.Normal_proximal

value: Ep


title: macrophage, mfap4:mCherry positive , UNCUT, 29hpA, rep 3

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

institute: CNRS

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing were performed using Illumina's conversion software (bcl2fastq v2.20). The quality of the raw data was assessed using FastQC (v0.11.9) from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). Contaminant screening was done using FastQ Screen (v0.15.1).
Adapters sequences were trimmed before alignment. Reads were aligned to the genome using TopHat (v2.1.1) and gene counts were obtained using featureCounts (v2.0.0 for 5hpA/29hpA samples, v2.0.3 for 2hpA samples).
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include geneID|gene symbol for 2hpA samples, gene symbols for 5hpA and 29hpA samples, and raw counts values for each sample

organism: Danio rerio

growth_protocol: Tg(mfap4:mCherry-F) embryos were maintained in embryo water at 28°C during 3 days.

extract_protocol:
Macrophages were sorted by FACS and RNA was harvested using Rneasy mini plus kit (Qiagen). Between 5ng-10ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit from Takara Bio and DNA Prep Kit from Illumina following manufacturer's protocols.
RNA-seq single read (100nt)

treatment_protocol:
At 3 days post-fertilization, the fin folds of Tg(mfap4:mCherry-F) embryos were amputated or kept intact.
Cell dissociation was done at 2 hours post-amputation (4 replicates), 5 hours post-amputation (4 replicates) and 29 hours post-amputation (4 replicates).

value: macrophage

value: mCherryF+

tag: time