title: Input of CORL47 cells expressing DOX-ON ASCL1del217-236

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: CORL47_ASCL1 del217-236_Flag_Input

data_processing:
Sequenced read were aligned to the UCSC hg38 reference genome using BWA (v0.7.15). Peaks are called by subtracting reads in each sample from its respective input using MACS3 (v.3). Common peaks between samples are derived using bedtools (v2.27.1). Differential analysis are performed using DiffBind (v.3.10.1). Motif analysis are performed using HOMER(v.4.11) and MEME_suite (v4.12.0). Heatmaps are generated using deeptools (v3.5.6).
Assembly: hg38
Supplementary files format and content: bigwig files of read coverage of each sample.

growth_protocol: CORL47 cells were cultured with RPMI-1640 with 10% FBS, 100 U/mL of penicillin, and 100 μg/mL of streptomycin and culture with 5% CO2 at 37C.

extract_protocol:
•Cells were collected and then cross-linked by incubation with 2 mM disuccinimidyl glutarate (DSG) prior to fixation step. Then cells were fixed in 1% paraformaldehyde. Crosslinking was then quenched by adding freshly made 1.25 M glycine. The cells were resuspended in 1 mL of lysis buffer (50 mM Hepes-NaOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) to collect nuclei. The intact nuclei were transferred to a 1 mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator. For each sample, 5% of the total lysate was used for the ChIP-seq input DNA and remaining lysate (95%) was used for either FLAG-ChIP or ASCL1-ChIP. 10 μg and 2 ug of FLAG and ASCL1 antibody, respectively, was  used for each ChIP. All samples were incubated overnight by rotating at 4°C. The next day all samples were washed through low salt, high salt and LiCl wash buffer. RNase A (Qiagen #19101) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, proteinase K was added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and after that an additional 6 hours of incubation at 65°C. DNA was then collected and purified by QIAquick gel extraction kit (Qiagen #28706). DNA concentration was determined using the Nanodrop 8000 (Thermofisher Scientific) and samples were stored at −80°C. For all experiments, an isotype matched control IgG ChIP (CST, #3900) used at same total amount as the experimental ChIP antibody described above and was performed with an equal number of cells for each ChIP sample. ChIP-seq library prep and sequencing were performed by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute.
ChIPseq libraries were prepared using IDT XGen DNAseq library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeq X Plus targeting 40 million 150bp read pairs.

treatment_protocol: CORL47 cells stably expressing DOX-ON ASCL1 variants (empty vector or ASCL1 WT or ASCL1 Δ217-236) cells were treated with DOX (1 µg/mL) for 72 hours

value: SCLC cell line

value: DOX-ON ASCL1 del217-236-Flag overexpression


title: Muscle_Patient35_Post-RYGB

status: Public on Jul 31 2026

type: genomic

city: Ottawa

first: Mary-Ellen

last: Harper

state: ON

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

hyb_protocol: QIAGEN, Epitect Bisulfite Kit

scan_protocol: Illumina iScan

data_processing:
GenomeStudio 2011.1
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Vastus Lateralis

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

treatment_protocol: Skeletal muscle biospsies (m. vastus lateralis) were collected from 35 individuals before Roux-en-Y-Gastric Bypass (RYGB) bariatric surgery and one-year (52 weeks) after RYGB surgery.

tag: tissue

value: Vastus Lateralis

tag: Sex

value: Female

tag: timepoint


title: ST39_H, Transcriptome library

type: SRA

city: San Francisco

first: Guohua

last: Yuan

state: CA

address: 1651 4th St Fl 5 521A, Weill Neurosciences Building

country: USA

institute: UCSF

description: Library name: ST39_H

library_source: transcriptomic single cell

data_processing:
scRNA-seq analysis 10X transcriptomic libraries were processed using CellRanger (version 7.2.0) and were aligned to the mouse transcriptome mm10-2020-A. Cellranger outputs were processed using Seurat (version 5.2.0). Datasets were processed to remove cells with fewer than 1,000 or greater than 100,000 reads, fewer than 500 or greater than 10,000 genes, or more than 20% of reads corresponding to mitochondrial genes. Doublets were identified and removed by using DoubletFinder (version 2.0.4). Libraries were integrated using Seurat’s “SCTransform” and Harmony (version 0.1.162). Libraries of the seurat project including all regions were integrated by Seurat’s “SCTransform”. Seurat projects of each brain region were integrated by Seurat’s “SCTransform” function and Harmony. To identify clusters, we constructed a shared nearest neighbor (SNN) graph using the 'FindNeighbors' function, and applied clustering through the 'FindClusters' function in Seurat. Iterative clustering to identify subtypes of cells was performed by subsetting into different major cell types (glutamatergic neurons, GABAergic neurons, glia) and using the “FindSubCluster” function in Seurat. Cell identities determined through analysis of iterative clusters were re-assigned to cells in the full Seurat object. Differential expression analysis was conducted using Seurat's “FindMarkers” and “FindAllMarkers” function, and gene expression in clusters was manually analyzed for known markers of given cell types.
STICR barcodes analysis STICR barcode analysis was performed using custom scripts, as previously described in Delgado et al57. First, BBMap (BBMap; sourceforge.net/projects/bbmap/) was used to remove low-quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments that were then aligned to our predefined fragment reference sets using Bowtie59 (version 5.2.1), allowing for up to two mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using awk. UMI of STICR barcodes with less than 10 reads were filtered by using awk to remove the noise UMI counts from the sequencing error. Finally, UMI-tools60 (version 0.5.1) was used to remove duplicate STICR barcode/cell barcode (CBC) reads by UMI, allowing for 1-bp mismatches in the UMI. STICR barcodes/CBC) pairings with at least three distinct UMIs were retained. For cells with multiple barcodes detected, only cells with all the same set of barcodes detected are considered as a shared clone, with Jaccard similarity of 1. Barcodes and their corresponding UMI counts were mapped to cells in the Seurat object of transcriptome data by aligning cell barcodes.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: rds

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Virally injected brains were collected from mouse pups at postnatal day 4. Brains were dissected in ice-cold pre-bubbled artificial cerebrospinal fluid (aCSF), and sectioned into coronal sections. Each brain region was manually dissected out from sliced brains based on the guidance of anatomy atlas from Allen institute. Collected tissue was then dissociated in the solution of papain (Worthington, LK003178) supplemented with 0.5 mg/ml DNase (Sigma Aldrich, DN25-1G) diluted with HBSS (Gibco,14025134) at 37℃. The tissues were incubated at 37℃ for 30-60 min, with gentle trituration every 15 min until samples had no visible chunks.  Papain was quenched by adding 1% BSA (Militeny) to the solution. Samples were spun down and resuspended in HBSS + 0.1% BSA and passed through the 35 um filter into a FACS tube (Falcon, 52235). To isolate and collect virally infected cells, flow cytometry was done using a BD FACSAria III Cell Sorter (BD FACSDiva Software, version 8.0.2) with a 100-µm nozzle. The cell suspensions were first gated on forward scatter, then within this population based on eGFP expression. eGFP-expressing cells were sorted into HBSS + 0.1% BSA for downstream processing on the 10x Genomics Chromium platform. Samples were kept on ice before and after FACS, and the chamber and collection tubes were maintained at 4℃ during sorting.
scRNA-seq library preparation Preparation of scRNA-seq libraries was carried out using a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000075). We input between 10 and 20k cells per lane on a Chromium Chip G and followed the manufacturer protocol for transcriptomic library preparation.  STICR barcode library preparation STICR barcodes were subamplified from each 10X cDNA library using the Q5 Hot Start High Fidelity 2× master mix (NEB, M0494). In brief, 10 μl of cDNA was used as template in a 50 μl PCR reaction containing STICR barcode read 1 and 2 primers (0.5 μM, each) targeting the region immediately upstream of the STICR viral index/barcode as well as the partial Illumina Read1 sequence added during cDNA library preparation (Extended Data Table 3), using the following program: 1, 98 °C, 30 s; 2, 98 °C, 10 s; 3, 62 °C, 20 s; 4, 72 °C, 10 s; 5, repeat steps 2–4 12 times; 6, 72 °C, 2 min; 7, 4 °C, hold. Following PCR amplification, a 0.8–0.6 dual-sided size selection was performed using Ampure XP beads (Beckman Coulter, A63881). The libraries were quantified by Tapestation (Agilent) and pooled for sequencing.

value: Brain

tag: genotype

value: Wild type


title: Input of CORL47 cells expressing empty vector

city: Boston

description: Library name: CORL47_EV_Input

library_source: genomic

tag: cell line

tag: cell type

value: DOX-ON empty vector overexpression


title: 1K8

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

library_source: transcriptomic

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

molecule: total RNA

organism: Mesocricetus auratus

source_name: Kidney, SARS-CoV-2, I.N., 1dpi, 4

growth_protocol: Golden hamstsers were housed in pairs in the ABSL3 facility of NYU-Langone/Mount Sinai Hospital, under 12 hour light/dark cycle. Water and Food (PicoLab Rodent Diet 20 5053) was provided ad libitum.

extract_protocol: RNA was extracted using Trizol reagent and following manufacturer's instructions. 100 ng of RNA were used for the construction ofn libraries.

treatment_protocol: Dexamethasone was prepared fresh each day at a dose of 1 mg/kg in 0.5 mL of 20% DMSO/60% PEG400/20% 2-hydroxypropyl-beta-cyclodextrin in water (w/w), and administered via subcutaneous injection.

value: Kidney

tag: time

value: 1 dpi

value: WT

tag: treatment

value: 1000 PFU SARSCOV2 IN


title: Muscle_Patient35_Pre-RYGB

value: Pre-RYGB


title: ST39_C, Transcriptome library

description: Library name: ST39_C


title: 1K7

source_name: Kidney, SARS-CoV-2, I.N., 1dpi, 3


title: Input of CORL47 cells expressing DOX-ON ASCL1WT-Flag

description: Library name: CORL47_ASCL1 WT_Flag_Input

value: DOX-ON ASCL1 WT-Flag overexpression


title: Muscle_Patient34_Post-RYGB


title: ST38_S_2, Transcriptome library

description: Library name: ST38_S_2


title: 1K6

source_name: Kidney, SARS-CoV-2, I.N., 1dpi, 2


title: P07 control sample

city: Jinan

first: Lin

last: Han

address: Wenhuaxi Road #107

country: China

institute: Shandong University

description: Library name: P07con

data_processing:
Raw reads were assessed using FastQC.
Adapters and low-quality bases were trimmed using fastp.
Clean reads were aligned to GRCh38 using STAR.
Gene-level counts were generated using featureCounts with GENCODE vXX annotation.
TPM values were calculated from gene-level counts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited matrix containing gene-level raw read counts for all samples. Rows represent genes and columns represent samples.

source_name: Stromal

extract_protocol:
Total RNA was extracted from each sample according to the standard RNA extraction protocol provided by the sequencing service provider. RNA quantity and quality were assessed prior to library construction.
RNA sequencing libraries were prepared from total RNA according to the standard bulk RNA-seq library preparation protocol provided by the sequencing service provider. Libraries were sequenced on an Illumina platform using paired-end sequencing.

treatment_protocol: Samples were treated with 5 μM 5-fluorouracil or 5 μM oxaliplatin. Immune checkpoint inhibitor treatment was performed at a concentration of 10 μg/mL. Untreated samples were included as controls.

value: Stromal

value: vehicle


title: FVB_Thymus_WT_rep4

city: Hangzhou

first: Xiaoping

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: FVB_Thymus_WT_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: Thymus

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Thymus

tag: strain

value: FVB/NJ

value: Male

tag: age

value: 8 weeks

tag: mouse id


title: Flag ChIP-seq on CORL47 cells expressing DOX-ON ASCL1del217-236-Flag Rep2

description: Library name: CORL47_ASCL1 del217-236_Flag_IP_Rep2

value: SCLC cell line

value: DOX-ON ASCL1 del217-236-Flag overexpression

tag: chip antibody

value: FLAG antibody (Sigma, Cat# F1804)

tag: batch


title: ST38_R, Transcriptome library

description: Library name: ST38_R

value: Brain

value: Wild type


title: 1K5

source_name: Kidney, SARS-CoV-2, I.N., 1dpi, 1

value: Kidney


title: Muscle_Patient34_Pre-RYGB

value: Vastus Lateralis

value: Female


title: Muscle_Patient33_Post-RYGB


title: Flag ChIP-seq on CORL47 cells expressing DOX-ON ASCL1del217-236-Flag Rep1

description: Library name: CORL47_ASCL1 del217-236_Flag_IP_Rep1


title: ST38_O, Transcriptome library

description: Library name: ST38_O


title: 8L

source_name: Lung, SARS-CoV-2, I.V., 3dpi, 4

value: Lung

value: 3 dpi

value: WT

value: 100000 PFU SARSCOV2 IV


title: ASCL1 ChIP-seq on CORL47 cells expressing empty vector Rep2

description: Library name: CORL47_EV_ASCL1_IP_Rep2

value: DOX-ON empty vector overexpression

value: ASCL1 (CST, Cat# E6Y1B)


title: Muscle_Patient33_Pre-RYGB

value: Pre-RYGB


title: ST38_H_2, Transcriptome library

description: Library name: ST38_H_2


title: STICR-ST5_L2, Clonal barcodes library

description: Library name: STICR-ST5_L2


title: 7L

source_name: Lung, SARS-CoV-2, I.V., 3dpi, 3


title: Muscle_Patient32_Post-RYGB


title: ASCL1 ChIP-seq on CORL47 cells expressing empty vector Rep1

description: Library name: CORL47_EV_ASCL1_IP_Rep1


title: ST38_H_1, Transcriptome library

description: Library name: ST38_H_1


title: 6L

source_name: Lung, SARS-CoV-2, I.V., 3dpi, 2


title: Flag ChIP-seq on CORL47 cells expressing DOX-ON ASCL1WT-Flag Rep2

description: Library name: CORL47_ASCL1 WT_Flag_IP_Rep2

value: DOX-ON ASCL1 WT-Flag overexpression


title: Muscle_Patient32_Pre-RYGB


title: FVB_Thymus_OE_rep4

description:
Library name: FVB_Thymus_OE_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: Thymus

value: MECP2 OE

value: FVB/NJ

value: Male

value: 8 weeks


title: 3K

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 3

value: 1000 PFU SARSCOV2 IN


title: ST38_C, Transcriptome library

description: Library name: ST38_C

value: Brain

value: Wild type


title: 5L

source_name: Lung, SARS-CoV-2, I.V., 3dpi, 1


title: Flag ChIP-seq on CORL47 cells expressing DOX-ON ASCL1WT-Flag Rep1

description: Library name: CORL47_ASCL1 WT_Flag_IP_Rep1

value: SCLC cell line

value: FLAG antibody (Sigma, Cat# F1804)


title: Muscle_Patient31_Post-RYGB

value: Vastus Lateralis

value: Female


title: ST31_T, Transcriptome library

description: Library name: ST31_T


title: 1L12

source_name: Lung, SARS-CoV-2, I.V., 1dpi, 4

value: Lung

value: 1 dpi

value: WT

value: 100000 PFU SARSCOV2 IV


title: CRC23509

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

description:
Library name: CRC23509
Column name in intercept_rna_raw_Intercept.txt: CRC23509

data_processing:
For bulk CD14+ seq, sequencing output was converted to FASTQ format and demultiplexed with bcl-convert (v4.2.4). Reads were mapped to the human reference genome (GRCh38.p13, Ensembl release 110) using STAR (v2.7.8a), and gene-level expression was quantified with RSEM (v1.3.1) based on Ensembl release 110 transcript annotations.
Assembly: Human reference genome (GRCh38.p13, Ensembl release 110)
Supplementary files format and content: tabular file with raw counts

source_name: Blood

extract_protocol:
CD14⁺ monocytes were extracted from PBMC using MACS MicroBeads.
For bulk CD14+ seq, libraries were generated using the sparQ RNA-Seq HMR kit (Quantabio) and sequenced on a NovaSeq X Plus system (Illumina, 10B flow cell) in paired-end 76 bp mode, producing an average of ~134 million reads per sample.

value: Blood

value: F

tag: immunotype

value: MIND


title: Muscle_Patient31_Pre-RYGB

value: Pre-RYGB


title: ST31_S, Transcriptome library

description: Library name: ST31_S


title: 1L11

source_name: Lung, SARS-CoV-2, I.V., 1dpi, 3


title: Muscle_Patient30_Post-RYGB


title: CRC23457

description:
Library name: CRC23457
Column name in intercept_rna_raw_Intercept.txt: CRC23457


title: ST31_R, Transcriptome library

description: Library name: ST31_R


title: Muscle_Patient30_Pre-RYGB


title: 1L10

source_name: Lung, SARS-CoV-2, I.V., 1dpi, 2


title: ST31_H, Transcriptome library

description: Library name: ST31_H


title: 1L9

source_name: Lung, SARS-CoV-2, I.V., 1dpi, 1


title: CRC23295

description:
Library name: CRC23295
Column name in intercept_rna_raw_Intercept.txt: CRC23295

value: M

value: SIND


title: ST31_C, Transcriptome library

description: Library name: ST31_C

source_name: Brain


title: Muscle_Patient29_Post-RYGB

source_name: Vastus Lateralis


title: CRC23244

description:
Library name: CRC23244
Column name in intercept_rna_raw_Intercept.txt: CRC23244


title: 12L

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 3dpi, 4

value: 3 dpi

value: 1000 PFU SARSCOV2 IN + DEX TREATMENT


title: Muscle_Patient29_Pre-RYGB


title: ST30_T, Transcriptome library

description: Library name: ST30_T

value: Brain

value: Wild type


title: CRC23218

description:
Library name: CRC23218
Column name in intercept_rna_raw_Intercept.txt: CRC23218


title: Muscle_Patient28_Post-RYGB


title: 11L

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 3dpi, 3


title: ST30_S, Transcriptome library

description: Library name: ST30_S


title: 10L

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 3dpi, 2


title: Muscle_Patient28_Pre-RYGB


title: CRC23187

description:
Library name: CRC23187
Column name in intercept_rna_raw_Intercept.txt: CRC23187


title: ST30_R, Transcriptome library

description: Library name: ST30_R


title: 9L

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 3dpi, 1


title: Muscle_Patient27_Post-RYGB


title: ST30_OB, Transcriptome library

description: Library name: ST30_OB


title: 4L

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 4

value: 1000 PFU SARSCOV2 IN


title: CRC22397

description:
Library name: CRC22397
Column name in intercept_rna_raw_Intercept.txt: CRC22397


title: Muscle_Patient27_Pre-RYGB

value: Vastus Lateralis


title: ST30_H, Transcriptome library

description: Library name: ST30_H


title: CRC22356

description:
Library name: CRC22356
Column name in intercept_rna_raw_Intercept.txt: CRC22356


title: 3L

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 3


title: ST30_C, Transcriptome library

description: Library name: ST30_C


title: 2L

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 2


title: Muscle_Patient26_Pre-RYGB

value: Female


title: ST29_S, Transcriptome library

description: Library name: ST29_S


title: 1L

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 1

value: Lung


title: CRC22318

description:
Library name: CRC22318
Column name in intercept_rna_raw_Intercept.txt: CRC22318


title: Muscle_Patient25_Post-RYGB


title: CRC22278

description:
Library name: CRC22278
Column name in intercept_rna_raw_Intercept.txt: CRC22278


title: Muscle_Patient25_Pre-RYGB


title: LU MOCK 3

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Lung mock 3

value: 1 dpi

value: MOCK


title: ST29_OB, Transcriptome library

description: Library name: ST29_OB


title: CRC22267

description:
Library name: CRC22267
Column name in intercept_rna_raw_Intercept.txt: CRC22267


title: Muscle_Patient24_Post-RYGB


title: ST29_H, Transcriptome library

description: Library name: ST29_H


title: LU MOCK 2

source_name: Lung mock 2

value: WT


title: CRC22258

description:
Library name: CRC22258
Column name in intercept_rna_raw_Intercept.txt: CRC22258

value: Blood


title: Muscle_Patient24_Pre-RYGB


title: LU MOCK

source_name: Lung mock 1


title: ST29_C, Transcriptome library

description: Library name: ST29_C


title: Muscle_Patient23_Post-RYGB


title: ST28_T, Transcriptome library

description: Library name: ST28_T


title: CRC22229

description:
Library name: CRC22229
Column name in intercept_rna_raw_Intercept.txt: CRC22229

source_name: Blood


title: IL24

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 1dpi, 4


title: CRC22223

description:
Library name: CRC22223
Column name in intercept_rna_raw_Intercept.txt: CRC22223


title: ST28_S, Transcriptome library

description: Library name: ST28_S


title: Muscle_Patient23_Pre-RYGB


title: CRC22195

description:
Library name: CRC22195
Column name in intercept_rna_raw_Intercept.txt: CRC22195


title: IL23

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 1dpi, 3


title: CRC23433

description:
Library name: CRC23433
Column name in intercept_rna_raw_Intercept.txt: CRC23433


title: Muscle_Patient22_Post-RYGB


title: ST28_R, Transcriptome library

description: Library name: ST28_R


title: CRC22188

description:
Library name: CRC22188
Column name in intercept_rna_raw_Intercept.txt: CRC22188


title: Muscle_Patient22_Pre-RYGB


title: IL22

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 1dpi, 2


title: ST28_OB, Transcriptome library

description: Library name: ST28_OB

source_name: Brain


title: IL21

source_name: Lung, SARS-CoV-2, I.N., Dexamethasone, 1dpi, 1


title: CRC22147

description:
Library name: CRC22147
Column name in intercept_rna_raw_Intercept.txt: CRC22147


title: ST28_H, Transcriptome library

description: Library name: ST28_H


title: Muscle_Patient21_Post-RYGB

source_name: Vastus Lateralis


title: CRC22124

description:
Library name: CRC22124
Column name in intercept_rna_raw_Intercept.txt: CRC22124

value: F


title: 1L8

source_name: Lung, SARS-CoV-2, I.N., 1dpi, 4


title: Muscle_Patient21_Pre-RYGB


title: CRC22122

description:
Library name: CRC22122
Column name in intercept_rna_raw_Intercept.txt: CRC22122

value: MIND


title: 1L7

source_name: Lung, SARS-CoV-2, I.N., 1dpi, 3


title: ST28_C, Transcriptome library

description: Library name: ST28_C


title: CRC23079

description:
Library name: CRC23079
Column name in intercept_rna_raw_Intercept.txt: CRC23079


title: Muscle_Patient20_Post-RYGB


title: CRC22117

description:
Library name: CRC22117
Column name in intercept_rna_raw_Intercept.txt: CRC22117


title: Muscle_Patient20_Pre-RYGB

value: Pre-RYGB


title: 1L6

source_name: Lung, SARS-CoV-2, I.N., 1dpi, 2


title: ST27_T, Transcriptome library

description: Library name: ST27_T


title: ST27_S, Transcriptome library

description: Library name: ST27_S


title: 1L5

source_name: Lung, SARS-CoV-2, I.N., 1dpi, 1


title: CRC22116

description:
Library name: CRC22116
Column name in intercept_rna_raw_Intercept.txt: CRC22116

value: M


title: Muscle_Patient26_Post-RYGB


title: CRC22342

description:
Library name: CRC22342
Column name in intercept_rna_raw_Intercept.txt: CRC22342


title: ST27_R, Transcriptome library

description: Library name: ST27_R


title: Muscle_Patient19_Post-RYGB


title: CRC22095

description:
Library name: CRC22095
Column name in intercept_rna_raw_Intercept.txt: CRC22095


title: E.coli114B_ASBLPP_8hrs_rep2

type: RNA

city: Subang Jaya

first: Vinod

last: Pallath

address: Jalan Lagoon Selatan, Bandar Sunway,

department: Jeffrey Cheah School of Medicine and Health Sciences.

country: Malaysia

institute: Monash University Malaysia

description: Gene expression of mid-log grown (8hrs) E. coli in Luria Bertani Broth

hyb_protocol: About 0.825μg of Cy3-labelled cRNA with specific activity =/>6 pmol Cy3/μg cRNA was fragmented at 60 °C for 30 min in a reaction volume of 25 μL containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturer’s instructions. After the fragmentation step, 25μl of the mixture was then combined with 25 μl of 2× Hi-RPM Hybridisation Buffer and immediately hybridised to Agilent SurePrint Escherichia coli  8x60K (Design ID: 086189) for 17 hours at 65 °C in a rotating Agilent microarray hybridisation oven. After hybridisation, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37 °C GE Wash Buffer 2 (Agilent).

scan_protocol: Slides were immediately scanned using Agilent SureScan Microarray Scanner (G4900DA) with 3 μm resolution at wavelengths of 532 nm (Cy3) using the extended dynamic range (10–100 %) setting.

data_processing: Normalised intensities were extracted using the Agilent Feature Extraction Software with protocol GE1_1200_Jun14, and all the 16 data (in .txt format) files were obtained.  The .txt files were then uploaded in Agilent GeneSpring Software version 14.9.1. for analysis.

organism: Escherichia coli

source_name: Urine specimen, ASBLPP, 8hrs, replicate 2

label_protocol: The concentration of all 16 RNA samples was normalised to 50ng before the preparation of Cyanine-3 (Cy3) labelled cRNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Valencia, Ca) according to the manufacturer’s instructions. Cy3 labelled cRNA was then purified by RNeasy Mini Kit (Qiagen, Valencia, CA) to purify the amplified cRNA samples. Dye incorporation and cRNA yield were checked with the NanoVue™ Plus Spectrophotometer (GE Healthcare, UK).

growth_protocol: All the E. coli from different disease categories of complicated UTI and asymptomatic bacteriuria included in this study were originally isolated from the urine specimens of the patients who attended the University Malaya Medical Centre between May 2017 and June 2019. The isolates were grown in Luria Bertani broth (HiMedia, India) until mid-log growth phase on a shaker incubator (37˚C) at 200 rpm prior to RNA extraction.

extract_protocol: RNA extraction was performed using RNA extraction kit were performed using RNA extraction kit (Favorgen, Biotech Corp, Taiwan) according to the manufacturer's guidelines. Contaminating genomic DNA was eliminated by DNase digestion kit (Favorgen, Biotech Corp, Taiwan) according to manufacturer instructions. The RNA concentration, purity, and RNA integrity were determined using a nano spectrophotometer (Nano-Drop Technology. Inc., Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA), respectively, according to the manufacturer's instruction.

treatment_protocol: No specific treatment protocol was applied in this study. All six complicated UTI isolates from cystitis, pyelonephritis, urosepsis,  recurrent UTI, catheter-associated UTI, and UTI with co-morbidities were treated as the test strains. As for the control, there were two asymptomatic bacteriuria E.coli isolates included in this study. The first control strain,  ASB E. coli  095 HPP (possessed with 12 UPEC associated virulence gene tested).  The second strain is ASB E. coli 114 LPP (lacked all the 12 UPEC associated genes tested). Both the test and control strains were grown under the same growth condition.

tag: type of uti

value: Asymptomatic bacteriuria

tag: uti category

value: ASB E.coli low pathogenic potential


title: CRC22042

description:
Library name: CRC22042
Column name in intercept_rna_raw_Intercept.txt: CRC22042

value: SIND


title: LU MOCK 4

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Lung mock 4


title: ST29_R, Transcriptome library

description: Library name: ST29_R

value: Brain


title: Muscle_Patient19_Pre-RYGB


title: Muscle_Patient18_Post-RYGB


title: ST27_OB, Transcriptome library

description: Library name: ST27_OB

value: Wild type


title: E.coli114A_ASBLPP_8hrs_rep1

source_name: Urine specimen, ASBLPP, 8hrs, replicate 1


title: ST27_H, Transcriptome library

description: Library name: ST27_H


title: CRC22008

description:
Library name: CRC22008
Column name in intercept_rna_raw_Intercept.txt: CRC22008


title: Muscle_Patient18_Pre-RYGB


title: E.coli095B_ASBHPP_8hrs_rep2

source_name: Urine specimen, ASBHPP, 8hrs, replicate 2

value: ASB E.coli high pathogenic potential


title: ST27_C, Transcriptome library

description: Library name: ST27_C


title: E.coli095A_ASBHPP_8hrs_rep1

source_name: Urine specimen, ASBHPP, 8hrs, replicate 1


title: CRC21434

description:
Library name: CRC21434
Column name in intercept_rna_raw_Intercept.txt: CRC21434


title: ST26_T, Transcriptome library

description: Library name: ST26_T


title: Muscle_Patient17_Post-RYGB

value: Vastus Lateralis


title: Muscle_Patient17_Pre-RYGB

value: Female


title: CRC21425

description:
Library name: CRC21425
Column name in intercept_rna_raw_Intercept.txt: CRC21425


title: CRC21424

description:
Library name: CRC21424
Column name in intercept_rna_raw_Intercept.txt: CRC21424


title: Muscle_Patient16_Post-RYGB


title: ST26_S, Transcriptome library

description: Library name: ST26_S


title: ST26_R, Transcriptome library

description: Library name: ST26_R


title: E.coli287B_cUTIwithcomorbidities_8hrs_rep2

source_name: Urine specimen, cUTIwithcomorbidities, 8hrs, replicate 2

value: Complicated UTI

value: cUTI with comorbidities


title: E.coli287A_cUTIwithcomorbidities_8hrs_rep1

source_name: Urine specimen, cUTIwithcomorbidities, 8hrs, replicate 1


title: CRC21377

description:
Library name: CRC21377
Column name in intercept_rna_raw_Intercept.txt: CRC21377

source_name: Blood


title: Muscle_Patient16_Pre-RYGB


title: ST26_OB, Transcriptome library

description: Library name: ST26_OB


title: E.coli299B_CAUTI_8hrs_rep2

source_name: Urine specimen, CAUTI, 8hrs, replicate 2

value: Catheter associated UTI


title: CRC21355

description:
Library name: CRC21355
Column name in intercept_rna_raw_Intercept.txt: CRC21355


title: ST26_H, Transcriptome library

description: Library name: ST26_H


title: E.coli299A_CAUTI_8hrs_rep1

source_name: Urine specimen, CAUTI, 8hrs, replicate 1


title: Muscle_Patient15_Post-RYGB


title: CRC21345

description:
Library name: CRC21345
Column name in intercept_rna_raw_Intercept.txt: CRC21345


title: Muscle_Patient15_Pre-RYGB


title: ST26_C, Transcriptome library

description: Library name: ST26_C

source_name: Brain


title: CRC21318

description:
Library name: CRC21318
Column name in intercept_rna_raw_Intercept.txt: CRC21318


title: Muscle_Patient14_Post-RYGB


title: E.coli240B_recurrentUTI_8hrs_rep2

source_name: Urine specimen, recurrentUTI, 8hrs, replicate 2

value: Recurrent UTI


title: CRC21300

description:
Library name: CRC21300
Column name in intercept_rna_raw_Intercept.txt: CRC21300

value: Blood


title: ST25_T, Transcriptome library

description: Library name: ST25_T


title: Muscle_Patient14_Pre-RYGB

source_name: Vastus Lateralis


title: ST25_S, Transcriptome library

description: Library name: ST25_S


title: E.coli285B_urosepsis_8hrs_rep2

source_name: Urine specimen, urosepsis, 8hrs, replicate 2

value: Urosepsis


title: E.coli240A_recurrentUTI_8hrs_rep1

source_name: Urine specimen, recurrentUTI, 8hrs, replicate 1


title: CRC21292

description:
Library name: CRC21292
Column name in intercept_rna_raw_Intercept.txt: CRC21292

value: F

value: MIND


title: Muscle_Patient13_Post-RYGB


title: Muscle_Patient13_Pre-RYGB

value: Pre-RYGB


title: CRC21268

description:
Library name: CRC21268
Column name in intercept_rna_raw_Intercept.txt: CRC21268

value: M


title: E.coli285A_urosepsis_8hrs_rep1

source_name: Urine specimen, urosepsis, 8hrs, replicate 1


title: CRC21239

description:
Library name: CRC21239
Column name in intercept_rna_raw_Intercept.txt: CRC21239


title: E.coli225A_pyelonephritis_8hrs_rep1

source_name: Urine specimen, pyelonephritis, 8hrs, replicate 1

value: Pyelonephritis


title: CRC21212

description:
Library name: CRC21212
Column name in intercept_rna_raw_Intercept.txt: CRC21212

value: SIND


title: Muscle_Patient12_Pre-RYGB


title: E.coli259A_cystitis_8hrs_rep1

source_name: Urine specimen, cystitis, 8hrs, replicate 1

value: Cystitis


title: ST24_T, Transcriptome library

description: Library name: ST24_T

value: Brain

value: Wild type


title: ∆oxyR anoxic, biol rep 3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description:
Library name: R_DoxyR_AN_5
Column Name in HTSeq-counts.txt : R_DoxyR_AN_5_HTseqOutput.txt

data_processing:
RNA-seq reads were processed with Trimmomatic version 0.39 and mapped to the Zymomonas mobilis ZM4 genome, GCF_003054575.1-RF_2023_03_19 genome using Bowtie 2 version 2.5.1 with default settings.
Read counts were calculated with HTSeq version 2.0.3 using the Z. mobilis ZM4 gene annotations using default settings.
Normalized read counts were determined as FPKM values
Assembly: GCF_003054575.1-RF_2023_03_19
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

organism: Zymomonas mobilis

source_name: bacteria

growth_protocol: Z. mobilis strains were grown in oxic or anoxic conditions in ZRMG to an OD600 of approximately 1.0-2.0 and the culture volume that yielded 2 x 108 cells was collected (for Z. mobilis ZM4: 6.55 x 107 CFU/OD=1).

extract_protocol:
RNA was harvested using the Qiagen RNeasy Mini Kit using standard protocols.
The sequencing libarary was constructed using the Qiagen RNeasy Mini Kit using standard protocols.

value: bacteria

value: oxyR deletion

value: Anoxic growth


title: Muscle_Patient11_Pre-RYGB

value: Vastus Lateralis

value: Female


title: ST24_R, Transcriptome library

description: Library name: ST24_R


title: CARD318

description:
Library name: CARD318
Column name in intercept_rna_raw_Intercept.txt: CARD318


title: ST24_OB, Transcriptome library

description: Library name: ST24_OB


title: ∆oxyR anoxic, biol rep 1

description:
Library name: R_DoxyR_AN_2
Column Name in HTSeq-counts.txt : R_DoxyR_AN_2_HTseqOutput.txt


title: BAL Male Organoid

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

description: Library name: male_organoid

data_processing:
Raw sequencing data were processed using CellRanger v8.0.1 with chemistry parameter set to SC3Pv4 (Single Cell 3' v4) and expected cell count of 10,000 cells per sample.
Ambient RNA contamination was addressed using SoupX v1.6.2 with 5% contamination fraction. Cell filtering criteria included: minimum 1,200 UMIs per cell, 500-Q3+(1.5×IQR) genes per cell, genes per UMI ratio >0.75, and <10% mitochondrial gene expression. Doublet detection was performed using both scDblFinder v1.22.0 and DoubletFinder v2.0.4 with 7.5% expected doublet rate.
Data analysis was performed in R using Seurat v5.1.0 with SCTransform normalization, reciprocal PCA integration, UMAP dimensionality reduction, and Louvain clustering at 0.1 resolution.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Comma-separated metadata table.

source_name: Lung airway organoid

growth_protocol: BAL-derived single cells were embedded in Growth Factor-Reduced, Phenol Red-free, LDEV-free Matrigel (Corning) at 100,000 live cells per 50 μL and cultured in airway medium containing Advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27 supplement, 100 μg/ml Primocin, 1.25 mM N-acetylcysteine, 5 mM nicotinamide, 500 ng/ml R-spondin-1, 25 ng/ml FGF7, 100 ng/ml FGF10, 100 ng/ml Noggin, 500 nM A83-01, 500 nM SB202190, and 5 μM Y-27632. HRG1-β1 was added at 50 ng/ml for the first 3-4 days. Organoids were maintained at 37°C, 5% CO2 with media changes every 3-4 days and passaged every 10-14 days.

extract_protocol:
Organoids were dissociated into single cells by incubation in TrypLE Express Enzyme at 37°C for 1-2 hours with gentle pipetting performed every 5-10 minutes. Cell viability was assessed using Trypan Blue exclusion. Cells were passed through a 40-μm nylon mesh filter to remove large clumps and debris, then centrifuged at 200g for 10 minutes. The cell pellet was resuspended in DMEM + 10% FBS to achieve a final concentration of 1000-1200 cells/μL for single-cell library preparation.
Single-cell RNA sequencing libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3' v3.1 kits for dual-index, paired-end sequencing. Library preparation was performed at the CHOP Single Cell Technology Core following manufacturer's protocols. Quality control of libraries was performed using Qubit for quantification and Bioanalyzer for size distribution analysis.

treatment_protocol: No treatments were applied to the organoids analyzed in this single-cell RNA-seq experiment. Organoids were maintained under standard culture conditions in room air (normoxic conditions) prior to single-cell dissociation and sequencing. This represents the baseline characterization of cellular heterogeneity in BAL-derived airway organoids.

value: Lung airway organoid

value: Epithelial cells

value: Male


title: ST24_C, Transcriptome library

description: Library name: ST24_C


title: 18513X13 CHOW KO

city: Salt Lake City

first: Dipayan

last: Chaudhuri

state: UT

institute: University of Utah

description: Library name: Sample 7

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 110 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: featureCount output files combined into a single tab-delimited matrix

source_name: Liver tissue

extract_protocol:
Livers were treated with trizole and then extracted using the Zymo RNA extraction kit (Cat #R2062)
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.

treatment_protocol: C57BL/6 mice we fed either a CHOW or a GAN diet for 28 weeks (diet begun at 8 weeks). At 28 weeks post diet, mice were sacrificed and their livers removed.

value: Liver tissue

value: EFHD1 KO

value: CHOW diet control


title: ∆oxyR oxic, biol rep 4

description:
Library name: R_DoxyR_AE_8
Column Name in HTSeq-counts.txt : R_DoxyR_AE_8_HTseqOutput.txt

value: Oxic growth


title: BAL Female Organoid

description: Library name: female_organoid


title: Muscle_Patient9_Post-RYGB


title: ST23_C, Transcriptome library

description: Library name: ST23_C


title: ∆oxyR oxic, biol rep 3

description:
Library name: R_DoxyR_AE_9
Column Name in HTSeq-counts.txt : R_DoxyR_AE_9_HTseqOutput.txt


title: ST25_R, Transcriptome library

description: Library name: ST25_R


title: Female Oxygen 3

description: Library name: Female_Oxygen_3

data_processing:
Quality control, preprocessing, and alignment were performed using the nf-core/rnaseq pipeline (version 3.17.0). Reads were aligned to the human reference genome using STAR aligner, and transcript abundance was quantified using Salmon. Quality metrics were assessed using MultiQC.
Transcript abundance estimates were summarized to gene-level counts using tximport (version 1.34.0). Differential expression analysis was performed using DESeq2 (version 1.46.0) with variance stabilizing transformation applied for visualization.
Assembly: GRCh38
Supplementary files format and content: Comma separated sample metadata, normalized counts and gene annotations for all samples.

growth_protocol: BAL-derived airway organoids were established from bronchoalveolar lavage fluid collected from intubated preterm neonates with established bronchopulmonary dysplasia. Single cells obtained from BAL were resuspended in Growth Factor-Reduced, Phenol Red-free, LDEV-free Matrigel (Corning) at a concentration of 100,000 live cells per 50 μL of Matrigel. Drops of 50 μl each were pipetted onto prewarmed 12-well plates and allowed to solidify for 25 minutes at 37°C. Organoids were cultured in airway medium containing Advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27 supplement (Thermo Fisher), 100 μg/ml Primocin (InvivoGen), 1.25 mM N-acetylcysteine, 5 mM nicotinamide (Millipore Sigma), 500 ng/ml R-spondin-1, 25 ng/ml FGF7, 100 ng/ml FGF10, 100 ng/ml Noggin (PeproTech), 500 nM A83-01 (Millipore Sigma), 500 nM SB202190 (Tocris), and 5 μM Y-27632 (ATCC). HRG1-β1 (PeproTech) was added at 50 ng/ml for the first 3-4 days. Organoids were maintained at 37°C, 5% CO2 with media changes every 3-4 days and passaged every 10-14 days. For the hyperoxia experiment, confluent organoids were passaged and reseeded in triplicate in prewarmed 12-well plates per experimental condition and allowed to recover for three days before treatment initiation.

extract_protocol:
Following 48-hour hyperoxia or room air exposure, organoids embedded in Matrigel were collected and immediately lysed in DNA/RNA shield (Zymo Research). Total RNA was extracted using the Quick RNA miniprep kit (#R1054, Zymo Research) according to manufacturer's instructions. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) prior to library preparation.
RNA library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dUTP instead of dTTP to maintain strand specificity. The directional library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit for quantification, real-time PCR for accurate quantification, and Bioanalyzer for size distribution detection.

treatment_protocol: On the day of experiment, fresh airway medium was replaced in all organoid cultures. For hyperoxia exposure, organoids were placed in a pre-calibrated ProOX model C21 oxygen chamber (Biospherix) and exposed to 85% oxygen at 37°C for 48 hours. Control organoids were maintained in parallel under room air conditions (37°C, standard atmospheric oxygen) for the same duration. No pharmacological treatments were applied.

value: Epithelial Cells

value: Hyperoxia


title: Muscle_Patient9_Pre-RYGB

value: Pre-RYGB


title: ST25_OB, Transcriptome library

description: Library name: ST25_OB

value: Brain


title: E.coli225B_pyelonephritis_8hrs_rep2

description: Gene expression of mid-log grown (8hrs) E. coli in Luria Bertani Broth

source_name: Urine specimen, pyelonephritis, 8hrs, replicate 2

value: Complicated UTI

value: Pyelonephritis


title: Muscle_Patient12_Post-RYGB


title: ST25_H, Transcriptome library

description: Library name: ST25_H

value: Wild type


title: CRC21221

description:
Library name: CRC21221
Column name in intercept_rna_raw_Intercept.txt: CRC21221

value: Blood

value: F

value: SIND


title: ∆oxyR oxic, biol rep 2

description:
Library name: R_DoxyR_AE_7
Column Name in HTSeq-counts.txt : R_DoxyR_AE_7_HTseqOutput.txt

value: bacteria

value: oxyR deletion


title: E.coli259B_cystitis_8hrs_rep2

source_name: Urine specimen, cystitis, 8hrs, replicate 2

value: Cystitis


title: ST25_C, Transcriptome library

description: Library name: ST25_C


title: Female Oxygen 2

description: Library name: Female_Oxygen_2

value: Lung airway organoid

value: Female


title: ST21_T, Transcriptome library

description: Library name: ST21_T


title: Muscle_Patient8_Post-RYGB

value: Vastus Lateralis


title: ST21_OB, Transcriptome library

description: Library name: ST21_OB


title: Muscle_Patient11_Post-RYGB


title: ∆oxyR oxic, biol rep 1

description:
Library name: R_DoxyR_AE_11
Column Name in HTSeq-counts.txt : R_DoxyR_AE_11_HTseqOutput.txt

value: Oxic growth


title: Female Oxygen 1

description: Library name: Female_Oxygen_1

value: Epithelial Cells


title: CARD338

description:
Library name: CARD338
Column name in intercept_rna_raw_Intercept.txt: CARD338

value: M

value: MIND


title: Muscle_Patient8_Pre-RYGB

value: Pre-RYGB


title: ST21_C, Transcriptome library

description: Library name: ST21_C

value: Brain


title: WT anoxic, biol rep 3

description:
Library name: R_AN_ZM4_3
Column Name in HTSeq-counts.txt : R_AN_ZM4_3_HTseqOutput.txt

value: Anoxic growth


title: Male Oxygen 3

description: Library name: Male_Oxygen_3

value: Hyperoxia

value: Male


title: Muscle_Patient7_Post-RYGB


title: ST20_RT, Transcriptome library

description: Library name: ST20_RT

value: Wild type


title: WT anoxic, biol rep 2

description:
Library name: R_AN_ZM4_2
Column Name in HTSeq-counts.txt : R_AN_ZM4_2_HTseqOutput.txt


title: Muscle_Patient7_Pre-RYGB


title: Male Oxygen 2

description: Library name: Male_Oxygen_2


title: ST20_RC, Transcriptome library

description: Library name: ST20_RC


title: Muscle_Patient10_Post-RYGB


title: WT anoxic, biol rep 1

description:
Library name: R_AN_ZM4_1
Column Name in HTSeq-counts.txt : R_AN_ZM4_1_HTseqOutput.txt


title: ∆oxyR anoxic, biol rep 2

description:
Library name: R_DoxyR_AN_3
Column Name in HTSeq-counts.txt : R_DoxyR_AN_3_HTseqOutput.txt


title: Muscle_Patient6_Post-RYGB


title: Male Oxygen 1

description: Library name: Male_Oxygen_1


title: ST20_CT, Transcriptome library

description: Library name: ST20_CT


title: WT oxic, biol rep 3

description:
Library name: R_AE_ZM4_3
Column Name in HTSeq-counts.txt : R_AE_ZM4_3_HTseqOutput.txt


title: Muscle_Patient6_Pre-RYGB


title: Female RoomAir 3

description: Library name: Female_RoomAir_3

value: Room Air


title: ST20_CC, Transcriptome library

description: Library name: ST20_CC


title: Female RoomAir 2

description: Library name: Female_RoomAir_2


title: Muscle_Patient5_Post-RYGB


title: WT oxic, biol rep 2

description:
Library name: R_AE_ZM4_2
Column Name in HTSeq-counts.txt : R_AE_ZM4_2_HTseqOutput.txt

value: bacteria


title: ST18-T, Transcriptome library

description: Library name: ST18-T


title: WT oxic, biol rep 1

description:
Library name: R_AE_ZM4_1
Column Name in HTSeq-counts.txt : R_AE_ZM4_1_HTseqOutput.txt


title: Muscle_Patient10_Pre-RYGB


title: Muscle_Patient5_Pre-RYGB


title: ST17-T, Transcriptome library

description: Library name: ST17-T


title: Female RoomAir 1

description: Library name: Female_RoomAir_1


title: *AB matched WT sibling zebrafish-M.marinum granuloma cells

city: Durham

first: David

last: Tobin

state: NC

address: 207 Research Drive

institute: Duke University

description:
Library name: Wtsib_del19_Gran
10X Genomics

data_processing:
The Molecular Genomics Core’s standard analytical pipeline was used for single cell RNAseq analysis. Briefly, raw base call (BCL) files generated by an Illumina sequencer were demultiplexed into FASTQ, then aligned to the Ensembl zebrafish genome assembly GRCz11.96. Filtering, barcode and UMI counting were performed using the most current version of 10X’s Cell Ranger software (9.0.1). The R package Seurat was used to perform quality control and linear dimensional reduction. Datasets were integrated using IntegrateLayers() and JoinLayers(). Cells were clustered de novo for unbiased cell type discovery using Seurat’s FindNeighbors() and FindClusters() functions, graph-based clustering approach with visualization of cells being achieved through the use of UMAP plots. Cluster specific markers were generated by FindConservedMarkers() and differentially expressed genes between datasets were generated by FindMarkers(). Expression of canonical gene markers were used to annotate clusters with specific cell types
Assembly: Zebrafish GRCz11.96
Supplementary files format and content: Tab-separated values and matrix files

organism: Danio rerio

source_name: Granulomas

extract_protocol:
Granulomas were transferred to a 1.5 mL tube and cells were dissociated using 1 mL of 0.05% trypsin/EDTA (ThermoFisher Scientific, 25300054) at 30_x000E_C for 35 minutes with rocking. Cells were collected by centrifugation for 5 min at 300 xg, resuspended in 1x DPBS with 10% FBS on ice, and passed through a 40 mm strainer.
Single cell samples were submitted to the Molecular Genomics Core at Duke Molecular Physiology Institute for library preparation, using Chromium Single Cell 3’ GEM, Library and Gel Bead Kit v4, and gem generation using the 10x Genomics platform. Libraries were sequenced was at Duke Sequencing and Genomic Technologies core facility.

treatment_protocol: M. marinum infection in apodb mutant compared to WT

value: Granulomas

value: Granuloma cells

value: immune and stromal

value: WT sibling


title: Male RoomAir 3

description: Library name: Male_RoomAir_3

value: Lung airway organoid


title: Muscle_Patient4_Post-RYGB

value: Vastus Lateralis

value: Female


title: ST17-CTX, Transcriptome library

description: Library name: ST17-CTX


title: Male RoomAir 2

description: Library name: Male_RoomAir_2

value: Epithelial Cells


title: *AB apodb mutant zebrafish-M.marinum granuloma cells

description:
Library name: apodb_del19_Gran
10X Genomics

value: apodb (xt75)


title: Muscle_Patient4_Pre-RYGB

value: Pre-RYGB


title: ST16-T, Transcriptome library

description: Library name: ST16-T

value: Brain


title: Muscle_Patient3_Post-RYGB


title: Male RoomAir 1

description: Library name: Male_RoomAir_1


title: ST16-R, Transcriptome library

description: Library name: ST16-R


title: Bemcentinib tri-culture of injured A375 + HMDM + HMDDC

city: Cambridge

first: Douglas

middle: A

last: Lauffenburger

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

description:
Library name: D24-16235
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were done using the Cell Ranger software v8.0.1
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: A375 + human monocyte-derived macrophage + human monocyte-derived dendritic cell

extract_protocol:
Co-culture samples for each donor were generated by pooling 6 wells across two 12-well plates (3 wells per plate) together, and tri-culture samples for each donor were generated by pooling 3 wells across one 12-well plate. After pooling the cells within each condition, samples were prepared as instructed in the Single Cell Gene Expression Flex Fixed RNA Profiling demonstrated protocols (10x Genomics) with the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics 1000414). Briefly, after cells were harvested and pooled, they were washed with PBS + 0.04% UltraPure BSA (ThermoFisher AM2616). The cell pellets were then fixed with Fixation Buffer overnight at 4°C. The next day, following centrifugation, the cell pellets were resuspended in Quenching Buffer and counted. Enhancer and glycerol (Sigma- Aldrich G5516) were then added to each sample, and the samples were stored at -80°C. Samples were then thawed, centrifuged, and resuspended as single cell suspensions in Quenchinig Buffer for submission to the MIT BioMicro Center for sample multiplexing by donor according to the manufacturer's instructions (10x Genomics 1000414) and downstream sequencing with the Element AVITI (https://bmcwiki.mit.edu/index.php/BioMicroCenter:SingleCell).
Library construction was performed according to the manufacter’s instructions (Chromium Human Transcriptome Probe Set v1.0.1, 10x Genomics).

value: malignant melanoma + macrophage + dendritic cell

value: trametinib + dabrafenib + bemcentinib


title: DMSO tri-culture of injured A375 + HMDM + HMDDC

description:
Library name: D24-16234
10x Genomics

value: A375 + human monocyte-derived macrophage + human monocyte-derived dendritic cell

value: trametinib + dabrafenib + dimethylsulfoxide


title: NGFR-positive 3

description: Library name: NGFR_High_3

growth_protocol: BAL-derived airway organoids were established and maintained in Growth Factor-Reduced, Phenol Red-free, LDEV-free Matrigel at 37°C, 5% CO2. Organoids were cultured in airway medium containing Advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27 supplement, 100 μg/ml Primocin, 1.25 mM N-acetylcysteine, 5 mM nicotinamide, 500 ng/ml R-spondin-1, 25 ng/ml FGF7, 100 ng/ml FGF10, 100 ng/ml Noggin, 500 nM A83-01, 500 nM SB202190, and 5 μM Y-27632. Media was changed every 3-4 days and organoids were passaged every 10-14 days until ready for cell sorting.

extract_protocol:
Organoids were dissociated into single cells using TrypLE Express Enzyme at 37°C with gentle pipetting every 5-10 minutes for up to 1-2 hrs. Cells were filtered through 40-μm nylon mesh, centrifuged at 200g for 10 minutes, and resuspended in FACS Buffer (PBS with 10% FBS, 2 mM EDTA, and 10 μM Y-27632). Cells were stained with anti-human NGFR APC-Cy7 (BioLegend 345126) at 1:50 dilution and other markers including EpCAM PE-Cy7 and CD45 APC. NGFR-positive and NGFR-negative cell populations were sorted using a 5-laser Cytek Cell Sorter. RNA was extracted from sorted cell populations using Quick RNA miniprep kit (#R1054, Zymo Research) according to manufacturer's instructions. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) prior to library preparation.
RNA library preparation was performed using standard bulk RNA-seq protocols. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dUTP instead of dTTP to maintain strand specificity. The directional library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed prior to sequencing.

treatment_protocol: No treatments were applied prior to cell sorting. Organoids were maintained under standard culture conditions in room air before fluorescence-activated cell sorting (FACS) based on NGFR expression to separate basal cell-enriched populations from other epithelial cell types.

tag: ngfr expression

value: High


title: Muscle_Patient3_Pre-RYGB

tag: tissue


title: ST16-C, Transcriptome library

description: Library name: ST16-C

value: Wild type


title: Bemcentinib tri-culture of untreated A375 + HMDM + HMDDC

description:
Library name: D24-16233
10x Genomics

value: dimethylsulfoxide + bemcentinib


title: Muscle_Patient2_Post-RYGB

tag: Sex


title: ST15_T, Transcriptome library

description: Library name: ST15_T


title: NGFR-positive 1

description: Library name: NGFR_High_1


title: ST15_C, Transcriptome library

description: Library name: ST15_C


title: Bemcentinib co-culture of injured A375 + HMDM

description:
Library name: D24-16231
10x Genomics

source_name: A375 + human monocyte-derived macrophage

value: malignant melanoma + macrophage


title: Muscle_Patient1_Post-RYGB

tag: timepoint


title: NGFR-negative 2

description: Library name: NGFR_Low_2

value: Low


title: Muscle_Patient1_Pre-RYGB


title: ST14_C, Transcriptome library

description: Library name: ST14_C

tag: genotype


title: ST14_T, Transcriptome library

description: Library name: ST14_T


title: DMSO co-culture of injured A375 + HMDM

description:
Library name: D24-16230
10x Genomics

tag: cell line

value: A375 + human monocyte-derived macrophage


title: Female Oxygen 2

description: Library name: Female_Oxygen_2

growth_protocol: BAL-derived airway organoids were established from bronchoalveolar lavage fluid collected from intubated preterm neonates with established bronchopulmonary dysplasia. Single cells obtained from BAL were resuspended in Growth Factor-Reduced, Phenol Red-free, LDEV-free Matrigel (Corning) at a concentration of 100,000 live cells per 50 μL of Matrigel. Drops of 50 μl each were pipetted onto prewarmed 12-well plates and allowed to solidify for 25 minutes at 37°C. Organoids were cultured in airway medium containing Advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27 supplement (Thermo Fisher), 100 μg/ml Primocin (InvivoGen), 1.25 mM N-acetylcysteine, 5 mM nicotinamide (Millipore Sigma), 500 ng/ml R-spondin-1, 25 ng/ml FGF7, 100 ng/ml FGF10, 100 ng/ml Noggin (PeproTech), 500 nM A83-01 (Millipore Sigma), 500 nM SB202190 (Tocris), and 5 μM Y-27632 (ATCC). HRG1-β1 (PeproTech) was added at 50 ng/ml for the first 3-4 days. Organoids were maintained at 37°C, 5% CO2 with media changes every 3-4 days and passaged every 10-14 days. For the hyperoxia experiment, confluent organoids were passaged and reseeded in prewarmed 12-well plates per experimental condition and allowed to recover for three days before treatment initiation.

value: Lung airway organoid

tag: cell type

value: Hyperoxia


title: O-DIO_3

city: Nanjing

first: Huichen

last: Song

state: Jiangsu

address: Qixia District, Xianlin Road No.163

institute: Nanjing university

description: Library name: SAMPLES6

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

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: DMSO co-culture of untreated A375 + HMDM

description:
Library name: D24-16228
10x Genomics

value: dimethylsulfoxide + dimethylsulfoxide


title: ST13_C, Transcriptome library

description: Library name: ST13_C

source_name: Brain


title: Tab_T2, rep4

city: NANTES

first: Emmanuel

last: SCOTET

state: Loire Atlantique

address: IRS UN, 8 quai Moncousu

institute: Emmanuel SCOTET

description:
Library name: 84_Tab_T2_4
Tab_T2_4

data_processing:
Base calling was performed directly by sequencing facility using phred-33 standard quality scores
Adapter sequences and low-quality reads were removed using SOAPnuke directly after FASTQ generation by the sequencing facility
Transcript count table from FASTQ files was generated  using subread (2.0.1) by alignment to the human genome (GRCh38) using STAR (2.7.10b) with Ensembl GTF (release 111)
Gene expression changes and statistics were realized using DESeq2 (1.34.0)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes counts after normalization, average expressions by conditions, and results of statistical analysis by DESeq2 (logFC, pval, padj)

source_name: ab T Cells

extract_protocol:
RNA was extracted by RNeasy Plus Micro Kits (Qiagen)
Messenger RNA-Seq libraries were prepared using a SMART-SeqII combined with transposase-based library construction, libraries were circularized, and sequencing was executed by DNA Nanoballs (DNBTM™) technology

value: ab T Cells

value: anti-CD3/CD28 + 7 days culture with IL-2 (30IU/mL)


title: O-DIO_1

description: Library name: SAMPLES4


title: Tab_T2, rep3

description:
Library name: 83_Tab_T2_3
Tab_T2_3


title: Male Oxygen 1

description: Library name: Male_Oxygen_1

value: Epithelial Cells

value: Male


title: ST12_T, Transcriptome library

description: Library name: ST12_T

value: Brain


title: O-Con_3

description: Library name: SAMPLES3


title: ST12_C, Transcriptome library

description: Library name: ST12_C


title: Tab_T2, rep2

description:
Library name: 82_Tab_T2_2
Tab_T2_2


title: Female RoomAir 2

description: Library name: Female_RoomAir_2

value: Room Air

value: Female


title: O-Con_2

description: Library name: SAMPLES2


title: O-Con_1

description: Library name: SAMPLES1


title: Female RoomAir 1

description: Library name: Female_RoomAir_1


title: Tab_T2, rep1

description:
Library name: 81_Tab_T2_1
Tab_T2_1


title: ST11_C, Transcriptome library

description: Library name: ST11_C


title: Tab_T1, rep4

description:
Library name: 80_Tab_T1_4
Tab_T1_4

value: SKOV3 + 4 days culture


title: Male RoomAir 2

description: Library name: Male_RoomAir_2


title: ST10_T, Transcriptome library

description: Library name: ST10_T

value: Wild type


title: Male RoomAir 1

description: Library name: Male_RoomAir_1


title: Sham 3

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample9

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: Rattus Norvegicus mRatBN7.2 release-110
Supplementary files format and content: .xlsx

organism: Rattus

source_name: Rat pelvic ganglion

extract_protocol:
2.1.1 extraction of Total RNA Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, the integrity of RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. Single library construction requires total RNA ≥1ug, concentration ≥35 ng/ΜL, OD260/280≥1.8, OD260/230≥1.0. 2.1.2oligo DT enrichment for mRNA Eukaryotic mrnas have a structure with a ployA tail at the 3′ end, and using magnetic beads with Oligo (DT) for A-T base pairing with Ploya, mrnas can be isolated from total RNA for analysis of transcriptome information. 2.1.3 fragmentation of mRNA The Illumina Novaseq 6000 platform is used to sequence short sequence fragments, and the enriched mrnas are complete RNA sequences with an average length of several KB, requiring random breaks. By adding fragmentation buffer, the mRNA was randomly cleaved, and small fragments of about 300 bp were isolated by magnetic bead screening. 2.1.4 cDNA synthesis by inversion Under the action of reverse transcriptase, random hexamers were added to synthesize one-stranded cDNA with mRNA as template, and then double-stranded cDNA was synthesized to form a stable double-stranded structure. 2.1.5 ligation of Adaptor The double-stranded cDNA has a sticky End, which is complemented by an End Repair Mix with a flat End, followed by the addition of an“A” base at the 3' End to connect the y-shaped linker. 2.1.6 in silico sequencing on the Illumina platform 1) library enrichment, PCR amplification for 15 cycles; 2) the target band was recovered by 2% agarose gel; 3) TBS380(Picogreen) quantification, mixed to data ratio on machine; 4) Bridge PCR amplification on cBot to generate clusters; 5) Illumina platform sequencing (PE library, read length 2 × 150 BP) .
1) the target RNA was interrupted by adding ion-interrupting reagent and random primer, and the random primer was combined with the target RNA; 2) the target RNA was reversely transcribed into cDNA by adding 1-strand reverse transcription reagent, and the hybrid chain of RNA and cDNA was formed; 3) the RNA in cDNA and RNA hybrid chain was cleaved by adding 2-strand synthetic reagent, and the double-stranded cDNA was synthesized by using the remaining RNA as the primer; 4) the double-stranded cDNA synthesis product was subjected to end-padding and a-addition; the“Y”-shaped linker was ligated; 5) the linker self-connecting fragment was removed by magnetic bead screening; 6) the library template was enriched by PCR amplification; 7) the library was recovered by magnetic beads. Reagent: VAHTS Universal V 8rna-seq Prep Library Kit for Illumina

value: Rat pelvic ganglion


title: Sham 2

description: Library name: Sample8


title: ST9_T, Transcriptome library

description: Library name: ST9_T


title: Tab_T1, rep2

description:
Library name: 78_Tab_T1_2
Tab_T1_2


title: ST9_C, Transcriptome library

description: Library name: ST9_C


title: Tab_T1, rep1

description:
Library name: 77_Tab_T1_1
Tab_T1_1


title: Female Dexamethasone 2

description: Library name: Female_Dexa_2

growth_protocol: BAL-derived airway organoids were established and maintained as described for single-cell experiments. Confluent organoids were passaged and reseeded in triplicate in prewarmed 12-well plates per experimental condition. Organoids were allowed to recover for three days in airway medium (Advanced DMEM/F12, 10 mM HEPES, 1X GlutaMAX, 1X B-27 supplement, 100 μg/ml Primocin, 1.25 mM N-acetylcysteine, 5 mM nicotinamide, 500 ng/ml R-spondin-1, 25 ng/ml FGF7, 100 ng/ml FGF10, 100 ng/ml Noggin, 500 nM A83-01, 500 nM SB202190, and 5 μM Y-27632) at 37°C, 5% CO2 before treatment initiation.

extract_protocol:
Following 24-hour dexamethasone or vehicle treatment, organoids embedded in Matrigel were collected and immediately lysed in DNA/RNA shield (Zymo Research). Total RNA was extracted using the Quick RNA miniprep kit (#R1054, Zymo Research) according to manufacturer's instructions. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) prior to library preparation.
RNA library preparation was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, first strand cDNA was synthesized using random hexamer primers, followed by second strand cDNA synthesis using dUTP instead of dTTP to maintain strand specificity. The directional library was completed through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit for quantification, real-time PCR for accurate quantification, and Bioanalyzer for size distribution detection.

treatment_protocol: On the day of experiment, fresh airway medium was replaced in all organoid cultures. Dexamethasone (Millipore Sigma) was added to treatment groups at a final concentration of 250 ng/ml, while control groups received vehicle only. Organoids were incubated with dexamethasone or vehicle for 24 hours at 37°C in room air conditions before harvest for RNA extraction.

value: Dexamethasone


title: Sacral NC 1

description: Library name: Sample6


title: Tab_NT, rep4

description:
Library name: 76_Tab_NT_4
Tab_NT_4

value: Untreated


title: Injury 2

description: Library name: Sample5


title: Female Dexamethasone 1

description: Library name: Female_Dexa_1


title: ST8_C, Transcriptome library

description: Library name: ST8_C

extract_protocol:
Virally injected brains were collected from mouse pups at postnatal day 4. Brains were dissected in ice-cold pre-bubbled artificial cerebrospinal fluid (aCSF), and sectioned into coronal sections. Each brain region was manually dissected out from sliced brains based on the guidance of anatomy atlas from Allen institute. Collected tissue was then dissociated in the solution of papain (Worthington, LK003178) supplemented with 0.5 mg/ml DNase (Sigma Aldrich, DN25-1G) diluted with HBSS (Gibco,14025134) at 37℃. The tissues were incubated at 37℃ for 30-60 min, with gentle trituration every 15 min until samples had no visible chunks.  Papain was quenched by adding 1% BSA (Militeny) to the solution. Samples were spun down and resuspended in HBSS + 0.1% BSA and passed through the 35 um filter into a FACS tube (Falcon, 52235). To isolate and collect virally infected cells, flow cytometry was done using a BD FACSAria III Cell Sorter (BD FACSDiva Software, version 8.0.2) with a 100-µm nozzle. The cell suspensions were first gated on forward scatter, then within this population based on eGFP expression. eGFP-expressing cells were sorted into HBSS + 0.1% BSA for downstream processing on the 10x Genomics Chromium platform. Samples were kept on ice before and after FACS, and the chamber and collection tubes were maintained at 4℃ during sorting.
scRNA-seq library preparation Preparation of scRNA-seq libraries was carried out using a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000075). We input between 10 and 20k cells per lane on a Chromium Chip G and followed the manufacturer protocol for transcriptomic library preparation.  STICR barcode library preparation STICR barcodes were subamplified from each 10X cDNA library using the Q5 Hot Start High Fidelity 2× master mix (NEB, M0494). In brief, 10 μl of cDNA was used as template in a 50 μl PCR reaction containing STICR barcode read 1 and 2 primers (0.5 μM, each) targeting the region immediately upstream of the STICR viral index/barcode as well as the partial Illumina Read1 sequence added during cDNA library preparation (Extended Data Table 3), using the following program: 1, 98 °C, 30 s; 2, 98 °C, 10 s; 3, 62 °C, 20 s; 4, 72 °C, 10 s; 5, repeat steps 2–4 12 times; 6, 72 °C, 2 min; 7, 4 °C, hold. Following PCR amplification, a 0.8–0.6 dual-sided size selection was performed using Ampure XP beads (Beckman Coulter, A63881). The libraries were quantified by Tapestation (Agilent) and pooled for sequencing.


title: Female Control 3

description: Library name: Female_Control_3

value: Control


title: Tab_NT, rep3

description:
Library name: 75_Tab_NT_3
Tab_NT_3


title: Female Dexamethasone 3

description: Library name: Female_Dexa_3

value: Lung airway organoid


title: Injury 1

description: Library name: Sample4


title: ST7_T, Transcriptome library

description: Library name: ST7_T


title: Female Control 2

description: Library name: Female_Control_2


title: Optic cup, P347S, P10, biol replicate 1

city: Pozzuoli

first: Santiago

last: Negueruela

address: Via Campi Flegrei, 34

department: Genetic Medicie

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description:
Library name: P347S_P10
10X Genomics

data_processing:
10x Genomics Cell Ranger v7.0.0
Assembly: mm10 [refdata version 2020-A from Cell Ranger]
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Optic cup

growth_protocol: Maintenance of the mice was on a regular 12/12-h light/dark cycle, temperature of 20–24°C, and humidity of 54–65%, with ad libitum access to food and water.

extract_protocol:
Eye samples were dissociated using the Worthington Papain Dissociation System, according to the manufacturer's instructions.
Single Cell 3′ Library and Gel Bead Kit V3.1 (10x Genomics)

value: Optic cup

tag: time point


title: Tab_NT, rep2

description:
Library name: 74_Tab_NT_2
Tab_NT_2

tag: treatment


title: shGFP_2_Input

first: Qi

last: Liu

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to human rRNA and tRNA sequence which were retrieved from Ensembl and GtRNAdb databases , respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the human gene models (GENCODE, hg19) using Bowtie with a maximum one mismatch allowed. The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 1.5 fold change of TE to define the differential translation genes.
Assembly: hg19
Supplementary files format and content: xls file containing translation efficiency for each sample
Library strategy: Ribo-Seq

growth_protocol: LPS853 cells were cultured in IMDM medium supplemented with 15% FBS and 1X penicillin/streptomycin

extract_protocol:
Ribosome footprinting was performed according to TruSeq® Ribo Profile system (Illumina)
For library preparation the NEBNext Multiplex Small RNA Library Prep set for Illumina (New England Biolabs) was used. In parallel, total RNA input samples were isolated, and fragmented and the library obtained using the TruSeq stranded total RNA Kit (Illumina).

treatment_protocol: 2 shRNAs for ADAT2. shGFP used as a control

value: shGFP

tag: molecule subtype

value: RiboMinus mRNA


title: H3K27ac_Cerebellum_WT

description:
Library name: H3K27ac_Cerebellum_WT_CUTnTag
CUT&Tag

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were aligned to mm10 using bowtie2 (v2.5.2). Reads with quality > 2 were selected and sorted by query names. BAM files were converted to BEDPE files then to fragment files (sorted BED files). Fragments in the blacklist regions of mm10 (https://www.encodeproject.org/files/ENCFF547MET/) were removed. BED files were converted to BW files for subsequent visualization.
The raw sorted BED files (blacklist regions were not removed) are supported as supplementary files for individual samples.
Assembly: mm10
Supplementary files format and content: BED  files including sorted fragments
Library strategy: CUT&Tag

source_name: Cerebellum

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Concanavalin A (ConA) coated magnetic beads were freshly activated with Ca²⁺ and Mn²⁺. Nuclei were extracted and a total of 10,000 nuclei were incubated with activated ConA beads. Supernatant was next removed, and beads were incubated with antibody (1:50) on a rotator at 4°C overnight, followed by incubated with secondary antibody (1:100) for 1 hr at room temperature. Beads were washed three times and suspended in dig300-wash buffer pre-mixed with pG-Tn5 (1:100), incubated for 1 hr at room temperature. After washing beads for three times, tag buffer was added to each well, then incubated on a rotator at 37 °C for 1 hr. After centrifugation, beads were washed once and resuspended. Lysis buffer was added to each well, and incubated for 2 hr at 65 °C. After adding 10% Tween20, TruePrep CUT&Tag Amplification Mix (Vazyme), 10 mM MGI-P5, and 10 mM MGI-P7 primer were added. Then PCR program was performed. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library.

value: Cerebellum

tag: antibody

value: WT

tag: strain

tag: age

value: 8 weeks


title: Female Control 1

description: Library name: Female_Control_1

value: Epithelial Cells


title: Sacral NC 3

description: Library name: Sample3

tag: batch


title: ST7_R, Transcriptome library

description: Library name: ST7_R

data_processing:
scRNA-seq analysis 10X transcriptomic libraries were processed using CellRanger (version 7.2.0) and were aligned to the mouse transcriptome mm10-2020-A. Cellranger outputs were processed using Seurat (version 5.2.0). Datasets were processed to remove cells with fewer than 1,000 or greater than 100,000 reads, fewer than 500 or greater than 10,000 genes, or more than 20% of reads corresponding to mitochondrial genes. Doublets were identified and removed by using DoubletFinder (version 2.0.4). Libraries were integrated using Seurat’s “SCTransform” and Harmony (version 0.1.162). Libraries of the seurat project including all regions were integrated by Seurat’s “SCTransform”. Seurat projects of each brain region were integrated by Seurat’s “SCTransform” function and Harmony. To identify clusters, we constructed a shared nearest neighbor (SNN) graph using the 'FindNeighbors' function, and applied clustering through the 'FindClusters' function in Seurat. Iterative clustering to identify subtypes of cells was performed by subsetting into different major cell types (glutamatergic neurons, GABAergic neurons, glia) and using the “FindSubCluster” function in Seurat. Cell identities determined through analysis of iterative clusters were re-assigned to cells in the full Seurat object. Differential expression analysis was conducted using Seurat's “FindMarkers” and “FindAllMarkers” function, and gene expression in clusters was manually analyzed for known markers of given cell types.
STICR barcodes analysis STICR barcode analysis was performed using custom scripts, as previously described in Delgado et al57. First, BBMap (BBMap; sourceforge.net/projects/bbmap/) was used to remove low-quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments that were then aligned to our predefined fragment reference sets using Bowtie59 (version 5.2.1), allowing for up to two mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using awk. UMI of STICR barcodes with less than 10 reads were filtered by using awk to remove the noise UMI counts from the sequencing error. Finally, UMI-tools60 (version 0.5.1) was used to remove duplicate STICR barcode/cell barcode (CBC) reads by UMI, allowing for 1-bp mismatches in the UMI. STICR barcodes/CBC) pairings with at least three distinct UMIs were retained. For cells with multiple barcodes detected, only cells with all the same set of barcodes detected are considered as a shared clone, with Jaccard similarity of 1. Barcodes and their corresponding UMI counts were mapped to cells in the Seurat object of transcriptome data by aligning cell barcodes.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: rds

value: Brain


title: Injury 3

description: Library name: Sample2


title: C57_Bladder_KO_Male5

description:
Library name: C57_Bladder_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Bladder

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Bladder

value: Mecp2 KO

value: Male

value: 7 weeks

tag: mouse id


title: ST7_C, Transcriptome library

description: Library name: ST7_C

value: Wild type


title: Male Dexamethasone 3

description: Library name: Male_Dexa_3

value: Dexamethasone


title: NGFR-positive 2

description: Library name: NGFR_High_2

value: High


title: DMSO tri-culture of untreated A375 + HMDM + HMDDC

description:
Library name: D24-16232
10x Genomics

value: A375 + human monocyte-derived macrophage + human monocyte-derived dendritic cell

value: malignant melanoma + macrophage + dendritic cell

value: dimethylsulfoxide + dimethylsulfoxide


title: Sacral NC 2

description: Library name: Sample1

value: Rat pelvic ganglion


title: Tgd_T2, rep4

description:
Library name: 72_Tgd_T2_4
Tgd_T2_4

source_name: Vg9Vd2 T Cells

value: Vg9Vd2 T Cells

value: SKOV3-Zoledronate + 4 days culture with IL-2 (30IU/mL)


title: Muscle_Patient2_Pre-RYGB

city: Ottawa

first: Mary-Ellen

institute: University of Ottawa

data_processing:
GenomeStudio 2011.1
Average Beta

source_name: Vastus Lateralis

extract_protocol: DNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)

value: Vastus Lateralis

value: Female

value: Pre-RYGB


title: ST6_L1, Transcriptome library

city: San Francisco

first: Guohua

institute: UCSF

description: Library name: ST6_L1

value: Brain


title: NGFR-negative 1

description: Library name: NGFR_Low_1

value: Lung airway organoid

value: Epithelial Cells

value: Low


title: Male Dexamethasone 2

description: Library name: Male_Dexa_2

value: Male


title: Tgd_T2, rep3

description:
Library name: 71_Tgd_T2_3
Tgd_T2_3


title: EC_8dpf

city: NanTong

first: Xiaofeng

last: Lu

address: 9# Seyuan Road

institute: Nantong University

description: Library name: EC_8dpf

data_processing:
Cell Ranger 3.0.2 (https://github.com/10XGenomics/cellranger) was used to convert the raw sequencing data to single-cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 (https://satijalab.org/seurat/install.html)
Assembly: The reference genome (fasta format) and gene annotation (gtf format) files were downloaded from Ensembl database (release version 94).
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: whole fish

growth_protocol: Tg(fli1ep:EGFP) embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.

extract_protocol:
Embryos were transferred into a 15 mL falcon tube with 10% FBS/MEM and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. The cells were collected by centrifuged at 1500 rpm for 10 min and resuspended in MEM with 10%  fetal calf serum (FCS) and filtered through a 40-µm cell mesh. Cells were resuspended in PBS and EGFP+ cells were sorted by Flow cytometric cell sorting (FACS).
Selected EGFP positive cells went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.

value: whole fish


title: Bemcentinib co-culture of untreated A375 + HMDM

description:
Library name: D24-16229
10x Genomics

value: A375 + human monocyte-derived macrophage

value: malignant melanoma + macrophage

value: dimethylsulfoxide + bemcentinib


title: ST13_T, Transcriptome library

description: Library name: ST13_T

value: Wild type


title: ST5_L2, Transcriptome library

description: Library name: ST5_L2


title: Male Dexamethasone 1

description: Library name: Male_Dexa_1

source_name: Lung airway organoid

value: Dexamethasone


title: EC_4dpf

description: Library name: EC_4dpf


title: ST5_L1, Transcriptome library

description: Library name: ST5_L1


title: Tgd_T2, rep2

description:
Library name: 70_Tgd_T2_2
Tgd_T2_2


title: Female Oxygen 1

description: Library name: Female_Oxygen_1

value: Hyperoxia


title: Tgd_T2, rep1

description:
Library name: 69_Tgd_T2_1
Tgd_T2_1

value: Vg9Vd2 T Cells


title: C57_Bladder_WT_Female2

description:
Library name: C57_Bladder_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

value: Bladder

value: WT

value: 7.5 months


title: Male Control 3

description: Library name: Male_Control_3

value: Control


title: E19_E, pNeuroD cell population, PolyI:C treatment, rep 1

first: Tabitha

last: Rücker

address: 25, rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

value: cerebral cortex

value: neuronal cells

tag: transgene constructs

value: pNeuroD-eGFP/pCAG-tDimer

value: 19 days old embryo (E19)

tag: harvest mode


title: Male Oxygen 2

description: Library name: Male_Oxygen_2

value: Lung airway organoid

value: Epithelial Cells

value: Male


title: O-DIO_2

description: Library name: SAMPLES5

value: liver


title: Surface stain of NK cells from Peripheral Blood donor NP7

city: Melbourne

first: Shihan

last: Li

state: Victoria

address: 792 Elizabeth Street

country: Australia

institute: Peter Doherty Institute, University of Melbourne

description: Library name: run7_PROT

library_source: other

data_processing:
Raw sequencing data were processed with Cell Ranger v7.1.0 (10x Genomics). Donors were demultiplexed based on differences in single nucleotide polymorphisms using cellsnp-lite v1.2.2 and vireo v0.2.3. Gene expression (GEX) and Feature Barcode (CITE-seq) matrices were analysed with the Seurat package v4.3.0.1
Assembly: GRCh38
Supplementary files format and content: Tab separated values and matrix count files
Supplementary files format and content: metadata of donor ids in comma separated format
Library strategy: CITE-seq

molecule: protein

source_name: PBMC

extract_protocol:
Sorted NK cells were encapsulated in gel beads in emulsion (GEMs) using a 10x Genomics Chromium Controller iX. Reverse transcription and cDNA amplification according to the 10x Genomics protocol CG000330: Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide RevD.
Gene expression and Feature Barcode libraries were prepared according to 10x Genomics protocol CG000330: Chromium Next GEM Single Cell 5-v2 Cell Surface Protein UserGuide RevD

value: PBMC

value: NK cells

tag: hto

tag: adt

value: See feature_reference.csv

tag: library type

value: ADT and HTO


title: EC_2dpf

description: Library name: EC_2dpf

tag: tissue

value: whole fish


title: Tgd_NT, rep4

description:
Library name: 64_Tgd_NT_4
Tgd_NT_4

value: Vg9Vd2 T Cells

value: Untreated


title: MCD cohort_MCD_DTMB_biol rep 3

city: Pohang-si

first: Jae

last: Lee

address: 77 Cheongam-ro, Nam-gu

country: South Korea

institute: POSTECH

description: Library name: MCD cohort_MCD_DTMB_biol rep 3

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.7).
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.38).
Filtered reads reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 (v2.1.0).
Transcript assembly and gene-level quantification were perfomed with StringTie (v2.1.3b).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain gene-level raw counts (Entrez Gene IDs) for each sample, with gene symbols annotated.

extract_protocol:
RNA was isolated from liver tissue using RNeasy Plus Mini Kit (QIAGEN, 74134) according to the manufacturer’s instructions. RNA concentration and integrity (RIN > 7.0) were assessed using 4200 TapeStation System (Agilent).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer's protocol.

treatment_protocol: DTMB was orally administered at a dose of 10mg/kg/day.

tag: Sex

value: male

tag: genotype

value: WT

tag: disease state

value: MASH

value: MCD


title: Male Control 2

description: Library name: Male_Control_2

tag: cell type

value: Control


title: MCD cohort_MCD_DTMB_biol rep 2

description: Library name: MCD cohort_MCD_DTMB_biol rep 2


title: EC_1dpf

description: Library name: EC_1dpf


title: Tgd_NT, rep3

description:
Library name: 63_Tgd_NT_3
Tgd_NT_3

tag: treatment


title: Tgd_NT, rep2

description:
Library name: 62_Tgd_NT_2
Tgd_NT_2


title: MCD cohort_MCD_DTMB_biol rep 1

description: Library name: MCD cohort_MCD_DTMB_biol rep 1


title: S15Te

city: San Juan

first: Elba

last: Caraballo Rivera

state: Puerto Rico

address: Av. Jose Kiko Custodio

institute: University of Puerto Rico Comprehensive Cancer Center

description: Library name: Sample 30

data_processing:
Quality assessment of the raw FASTQ reads was conducted using FastQC to evaluate data integrity. Adapter trimming and low-quality base removal were performed using Trimmomatic, followed by alignment of the reads to the human reference genome GRCh38 (hg38) using the STAR. Gene-level quantification was carried out using RSEM, and the resulting expression data was imported into R/RStudio.
Assembly: hg38
Supplementary files format and content: rna-seq-normalized-counts_allSamples.csv-CSV file that contains gene-level raw read counts for each RNA-seq sample.
Supplementary files format and content: differential_gene_expression_te_me.csv-CSV file that contains differential gene expression results when comparing early-stage CRC tumors with adjacent mucosal tissue.
Supplementary files format and content: differential_gene_expression_ta_ma.csv-CSV file that contains differential gene expression results when comparing advanced-stage CRC tumors with adjacent mucosal tissue.

source_name: Early CRC

growth_protocol: This study was a secondary data analysis and uses previously collected tissue from PRH enrolled in the Puerto Rico Familial Colorectal Cancer Registry (PURIFICAR) IRB #2290034759. Tissue was stored at 80°C

extract_protocol:
RNA was extracted from frozen tumor and adjacent mucosal tissue samples using the Qiagen RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.  RNA quality and concentration were assessed prior to library preparation using a NanoDrop 2000 (Thermo Fisher Scientific).
RNA-seq libraries were prepared from total RNA using a poly(A)-selected library preparation kit according to the manufacturer’s protocol.

treatment_protocol: No in vitro treatment was applied. Samples represent primary early and advanced CRC tumors and adjacent mucosal tissue collected at the time of surgery.

value: Colorectal

value: Tumor tissue


title: Male Control 1

description: Library name: Male_Control_1

data_processing:
Quality control, preprocessing, and alignment were performed using the nf-core/rnaseq pipeline (version 3.17.0). Reads were aligned to the human reference genome using STAR aligner, and transcript abundance was quantified using Salmon. Quality metrics were assessed using MultiQC.
Transcript abundance estimates were summarized to gene-level counts using tximport (version 1.34.0). Differential expression analysis was performed using DESeq2 (version 1.46.0) with variance stabilizing transformation applied for visualization.
Assembly: GRCh38
Supplementary files format and content: Comma separated sample metadata, normalized counts and gene annotations for all samples.

value: Lung airway organoid

value: Epithelial Cells


title: Nanostring of human22

city: Beijing

first: Junping

last: Zhang

state: Beijing

address: No. 50, Yikesong Road, District Haidian, Beijing

institute: Sanbo Brain Hospital Capital Medical University

description: MiniBenifit

hyb_protocol: hybridization of 100 ng RNA to a version of the NanoString PanCancer code set for reading on the nCounter platform

scan_protocol: nCounter

data_processing: nSolver Analysis software, IO 360 Data Analysis Service

label: brain glioma

source_name: SD/PD

label_protocol: As little as 10 ng with nCounter RNA Low Input Kit and Panel specific primer pools (sold separately)

extract_protocol: The tumor tissue was divided into two parts. MagMAX FFPE RNA Ultra Kit (item No. A31881 ThermoFisher) was used to extract RNA from the tumor tissue, and the RNA was inspected according to relevant quality inspection standards. After the quality inspection was qualified, the RNA sequencing library was constructed

tag: gender


title: Tgd_NT, rep1

description:
Library name: 61_Tgd_NT_1
Tgd_NT_1


title: Nanostring of human21

description: MiniBenifit


title: S15Me

description: Library name: Sample 29

value: Adjacent mucosal tissue