title: AB1546_Roi-IN3_non-phago myeloid_3

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

institute: Tel Aviv University

description:
Library name: AB1546
mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol41. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.
invivolung_qc.h5ad

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a). Reads with multiple mapping positions were excluded. We then assigned gene names for exonic, genomic and mitochondrial regions using featureCounts (v.2.0.0), processed the resulting BAM file using samtools (v.1.10) and finally created gene-cell UMI matrices using the UMI-tools software package (v.1.1.2). Using the Scanpy package (v.1.9.8), we loaded these files to a unified data object.
We performed QC by excluding cells with <500 or >10,000 UMIs, >30% mitochondrial genes or >1 UMIs of hemoglobin genes. We also excluded cells from the in vitro model with any expression of T cell genes (Tcf7, Trbc2, Cd3d, Trbc1, Cd3g, Cd3e, Trac, Cd8b1) and from the in vivo lung model with >1 UMIs of endothelial genes (Pecam1, Cdh5, Col4a1, Plvap).
Assembly: GRCm39
Supplementary files format and content: h5ad files - unified post-QC scRNA-seq data, containing a gene-cell UMI matrix
Supplementary files format and content: csv files - flourescence intensity data where relevant (pHrodo+ cells)

source_name: Lung

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
in-vitro: For macrophage-thymocyte co-culture, BM-derived macrophages were washed with cold PBS and seeded in 24-well plates at 2.5 x 105 cells per well in culture medium supplemented with 10 ng/ml M-CSF and incubated at 37 °C for 3 hours to settle. pHrodo-labeled apoptotic thymocytes were added to the BM-derived macrophages at 1.25 x 106 cells per well. Cells were co-cultured for 3 or 24 hours before they were collected by gentle scraping. in-vivo lung: To obtain single cell suspensions of lungs from mice inoculated with apoptotic thymocytes or PBS, the mice were perfused with PBS through the right ventricle. Lungs were dissociated using the mouse lung dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions with the following modifications: After mechanical dissociation using the gentleMACS dissociator program “m_lung_01”, lungs were incubated at 37 °C for 10 minutes with agitation. The sample was subsequently pipetted through 16G, 18G and 19G needles and then incubated again at 37 °C for 10 minutes with agitation and then washed with ice-cold sorting buffer (PBS supplemented with 0.2 mM EDTA, pH 8 and 0.5% BSA), filtered through a 100-µm cell strainer and pelleted. B16: To obtain single cell suspensions of B16 tumors, the tumors were removed and weighed using an analytical scale, and then placed in RPMI-1640 supplemented with DNase (28 μg/ml, Sigma-Aldrich) and collagenase IV (1 mg/ml, Worthington). Tissues were incubated at 37 °C for 10 minutes with agitation and then pipetted through 16G, 18G, 19G and 21G needles before they were incubated again at 37 °C for 10 minutes with agitation. Cell suspensions were then washed with cold sorting buffer and pelleted.
The library preparation was conducted following the previously reported protocol {Jaitin, 2014}. In brief, mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol {Jaitin, 2014}. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

value: Lung

value: non-phago myeloid


title: RNA-seq in Donor 30 macrophages, treated with 10 mM butyrate

status: Public on Jun 04 2026

type: SRA

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

library_source: transcriptomic

data_processing:
RNA-seq data was aligned to the hg38 assembly of the human genome using STAR v2.7.10b (parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Gene counts were computed using featureCounts v2.0.0 and the latest refFlat annotation from UCSC (parameters: -M -p). Differential expression analysis was performed using DESeq2 v1.40.1. Pathway enrichment analysis was performed using the package pathfindR v2.2.0.
Assembly: hg38
Supplementary files format and content: BigWig files of RNA-seq coverage

molecule: polyA RNA

organism: Homo sapiens

source_name: macrophage

growth_protocol: CD14+ peripheral blood mononuclear cells (PBMC) were obtained from buffy coats of human blood donors from the Dutch blood bank. All blood donors were informed about the research and granted their consent to the blood bank. The research is exempt from ethical approval by the Dutch Medical Research with Human Subjects Law, because samples were provided fully anonymized to the researchers and the blood donors did not have to undergo extra procedures. Gradient centrifugation was performed at 1250 ×g for 22 minutes at room temperature in SepMate-50 tubes (STEMCELL, 85450) containing ficoll (STEMCELL, 07851). CD14+ monocytes were isolated from PBMC using CD14 MicroBeads (Miltenyi Biotech, 130-050-201) for LS column (Miltenyi Biotech, 130-042-401) magnetic antibody cell sorting (MACS) according to the manufacturer’s supplied protocol. Human peripheral blood monocyte-derived macrophages were generated in ultra-low adherent 6-well plates (Corning, 3471) in 2 mL complete RPMI 1640 Medium (Gibco, 11875093) including 10% Fetal Bovine Serum (FBS) (Hyclone, 10309433), 1% antibiotic-antimitotic (Gibco, 15240062), 1% L-glutamine (Gibco, 15430614), and 100 ng/mL M-CSF (RnD, 216-MC) in 5% CO2 at 37 °C and for 7 days. On day 4, macrophages were supplemented with 1 mL complete RPMI 1640 Medium containing 50 ng/mL M-CSF.

extract_protocol:
Samples were washed twice in PBS and lysed by direct addition of 1 mL TRIzol reagent (ThermoFisher Scientific, 15596026). RNA extraction was performed as per manufacturer instructions, and RNA integrity was assessed by electrophoresis.
Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7770L), as per manufacturer instructions.

treatment_protocol: PBMC-differentiated macrophages were seeded in 6-well plate at 1,000,000 cells/well, cells were treated with 1 μg/mL LPS, 20 ng/mL IFN-γ and 0.1 mM, 1 mM or 10 mM sodium butyrate for 24 hours.

tag: cell type

value: macrophage


title: female, intestinal epithelium, Tacr2null, low fat diet, biological replicate 2

city: La Jolla

first: Supriya

last: Srinivasan

state: CA

address: 10550 North Torrey Pines Road

country: USA

institute: The Scripps Research Institute

description: Library name: Sample 26

data_processing:
Raw sequencing reads were quality-assessed using FastQC, and adapters were removed using Cutadapt.
Trimmed reads were aligned to the mouse reference genome (ENSEMBL GRCm38) using STAR aligner version 2.6.1d.
The distribution of mapped reads across genomic features was analyzed with RSeQC v3.0.1.
Differential gene expression analysis was performed using DESeq2 (v2.11.40.8) implemented in R (v4.2.2) via the Galaxy platform.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: intestinal epithelium

extract_protocol:
NOTE for intestinal intestinal epithelium: the small intestine was cut longitudanally, and the intestinal epithelium was scraped using microscope slides from the middle of the length of the entire intestine (roughly 16-20 cm in a typical 34 cm small intestine). The tissues (isolated intestinal epithelium or perigonadal white adipose tissues) were processed via commercial RNeasy RNA purification kits using manufacturers protocols.
Total RNA samples were prepared into RNA-Seq libraries using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommended protocol. Briefly, for each sample, 200 ng total RNA was polyA selected, and converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq 2000 for 100 base single-read sequencing.

treatment_protocol: Mice (8-12 weeks) were maintained on a low fat diet. Test mice were then given an high fat diet for 1 or 12 weeks. The intestines and perigonadal tissues were collected and flash frozen.

tag: tissue

value: intestinal epithelium

tag: Sex

value: female

tag: genotype

tag: treatment

value: low fat diet


title: Panc1_ScrKD2

city: Göttingen

first: Adi

last: Mackay

address: Robert-Koch-Straße 40

department: Pathology

country: Germany

institute: University Medical Center Göttingen

description: Library name: Panc1_ScrKD2

data_processing:
Alignment with STAR V2.7.31 followign by sorting and indexing with samtools V1.9
Gene counts were generated using Featurecounts from the subread v1.6.3 package
DESeq2 with RUVseq normalization, Differentially expressed genes were filtered according to adjusted P value <0.05
Assembly: hg38
Supplementary files format and content: FeatureCounts_Panc1_Scr1.txt, FeatureCounts_Panc1_Scr2.txt, FeatureCounts_Panc1_HMGB2KD1.txt, FeatureCounts_Panc1_HMGB2KD2.txt: Raw count files, output of Featurecounts
Supplementary files format and content: DGE_Panc1_HMGB2KD_GRCh38_qval0.01.xlsx: Filtered differential expression of control/HMGB2 KD

source_name: Pancreas

extract_protocol:
harvested with TRIzol® Reagent (Life Technologies, 15596018). Total RNA was isolated using the Direct-zol RNA Miniprep Kit (Zymo Research, R2052) according to the manufacturer’s protocol.
costumised PolyA library construction by Novogene

value: Pancreas

tag: cell line

value: Cell line

value: Scramble siRNA


title: Naïve ESCs, Input, ChIP-seq

city: Haifa

first: Evgeny

last: Potapenko

address: Abba Khoushy Ave 199

department: Institute of Evolution

country: Israel

institute: University of Haifa

library_source: genomic

data_processing:
Firstly, reads were trimmed by fastp tool with default settings.
Trimmed reads were aligned to GRCm38/mm10 reference genome by Bowtie2 with default parameters.
Picard Markduplicates was used to mark duplicates.
Peak calling was performed using macs2 callpeak with such parameters: -g mm -q 0.01 –nomodel –SPMR. Input DNA for corresponding sample was used as controls.
BigWig files were generated with macs2 bdgcmp by subtracting bedgraph pileup of treatment from input sample.
Assembly: mm10
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: E14 Tg2a Bay Genomics

growth_protocol: Mouse ESCs were adapted for 3 passages in serum-free 2i-LIF-N2B27 medium (2i – MEK inhibitor PD0325901 (1uM, Axon) and GSK3β inhibitor CHIR99021 (3uM, Axon)) in tissue culture plastic preliminary treated with 0.01% poly-L-ornithine (Sigma). For EpiLC derivation, ESCs were trypsinized, washed with PBS and seeded in the amount of 250.000 cells to 6 well culture plate, pretreated with 15ug/ml of Fibronectin (Merck) in N2B27 medium supplemented with 12ng/ml bFGF (Peprotech), 20ng/ml Activin A (Peprotech) and 1% of KOSR (Gibco) for 48 hours.

extract_protocol:
Cells were fixed with 1% Formaldehyde for 10 minutes, then quenched with 0.125M Glycine. Chromatin was lysed in SDS-containing buffer with protease inhibitors cocktail (Roche) and sheared to fragments around 500 bp by sonicator FisherScientific CL-18. For precipitation chromatin of 1.5 million cells and 12ug of antibodies conjugated with MabSelect sure Sepharose (Cytiva) were taken. The precipitated chromatin was sequentially washed with SDS-containing buffer and with TE. Precipitated chromatin complexes were then eluted and subjected to cross-link reversal reaction. DNA was extracted with a phenol/chloroform, then precipitated with isopropanol and washed by ethanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Each ChIP was validated using q-PCR against selected loci.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: E14 Tg2a Bay Genomics

value: Mouse embryonic stem cells

tag: condition

value: Naive

tag: chip antibody


title: female, intestinal epithelium, Tacr2null, low fat diet, biological replicate 1

description: Library name: Sample 25


title: Panc1_ScrKD1

description: Library name: Panc1_ScrKD1


title: CCL17-rep4

city: JiNan

first: Anda

last: Shi

address: Culture West Road num 107

country: China

institute: Qilu Hospital

description: human bile duct

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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: CCA Tumor

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CCA Tumor

value: QBC-939 cell line

value: CCA cell


title: RNA-seq in Donor 30 macrophages, treated with 0.1 mM butyrate


title: Panc1_HMGB2KD2

description: Library name: Panc1_HMGB2KD2

value: HMGB2 siRNA


title: CCL17-rep3

description: human bile duct


title: MitoRibo_HAP1_1

status: Public on Jun 05 2026

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

description: Library name: L21

library_source: other

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Assembly: Read quantitation using custom scripts
Supplementary files format and content: The human or mouse nuclear genomes (human, hg38; mouse, mm10) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpframing text files contain nine columns:  1. the length of ribosome footprint; 2. the fraction of ribosome footprint; 3~5. the number of ribosome footprint at each frames;  6~8,the fraction of ribosome footprint at each frames; 9. the relative entropy of ribosome footprint.
Library strategy: MitoIP-Thor-Ribo-Seq

molecule: other

extract_protocol:
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. Ribo-Seq and RNA-Seq: Cells in a 10-cm dish were lysed with 600 µl of lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol) and treated with 25 U/ml TURBO DNase (Thermo Fisher Scientific). Then, the lysate was clarified by centrifugation at 20,000 × g for 10 min at 4°C.
MitoIP-Thor-Ribo-Seq and MitoIP-Thor-Disome-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).


title: RNA-seq in Donor 29 macrophages, treated with 10 mM butyrate


title: Panc1_HMGB2KD1

description: Library name: Panc1_HMGB2KD1


title: male, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 3

description: Library name: Sample 23

value: male

value: wildtype

value: high fat diet 12 weeks


title: RNA-seq in Donor 29 macrophages, untreated

value: macrophage


title: male, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 2

description: Library name: Sample 22

value: intestinal epithelium


title: Subject 12

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Subject 12
Bronchoalveolar lavage cells from healthy adult

library_source: transcriptomic single cell

data_processing:
Initial pre-processing of the 10 subjects’ 10X scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics)
Assembly: hg38
Supplementary files format and content: comma separated (.csv) matrix of raw counts. Rows are features and columns are cells.

source_name: Bronchoalveolar lavage cells

extract_protocol:
Enrolled subjects underwent flexible fiberoptic bronchoscopy and bronchoalveolar lavage with serial installation and aspiration of normal saline. Lavage fluid was centrifuged to pellet cells. Cell pellet was resuspended  at 1x10^6 cells per ml in PBS containing 0.04% bovine serum albumin.
Single cells were captured using The Chromium Box (10x Genomics, Pleasanton, CA). The Chromium Single Cell 3’ GEM, library, and gel bead kit PN-1000075 were used along with Bead Chip B PN-1000092 for cell capture and library construction. Libraries were sequenced with the Illumina NovaSEQ 6000 sequencer (Illumina, Inc., San Diego, CA) using an S4 flow cell.

tag: age

value: Bronchoalveolar lavage cells

tag: diagnosis

value: healthy


title: CCL17-rep1

description: human bile duct


title: RNA-seq in Donor 29 macrophages, treated with 0.1 mM butyrate


title: MitoRibo_HeLa_mtRF1_KO_1

description: Library name: L3

source_name: HeLa

value: HeLa


title: MitoRibo_HeLa_7

description: Library name: L15


title: MitoRibo_HeLa_1

description: Library name: L1


title: male, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 1

description: Library name: Sample 21


title: CCL17+C-021-rep4

description: human bile duct


title: Input DNA

data_processing:
ChIP-seq data was aligned to the hg38 assembly of the human genome using Bowtie v1.3.1 (parameters: -l 28 -n 2 -m 1 --best --strata --chunkmbs 3200), retaining only uniquely aligned reads. Correlation, principal component analysis, heatmap generation were performed using deepTools v3.5.0.
Assembly: hg38
Supplementary files format and content: BigWig files of ChIP-seq coverage

source_name: peripheral blood

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific), 1% antibiotic-antimitotic solution (AA, Gibco), and 1% L-glutamine (Gibco) at 37 ℃ and 5% CO2. Peripheral blood mononuclear cells (PBMC) were obtained from buffy coats of human blood donors by ficoll gradient centrifugation. Buffy coats were obtained anonymized from the Dutch blood bank, Sanquin. The research of the Department of Molecular Immunology was approved by the ethics committee of Sanquin, and an access use agreement was signed. All blood donors were informed about the research and granted their consent to Sanquin. The research is exempt from ethical approval by the Dutch Medical Research with Human Subjects Law, because samples were provided fully anonymized to the researchers and the blood donors did not have to undergo extra procedures. CD14+ monocytes were isolated from PBMC using CD14 MicroBeads (Miltenyi). Human peripheral blood monocyte-derived macrophages were generated in Ultra-low adherent 6-well plates (Corning) in 2 ml RPMI 1640 medium (Gibco) supplemented 10% FBS, 1% antibiotic-antimitotic solution (AA, Gibco), and 1% L-glutamine (Gibco) and M-CSF (RnD 216-MC, 100 ng/ml) at 37 °C and 5% CO2 for seven days. On day 4, macrophages were supplemented with 1 ml medium containing 50 ng/ml M-CSF.

extract_protocol:
Chromatin preparation and library construction were carried out using on the standard 2014 Blueprint Histone ChIP and Kapa Hyper Prep kit protocol (http://www.blueprint-epigenome.eu) and the reagents described therein.
For chromatin preparation, we established the optimal fixation time to be 5 minutes in 1% formaldehyde at room temperature. The shearing time was 10 or 12 minutes using the Covaris Focused-ultrasonicator (S220) and the low cell protocol for chromatin shearing, which is optimized for chromatin shearing of 1 to 3 million cells using the microTUBE-130 with AFA fiber screw cap (Covaris, cat 520216). Immunoprecipitation was carried out with polyclonal rabbit H3AcK27 antibody (Diagnode, C15410196). After the library construction, samples were PAGE-purified, quantified on the Agilent tapestation 2200 bioanalyzer, and equimolarly pooled. Sequencing was done on the DNBseq platform using Paired-End 100 sequencing.

treatment_protocol: 1×10^6 human peripheral blood monocyte-derived macrophages per condition were treated with 1 μg/mL LPS, 20 ng/mL IFN-γ and 0.1 mM or 10 mM sodium butyrate for 24 hours.

value: peripheral blood

value: macrophages


title: MitoRibo_HeLa_4

description: Library name: L6


title: RNA-seq in Donor 28 macrophages, treated with 10 mM butyrate


title: male, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 4

description: Library name: Sample 20

value: high fat diet one week


title: ChIP-seq of H3K27ac in Donor 9A cells, treated with 10 mM butyrate

tag: agent

value: 10 mM butyrate

tag: antibody


title: CCL17+C-021-rep3

description: human bile duct


title: MitoRibo_HeLa_mtRF1_KO_2

description: Library name: L4


title: RNA-seq in Donor 28 macrophages, untreated


title: ChIP-seq of H3K27ac in Donor 9A cells, treated with 0.1 mM butyrate

value: 0.1 mM butyrate


title: CCL17+C-021-rep2

description: human bile duct

value: CCA Tumor


title: RNA-seq in Donor 28 macrophages, treated with 0.1 mM butyrate


title: ChIP-seq of H3K27ac in Donor 9A cells, treated with 0 mM butyrate

value: 0 mM butyrate


title: male, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 2

description: Library name: Sample 18


title: CCL17+C-021-rep1

description: human bile duct

value: QBC-939 cell line

value: CCA cell


title: RNA-seq in Donor 27 macrophages, treated with 10 mM butyrate


title: male, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 1

description: Library name: Sample 17

value: male


title: MitoRibo_HeLa_ICT1_KO_1

description: Library name: L7


title: ChIP-seq of H3K27ac in Donor 6B cells, treated with 10 mM butyrate


title: Control-rep4

description: human bile duct


title: RNA-seq in Donor 27 macrophages, untreated


title: Control-rep3

description: human bile duct


title: RNA-seq in Donor 27 macrophages, treated with 0.1 mM butyrate


title: male, intestinal epithelium, wildtype, low fat diet, biological replicate 3

description: Library name: Sample 15

value: wildtype

value: low fat diet


title: ChIP-seq of H3K27ac in Donor 6B cells, treated with 0 mM butyrate


title: male, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 4

description: Library name: Sample 24

value: high fat diet 12 weeks


title: Control-rep2

description: human bile duct


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 20-hour time point (biol rep 3).

city: Duarte

first: Ching

last: Ouyang

address: 1500 E. Duarte Rd.

institute: City of Hope National Medical Center

description: Library name: 54539_5pct_EtOH_20hr_rep3

data_processing:
Sequence reads passing quality check were preprocessed for adaptor and polyA removal using trimmomatic v.0.39 and fastp v.0.23.2.
Trimmed sequence reads were mapped to C. elegans reference genome ce10 with an index build containing the transcript/gene annotations using STAR v.2.7.9a.
Strand-specific paired-end fragment counts of each gene annotated in RefGene were calculated using the featureCounts function in the Subread package v.2.0.3.
Assembly: ce10
Supplementary files format and content: Tab-delimited text file containing read counts for each sample.

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were synchronized by bleaching and grown at 20 °C on agar plates seeded with E. coli OP50 until they reached the L3 stage.

extract_protocol:
Total RNA was extracted from whole C. elegans L3 larvae using TRI Reagent® (Molecular Research Center, Inc., TR118) according to the manufacturer’s instructions. Approximately 1,500 synchronized L3 larvae were collected after ethanol treatment and homogenized in 0.5 mL TRI Reagent® using a plastic pestle. After homogenization, 50 µL of 1-bromo-3-chloropropane was added, followed by vigorous shaking for 15 seconds. Samples were incubated at room temperature for 15 minutes and centrifuged at 12,000 × g for 15 minutes at 4°C. The aqueous phase was transferred to a new tube and RNA was precipitated with isopropanol, followed by washing with 75% ethanol. The RNA pellet was air-dried and dissolved in RNase-free water.
Libraries were prepared with Kapa RNA mRNA HyperPrep kit (Roche) according to the manufacturer's protocol.

treatment_protocol: Age-synchronized approximately 1500 worms L3 larvae were washed off E. coli OP50 and transferred into S-basal buffer containing either 0% (control) or 5% ethanol (v/v). Worms were incubated in these solutions at 20 °C for 1, 4, or 20 hours. After each exposure time, worms were collected for RNA extraction.

value: Whole worm


title: male, intestinal epithelium, wildtype, low fat diet, biological replicate 2

description: Library name: Sample 14

value: intestinal epithelium


title: ChIP-seq of H3K27ac in Donor 11B cells, treated with 10 mM butyrate


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 20-hour time point (biol rep 2).

description: Library name: 54538_5pct_EtOH_20hr_rep2


title: Control-rep1

description: human bile duct


title: male, intestinal epithelium, wildtype, low fat diet, biological replicate 1

description: Library name: Sample 13


title: CCL17-rep2

description: human bile duct


title: EpiLC cells, PCBP1 KO, rep 2

description:
11
EpiLC_KO_R2

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using fastp software with default parameters, and quality control was assessed by FastQC.
Trimmed high quality sequences were mapped to GRCm38/mm10 genome using STAR tool in the two-pass mode.
Quality control of the RNA-seq experiment was analyzed with the ReadDistribution and the GeneBodyCoverage tools from the RseQC.
Read counts for each gene was estimated by featureCounts tool.
Differential expression analysis of two groups (KO samples and WT samples) was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: Bigwig file format of reads aligned to the genome.

extract_protocol:
RNAs from each biological replicate of ESC and of EpiLC was extracted with Trizol (Invitrogen) following the manufacturer's recommendations.
The libraries for NGS analyses were constructed using TruSeq Stranded mRNA kit (Illumina) following the manufacturer's recommendations. 1 μg of total RNA was taken as input material for the protocol.

value: E14 Tg2a Bay Genomics

value: Mouse embryonic stem cells

value: PCBP1 knockout

value: 48h of Naive-to-EpiLC transition


title: ChIP-seq of H3K27ac in Donor 11B cells, treated with 0.1 mM butyrate

value: peripheral blood

value: macrophages


title: CBDS bile stimulate-rep3

description: human bile duct

value: primary mast cell

value: mast cell


title: female, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 4

description: Library name: Sample 12

value: female


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 20-hour time point (biol rep 1).

description: Library name: 54537_5pct_EtOH_20hr_rep1


title: male, intestinal epithelium, Tacr2null, high fat diet, acute, biological replicate 2

description: Library name: Sample 42

value: high fat diet one week


title: ChIP-seq of H3K27ac in Donor 11B cells, treated with 0 mM butyrate

value: 0 mM butyrate


title: CBDS bile stimulate-rep2

description: human bile duct

value: CCA Tumor


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 4-hour time point (biol rep 3).

description: Library name: 54536_5pct_EtOH_4hr_rep3


title: female, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 3

description: Library name: Sample 11

value: wildtype


title: mPFC, K4-2, Day15

city: Yokohama City

first: Waki

last: Nakajima

state: Kanazawa-Ku

address: 3-9, Fukuura

department: Physiology

institute: Yokohama City University

description: Library name: Sample 5

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain (mPFC)

extract_protocol:
Total RNA was harvested using the RNeasy plus universal kits (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacture's protocols.

treatment_protocol: In control group, rats were recieved no treatment. In K4 group, rats were administered K4 intravenously through a cannula for 7 days. In ketamine group, rats were administered ketamine subcutaneously for 7days. After continuous treatment, withdrawal was done for 7 days.

value: Brain (mPFC)

value: Wistar Kyoto rats


title: CBDS bile stimulate-rep1

description: human bile duct


title: ChIP-seq of H3K27ac in Donor 10A cells, treated with 0.1 mM butyrate

value: 0.1 mM butyrate


title: ChIP-seq of H3K27ac in Donor 10A cells, treated with 10 mM butyrate

value: 10 mM butyrate


title: female, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 2

description: Library name: Sample 10

value: intestinal epithelium

value: high fat diet 12 weeks


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 4-hour time point (biol rep 2).

description: Library name: 54535_5pct_EtOH_4hr_rep2

value: Whole worm


title: CCA bile stimulate-rep3

description: human bile duct


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 4-hour time point (biol rep 1).

description: Library name: 54534_5pct_EtOH_4hr_rep1


title: ChIP-seq of H3K27ac in Donor 10A cells, treated with 0 mM butyrate


title: female, intestinal epithelium, wildtype, high fat diet chronic, biological replicate 1

description: Library name: Sample 9


title: CCA bile stimulate-rep2

description: human bile duct


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 1-hour time point (biol rep 3).

description: Library name: 54533_5pct_EtOH_1hr_rep3


title: female, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 4

description: Library name: Sample 8


title: Trachemys scripta peripheral nerve stage 21 - R2

city: Toluca

first: Rodolfo Daniel

last: Avila Aviles

address: Intituto Literario

country: Mexico

institute: Universidad Autonoma del Estado de Mexico

description:
Library name: Ts_21_R2
Embryonic peripheral nerve tissue from T. scripta at developmental stage 21

data_processing:
Sequencing data were aligned to the T. scripta elegans genome using Hisat2.
Gene counts were obtained using featureCounts with the genome annotation in GTF format.
Raw count data were imported into edgeR 3.42.4 in R. Genes with low expression were filtered out by excluding those with counts per million (CPM) less than 1 in fewer than two samples.
Data normalization was performed using calcNormFactors to account for differences in sequencing depth, followed by dispersion estimation using estimateDisp
RPKM/FPKM and TPM values were calculated for the RNA-seq data.
Assembly: NCBI RefSeq assembly GCF_013100865.1.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: csv or tab-delimited files include RPKM/FPKM and TPM values for each sample.

organism: Trachemys scripta

source_name: peripheral nerve

growth_protocol: Adult female Trachemys scripta were injected with oxytocin to induce oviposition, and collected eggs were incubated in a mixture of vermiculite and water at 28°C.

extract_protocol:
Total RNA was extracted from embryonic nerve tissues stored in RNA-later using the Thermo GeneJET RNA Purification Kit. RNA concentration was measured using a Thermo Scientific NanoDrop 2000.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit.

treatment_protocol: Embryos at developmental stages 19 and 21 were collected, and parts of the brachial and sacral plexus (peripheral nerves) were dissected and stored in RNA-later at -20°C.

value: peripheral nerve


title: Trachemys scripta peripheral nerve stage 21 - R1

description:
Library name: Ts_21_R1
Embryonic peripheral nerve tissue from T. scripta at developmental stage 21


title: CCA bile stimulate-rep1

description: human bile duct


title: female, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 3

description: Library name: Sample 7


title: Control-rep3

description: human bile duct


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 1-hour time point (biol rep 2).

description: Library name: 54532_5pct_EtOH_1hr_rep2


title: female, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 2

description: Library name: Sample 6


title: Trachemys scripta peripheral nerve stage 19 - R2

description:
Library name: Ts_19_R2
Embryonic peripheral nerve tissue from T. scripta at developmental stage 19


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 20-hour time point (biol rep 3).

description: Library name: 54530_0pct_EtOH_20hr_rep3


title: Control-rep1

description: human bile duct


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 20-hour time point (biol rep 2).

description: Library name: 54529_0pct_EtOH_20hr_rep2


title: ArPHR4-3

city: Hangzhou

first: Shuguang

last: Wang

state: zhejiang

address: Zhejiang A&F University

institute: Zhejiang A&F University

description: Library name: SAMPLES9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: tab-delimited text file includes FPKM and raw counts for each Sample

organism: Anoectochilus roxburghii

source_name: Leave

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was usedfor the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols

value: Leave

value: WT

value: Anoectochilus roxburghii Leaves

tag: group

value: OE

value: transient overexpression

tag: time

value: Days 3


title: RMb2-12

city: Chapel Hill

first: Robert

middle: G

last: Mealer

state: NC

address: 120 Mason Farm Road, 5023F

institute: University of North Carolina at Chapel Hill

description: iE KO + DOX

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of hg19 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Assembly: hg19
Supplementary files format and content: not_stranded_htseq_output.txt

source_name: cell line

growth_protocol: Standard iPCS culture practices were used for all cell line maintenance. In brief, Matrigel (VWR Cat # 354277) coated plates were used with daily mTeSR+ (Stem Cell Technologies Cat #100-0276) media changes. Cells were aggregate or single-cell passaged, depending on the downstream application, with Gentle Cell Dissociation Reagent (Stem Cell Technologies Cat # 7174). Cells were gently thawed by rolling the cryovial between gloved hands until fully liquid and then placed directly into newly prepared plates with media. Rock inhibitor (StemCell Technologies Cat # 72304) was used in all media for thawing, passaging and in any case where colony size was significantly small, less than ~10 cells. Cells were frozen down in dissociated suspensions of ~1,000,000 cells per ml in mFreSR media (Stem Cell Technologies Cat # 05854). Mr. Frosty (ThermoFisher Scientific Cat # 5100-0001) was used to slowly cool cells during the freezing process. Cells were transferred to –140°C when fully frozen. All cell lines were generated from the same previously published human iPSC line, termed PGP129.

extract_protocol:
RNA from snap frozen cell pellets was extracted using the Monarch Total RNA Miniprep Kit (Cat # T2010S).
In brief RNA-seq libraries were prepared from total RNA using polyA selection followed by the NEBNext Ultra II Directional RNA Library Prep Kit protocol (New England Biolabs, E7760S).

treatment_protocol: A Matrigel-coated 24-well plate of PGP1 cells at 50% confluency were incubated with filtered virus at 3 different concentrations, 1:4, 1:12 & 1:36 virus:media, in a total volume of  400 ml plus 10 mg/ml Polybrene mTeSR+ media with Rock for each well. Virus-containing media was allowed to sit on cells for 24 hours before being changed. The resulting polyclonal populations were expanded and underwent 2 passages before further analysis. 5 mg of Doxycycline Hyclate (DOX) (Sigma-Aldrich Cat# D9891) was resuspended in nuclease free water H2O to bring to make a 10 mg/ml stock, which was then aliquoted and stored at –20C. DOX was added to the media of newly seeded 6-well plates at a 5 M concentration. Media was changed every 2-3 days for iNN and iAD cells, and daily for iE cells due to there more rapid proliferation.

value: cell line

value: hiPSC

value: iE

value: KO

value: + DOX


title: Control-rep2

description: human bile duct

value: CCA Tumor

value: primary mast cell

value: mast cell


title: female, intestinal epithelium, wildtype, high fat diet, acute, biological replicate 1

description: Library name: Sample 5

value: intestinal epithelium

value: female

value: wildtype

value: high fat diet one week


title: female, intestinal epithelium, wildtype, low fat diet, biological replicate 3

description: Library name: Sample 3

value: low fat diet


title: ArPHR4-2

description: Library name: SAMPLES8

value: Leave

value: WT

value: Anoectochilus roxburghii Leaves


title: RMb2-11

description: iNN KO + DOX

value: iNN


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 4-hour time point (biol rep 3).

description: Library name: 54527_0pct_EtOH_4hr_rep3

value: Whole worm


title: RMb2-10

description: iAD KO + DOX

value: cell line

value: hiPSC

value: iAD


title: female, intestinal epithelium, wildtype, low fat diet, biological replicate 2

description: Library name: Sample 2


title: female, intestinal epithelium, wildtype, low fat diet, biological replicate 1

description: Library name: Sample 1


title: ArPHR2-3

description: Library name: SAMPLES6

value: OE

value: transient overexpression

value: Days 3


title: RMb2-9

description: iE WT + DOX

value: iE

value: + DOX


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 4-hour time point (biol rep 1).

description: Library name: 54525_0pct_EtOH_4hr_rep1


title: scATAC_PDO84T_ICM

description: Library name: scATAC_PDO84T_ICM

library_source: genomic single cell

data_processing:
cell_ranger_atac/1.1.0
Assembly: refdata-cellranger-atac-GRCh38-1.1.0
Supplementary files format and content: XXX.barcodes.tsv: text file containing cellular barcodes of the sample.
Supplementary files format and content: XXX.matrix.mtx: accessibility matrix per cell
Supplementary files format and content: xxx.peaks.bed: peak file with chromosome, start and end positions for each detected peak

extract_protocol:
according to the 10x “Nuclei isolation for Single Cell ATAC Sequencing” demonstrated protocol (Document CG000169 Rev E) with centrifugation speed of 500 xg instead of 300 xg.
according to the respective 10x user guide “Chromium Next GEM Single Cell ATAC Reagent Kits V2” (document CG000496 Rev B)

value: Pancreas

value: Patient derived organoids

value: Inflachromene


title: RMb2-8

description: iNN WT + DOX


title: RMb2-7

description: iAD WT + DOX


title: ArPHR2-1

description: Library name: SAMPLES4


title: scATAC_PDO54T_ICM

description: Library name: scATAC_PDO54T_ICM


title: CK3

description: Library name: SAMPLES3

value: EV


title: RMb2-6

description: iE KO - DOX

value: KO

value: - DOX


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 1-hour time point (biol rep 1).

description: Library name: 54522_0pct_EtOH_1hr_rep1


title: scATAC_PDO54T

description: Library name: scATAC_PDO54T


title: CK2

description: Library name: SAMPLES2

value: Leave

value: WT

value: Anoectochilus roxburghii Leaves


title: RMb2-5

description: iNN KO - DOX

value: cell line

value: iNN


title: RNA extracted from C. elegans grown without ethanol was analyzed at time zero (biol rep 4).

description: Library name: 54521_0pct_EtOH_0hr_rep4

value: Whole worm


title: scATAC_PDO51T_ICM

description: Library name: scATAC_PDO51T_ICM


title: CK1

description: Library name: SAMPLES1


title: RMb2-4

description: iAD KO - DOX

value: hiPSC

value: iAD


title: RNA extracted from C. elegans grown without ethanol was analyzed at time zero (biol rep 3).

description: Library name: 54520_0pct_EtOH_0hr_rep3


title: scATAC_PDO51T

description: Library name: scATAC_PDO51T


title: scATAC_PDO84T

description: Library name: scATAC_PDO84T


title: USZ-23_EMC3

city: Zurich

first: Lara

last: Planas-Paz

address: Schmelzbergstrasse 12

department: Pathology and Molecular Pathology

country: Switzerland

institute: University Hospital Zurich

description: Library name: USZ-23_EMC3

data_processing:
Dragen RNA
Assembly: Homo_sapiens_assembly38.fasta.gz, hg38.ncbiRefSeq.gtf.gz
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample

source_name: cells

growth_protocol: Cells were maintained in advanced Dulbecco’s modified Eagle medium (DMEM; Gibco, 12634028) supplemented with 10% heat-inactivated horse serum (Gibco, 260500888), 1x Glutamax (Gibco 35050038) and 0.2 % Primocin (InvivoGen, ant-pm-2). For cell expansion, the previous media was mixed 1:1 with DMEM containing 1 mM N-acetylcyteine (Sigma-Aldrich, A9165), 50 ng/ml recombinant human epidermal growth factor (Sigma-Aldrich, E9644), 100 ng/ml recombinant human fibroblast growth factor 10 (PeproTech, 100-26), 10 µM Y-27632 (Sellekchem, S1049), 5 µM A-83-01 (Sigma-Aldrich, SLM0788), 10 mM nicotinamide (Sigma-Aldrich, N0636), 10 % R-Spondin conditioned media (self-produced), B27 supplement (Gibco, 17504001), 10 mM HEPES (Gibco, 15630-080), 36 ng/ml hydrocortisone (Sigma-Aldrich, H6909) and 500 ng/ml epinephrine (Sigma-Aldrich, E4250). All cells were passaged when subconfluent  conditions were reached in cell culture‐treated flasks, incubated at 37°C in a humidified atmosphere with 5% CO2, and routinely tested for Mycoplasma.

extract_protocol:
RNA from fresh frozen sarcoma patient samples or patient-derived cells was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega AS1340). The extracted RNA was quantified with a Nanodrop (ThermoFisher Scientific) and the High Sensitivity RNA ScreenTape Assay for TapeStation systems (Agilent 5067).
RNA sequencing libraries were prepared using the Illumina Stranded mRNA sample preparation protocol

value: cells

value: extraskelletal myxoid chondrosarcoma


title: RMb2-3

description: iE WT - DOX

value: iE


title: RNA extracted from C. elegans grown without ethanol was analyzed at time zero (biol rep 2).

description: Library name: 54519_0pct_EtOH_0hr_rep2


title: scATAC_PDO35T_ICM

description: Library name: scATAC_PDO35T_ICM

value: Pancreas


city: Kanazawa

first: Tomohiro

last: Iba

state: Ishikawa

address: 13-1, Takara-machi

institute: Kanazawa University School of Medicine

description: Library name: Vascular endothelial cells of human limb muscle No2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Seurat (v4.4.0) for downstream single cell analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix files

source_name: limb muscle

extract_protocol:
Fluorescence-activated cell sorting (FACS)-purified cells were processed using the Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the standard protocol.
Chromium Single Cell 3’ Kit v3.1 (10X Genomics, Pleasanton, CA)

value: limb muscle


title: RMb2-2

description: iNN WT - DOX


title: RNA extracted from C. elegans grown without ethanol was analyzed at time zero (biol rep 1).

description: Library name: 54518_0pct_EtOH_0hr_rep1


title: Vascular endothelial cells of human limb muscle No1

description:
Library name: Vascular endothelial cells of human limb muscle
Human_EC

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Seurat (v4.4.0) for downstream single cell analysis.
Assembly: GRCm38/GRCh38
Supplementary files format and content: barcodes, features, matrix files


title: RMb2-1

description: iAD WT - DOX


title: Chicken spinal cord, Ch2, scRNA-seq 2

status: Public on Jun 03 2026

city: Dalseong-gun

first: Tery

last: Yun

state: Daegu

address: 333 Technojungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

country: South Korea

institute: DGIST

description: Library name: Ch2-chicken

data_processing:
Raw FASTQ files were processed using Cell Ranger v7.2.0. Fugu reads were mapped to Takifugu rubripes genome (Ensembl release 113). Mudskipper reads were mapped to Periophthalmus magnuspinnatus genome (Ensembl release 113). Chicken reads were mapped to Gallus gallus genome (Ensembl release 113). Empty droplets removed using emptyDrops (FDR ≤ 0.01, DropletUtils v1.26.0). Doublets identified using scDblFinder v1.23.4. Downstream analysis performed in Seurat v5.3.0 with Monocle3 pseudotime and CAME cross-species cell type mapping.
Assembly: Fugu: Takifugu rubripes (Ensembl release 113); Mudskipper: Periophthalmus magnuspinnatus (Ensembl release 113); Chicken: Gallus gallus (Ensembl release 113)
Supplementary files format and content: Tab-separated gzipped files in 10x Genomics sparse matrix format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs and names), and matrix.mtx.gz (UMI count matrix). Generated by Cell Ranger v7.2.0.

organism: Gallus gallus

source_name: spinal cord

growth_protocol: Fugu (Takifugu obscurus) and mudskipper (Periophthalmus magnuspinnatus) were dissected approximately one month post-hatching. Chicken (Gallus gallus) spinal cord was collected at embryonic days 10-11 (Hamburger-Hamilton stage 36-37). All procedures were approved by IACUC of DGIST (Approval No: DGIST-IACUC-23052304-0002).

extract_protocol:
Spinal cord tissue from multiple individuals was pooled per library. Cell dissociation was performed by incubation in pronase solution for 40 min at room temperature, followed by trituration in 100 µL ACSF containing 1% FBS. Volume was adjusted to 3 mL and live cells were enriched by FACS (BD FACSAria III) using propidium iodide (1 µg/mL) exclusion. Cell viability exceeded 80%. Sorted cells were resuspended in 1× DPBS containing 0.04% BSA.
Libraries were prepared using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics). Target cell recovery was 1,000-9,000 cells per replicate depending on tissue availability. Reverse transcription was performed using a C1000 Touch Thermal Cycler (Bio-Rad). Libraries were sequenced on an Illumina HiSeq X platform (paired-end 100 bp reads) targeting an average of 20,000 read pairs per cell.

value: spinal cord


title: ChIP-seq of H3K27ac in Donor 6B cells, treated with 0.1 mM butyrate

value: 0.1 mM butyrate

value: peripheral blood

value: macrophages


title: male, intestinal epithelium, wildtype, low fat diet, biological replicate 4

description: Library name: Sample 16

data_processing:
Raw sequencing reads were quality-assessed using FastQC, and adapters were removed using Cutadapt.
Trimmed reads were aligned to the mouse reference genome (ENSEMBL GRCm38) using STAR aligner version 2.6.1d.
The distribution of mapped reads across genomic features was analyzed with RSeQC v3.0.1.
Differential gene expression analysis was performed using DESeq2 (v2.11.40.8) implemented in R (v4.2.2) via the Galaxy platform.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
NOTE for intestinal intestinal epithelium: the small intestine was cut longitudanally, and the intestinal epithelium was scraped using microscope slides from the middle of the length of the entire intestine (roughly 16-20 cm in a typical 34 cm small intestine). The tissues (isolated intestinal epithelium or perigonadal white adipose tissues) were processed via commercial RNeasy RNA purification kits using manufacturers protocols.
Total RNA samples were prepared into RNA-Seq libraries using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina following the manufacturer’s recommended protocol. Briefly, for each sample, 200 ng total RNA was polyA selected, and converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq 2000 for 100 base single-read sequencing.

value: intestinal epithelium

value: male

value: wildtype

value: low fat diet


title: Matched adjacent non-tumor lung tissue sample N120

city: Suzhou

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

description:
Library name: N120
Local paired bulk RNA-seq library; pair_id=120; tissue_status=adjacent non-tumor; sample_id=N120.

data_processing:
Raw sequencing reads were processed by the sequencing provider to generate a gene-level raw-count matrix.
Assembly: GRCh38
Supplementary files format and content: CSV file containing gene-level raw counts. Rows correspond to Ensembl gene identifiers and columns correspond to sample IDs.

source_name: matched adjacent non-tumor lung tissue

extract_protocol:
Total RNA was extracted from each surgically resected tissue specimen using a standard total-RNA extraction workflow according to the sequencing provider's protocol. RNA quantity and quality were assessed before library construction, and samples passing RNA quality-control criteria were used for bulk RNA-seq.
Bulk RNA-seq libraries were prepared from total RNA using an Illumina-compatible RNA-seq library preparation workflow according to the sequencing provider's protocol. Libraries were generated for paired-end sequencing.

value: matched adjacent non-tumor lung tissue

value: bulk tissue


title: NSCLC tumor tissue sample C120

description:
Library name: C120
Local paired bulk RNA-seq library; pair_id=120; tissue_status=tumor; sample_id=C120.

source_name: non-small cell lung cancer tumor tissue

value: non-small cell lung cancer tumor tissue


title: Matched adjacent non-tumor lung tissue sample N119

description:
Library name: N119
Local paired bulk RNA-seq library; pair_id=119; tissue_status=adjacent non-tumor; sample_id=N119.


title: NSCLC tumor tissue sample C119

description:
Library name: C119
Local paired bulk RNA-seq library; pair_id=119; tissue_status=tumor; sample_id=C119.


title: Sample2A HTO

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

data_processing:
Alignment to human reference and assembly of VDJ contigs using Cellranger (v6.0.2) multi pipeline
Assembly: GRCh38, GENCODE v32/Ensembl 98
Supplementary files format and content: h5 filtered matrices

source_name: PBMC

extract_protocol:
PCR cycle number for the cDNA amplification was set to 16 cycles for a target recovery of <2000 cells. cDNA QC and Quantification via Tapestation. 2uL cDNA was used as input for the V(D)J amplification. 50ng cDNA was used as input for the 5’ Gene Expression Library Construction. Remaining cDNA was stored at -20°C.
50ng amplified V(D)J products was used as input for the V(D)J Library Construction. For the GEX library sample 50ng cDNA was used and index PCR cycle number was set to 14 cycles with a cDNA input of 26-50 ng. For surface protein library construction 5uL cleaned up supernatant product was used.
Library QC and Quantification via Tapestation.

treatment_protocol: Cells were surface stained and sorted based on positive tetramer staining into 50% FBS/PBS. Cells were pelleted and resuspended ~30uL 0.04% BSA/PBS solution. GEMs were produced using the Chromium Next GEM Single Cell 5'v2 (Dual Index) kit with Feature Barcoding technology and a Chromium Controller from 10X Genomics (Model GCG-SR-1).

value: PBMC

value: T cell

value: Nivolumab

tag: library type

value: HTO


title: Matched adjacent non-tumor lung tissue sample N118

description:
Library name: N118
Local paired bulk RNA-seq library; pair_id=118; tissue_status=adjacent non-tumor; sample_id=N118.


title: NSCLC tumor tissue sample C118

description:
Library name: C118
Local paired bulk RNA-seq library; pair_id=118; tissue_status=tumor; sample_id=C118.


title: Matched adjacent non-tumor lung tissue sample N117

description:
Library name: N117
Local paired bulk RNA-seq library; pair_id=117; tissue_status=adjacent non-tumor; sample_id=N117.


title: NSCLC tumor tissue sample C117

description:
Library name: C117
Local paired bulk RNA-seq library; pair_id=117; tissue_status=tumor; sample_id=C117.


title: Matched adjacent non-tumor lung tissue sample N116

description:
Library name: N116
Local paired bulk RNA-seq library; pair_id=116; tissue_status=adjacent non-tumor; sample_id=N116.


title: NSCLC tumor tissue sample C116

description:
Library name: C116
Local paired bulk RNA-seq library; pair_id=116; tissue_status=tumor; sample_id=C116.


title: Matched adjacent non-tumor lung tissue sample N115

description:
Library name: N115
Local paired bulk RNA-seq library; pair_id=115; tissue_status=adjacent non-tumor; sample_id=N115.


title: A549 cells, alisertib 500 nmol/L, day 3, DUL, rep1

city: Salt

first: Javier

middle: Abel

last: Menendez

state: Girona

address: Dr Castany s/n. Parc hospitalari Marti i Julia

country: Spain

institute: Girona Biomedical Research Institute

description:
Library name: A549_D3_DUL_ALI_500_R1_1
colum name in Read_counts_ALL_samples:  A549_D3_DUL_ALI_500_R1_Read_Count

data_processing:
BCL/cBCL (base call) binary files are converted into FASTQ files using bcl2fastq
Trimmed reads are mapped to reference genome with HISAT2
Stringtie was used for transcript assembly
read count data was normalized with Relative Log Expression (RLE) method in DESeq2 R library
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes read counts for each sample

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA Plus kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit acording to standard Illumina protocols. Reference Guide # 1000000040498 v00

value: Lung cells

value: Day 3

value: alisertib 500 nmol/L


title: NSCLC tumor tissue sample C115

description:
Library name: C115
Local paired bulk RNA-seq library; pair_id=115; tissue_status=tumor; sample_id=C115.


title: Matched adjacent non-tumor lung tissue sample N114

description:
Library name: N114
Local paired bulk RNA-seq library; pair_id=114; tissue_status=adjacent non-tumor; sample_id=N114.


title: NSCLC tumor tissue sample C114

description:
Library name: C114
Local paired bulk RNA-seq library; pair_id=114; tissue_status=tumor; sample_id=C114.


title: RNA extracted from C. elegans grown with 5% ethanol was analyzed at the 1-hour time point (biol rep 1).

description: Library name: 54531_5pct_EtOH_1hr_rep1

value: Whole worm


title: Matched adjacent non-tumor lung tissue sample N113

description:
Library name: N113
Local paired bulk RNA-seq library; pair_id=113; tissue_status=adjacent non-tumor; sample_id=N113.


title: NSCLC tumor tissue sample C113

description:
Library name: C113
Local paired bulk RNA-seq library; pair_id=113; tissue_status=tumor; sample_id=C113.


title: Matched adjacent non-tumor lung tissue sample N112

description:
Library name: N112
Local paired bulk RNA-seq library; pair_id=112; tissue_status=adjacent non-tumor; sample_id=N112.


title: Trachemys scripta peripheral nerve stage 19 - R1

description:
Library name: Ts_19_R1
Embryonic peripheral nerve tissue from T. scripta at developmental stage 19

value: peripheral nerve


title: scATAC_PDO35T

description: Library name: scATAC_PDO35T

source_name: Pancreas

value: Pancreas

value: Patient derived organoids


title: NSCLC tumor tissue sample C112

description:
Library name: C112
Local paired bulk RNA-seq library; pair_id=112; tissue_status=tumor; sample_id=C112.


title: Matched adjacent non-tumor lung tissue sample N111

description:
Library name: N111
Local paired bulk RNA-seq library; pair_id=111; tissue_status=adjacent non-tumor; sample_id=N111.


title: female, intestinal epithelium, wildtype, low fat diet, biological replicate 4

city: La Jolla

first: Supriya

last: Srinivasan

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description: Library name: Sample 4

source_name: intestinal epithelium

value: intestinal epithelium

value: female


title: NSCLC tumor tissue sample C111

description:
Library name: C111
Local paired bulk RNA-seq library; pair_id=111; tissue_status=tumor; sample_id=C111.


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 20-hour time point (biol rep 1).

description: Library name: 54528_0pct_EtOH_20hr_rep1


title: Matched adjacent non-tumor lung tissue sample N110

description:
Library name: N110
Local paired bulk RNA-seq library; pair_id=110; tissue_status=adjacent non-tumor; sample_id=N110.


title: NSCLC tumor tissue sample C110

description:
Library name: C110
Local paired bulk RNA-seq library; pair_id=110; tissue_status=tumor; sample_id=C110.


title: Matched adjacent non-tumor lung tissue sample N108

description:
Library name: N108
Local paired bulk RNA-seq library; pair_id=108; tissue_status=adjacent non-tumor; sample_id=N108.


title: NSCLC tumor tissue sample C108

description:
Library name: C108
Local paired bulk RNA-seq library; pair_id=108; tissue_status=tumor; sample_id=C108.


title: Matched adjacent non-tumor lung tissue sample N107

description:
Library name: N107
Local paired bulk RNA-seq library; pair_id=107; tissue_status=adjacent non-tumor; sample_id=N107.


title: NSCLC tumor tissue sample C107

description:
Library name: C107
Local paired bulk RNA-seq library; pair_id=107; tissue_status=tumor; sample_id=C107.


title: Matched adjacent non-tumor lung tissue sample N106

description:
Library name: N106
Local paired bulk RNA-seq library; pair_id=106; tissue_status=adjacent non-tumor; sample_id=N106.


title: NSCLC tumor tissue sample C106

description:
Library name: C106
Local paired bulk RNA-seq library; pair_id=106; tissue_status=tumor; sample_id=C106.


title: Matched adjacent non-tumor lung tissue sample N105

description:
Library name: N105
Local paired bulk RNA-seq library; pair_id=105; tissue_status=adjacent non-tumor; sample_id=N105.


title: Chicken spinal cord, Ch1, scRNA-seq 1

description: Library name: Ch1-chicken

value: spinal cord


title: NSCLC tumor tissue sample C105

description:
Library name: C105
Local paired bulk RNA-seq library; pair_id=105; tissue_status=tumor; sample_id=C105.


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 4-hour time point (biol rep 2).

description: Library name: 54526_0pct_EtOH_4hr_rep2


title: ArPHR4-1

description: Library name: SAMPLES7

value: Leave

value: WT

value: Anoectochilus roxburghii Leaves

value: OE

value: transient overexpression

value: Days 3


title: Matched adjacent non-tumor lung tissue sample N104

description:
Library name: N104
Local paired bulk RNA-seq library; pair_id=104; tissue_status=adjacent non-tumor; sample_id=N104.

value: matched adjacent non-tumor lung tissue

value: bulk tissue


title: NSCLC tumor tissue sample C104

description:
Library name: C104
Local paired bulk RNA-seq library; pair_id=104; tissue_status=tumor; sample_id=C104.

value: non-small cell lung cancer tumor tissue


title: Matched adjacent non-tumor lung tissue sample N103

description:
Library name: N103
Local paired bulk RNA-seq library; pair_id=103; tissue_status=adjacent non-tumor; sample_id=N103.


title: NSCLC tumor tissue sample C103

description:
Library name: C103
Local paired bulk RNA-seq library; pair_id=103; tissue_status=tumor; sample_id=C103.


title: Matched adjacent non-tumor lung tissue sample N102

description:
Library name: N102
Local paired bulk RNA-seq library; pair_id=102; tissue_status=adjacent non-tumor; sample_id=N102.


title: Matched adjacent non-tumor lung tissue sample N101

description:
Library name: N101
Local paired bulk RNA-seq library; pair_id=101; tissue_status=adjacent non-tumor; sample_id=N101.


title: NSCLC tumor tissue sample C101

description:
Library name: C101
Local paired bulk RNA-seq library; pair_id=101; tissue_status=tumor; sample_id=C101.


title: NSCLC tumor tissue sample C100

description:
Library name: C100
Local paired bulk RNA-seq library; pair_id=100; tissue_status=tumor; sample_id=C100.


title: Matched adjacent non-tumor lung tissue sample N99

description:
Library name: N99
Local paired bulk RNA-seq library; pair_id=99; tissue_status=adjacent non-tumor; sample_id=N99.


title: ArPHR2-2

description: Library name: SAMPLES5


title: Matched adjacent non-tumor lung tissue sample N100

description:
Library name: N100
Local paired bulk RNA-seq library; pair_id=100; tissue_status=adjacent non-tumor; sample_id=N100.


title: NSCLC tumor tissue sample C99

description:
Library name: C99
Local paired bulk RNA-seq library; pair_id=99; tissue_status=tumor; sample_id=C99.


title: Matched adjacent non-tumor lung tissue sample N98

description:
Library name: N98
Local paired bulk RNA-seq library; pair_id=98; tissue_status=adjacent non-tumor; sample_id=N98.


title: NSCLC tumor tissue sample C98

description:
Library name: C98
Local paired bulk RNA-seq library; pair_id=98; tissue_status=tumor; sample_id=C98.


title: NSCLC tumor tissue sample C97

description:
Library name: C97
Local paired bulk RNA-seq library; pair_id=97; tissue_status=tumor; sample_id=C97.


title: Matched adjacent non-tumor lung tissue sample N97

description:
Library name: N97
Local paired bulk RNA-seq library; pair_id=97; tissue_status=adjacent non-tumor; sample_id=N97.


title: Matched adjacent non-tumor lung tissue sample N96

description:
Library name: N96
Local paired bulk RNA-seq library; pair_id=96; tissue_status=adjacent non-tumor; sample_id=N96.


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 1-hour time point (biol rep 3).

description: Library name: 54524_0pct_EtOH_1hr_rep3


title: NSCLC tumor tissue sample C96

description:
Library name: C96
Local paired bulk RNA-seq library; pair_id=96; tissue_status=tumor; sample_id=C96.


title: NSCLC tumor tissue sample C95

description:
Library name: C95
Local paired bulk RNA-seq library; pair_id=95; tissue_status=tumor; sample_id=C95.


title: Matched adjacent non-tumor lung tissue sample N95

description:
Library name: N95
Local paired bulk RNA-seq library; pair_id=95; tissue_status=adjacent non-tumor; sample_id=N95.


title: NSCLC tumor tissue sample C94

description:
Library name: C94
Local paired bulk RNA-seq library; pair_id=94; tissue_status=tumor; sample_id=C94.


title: Matched adjacent non-tumor lung tissue sample N94

description:
Library name: N94
Local paired bulk RNA-seq library; pair_id=94; tissue_status=adjacent non-tumor; sample_id=N94.


title: RNA extracted from C. elegans grown without ethanol was analyzed at the 1-hour time point (biol rep 2).

description: Library name: 54523_0pct_EtOH_1hr_rep2


title: Matched adjacent non-tumor lung tissue sample N92

description:
Library name: N92
Local paired bulk RNA-seq library; pair_id=92; tissue_status=adjacent non-tumor; sample_id=N92.


title: NSCLC tumor tissue sample C93

description:
Library name: C93
Local paired bulk RNA-seq library; pair_id=93; tissue_status=tumor; sample_id=C93.


title: NSCLC tumor tissue sample C92

description:
Library name: C92
Local paired bulk RNA-seq library; pair_id=92; tissue_status=tumor; sample_id=C92.


title: Matched adjacent non-tumor lung tissue sample N91

description:
Library name: N91
Local paired bulk RNA-seq library; pair_id=91; tissue_status=adjacent non-tumor; sample_id=N91.


title: Matched adjacent non-tumor lung tissue sample N89

description:
Library name: N89
Local paired bulk RNA-seq library; pair_id=89; tissue_status=adjacent non-tumor; sample_id=N89.


title: NSCLC tumor tissue sample C90

description:
Library name: C90
Local paired bulk RNA-seq library; pair_id=90; tissue_status=tumor; sample_id=C90.


title: NSCLC tumor tissue sample C102

description:
Library name: C102
Local paired bulk RNA-seq library; pair_id=102; tissue_status=tumor; sample_id=C102.


title: Matched adjacent non-tumor lung tissue sample N90

description:
Library name: N90
Local paired bulk RNA-seq library; pair_id=90; tissue_status=adjacent non-tumor; sample_id=N90.


title: NSCLC tumor tissue sample C89

description:
Library name: C89
Local paired bulk RNA-seq library; pair_id=89; tissue_status=tumor; sample_id=C89.


title: NSCLC tumor tissue sample C91

description:
Library name: C91
Local paired bulk RNA-seq library; pair_id=91; tissue_status=tumor; sample_id=C91.


title: Matched adjacent non-tumor lung tissue sample N93

description:
Library name: N93
Local paired bulk RNA-seq library; pair_id=93; tissue_status=adjacent non-tumor; sample_id=N93.


title: Matched adjacent non-tumor lung tissue sample N88

description:
Library name: N88
Local paired bulk RNA-seq library; pair_id=88; tissue_status=adjacent non-tumor; sample_id=N88.


title: Matched adjacent non-tumor lung tissue sample N87

description:
Library name: N87
Local paired bulk RNA-seq library; pair_id=87; tissue_status=adjacent non-tumor; sample_id=N87.


title: NSCLC tumor tissue sample C88

description:
Library name: C88
Local paired bulk RNA-seq library; pair_id=88; tissue_status=tumor; sample_id=C88.


title: Matched adjacent non-tumor lung tissue sample N86

description:
Library name: N86
Local paired bulk RNA-seq library; pair_id=86; tissue_status=adjacent non-tumor; sample_id=N86.


title: NSCLC tumor tissue sample C86

description:
Library name: C86
Local paired bulk RNA-seq library; pair_id=86; tissue_status=tumor; sample_id=C86.


title: NSCLC tumor tissue sample C87

description:
Library name: C87
Local paired bulk RNA-seq library; pair_id=87; tissue_status=tumor; sample_id=C87.


title: Matched adjacent non-tumor lung tissue sample N85

description:
Library name: N85
Local paired bulk RNA-seq library; pair_id=85; tissue_status=adjacent non-tumor; sample_id=N85.


title: Matched adjacent non-tumor lung tissue sample N84

description:
Library name: N84
Local paired bulk RNA-seq library; pair_id=84; tissue_status=adjacent non-tumor; sample_id=N84.


title: NSCLC tumor tissue sample C85

description:
Library name: C85
Local paired bulk RNA-seq library; pair_id=85; tissue_status=tumor; sample_id=C85.


title: NSCLC tumor tissue sample C84

description:
Library name: C84
Local paired bulk RNA-seq library; pair_id=84; tissue_status=tumor; sample_id=C84.


title: alx3 Mutant 48hpf CNCCs

city: Aurora

first: James

middle: T

last: Nichols

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: alx3_Mutant
10x genomics

data_processing:
Recovered sequencing reads were mapped to a custom Cell Ranger reference based on the GRCz11/danRer11 genome assembly using the Cell Ranger pipeline (10X Genomics). This Cell Ranger reference contained the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7. The 10X Genomics Cell Ranger pipeline was used to identify cell-associate barcodes.
Assembly: GRCz11/danRer11 genome assembly with the alx3 transcript from Ensembl release 91 (GRCz10) mapped to the GCRz11 genome in place of the release 101 (GRCZ11) version due to inaccurate truncation of the 3’ UTR in the most recent version7.
Supplementary files format and content: wt.barcodes.tsv.gz : barcodes for WT dataset in tsv file
Supplementary files format and content: alx3M.barcodes.tsv.gz : barcodes for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.barcodes.tsv.gz : barcodes for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.features.tsv.gz : features for WT dataset in tsv file
Supplementary files format and content: alx3M.features.tsv.gz : features for alx3M dataset in tsv file
Supplementary files format and content: alx3Malx4aM.features.tsv.gz : features for alx3Malx4aM dataset in tsv file
Supplementary files format and content: wt.matrix.mtx.gz : matrix for WT dataset in mtx file
Supplementary files format and content: alx3M.matrix.mtx.gz : matrix for alx3M dataset in mtx file
Supplementary files format and content: alx3Malx4aM.matrix.mtx.gz : matrix for alx3Malc4aM dataset in mtx file
Supplementary files format and content: 230724_A00405_0714_BH55GNDSX7_L3_Nichols_demux.csv : csv of all data files

organism: Danio rerio

source_name: 48hpf zebrafish embryo

growth_protocol: Zebrafish were grown to 48hpf in E2 embryo media

extract_protocol:
33 double transgenic fli1:EGFP;sox10:mRFP embryos per genotype were dissociated into single-cell suspension using cold-active protease from Bacillus licheniformis, DNase, EDTA, and trituration.
Sorted cells (at 3.27 x 105 cells/ml in wild type, at 2.72 x 105 cells/ml in alx3-/-, and at 2.86 x 105 cells/ml in alx3-/-;alx4a-/- with ~85% viability) were loaded into the 10X Chromium Controller aiming to capture > 10,000 cells per sample. 2x150 paired-end sequencing Chromium 10X Genomics libraries were sequenced using the NovaSEQ6000.

value: 48hpf zebrafish embryo

value: Cranial neural crest

value: alx3 mutant


title: Matched adjacent non-tumor lung tissue sample N82

description:
Library name: N82
Local paired bulk RNA-seq library; pair_id=82; tissue_status=adjacent non-tumor; sample_id=N82.


title: NSCLC tumor tissue sample C83

description:
Library name: C83
Local paired bulk RNA-seq library; pair_id=83; tissue_status=tumor; sample_id=C83.


title: NSCLC tumor tissue sample C82

description:
Library name: C82
Local paired bulk RNA-seq library; pair_id=82; tissue_status=tumor; sample_id=C82.


title: Matched adjacent non-tumor lung tissue sample N83

description:
Library name: N83
Local paired bulk RNA-seq library; pair_id=83; tissue_status=adjacent non-tumor; sample_id=N83.


title: NSCLC tumor tissue sample C81

description:
Library name: C81
Local paired bulk RNA-seq library; pair_id=81; tissue_status=tumor; sample_id=C81.


title: Matched adjacent non-tumor lung tissue sample N81

description:
Library name: N81
Local paired bulk RNA-seq library; pair_id=81; tissue_status=adjacent non-tumor; sample_id=N81.


title: Matched adjacent non-tumor lung tissue sample N80

description:
Library name: N80
Local paired bulk RNA-seq library; pair_id=80; tissue_status=adjacent non-tumor; sample_id=N80.


title: NSCLC tumor tissue sample C80

description:
Library name: C80
Local paired bulk RNA-seq library; pair_id=80; tissue_status=tumor; sample_id=C80.


title: Matched adjacent non-tumor lung tissue sample N79

description:
Library name: N79
Local paired bulk RNA-seq library; pair_id=79; tissue_status=adjacent non-tumor; sample_id=N79.


title: NSCLC tumor tissue sample C79

description:
Library name: C79
Local paired bulk RNA-seq library; pair_id=79; tissue_status=tumor; sample_id=C79.


title: Matched adjacent non-tumor lung tissue sample N78

description:
Library name: N78
Local paired bulk RNA-seq library; pair_id=78; tissue_status=adjacent non-tumor; sample_id=N78.


title: NSCLC tumor tissue sample C78

description:
Library name: C78
Local paired bulk RNA-seq library; pair_id=78; tissue_status=tumor; sample_id=C78.


title: Matched adjacent non-tumor lung tissue sample N77

description:
Library name: N77
Local paired bulk RNA-seq library; pair_id=77; tissue_status=adjacent non-tumor; sample_id=N77.


title: NSCLC tumor tissue sample C77

description:
Library name: C77
Local paired bulk RNA-seq library; pair_id=77; tissue_status=tumor; sample_id=C77.


title: B4galt1 WT, replicate 3

city: Milwaukee

first: Karin

last: Hoffmeister

state: WI

address: 8727 Watertown Plank Road

institute: Versiti Blood Research Institute

data_processing:
Sequenced libraries were demultiplexed and aligned to the Mus musculus mm10 genome using Illumina BaseSpace (workflow version 1.1.0).
Illumina adapters were trimmed with CutAdapt
Read counts per gene were quantified using the pseudoaligner salmon-0.11.2
Assembly: mm10
Supplementary files format and content: SALMON quant files from Salmon pseudoalignment

source_name: Bone marrow

extract_protocol:
Bone marrow (BM) cells were obtained by flushing mice tibia and femur shafts in 1×PBS supplemented with 3% FBS and 5 mM EDTA (flushing buffer) through a 70mm filter, followed by erythrocyte lysis 1× RBC Lysis Buffer (eBiosciences).
Library preparation followed manufacture’s recommendations in the SMART-Seq v4 Ultra Low Input RNA kit (Takara) Final preparation and amplification of libraries was completed with the SMARTer ThruPLEX DNA-seq Kit (Takara) utilizing dual 8bp indexes.  Final libraries were check by fragment analysis (Agilent, Bioanalyzer), quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems).  Samples were sequenced over 2 lanes on the HiSeq2500, run in rapid mode with 2x150bp read lengths captured

value: Bone marrow

value: LT-HSC


title: B4galt1 WT, replicate 2


title: B4galt1 WT, replicate 1


title: NSCLC tumor tissue sample C76

description:
Library name: C76
Local paired bulk RNA-seq library; pair_id=76; tissue_status=tumor; sample_id=C76.


title: NSCLC tumor tissue sample C75

description:
Library name: C75
Local paired bulk RNA-seq library; pair_id=75; tissue_status=tumor; sample_id=C75.


title: B4galt1 KO, replicate 3


title: B4galt1 KO, replicate 2


title: B4galt1 KO, replicate 4


title: Matched adjacent non-tumor lung tissue sample N74

description:
Library name: N74
Local paired bulk RNA-seq library; pair_id=74; tissue_status=adjacent non-tumor; sample_id=N74.


title: B4galt1 KO, replicate 1


title: Matched adjacent non-tumor lung tissue sample N73

description:
Library name: N73
Local paired bulk RNA-seq library; pair_id=73; tissue_status=adjacent non-tumor; sample_id=N73.


title: NSCLC tumor tissue sample C73

description:
Library name: C73
Local paired bulk RNA-seq library; pair_id=73; tissue_status=tumor; sample_id=C73.


title: NSCLC tumor tissue sample C74

description:
Library name: C74
Local paired bulk RNA-seq library; pair_id=74; tissue_status=tumor; sample_id=C74.


title: Sextuple-AA rep2

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
HiSeq2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. 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: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA was isolated usingTRIzol for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ten day old seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours (sample named as Col_AA), or treated with DMSO (sample named as Col_CK).

value: whole seedling

value: ten day old

value: sextuple mutant line

value: AA


title: 2582, Cre+, Saline

city: Los Angeles

first: Jonathan

middle: William

last: Nelson

address: 1333 San Pablo St.

department: Medicine

institute: University of Southern California

description:
10x Genomics
NUC230517SG_5

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 7.1.0 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.2
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.3.0
Assembly: mm10
Supplementary files format and content: Raw and filtered feature-barcode matrices from each replicate
Supplementary files format and content: Integrated seurat objects containing multiple replicates

molecule: nuclear RNA

source_name: Whole Kidney

extract_protocol:
Kidney cortex was dissected out after PBS washout via aortic perfusion and snap-frozen in liquid nitrogen immediately after dissection. Frozen tissue was stored at -80 °C until subsequent tissue processing. Prepare the nuclei isolation buffer (NIB, includes 146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA, pH 7.5), and add 1 tablet of cOmplete ULTRA per 10 ml NIB. The samples were ground for 30 times in 2ml NIB1 (4mL NIB + 20µl RNasin Plus + 20µl SUPERaseIN) with a 2ml Dounce grinder and a loose pestle, then homogenate was passed through a 200 µm strainer. The homogenate was ground for 15 times with a tight pestle, then 2 ml NIB1 was added and the homogenate was incubated for 5 min on ice. The homogenate was passed through a 40 µm strainer, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 4 ml NIB2 (4mL NIB + 4µl RNasin Plus + 4µl SUPERaseIN) and the suspension was incubated on ice for 5 min, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 1.5 ml of nuclei resuspension buffer (NSB, 10mL DPBS + 10µl RNasin Plus), then centrifuged at 500g for 5 min at 4°C. Repeat this step, then the suspension was passed through a 5 µm strainer. The suspension was centrifuged at 500g for 5 min at 4°C, and the pellet was resuspended in 10 ml NSB. The nuclei suspension was mixed with 5µl Vybrant Ruby stain and incubated on ice for 15 min. The nuclei were sorted in 500 µl final resuspension buffer (FSB, 1ml DPBS with 1% BSA + 5 µl Protector RNase inhibitor) with a low flow rate and pressure to ensure high viability.A 561+683 emission gate was used to select for ruby stained nulcei. Low trigger pulse width was used as singlet discriminator. One hundred thousand nuclei were collected and centrifuged at 500g for 5 min at 4°C. The top supernatant was carefully removed, and 50 µl volume was left to resuspend the nuclei pellet.
Single nucleus RNA-seq was performed using a Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Single nuclei were partitioned in droplets with single Gel Beads, which contained primers with cell-tagging indexes. Single nucleus suspensions with concentration of at least 300/µl were loaded targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. ( https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry )

tag: strain

value: Male

value: Cre+

value: Whole Kidney

value: All Kidney Cells

value: Saline


title: Sextuple-AA rep1


title: NSCLC tumor tissue sample C72

description:
Library name: C72
Local paired bulk RNA-seq library; pair_id=72; tissue_status=tumor; sample_id=C72.


title: Matched adjacent non-tumor lung tissue sample N72

description:
Library name: N72
Local paired bulk RNA-seq library; pair_id=72; tissue_status=adjacent non-tumor; sample_id=N72.

value: matched adjacent non-tumor lung tissue


title: Sextuple1-CK rep2

value: CK


title: Sextuple1-CK rep1


title: Matched adjacent non-tumor lung tissue sample N71

description:
Library name: N71
Local paired bulk RNA-seq library; pair_id=71; tissue_status=adjacent non-tumor; sample_id=N71.

value: bulk tissue


title: Matched adjacent non-tumor lung tissue sample N70

description:
Library name: N70
Local paired bulk RNA-seq library; pair_id=70; tissue_status=adjacent non-tumor; sample_id=N70.


title: 6OX-AA rep3

value: MCU6 overexpression line


title: 6OX-AA rep2


title: 6OX-AA rep1


title: 6OX-CK rep3


title: 6OX-CK rep2


title: 6OX-CK rep1


title: Matched adjacent non-tumor lung tissue sample N67

description:
Library name: N67
Local paired bulk RNA-seq library; pair_id=67; tissue_status=adjacent non-tumor; sample_id=N67.


title: NSCLC tumor tissue sample C67

description:
Library name: C67
Local paired bulk RNA-seq library; pair_id=67; tissue_status=tumor; sample_id=C67.

value: non-small cell lung cancer tumor tissue


title: 4OX-AA rep3

value: MCU4 overexpression line


title: 4OX-AA rep1


title: 4OX-AA rep2


title: NSCLC tumor tissue sample C66

description:
Library name: C66
Local paired bulk RNA-seq library; pair_id=66; tissue_status=tumor; sample_id=C66.


title: 4OX-CK rep3


title: Matched adjacent non-tumor lung tissue sample N65

description:
Library name: N65
Local paired bulk RNA-seq library; pair_id=65; tissue_status=adjacent non-tumor; sample_id=N65.


title: 4OX-CK rep2


title: Matched adjacent non-tumor lung tissue sample N64

description:
Library name: N64
Local paired bulk RNA-seq library; pair_id=64; tissue_status=adjacent non-tumor; sample_id=N64.


title: NSCLC tumor tissue sample C65

description:
Library name: C65
Local paired bulk RNA-seq library; pair_id=65; tissue_status=tumor; sample_id=C65.


title: NSCLC tumor tissue sample C64

description:
Library name: C64
Local paired bulk RNA-seq library; pair_id=64; tissue_status=tumor; sample_id=C64.


title: 2OX-AA rep3

value: MCU2 overexpression line


title: 2OX-AA rep2


title: Matched adjacent non-tumor lung tissue sample N63

description:
Library name: N63
Local paired bulk RNA-seq library; pair_id=63; tissue_status=adjacent non-tumor; sample_id=N63.


title: NSCLC tumor tissue sample C63

description:
Library name: C63
Local paired bulk RNA-seq library; pair_id=63; tissue_status=tumor; sample_id=C63.


title: 2OX-CK rep3


title: Matched adjacent non-tumor lung tissue sample N62

description:
Library name: N62
Local paired bulk RNA-seq library; pair_id=62; tissue_status=adjacent non-tumor; sample_id=N62.


title: 2OX-CK rep2


title: NSCLC tumor tissue sample C62

description:
Library name: C62
Local paired bulk RNA-seq library; pair_id=62; tissue_status=tumor; sample_id=C62.


title: 2OX-CK rep1


title: Matched adjacent non-tumor lung tissue sample N61

description:
Library name: N61
Local paired bulk RNA-seq library; pair_id=61; tissue_status=adjacent non-tumor; sample_id=N61.


title: Col-0-AA rep3

value: wild type Col-0


title: Col-0-AA rep2

value: whole seedling


title: Matched adjacent non-tumor lung tissue sample N60

description:
Library name: N60
Local paired bulk RNA-seq library; pair_id=60; tissue_status=adjacent non-tumor; sample_id=N60.


title: NSCLC tumor tissue sample C61

description:
Library name: C61
Local paired bulk RNA-seq library; pair_id=61; tissue_status=tumor; sample_id=C61.


title: Col-0-AA rep1

value: ten day old


title: NSCLC tumor tissue sample C60

description:
Library name: C60
Local paired bulk RNA-seq library; pair_id=60; tissue_status=tumor; sample_id=C60.


title: Col-0-CK rep3


title: Col-0-CK rep2


title: Matched adjacent non-tumor lung tissue sample N59

description:
Library name: N59
Local paired bulk RNA-seq library; pair_id=59; tissue_status=adjacent non-tumor; sample_id=N59.


title: NSCLC tumor tissue sample C59

description:
Library name: C59
Local paired bulk RNA-seq library; pair_id=59; tissue_status=tumor; sample_id=C59.


title: Col-0-CK rep1


title: Matched adjacent non-tumor lung tissue sample N58

description:
Library name: N58
Local paired bulk RNA-seq library; pair_id=58; tissue_status=adjacent non-tumor; sample_id=N58.


title: NSCLC tumor tissue sample C69

description:
Library name: C69
Local paired bulk RNA-seq library; pair_id=69; tissue_status=tumor; sample_id=C69.


title: C4-2 cells, BG4 (ChIP), input

city: Xi'an

first: Yue

last: Hou

state: ShaanXi

address: Changle west road

institute: the Fourth military medical university

description: Library name: C4-2_INPUT

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After removing adaptor sequences, the reads were mapped to the reference human genome (hg19) with bowtie v2.2.5 with the default parameters.
Unmapped reads, non-uniquely mapped reads, reads with mapping quality below ten or marked as duplicates were removed by using samtools v1.11.
MACS2 v2.1.1 was used to identify peaks with a cutoff p-value of 0.01.
Assembly: hg19
Supplementary files format and content: narrowPeak files

source_name: Prostate cancer tissue

growth_protocol: C4-2 cells were cultured at 378C in a humidifiedenvironment of 5% CO2in air, and the medium wasreplenished twice weekly.

extract_protocol:
Chromatin was isolated from C4-2 cells that were cross-linked using 1% formaldehyde. Chromatin was sonicated using a Bioruptor Plus to give a fragment distribution of 100-500 bp. For further details see methods section in the associated manuscript.
BG4 ChIP-seq was modified from a previously published protocol (Hansel-Hertsch et al., 2018).

value: Prostate cancer tissue


title: Matched adjacent non-tumor lung tissue sample N57

description:
Library name: N57
Local paired bulk RNA-seq library; pair_id=57; tissue_status=adjacent non-tumor; sample_id=N57.


title: C4-2 cells, BG4 (ChIP), rep3

description: Library name: C4-2_IP3


title: NSCLC tumor tissue sample C57

description:
Library name: C57
Local paired bulk RNA-seq library; pair_id=57; tissue_status=tumor; sample_id=C57.


title: Matched adjacent non-tumor lung tissue sample N56

description:
Library name: N56
Local paired bulk RNA-seq library; pair_id=56; tissue_status=adjacent non-tumor; sample_id=N56.


title: DHGZ_Day_70

city: Durham

first: Andrew

last: Hudson

address: 1328 Campus Drive

department: Surgery

institute: Duke University

description: Library name: DHGZ_Day_70

data_processing:
Raw sequence reads were trimmed using Trimmomatic1
Raw sequence reads were trimmed using Trimmomatic1
Sequenced reads were aligned to the reference genome (MMul_10, GCA_003339765.3) using the STAR aligner2.
Transcripts were annotated using Ensembl build Mmul_10.109.
Assembly: MMul_10 (Available at https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003339765.1/)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Macaca mulatta

source_name: Peripheral NK

extract_protocol:
Peripheral NK cells were isolated from PBMC by fluorescence-activated cell sorting. RNA extraction was performed from frozen cell pellets using the QIAGEN AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, Maryland), following the manufacturer’s instructions.
Library prep was conducted using the Takara v4 ultra-low input kit (Takara Bio, Otsu, Shiga, Japan), and indexed sequence libraries were sequenced using Illumina NovaSeq X Plus instrument.

treatment_protocol: Macaques were infected intrarectally with SIVmac251 as described [Hudson et al. J Virol 2025]

value: Peripheral NK


title: 2C10_D8

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

description: Library name: 2C10_D8

data_processing:
Nextpresso pipeline was used for analysis. Brieffly, reads were aligned to hg19 genome using bowtie and TopHat aligners. Feature counting was performed by htseq count command. Read count normalization and diffrential expression analysis was performed using DEseq2 package.
Assembly: hg19
Supplementary files format and content: raw counts as plain text file

source_name: H&N squamous cel carcinoma

extract_protocol:
Tumor biopies were obtained prior to treatment, on day 8, and day 28 after treatment and and placed in RNAlater® (Invitrogen). RNA wasextracted using the guanidine isothiocyanate (GTC) method.
Total RNA samples [1µg, but 70-100ng from samples 1S24RNAD-7 and 1S25RNASCR; RQS/RIN= 7.3, range 5.3-9.3 (samples 1S24RNAD-7 and 1S25RNASCR RQS under 6)] were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760), as recommended by the manufacturer. Briefly, polyA+ fraction is purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library is completed by PCR with Illumina PE primers. {This kit generates directional libraries stranded in the antisense orientation [the read1 (the only read in single read format) has the antisense orientation (--library-type fr-firststrand in TopHat, --stranded=reverse in HTSeq]} The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: H&N squamous cel carcinoma

value: Arm I LD D8


title: NSCLC tumor tissue sample C56

description:
Library name: C56
Local paired bulk RNA-seq library; pair_id=56; tissue_status=tumor; sample_id=C56.


title: 2C04_D8

description: Library name: 2C04_D8


title: DHGZ_Day_7

description: Library name: DHGZ_Day_7


title: Matched adjacent non-tumor lung tissue sample N54

description:
Library name: N54
Local paired bulk RNA-seq library; pair_id=54; tissue_status=adjacent non-tumor; sample_id=N54.


title: 2C04_SCR

description: Library name: 2C04_SCR

value: Arm I LD D0


title: N035_Day_70

description: Library name: N035_Day_70


title: 1S24_D7

description: Library name: 1S24_D7

value: Arm II HD D8


title: NSCLC tumor tissue sample C54

description:
Library name: C54
Local paired bulk RNA-seq library; pair_id=54; tissue_status=tumor; sample_id=C54.


title: 1S18_D7

description: Library name: 1S18_D7

value: Arm II LD D8


title: M636_Day_0

description: Library name: M636_Day_0


title: 1S03_D7

description: Library name: 1S03_D7


title: NSCLC tumor tissue sample C58

description:
Library name: C58
Local paired bulk RNA-seq library; pair_id=58; tissue_status=tumor; sample_id=C58.


title: C4-2 cells, BG4 (ChIP), rep4

description: Library name: C4-2_IP4


title: Matched adjacent non-tumor lung tissue sample N53

description:
Library name: N53
Local paired bulk RNA-seq library; pair_id=53; tissue_status=adjacent non-tumor; sample_id=N53.

value: matched adjacent non-tumor lung tissue


title: C4-2 cells, BG4 (ChIP), rep2

description: Library name: C4-2_IP2


title: 1S24_SCR

description: Library name: 1S24_SCR

value: Arm II HD D0


title: C4-2 cells, BG4 (ChIP), rep1

description: Library name: C4-2_IP1


title: M636_Day_70

description: Library name: M636_Day_70


title: 1S18_SCR

description: Library name: 1S18_SCR

value: Arm II LD D0


title: NSCLC tumor tissue sample C53

description:
Library name: C53
Local paired bulk RNA-seq library; pair_id=53; tissue_status=tumor; sample_id=C53.

value: bulk tissue


title: M488_Day_0

description: Library name: M488_Day_0


title: 1S03_SCR

description: Library name: 1S03_SCR


title: 1S22_D7

description: Library name: 1S22_D7


title: Matched adjacent non-tumor lung tissue sample N52

description:
Library name: N52
Local paired bulk RNA-seq library; pair_id=52; tissue_status=adjacent non-tumor; sample_id=N52.


title: 2S13_D7

description: Library name: 2S13_D7


title: M491_Day_7

description: Library name: M491_Day_7


title: 1S21_D7

description: Library name: 1S21_D7


title: 2C10_SCR

description: Library name: 2C10_SCR


title: NSCLC tumor tissue sample C52

description:
Library name: C52
Local paired bulk RNA-seq library; pair_id=52; tissue_status=tumor; sample_id=C52.

value: non-small cell lung cancer tumor tissue


title: 2S11_D7

description: Library name: 2S11_D7


title: Matched adjacent non-tumor lung tissue sample N76

description:
Library name: N76
Local paired bulk RNA-seq library; pair_id=76; tissue_status=adjacent non-tumor; sample_id=N76.


title: DHGZ_Day_0

description: Library name: DHGZ_Day_0


title: 2S08_D7

description: Library name: 2S08_D7