title: Day5_Untreated

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

institute: University of Toronto

description: 3pr snRNA-seq, 10x Genomics

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Assembly: Genome_build: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of barcodes (raw feature matrix)
Supplementary files format and content: features.tsv.gz: list of gene IDs (raw feature matrix)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format (raw feature matrix)
Supplementary files format and content: possorted_genome_bam.bam: raw data

source_name: Mouse liver

extract_protocol:
Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

value: Mouse liver


title: CR-D21-6: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

status: Public on Sep 26 2025

type: SRA

city: Beijing

first: Qiang

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District, Beijing

country: China

institute: China Agricultural University

description: Library name: Unknown_AU543-01T0030

library_source: transcriptomic

data_processing:
In the preprocessing stage, Cutadapt (version 4.4)  was used to eliminate adapter sequences and low-quality reads for all samples. The clean data were subsequently aligned to the chicken reference genome (GRCg7b) using HISAT 2 (version 2.2.1)  with default parameters. Based on the alignment data, transcripts were assembled and quantified using StringTie. To generate the gene count matrix, we utilized the prepDE.py Python script, which is distributed as part of the StringTie, to process the output files generated by StringTie. The gene expression data for each group was filtered in R program to retain only protein-coding genes.
Assembly: GRCg7b
Supplementary files format and content: All_samples_read_counts.csv files include read counts for each Sample
Supplementary files format and content: D42/D21/D1/E17_DEGs.csv include differentially expressed genes for each growth points

molecule: total RNA

organism: Gallus gallus

source_name: breast muscle myofibroblasts

extract_protocol:
Approximately 20 mg of frozen breast muscle tissue per sample was homogenized in the lysis buffer provided in the RNA extraction kit (LS1040, Promega, Shanghai, China) following the manufacturer’s instructions. Total RNA was then extracted according to the kit protocol. The quality of the isolated RNA was assessed by detecting degradation and potential contamination using 1% agarose gels.
The cDNA libraries were constructed using Illumina Truseq TM RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's guide.

tag: cell line

value: breast muscle myofibroblasts

tag: Sex

value: male broiler

tag: time

value: 21 days old


title: PCBP1/2 shRNA in DMSO, Rep3

city: Chapel Hill

first: Maria

last: Aleman

state: NC

address: 120 Mason Farm Rd.

country: USA

institute: University of North Carolina at Chapel Hill

description: Library name: DMSO_shPCBP_3

data_processing:
Quality of sequencing fastq files was checked using FastQC and MultiQC. Salmon (v1.10.2) was used for transcript abundance quantification which was then analyzed for differential gene expression using DESeq2 (v3.19).
Significant genes were quantified by passing a read count threshold greater than 10, having an absolute log2 fold change greater than 1 and an adjusted P value less than 0.05. To capture alternative splicing, reads were first mapped to human genome build hg38 from Ensembl{Harrison, 2024 #297} using STAR (v2.7.11b){Dobin, 2013 #298}.
Chi-square tests were used to determine significant differences between observed and expected results. Hypergeometric tests were used to calculate the significance of overlapping datasets, where only co-detected genes or events were used as background.
Spearman's rank correlation test was used in correlation analysis.
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: K562 cells were cultured in RPMI 1640 with 10% fetal bovine serum and 1x Anti-Anti and incubated at 37° C with 5% CO2.

extract_protocol:
RNeasy Kit with DNase I treatment (Qiagen).
PolyA selection using KAPA mRNA Hyperprep Kit and NEBNext Multiplex Illumina Adaptors

tag: genotype

value: PCBP1 and PCBP2 Knockdown

tag: treatment

value: DMSO


title: Day3_IL4treated

country: Canada

description: 3pr snRNA-seq, 10x Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA

organism: Mus musculus

tag: tissue


title: CR-D21-5: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0029


title: Treatment (Z2A)

city: Jinan

first: Mingyang

last: Li

state: --- Select One ---

address: 324 Jingwu Road, Jinan 250021, China

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

description: Library name: Sample11

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). Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm39
Supplementary files format and content: excel files include fpkm values and read_count for each Sample (rna_expression.txt)

source_name: lung cancer

growth_protocol: Before constructing a mouse tumor model, LLCs cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using AG RNAex Pro. 1.0 ug of total RNA was used for the construction of sequencing libraries.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Before constructing mouse lung cancer models, LLCs in sample1-3 were transfected with negative control lentivirus and LLCs in sample4-6 transfected with OTUB1 knockdown lentivirus. In animals, sample 7-9 were treated with physiological saline, and sample 10-12 were treated with SFD@M.

value: lung cancer

value: WT


title: PCBP1/2 shRNA in DMSO, Rep2

description: Library name: DMSO_shPCBP_2


title: Treatment (Z3A)

description: Library name: Sample12


title: Day3_Untreated

description: 3pr snRNA-seq, 10x Genomics


title: PCBP1/2 shRNA in DMSO, Rep1

description: Library name: DMSO_shPCBP_1


title: CR-D21-3: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0027


title: CR-D21-4: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0028


title: Treatment (Z1A)

description: Library name: Sample10


title: Day1_IL4Treated

description: 3pr snRNA-seq, 10x Genomics


title: Day1_Untreated

description: 3pr snRNA-seq, 10x Genomics


title: Day5_IL4Treated

description: 3pr snRNA-seq, 10x Genomics


title: Blank (KD3A)

description: Library name: Sample9

value: physiological saline


title: CR-D21-2: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0026


title: Control shRNA in 21H7, Rep3

description: Library name: CHEL_shCtrl_3

value: Control


title: CC-D21-5: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0023


title: CR-D21-1: Crossbred progeny, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0025


title: Blank (KD2A)

description: Library name: Sample8


title: Day10_passaged_IWP2

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

data_processing:
The raw paired-end reads underwent trimming and filtering using the Drop-seq_tools-2.5.3 software, utilizing default parameters. Subsequently, alignment to the human genome GRCh38 (hg38) was carried out.
The default threshold of 200 genes per cell was used as the minimum requirement. Further filtration steps were applied to generate the cell expression matrix.
Assembly: hg38
Supplementary files format and content: Text files containing the expression matrix

extract_protocol:
Cells were harvested and encapsulated on the Nadia instrument. After reverse transcription and PCR amplification, 800 STAMPs were purified and used for library preparation.
Tagmentation of cDNA was carried out with Nextera XT Kit

treatment_protocol: H1 hESCs were induced to mesendodermal progenitors using WNT activator, and then allowed to differentiate with or without intermediate passaging on Day 2, in the presence or absence of WNT inhibitor IWP2. Samples were collected on Day 2, 3 and 10.

tag: cell type

value: human embryonic stem cells (hESCs)

value: Mesendoderm differentiation with IWP2, D2 passaged


title: CC-D21-6: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0024


title: Control shRNA in 21H7, Rep2

description: Library name: CHEL_shCtrl_2


title: Control shRNA in 21H7, Rep1

description: Library name: CHEL_shCtrl_1


title: Day0_Untreated

description: 3pr snRNA-seq, 10x Genomics


title: OTUB1 knockdown (sh2A)

description: Library name: Sample5

value: OTUB1 knockdown


title: Blank (KD1A)

description: Library name: Sample7


title: Control shRNA in DMSO, Rep1

description: Library name: DMSO_shCtrl_1


title: Day10_NP_ctrl

value: Mesendoderm spontaneous differentiation, not passaged


title: Control shRNA in DMSO, Rep2

description: Library name: DMSO_shCtrl_2


title: OTUB1 knockdown (sh1A)

description: Library name: Sample4


title: CC-D21-4: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0022


title: Day3_passaged_IWP2


title: Negative control (NC3A)

description: Library name: Sample3


title: FFPE tissue, DCIS 15

city: Ann Arbor

first: Sunitha

last: Nagrath

state: MI

address: 2800 Plymouth Rd

department: Chemical Engineering

institute: University of Michigan

description:
Library name: 10977YC16
10x genomics

data_processing:
The Advanced Genomics Core at the University of Michigan provided pooled FASTQ files  for multiplexed samples, per sample BAM files, and per sample processed barcodes, matrix, and genes files. BAM files for each sample are provided as the raw files here along with the number of cells determined by cellranger multi (from 10x's web summary). Barcodes, matrix, and genes files were used as input in R and processed according to the Seurat Guided Clustering workflow (Satija Lab).
Cells detected by cellranger multi for each of the BAM files: 9378NN3 = 3358 cells; 9597NN2 = 261 cells; 9597NN3 = 1659 cells; 9597NN4 = 5631 cells; 9597NN6 = 2288 cells; 10977YC9 = 15516; 10977YC10 = 2147; 10977YC11 = 1747; 10977YC12 = 8306; 10977YC13 = 3031; 10977YC14 = 5323; 10977YC16 = 5686
Assembly: GRCh38
Supplementary files format and content: Tab separated values for matrix, barcodes, and genes

source_name: Breast tissue biopsy

extract_protocol:
Blood samples were collected into CellRescue tubes (Menarini) and processed on the microfluidic Labyrinth system. Downstream, the enriched CTCs were supplemented with additional white blood cells until the cell count reached ~ 800,000 total cells. Then, these cells were used as input into 10X Genomics' Flex Protocol. At the end of the protocol, cells were frozen at -80C with Glycerol and Thaw Enhancer following the protocol's recommendation. Frozen samples were submitted to the university's Genomics core for processing on the 10X Chromium system.
The library construction was performed by the University of Michigan's Advanced Genomics Core and in accordance with 10X Genomics' Flex/Chromium Fixed RNA profiling protocol.

value: Breast tissue biopsy

value: Tissue epithelial, stromal, and immune cells


title: FFPE tissue, DCIS 25

description:
Library name: 10977YC14
10x genomics


title: Day3_passaged

value: Mesendoderm spontaneous differentiation, D2 passaged


title: CC-D21-1: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0019


title: Negative control (NC2A)

description: Library name: Sample2


title: Day3_NP_IWP2

value: Mesendoderm differentiation with IWP2, not passaged


title: vehicle, scRNAseq

first: Pengda

middle: P.

last: Lie

address: 21-246 Lineberger Cancer Center

department: Biochemistry and Biophysics

description: 10x Genomics

data_processing:
Resulting datasets were analyzed via the Seurat package (v5.1.0) in R (v4.3.1). Raw counts were processed following standard quality control measures and low-quality cells were excluded, including dead and suspected doublets. The minimum number of principal components needed to represent the data were calculated using a Jack Straw Plot, and next clustering was performed at a resolution of 0.7
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: B16 tumors

extract_protocol:
On day 14, tumor tissues were digested using the tumor dissociation kit, mouse and gentleMACS Dissociator. Tumor debris and melanin were removed by filtration and PBS washing. Tumor-infiltrating CD45+ cells in B16 tumors were enriched through positive selection via anti-CD45 biotinylated antibody staining for 20 min at room temperature, streptavidin-labeled microbeads and Miltenyi MACS LS columns. CD45+ cells from three mice in each treatment group were pooled together in PBS and sent for sample preparation.
PE-CD45+/Annexin V- cells were sorted on a SONY XYZ instrument, and 10000 cells were loaded in 10x Genomics Chromium Single Cell 3’ inlets (one inlet per sample). Barcoding and library preparation were performed following manufacture instructions with the 10x Genomics Chromium GEM-X Single Cell 3’ kit v4

treatment_protocol: B16 tumor-beraring C57BL/6J mice were treated with or without 60 mg/kg of SPOP-IN-6b for 9 consecutive days starting from 5 days after subcutaneous inoculation of B16 cells.

value: B16 tumors

tag: strain

tag: age

value: CD45+ lymphocytes

value: solvent


title: OTUB1 knockdown (sh3A)

description: Library name: Sample6


title: Control shRNA in DMSO, Rep3

description: Library name: DMSO_shCtrl_3


title: Day10_passaged


title: Day10_NP_IWP2


title: Day3_NP_ctrl


title: Negative control (NC1A)

description: Library name: Sample1


title: RR-D42-6: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0018

value: breast muscle myofibroblasts

value: male broiler

value: 42 days old


title: FFPE tissue, DCIS 14

description:
Library name: 10977YC11
10x genomics


title: FFPE tissue, DCIS 12

description:
Library name: 10977YC10
10x genomics


title: 8-2

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

data_processing:
RNA-seq reads were aligned to Mus musculus genome and annotation (assembly GCF_000001635.26_GRCm38.p6) using HISAT. The aligned short reads were counted using RSEM.
Assembly: assembly GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel file include FPKM for each sample.

growth_protocol: CBA/N male/ female mice were obtained from a local dealer (Nihon SLC, Hamamatsu), and kept under winter-like condition (Light: Dark=8:16, 10℃) /  summer-like condition (Light: Dark=16:8, 30℃) for 4 weeks.

extract_protocol:
Total RNA of whole brain (Exclusion of cerebellum and olfactory bulb) was isolated with elimination of DNA contamination using DNase. mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE100 strand specific sequencing libraries.
Strand-specific RNA-seq

treatment_protocol: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:00 (JST).

value: CBA/N

value: Wild-type

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:10 (JST).


title: RR-D42-4: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0016


title: RR-D42-5: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0017


title: 8-3

source_name: whole brain (Exclusion of cerebellum and olfactory bulb)

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:11 (JST).


title: CC-D21-2: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0020

value: 21 days old


title: CC-D21-3: Cornish purebred, Transcriptome sequencing of breast muscles, 21 days old

description: Library name: Unknown_AU543-01T0021


title: Day2

value: human embryonic stem cells (hESCs)

value: WT

value: Mesendoderm spontaneous differentiation


title: 8-1

value: whole brain (Exclusion of cerebellum and olfactory bulb)

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:09 (JST).


title: FFPE tissue, DCIS 4

description:
Library name: 10977YC9
10x genomics

value: Breast tissue biopsy

value: Tissue epithelial, stromal, and immune cells


title: 7-3

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:08 (JST).


title: Enriched CTCs and white blood cells, DCIS 25

description:
Library name: 10977YC13
10x genomics

source_name: White blood cells and circulating tumor cells


title: Has2+/- KO mice 4days after elastase stimulation 5

city: Tsukuba

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

institute: University of Tsukuba

description: Library name: LAB_341_26

data_processing:
CLC Genomics Workbench version 10.1.1
Assembly: mm10
Supplementary files format and content: Excel files include total counts, RPKM, and TPM values for each sample.

source_name: lung

extract_protocol:
Lung were removed, flash frozen on dry ice, and total RNA was extracted from mouse lungs using the TRIzol® reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using a NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich) and an ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions using 500 ng of total RNA samples.

value: lung

value: Has2 heterozygous-deficient (C57BL6 background)

value: elastase treated with intratracheal


title: RR-D42-3: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0015

value: breast muscle myofibroblasts

value: male broiler

value: 42 days old


title: RR-D42-2: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0014


title: Enriched CTCs and white blood cells, DCIS 17

description:
Library name: 9597NN6
10x genomics

value: White blood cells and circulating tumor cells


title: Has2+/- KO mice 4days after elastase stimulation 4

description: Library name: LAB_341_25


title: 7-2

value: CBA/N

value: Wild-type

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:07 (JST).


title: Has2+/- KO mice 4days after elastase stimulation 3

description: Library name: LAB_341_24


title: FFPE tissue, DCIS 17

description:
Library name: 10977YC12
10x genomics


title: CR-D42-6: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0012


title: Enriched CTCs and white blood cells, DCIS 15

description:
Library name: 9597NN4
10x genomics


title: Has2+/- KO mice 4days after elastase stimulation 2

description: Library name: LAB_341_23


title: Has2+/- KO mice 4days after elastase stimulation 6

description: Library name: LAB_341_27


title: Has2+/- KO mice 4days after elastase stimulation 1

description: Library name: LAB_341_22


title: CR-D42-5: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0011


title: Enriched CTCs and white blood cells, DCIS 4

description:
Library name: 9597NN3
10x genomics


title: 2-2

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:04 (JST).


title: CR-D42-3: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0009


title: 7-1

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:06 (JST).


title: 2-1

value: whole brain (Exclusion of cerebellum and olfactory bulb)

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:03 (JST).


title: Enriched CTCs and white blood cells, DCIS 12

description:
Library name: 9378NN3
10x genomics


title: 1-3

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:02 (JST).


title: WT mice 4days after elastase stimulation 7

description: Library name: LAB_341_21

value: WT(C57BL6 background)


title: PCBP1 OE, rep3

data_processing:
Quality of sequencing fastq files was checked using FastQC and MultiQC. Salmon (v1.10.2) was used for transcript abundance quantification which was then analyzed for differential gene expression using DESeq2 (v3.19).
Significant genes were quantified by passing a read count threshold greater than 10, having an absolute log2 fold change greater than 1 and an adjusted P value less than 0.05. To capture alternative splicing, reads were first mapped to human genome build hg38 from Ensembl{Harrison, 2024 #297} using STAR (v2.7.11b){Dobin, 2013 #298}.
The resulting bam files were then analyzed with rMATS. Significant alternative splicing events had an FDR less than 0.05, an absolute ∆PSI > 5 percent, and having either an average inclusion read count or exclusion read count >= 10.
Chi-square tests were used to determine significant differences between observed and expected results. Hypergeometric tests were used to calculate the significance of overlapping datasets, where only co-detected genes or events were used as background.
Spearman's rank correlation test was used in correlation analysis.
Assembly: hg38
Supplementary files format and content: text files include TPM for each sample

growth_protocol: K562 cells were electroporated using the NeonTM Transfection System with AAVS1 guide RNA, Cas9-NLS, and a donor plasmid containing a blasticidin-resistance cassette flanked by loxP and lox2272 sites under an EF-1 promotor with homology regions to the AAV1 locus that is compatible with the pRD-RIPE system for recombinase-mediated cassette exchange (RMCE) {Khandelia, 2011 #219}.

extract_protocol:
RNA isolated from cells after treatments was sent to Novogene (Sacramento, CA) for polyA selection and library preparation followed by Illumina sequencing (paired end, 150 cycles). Eighteen to 30 GB of data per sample were collected.
Poly A selection. Performed by Novogene.

treatment_protocol: Cells were selected with 10 µg/mL blasticidin  and plated for single cell clonal expansion. The final clone was genotyped using sanger sequencing.

value: Dox


title: CR-D42-4: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0010


title: WT mice 4days after elastase stimulation 6

description: Library name: LAB_341_20

value: lung


title: CR-D42-2: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0008


title: Enriched CTCs and white blood cells, DCIS 14

description:
Library name: 9597NN2
10x genomics


title: RR-D42-1: White Plymouth Rock purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0013


title: 1-2

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:01 (JST).


title: PCBP1 OE, rep1


title: PCBP1 OE, rep2


title: WT mice 4days after elastase stimulation 5

description: Library name: LAB_341_19

value: elastase treated with intratracheal


title: WT mice 4days after elastase stimulation 4

description: Library name: LAB_341_18


title: CR-D42-1: Crossbred progeny, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0007

value: breast muscle myofibroblasts


title: 2-3

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:05 (JST).


title: CC-D42-6: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0006

value: male broiler

value: 42 days old


title: 1-1

value: CBA/N

value: Whole brain (Exclusion of cerebellum and olfactory bulb) was collected from mouse and saved in 1.5ml sampling tube under -80℃ around 13:00 (JST).


title: WT mice 4days after elastase stimulation 3

description: Library name: LAB_341_17


title: Control, rep3

value: Control


title: CC-D42-5: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0005


title: cko-42dpMI-4

city: 深圳

first: Xueting

address: 广东省深圳市盐田区华大公寓

institute: University of Chinese Academy of Sciences

description: Library name: R24

data_processing:
Raw sequencing data processing (alignment, filtering, and UMI counting) was performed using CellRanger toolkit (v2.1.0.). The cDNA reads were mapped with a mouse genome reference (mm10).
Assembly: Mouse mm10
Supplementary files format and content: R serialized data file (.rds) containing a normalized gene expression matrix and associated metadata.

source_name: heart

extract_protocol:
For each experimental condition, heart tissues were first rinsed and minced into 1 mm pieces on ice, then the minced tissues were pooled and digested in tissue dissociation media (0.1% Collagenase with 2.5 U/mL Dispase II, 9:1 in volume) for 40 minutes in 37°C water bath, pipetted every 5 minutes, to ensure an adequate number of cells and a robust representation of cardiac cell types. Single-cell suspension was passed through a 40 µm filter. Cell suspension was stained with PE Rat anti mouse CD31 (BD Pharmingen, 553373) or APC Rat anti mouse CD45 (BD Pharmingen, 559864), then followed incubated with anti-PE microbeads (MACS,130-105-639) or Anti-APC microbeads (MACS,130-090-855). Single cells from CD31+ or CD45+ cell populations were collected by FACS sorting.
The DNBelab C Series Single-Cell Library Prep Set (MGI, 1000021082) was used as previously described. In brief, single cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription and cDNA amplification to generate barcoded libraries. Libraries were sequenced on DNBSEQ-T1 sequencers with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2.

value: heart

value: cko

tag: group


title: cko-42dpMI-3

address: 广东省深圳市盐田区华大公寓

description: Library name: R23


title: Control, rep2


title: CC-D42-4: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0004


title: WT mice 4days after elastase stimulation 1

description: Library name: LAB_341_15


title: WT mice 4days after elastase stimulation 2

description: Library name: LAB_341_16


title: CC-D42-3: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0003


title: Control, rep1


title: cko-42dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R21


title: PCBP1 shRNA, Rep3

extract_protocol:
RNA isolated from cells after treatments was sent to Novogene (Sacramento, CA) for polyA selection and library preparation followed by Illumina sequencing (paired end, 150 cycles). Eighteen to 30 GB of data per sample were collected.
PolyA selection. Performed by Novogene.

treatment_protocol: Lentiviral particles containing pLKO.1 plasmids with shRNA genes for Luciferase (shCtrl) or PCBP1 (shPCBP1) were generated as described from HEK293T cells{Addgene, 2006 #319;Moffat, 2006 #320}. K562 cells were treated with media containing lentiviral particles and 8µg/mL polybrene, overnight at 37° C with 5% CO2. The following morning, cells were spun down (500 x g, 3 min) and resuspended in selection media (3 µg/mL puromycin, 10% FBS, RPMI 1640) for four days before collection.

value: PCBP1 Knockdown


title: CC-D42-2: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0002


title: cko-42dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R22


title: Has2+/- KO mice  control 7 (without elastase stimulation)

description: Library name: LAB_341_14

value: Has2 heterozygous-deficient (C57BL6 background)

value: unstimulated


title: Has2+/- KO mice  control 6 (without elastase stimulation)

description: Library name: LAB_341_13


title: CC-D42-1: Cornish purebred, Transcriptome sequencing of breast muscles, 42 days old

description: Library name: Unknown_AU543-01T0001


title: PCBP1 shRNA, Rep1


title: PCBP1 shRNA, Rep2


title: Has2+/- KO mice  control 5 (without elastase stimulation)

description: Library name: LAB_341_12


title: cko-21dpMI-3

address: 广东省深圳市盐田区华大公寓

description: Library name: R19


title: Has2+/- KO mice  control 4 (without elastase stimulation)

description: Library name: LAB_341_11


title: cko-21dpMI-4

address: 广东省深圳市盐田区华大公寓

description: Library name: R20


title: Control shRNA, Rep3


title: cko-21dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R18


title: Right gonad, female, E9.5, Rep2

city: University Park

first: Tae Hyun

last: Kim

state: PA

address: 317 AVBS

institute: Penn State University

data_processing:
Read trim & QC - TrimGalore (0.6.7)
Read alignment - STAR (2.7.10a)
Read count - HTSeq-count (2.0.0)
Assembly: GRCg6a NCBI Gallus gallus Annotation Release 104
Supplementary files format and content: csv, raw readcount per gene for each sample

source_name: Gonad

extract_protocol:
Zymo direct-zol miniprep kit
NEB

value: Gonad

value: gonadal cells

value: Leghorn


title: Has2+/- KO mice  control 3 (without elastase stimulation)

description: Library name: LAB_341_10

value: lung


title: cko-21dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R17


title: Right gonad, female, E9.5, Rep1


title: Has2+/- KO mice  control 2 (without elastase stimulation)

description: Library name: LAB_341_09


title: Left gonad, female, E9.5, Rep3


title: Control shRNA, Rep1


title: cko-7dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R16


title: Has2+/- KO mice  control 1 (without elastase stimulation)

description: Library name: LAB_341_08


title: WT mice control 7 (without elastase stimulation)

description: Library name: LAB_341_07

value: WT(C57BL6 background)


title: Left ventricle, SHR_OMT, replicate 3

city: Chongqing

first: Chaohong

address: Yuzhong Road

institute: Chongqing Medical University

description: Library name: SHR_OMT3

data_processing:
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)
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
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 DEGseqor PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001)
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Left ventricle

extract_protocol:
RNA was extracted using Trizol reagent (Thermo Fisher Scientific). 200 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols on the BGISEQ-500 sequencing platform

value: Left ventricle


title: Right gonad, female, E9.5, Rep3


title: NPM6_DOX

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Sequencing data from the Illumina NovaSeq were aligned to human GRCh38 in CellRanger v5.0.1.
Assembly: GRCh38
Supplementary files format and content: HDF5 file

source_name: Human embryonic stem cells (RUES1 cell line)

extract_protocol:
The tissue samples were incubated in 20mM EDTA-PBS while rocking in a cold room for 90 minutes. Every 30 minutes, the tubes containing the intestinal tissues were shaken vigorously for one minute to collect dissociated epithelial fractions. After 90 minutes, the three collections from each tissue were combined and dissociated into single cells using TrypLE for one minute at 37°C.The single-cell suspensions in FACS buffer (containing 1% glucose, 10mM HEPES, 10μM Y-27632, 1mM N-acetyl-L-cysteine, and 2% FBS in DPBS) were passed through a 40μm filter. The cells were then stained with anti-mouse CD326 (EpCam, Key Resources Table). Live EpCam+ epithelial cells were sorted using a Symphony S6 II cell sorter in FACS buffer.
For each sample, 10,000 cells were loaded into each channel of the Chromium Controller cartridge to produce droplets. Beads-in-emulsion (GEMs) were transferred, and GEM reverse transcription (GEM-RT) was performed in droplets via PCR incubation. After the post-GEM-RT reaction, first-strand cDNA was purified. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. TruSeq Read 1 (read 1 primer sequence) was added during GEM incubation. A sample index and TruSeq Read 2 (read 2 primer sequence) were added through end-repair, A-tailing, adaptor ligation, and PCR. The final libraries were assessed using an Agilent Technology 2100 Bioanalyzer and sequenced on an Illumina NovaSeq sequencer.

value: Epithelial cells


title: Left ventricle, SHR_OMT, replicate 2

description: Library name: SHR_OMT2


title: Left gonad, female, E9.5, Rep2


title: cko-3dpMI-4

address: 广东省深圳市盐田区华大公寓

description: Library name: R14


title: Left gonad, female, E9.5, Rep1


title: Right gonad, female, E8, Rep3


title: WT mice control 6 (without elastase stimulation)

description: Library name: LAB_341_06


title: cko-3dpMI-3

address: 广东省深圳市盐田区华大公寓

description: Library name: R13


title: WT mice control 5 (without elastase stimulation)

description: Library name: LAB_341_05


title: cko-7dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R15


title: Left ventricle, SHR, replicate 3

description: Library name: SHR3


title: Right gonad, female, E8, Rep2


title: cko-3dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R12


title: Left ventricle, SHR, replicate 2

description: Library name: SHR2


title: WT mice control 3 (without elastase stimulation)

description: Library name: LAB_341_03


title: Left ventricle, SHR_OMT, replicate 1

description: Library name: SHR_OMT1


title: Control shRNA, Rep2


title: Right gonad, female, E8, Rep1


title: ctrl-42dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R10

value: ctrl


title: Left gonad, female, E8, Rep3


title: WT mice control 2 (without elastase stimulation)

description: Library name: LAB_341_02


title: ctrl-42dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R9


title: Left gonad, female, E8, Rep2


title: WT mice control 1 (without elastase stimulation)

description: Library name: LAB_341_01


title: mE6_NPC_H3K27ac_Ab Biological repliacate 1

city: Stanford

first: Christy

last: Luong

state: CA

address: 269 Campus Dr

department: Department of Dermatology

institute: Stanford University School of Medicine

description:
Library name: mE6_NPC_H3K27ac_Ab_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.

library_source: genomic

data_processing:
Reads were aligned with Bowtie2 with a custom N-masked genome. Reads were then deduplicated and indexed with samtools. For allele-specific analysis, reads were split based on informative SNPs using SNPSplit.
Assembly: mm10
Supplementary files format and content: BigWig files: created using bamCovarage with normalization using RPGC and bin size of 10 Genome 1 is the 129 allele and genome 2 is the CAST allele.

molecule: genomic DNA

growth_protocol: NPC were ifferentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. mESCs were grown on 0.1% gelatin with 2i+lif medium.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins and lysed with nuclear lysis buffer containing NP-40. Chromtain was then sheared with a Covaris. Sonicated chromatin underwent immunoprecipitation with antibody of choice then DNA was purified.
NEB II Ultra DNA library prep kit was used for library prep with the ChIP DNA.

value: male

value: neuronal progenitor cells

tag: chip-antibody


title: Left ventricle, SHR, replicate 1

description: Library name: SHR1


title: ctrl-21dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R8


title: Left gonad, female, E8, Rep1


title: cko-3dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R11


title: ctrl-21dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R7


title: WT mice control 4 (without elastase stimulation)

description: Library name: LAB_341_04


title: Left ventricle, WKY, replicate 2

description: Library name: WKY2


title: Right gonad, female, E6.5, Rep3


title: Left ventricle, WKY, replicate 3

description: Library name: WKY3


title: ctrl-7dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R6


title: Right gonad, female, E6.5, Rep1


title: ctrl-3dpMI-4

address: 广东省深圳市盐田区华大公寓

description: Library name: R4


title: Left ventricle, WKY, replicate 1

description: Library name: WKY1


title: F123 mouse embryonic stem cell (bisulfite-seq) biol rep 1

description:
Library name: F123_mESC_methyl_R1
bisulfite-seq on mESCs with PE 150 and ~15 million PE reads

data_processing:
Reads were aligned and deduplicated using an N-masked custom genome and Bismark in allele-specific mode. Aligned reads were then split using SNPsplt on informative SNPs. Resulting bam files were they visualized using bamCoverage to create BigWig files.
Assembly: mm10
Supplementary files format and content: BigWig files were created using bamCoverage from allele-specific bam files using RPGC and a bin of 10. Genome 1 the 129 allele and genome 2 is the CAST allele.

growth_protocol: NPCs were differentiated from mESCs from 2i+Lif. NPCs were grown on 0.1% gelatin with N2B27 medium with FGF and EGF. F123 mESCs were growon on 0.1% gelatin with N2B27 medium with 2i+Lif

extract_protocol:
Genomic DNA was extracted using genomic lysis buffer followed by phenol chloroform purification and isoporanol precipitation.
Library was constructed using illumina's TruSeq Methyl Epic Capture library prep kit.

value: Male

value: embryonic stem cells


title: mE6 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 1

description:
Library name: mE6_NPC_methyl_R1
bisulfite-seq on NPC with PE 150 and ~15 million PE reads

value: Neuronal progenitor cells


title: Ch1_NPC_H3K27ac_Ab Biological repliacate 1

description:
Library name: Ch1_NPC_H3K27ac_Ab_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: H_8_8+I_(3) ; HEK293T_8h_10uM-A8+Isrib(biol. rep 3)

city: La Jolla

first: Jeffery

last: Kelly

state: California

address: 10550 North Torrey Pines Road

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Alignment of reads was performed using DNAstar Lasergene SeqMan NGen 17 to the human genome GRCh37-dbSNP150 assembly.
Aligned reads were imported into ArrayStar 17 as linear counts data.
Differential expression analysis and statistical significance comparisons were assessed using DESeq 2 v. 1.34 in R compared to vehicle-treated cells.
Assembly: human genome GRCh37-dbSNP150 assembly
Supplementary files format and content: Raw counts of sequencing reads for each gene following alignment. Format is .csv.
Supplementary files format and content: Normalized abundance measurements for each gene following DESeq2. Format is .csv.

growth_protocol: HEK293 cells were plated at 200,000 cells/well in a 6-well plate in DMEM with 10% FBS and 1% PennStrep

extract_protocol:
Cells were collected with 0.25% trypsin, neutralized with cell culture media, and pelleted at 200 x g for 5 min. Total RNA was extracted using the Quick-RNA MiniPrepKit (Zymo Research), following the protocol suggested by the manufacturer.
Libraries were constructed by BGI using their standard methodology. mRNA was enriched from total RNA samples via their polyA tails using oligo dT beads. mRNA was then fragmented and converted to cDNA using random primers to synthesize the first cDNA strand. The second cDNA strand was synthesized using dUTP instead of dTTP. The cDNA was subjected to end-repair and 3’ adenylated. Adaptors were ligated to the ends of these cDNA fragments. The U-labeled second-strand template was digested with uracil-DNA-glycosylase. The remaining cDNA fragments were then amplified by PCR. The library was quality controlled, then circularized and amplified to make a DNA nanoball (DNB). Finally, the library was sequenced using the DNBSEQ platform.

treatment_protocol: After 24 hours, the cells were treated with the indicated concentration of compound for 4 h.

value: 8 hour

value: A8 (10 uM) + Isrib


title: Left gonad, female, E6.5, Rep3


title: ctrl-3dpMI-3

address: 广东省深圳市盐田区华大公寓

description: Library name: R3

value: heart


title: H_8_8+I_(2) ; HEK293T_8h_10uM-A8+Isrib(biol. rep 2)


title: H_8_8+I_(1) ; HEK293T_8h_10uM-A8+Isrib(biol. rep 1)


title: Left gonad, female, E6.5, Rep2


title: Left gonad, female, E6.5, Rep1


title: Ch8_NPC_H3K27ac_Ab Biological repliacate 1

description:
Library name: Ch8_NPC_H3K27ac_Ab_R1
Chromatin immunoprecipitation libraries with antibody for protein of interest. Libraries were sequenced PE 150 for ~100 million reads.


title: H_8_10uM_A8_(3) ; HEK293T_8h_10uM-A8(biol. rep 3)


title: ctrl-7dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R5


title: Right gonad, female, E6.5, Rep2


title: Ch8 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 1

description:
Library name: Ch8_NPC_methyl_R1
bisulfite-seq on NPC clonal line with PE 150 and ~15 million PE reads


title: Ch1 neuronal progenitor cell clonal line (bisulfite-seq) biol rep 1

description:
Library name: Ch1_NPC_methyl_R1
bisulfite-seq on NPC clonal line with PE 150 and ~15 million PE reads


title: ctrl-3dpMI-2

address: 广东省深圳市盐田区华大公寓

description: Library name: R2


title: Right gonad, female, E5, Rep3


title: H_8_10uM_A8_(2) ; HEK293T_8h_10uM-A8(biol. rep 2)


title: ctrl-3dpMI-1

address: 广东省深圳市盐田区华大公寓

description: Library name: R1


title: H_8_D+I_(3) ; HEK293T_8h_DMSO+Isrib(biol. rep 3)

description: Biological replicate 2 excluded due to poor sample quality.

value: DMSO + Isrib


title: H_8_10uM_A8_(1) ; HEK293T_8h_10uM-A8(biol. rep 1)


title: Right gonad, female, E5, Rep1

value: Gonad


title: PTEN ko macrophages, GM-CSF,3

city: Zhengzhou

first: chen

last: lin

state: Henan

address: Erqi District, University North Road

institute: ZHENGZHOU University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated
Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software.
Assembly: mm10
Supplementary files format and content: fastq.gz
Supplementary files format and content: fastq.gz

source_name: bone marrow

growth_protocol: BMDM(bone marrow derived macrophages) were maintained in DMEM suppledmented with 10%fetal serum(FBS) and 1%antibiotics in humidified atmosphere with 5% CD2 at 37C

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: BMDM differentiated in a medium containing GM-CSF for 7 days

value: bone marrow

value: bone marrow -derived macrophages

value: PTEN knockdown

value: GM-CSF


title: 4NQO + SP2509 Rep 2

city: Boston

first: Lina

last: Kroehling

state: MA

address: 91 E Concord St

institute: Boston Unviersity

description: 10x Genomics

data_processing:
CellRanger Version 3.1.0 was used for data processing with mm10
Assembly: mm10
Supplementary files format and content: barcods,matrix,features tsv per sample

source_name: Tongue

extract_protocol:
Single-cell suspensions from mouse oral cavities and oral cavity lesions dissociated as described above were loaded on a 10X genomics chip B at concentrations varying between 805,000 and 1,930,000 cells/mL with viability over 90% for a targeted cell recovery of 6,000 cells per sample and processed using the 10X Genomics 3’v3  kit according to the manufacturer’s protocol (10x Genomics, CA, USA). Following the 10X Genomics Chromium controller, the gel beads in emulsion (GEMs) were transferred to strip tubes and subsequently placed into a thermal cycler using the following parameters: 45 min at 53 °C, 5 min at 85 °C, and hold at 4 °C. The samples were then stored overnight at -20 °C. The next day, the samples were thawed at room temperature before adding the recovery agent to break the GEMs. Subsequently, the cDNA was purified and amplified, and gene expression libraries were generated and purified
10X Genomics 3’v3  kit according to the manufacturer’s protocol (10x Genomics, CA, USA).

value: Tongue


title: 4NQO + SP2509 Rep 1

description: 10x Genomics


title: 4NQO Control Rep 2

description: 10x Genomics


title: Right gonad, female, E5, Rep2

value: gonadal cells

value: Leghorn


title: Left gonad, female, E5, Rep3


title: PTEN ko macrophages, GM-CSF,1


title: H_8_D_(3) ; HEK293T_8h_DMSO(biol. rep 3)

value: DMSO


title: PTEN ko macrophages, GM-CSF,2


title: 4NQO Control Rep 1

description: 10x Genomics


title: macrophages ,GM-CSF,3

value: WT


title: H_8_D_(2) ; HEK293T_8h_DMSO(biol. rep 2)


title: WT replicate 2

description: 10x Genomics

value: Vehicle


title: Left gonad, female, E5, Rep2


title: Left gonad, female, E5, Rep1


title: macrophages ,GM-CSF,2


title: H_8_D_(1) ; HEK293T_8h_DMSO(biol. rep 1)


title: WT replicate 1

description: 10x Genomics


title: PK-15 cells_bio rep 2

status: Public on Sep 25 2025

first: Xiwang

last: Yang

state: Chongqing

address: 2# Tiansheng Street

institute: Southwest University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data of fastq format were firstly processed through in-house perlscripts. In this step, clean data were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using Bowtie
The circRNA were detected and identified using find_circ and CIRI2. The raw counts were first normalized using TPM. Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value found by DESeq were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis for host genes of differentially expressed circRNAs were implemented by the GOseq R package, in which gene length bias was corrected . GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways
Assembly: Sscrofa11.1
Supplementary files format and content: Excel Workbook files include TPM values for each Sample

organism: Sus scrofa

source_name: Kidney

extract_protocol:
RNA simple Total RNA Kit (Tiangen) was used to extract the total RNA. A total amount of 5 μg RNA per sample was used as input material for the construction of sequencing libraries.
The sequencing libraries were generated by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Kidney

value: Porcine kidney cells


title: PK-15 cells_bio rep 3


title: PK-15 cells, TGEV_bio rep 3


title: PK-15 cells_bio rep 1


title: macrophages ,GM-CSF,1


title: CHATCre-Ribotag_Input_AMPH4

city: Bellaterra (Cerdanyola del Vallès)

first: Laura

last: Cutando Ruiz

state: Barcelona

address: Facultat de Medicina, M1/125, Av. de Can Domènech Campus de la UAB · 08193 Bellaterra

department: Department of Cellular Biology, Physiology and Immunology - Institute of Neurosciences

country: Spain

institute: Universitat Autònoma de Barcelona

description: Library name: ABA33072

data_processing:
Reads were mapped to the GRCm39 genome with STAR v2.7.8a (ENCODE parameters) and quantified using RSEM v1.3.0 with GENCODE M34 annotation. Dataset followed ENCODE RNA-seq processing guidelines to generate gene-level expression estimates from raw FASTQ files.
Assembly: GRCm39 (GENCODE M33, mm39)
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: Brain, striatum

extract_protocol:
RNA was extracted using the RNeasy micro kit (Qiagen)
RNA sequencing libraries from Pvalb-RiboTag mouse striatal tissue were prepared using a modified SMART-seq2 protocol (Picelli et al., 2014). Total RNA (6–11 ng) was quantified (Qubit RNA BR Assay) and integrity assessed (Agilent Fragment Analyzer). Reverse transcription was performed with SuperScript II, oligo-dT30VN primers, template-switching oligonucleotides, and betaine. The resulting cDNA was amplified by 8 PCR cycles (KAPA HiFi HotStart), purified (AMPure XP beads), and quality-checked (Bioanalyzer HS DNA Kit). Two hundred nanograms of amplified cDNA was tagmented (Nextera XT Kit) and subjected to 12 cycles of indexed PCR amplification. Libraries were further purified, quantified, and sequenced on an Illumina NovaSeq 6000 system (paired-end 2 × 51 bp) with dual indexing, followed by image analysis and quality scoring using RTA v3.4.4.

value: Brain, striatum

value: Whole striata cell types

value: Chat-Cre;RiboTag

value: Chronic Amphetamine


title: CHATCre-Ribotag_Input_AMPH1

description: Library name: ABA33070


title: CHATCre-Ribotag_Pellet_AMPH3

description: Library name: ABA33065

value: Chat-expressing neurons


title: CHATCre-Ribotag_Pellet_AMPH4

description: Library name: ABA33066


title: CHATCre-Ribotag_Input_SAL2

description: Library name: ABA33068

value: Chronic Saline


title: CHATCre-Ribotag_Pellet_SAL3

description: Library name: ABA33063


title: CHATCre-Ribotag_Pellet_SAL1

description: Library name: ABA33059


title: H_8_D+I_(1) ; HEK293T_8h_DMSO+Isrib(biol. rep 1)

value: 8 hour

value: DMSO + Isrib


title: CHATCre-Ribotag_Input_AMPH3

description: Library name: ABA33071


title: PVCre-Ribotag_Input_AMPH2

description: Library name: ABA33057

value: Pvalb-Cre;RiboTag


title: CHATCre-Ribotag_Input_SAL3

description: Library name: ABA33069


title: CHATCre-Ribotag_Input_SAL1

description: Library name: ABA33067


title: PVCre-Ribotag_Input_SAL3

description: Library name: ABA33055


title: CHATCre-Ribotag_Pellet_SAL2

description: Library name: ABA33061


title: CHATCre-Ribotag_Pellet_AMPH1

description: Library name: ABA33064


title: PVCre-Ribotag_Input_AMPH3

description: Library name: ABA33058


title: PVCre-Ribotag_Input_SAL2

description: Library name: ABA33054


title: PVCre-Ribotag_Input_AMPH1

description: Library name: ABA33056


title: PVCre-Ribotag_Pellet_AMPH3

description: Library name: ABA33052

value: Parvalbumin-expressing neurons


title: PVCre-Ribotag_Pellet_AMPH2

description: Library name: ABA33050


title: PK-15 cells, TGEV_bio rep 1


title: PVCre-Ribotag_Input_SAL1

description: Library name: ABA33053


title: PVCre-Ribotag_Pellet_SAL2

description: Library name: ABA33047


title: PVCre-Ribotag_Pellet_SAL1

description: Library name: ABA33046


title: PK-15 cells, TGEV_bio rep 2


title: PVCre-Ribotag_Pellet_SAL3

description: Library name: ABA33048


title: KO2CCL4

city: New Haven

first: Suyavaran

last: Arumugam

state: Connecticut

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

description:
Library name: Sample 8
10x Genomics

data_processing:
Data were demultiplexed, barcode processed, gene counted and aggregated using Cell Ranger software v 2.1.1
Assembly: Mouse mm10
Supplementary files format and content: tab separated value and matrix files

source_name: Liver

extract_protocol:
Livers were perfused with HBSS and then EMEM-containing collagenase type 4, 40-mg pronase, and 25 mg/mL of DNAase 1. Suspension was centrifuged to isolate hepatocytes in pellet and the supernatant was saved for non-parenchymal cells. The suspension was subjected to purification with 20% percoll gradient. The purified hepatocytes were added to final non parenchymal cells suspension, and the final cell suspension (1200/μL and 100 μL in total) was prepared in phosphate buffered saline containing 0.04% bovine serum albumin and were submitted to Yale Center for Genome Analysis. Cells were subjected to 10X chromium using 3′ gene expression V3kit for library preparation according to manufacturer’s guidelines and were sequenced using Novaseq. The count matrix was generated using 10X Genomics Cell Ranger software. The barcode matrices from Cell Ranger output were demultiplexed using Seruat pipeline for QC. The liver sections from rest of the mice were subjected to Sirius red staining to assess the grade of fibrosis.
Cells were subjected to 10X chromium using 3′ gene expression V3kit for library preparation according to manufacturer’s guidelines and were sequenced using Novaseq. The count matrix was generated using 10X Genomics Cell Ranger software. The barcode matrices from Cell Ranger output were demultiplexed using Seruat pipeline for QC.

treatment_protocol: Study groups were as follows: (1) Wild type C57BL6/J mice injected with corn oil (100ul injection, 3×per week for 4 weeks) (n=6) (2) Wild type mice injected with CCl4 0.5 ml/kg b.wt  intraperitoneally (i.p.) 1 in 4 dilution in corn oil, 3×week for 4 weeks (n=6); (3) Col1a2/STING-/- mice injected with corn oil (100ul injection, 3×per week for 4 weeks) (n-6) (4) Col1a2/STING-/- mice injected with CCl4 0.5 ml/kg b.wt  intraperitoneally 1 in 4 dilution in corn oil, 3×week for 4 weeks (n=6). Two mice from each group were subjected to single-cell isolation.

value: Liver

value: 6-8 weeks old

value: Male

value: Col1A2 STING-/-

value: CCL4 0.5mg/kg b.wt (4weeks)


title: WT2CCL4

description:
Library name: Sample 6
10x Genomics

value: Col1A2 STING fl/fl


title: KO1CCL4

description:
Library name: Sample 7
10x Genomics


title: PVCre-Ribotag_Pellet_AMPH1

description: Library name: ABA33049


title: WT1CCL4

description:
Library name: Sample 5
10x Genomics


title: KO2

description:
Library name: Sample 4
10x Genomics

value: Corn oil


title: KO1

description:
Library name: Sample 3
10x Genomics


title: HS_Plac_24

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the mouse genome (mm10) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R (v4.05) and analysis of differential expression between groups was done using the limma-voom pipeline
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Placenta

extract_protocol:
RNA was extracted using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries (n = 4 per group) were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (Illumina, Cat. No. RS-122-2303) using dual-indexed barcodes. Bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and size distribution ws confirmed using TapeStation.

value: Placenta

tag: tempertaure

tag: temp

value: MMV


title: HS_Plac_23


title: HS_Plac_21

value: Female


title: HS_Plac_18


title: HS_Plac_22


title: HS_Plac_19


title: WT1

description:
Library name: Sample 1
10x Genomics

value: Col1A2cre STING fl/fl


title: HS_Plac_14


title: HS_Plac_16


title: HS_Plac_17


title: HS_Plac_8

value: Control


title: HS_Plac_10


title: HS_Plac_12


title: HS_Plac_9


title: HS_Plac_7


title: HS_Plac_6


title: HS_Plac_4


title: HS_Plac_5


title: HS_Plac_2


title: WT2

description:
Library name: Sample 2
10x Genomics


title: CR+Immob-Salbutamol-right-105

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus. GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: quadriceps (leg muscle)

growth_protocol: All animal care and experimental procedures were approved by the Ethical Committee on Animal Care and Experimentation (Zeist, The Netherlands; approval reference number TNO-534, date: 18th of April 2023), and were in compliance with European Community specification regarding the use of laboratory animals. Ten-week-old C57BL/6J mice were obtained from Charles River Laboratories (L’Arbresle, France) and all mice were kept on chow maintenance diet (Ssniff Spezialdieten GmbH, Soest, Germany). Male mice were chosen due to their increased translatability for human muscle atrophy and since they have more muscle mass compared to female mice, making it easier to detect effects of immobilization and salbutamol treatment.

extract_protocol:
Total RNA was extracted from mouse quadriceps muscle samples using glass beads and RNA-Bee (Campro Scientific, Veenendaal, The Netherlands). RNA concentrations were determined using Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-40 million read counts per sample.
Clustering and DNA sequencing using Illumina NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: The number of mice was calculated with G*Power software (Heinrich Heine University Dusseldorf, Dusseldorf, Germany) using a one-way ANOVA with a significance threshold of 0.05, a power of 80% and an effect size f of 0.45 (as determined using pilot-study data). Upon arrival, mice were initially housed with at least one littermate in a temperature-controlled room on a 12h light-dark cycle (7:00 AM – 7:00 PM, light during daytime and dark during nighttime) and had free access to chow and water. Wood gnawing blocks and nesting material were provided. After two weeks, mice were housed individually for another two weeks and food intake was measured during the second week to assess the individual food intake. After this acclimatization period, the two-weeks intervention period started. Mice were divided into three groups which were matched for body weight and lean body mass, i.e. 1) A healthy reference group receiving ad libitum food; 2) An untreated control group receiving 60% of their normal food intake, unilateral immobilization and an osmotic pump filled with vehicle (PBS); and 3) A group receiving 60% of their normal food intake, unilateral immobilization and an osmotic pump releasing 1 mg salbutamol per kg body weight per day. Mice in the untreated control and salbutamol treated groups received an osmotic pump (ALZET model 1004, Charles River Laboratories, Massachusetts, USA) which was placed underneath the skin through a small incision on the left lateral side of the mouse, just above the hip. Pump placement was performed while using isoflurane inhalation anesthesia and as analgesia carprofen was added to the drinking water (0.067mg/ml) the day prior to pump placement till two days after pump placement. The pump was orientated in parallel to the spine of the mouse with its opening facing the cranial side of the body. The pumps were filled with either PBS (untreated control group) or salbutamol dissolved in PBS. The pumps were incubated in PBS at 37°C for 24 hours prior to inserting them in the mouse, to activate the osmotic pumps. After placing the pumps, the right legs of the mice in the untreated control and salbutamol treated groups were immobilized (fig. 1B). This was achieved through fixation using adhesive bandage and surgical tape. The quality of the immobilization was checked daily and the bandage and tape were replaced if they became loose. The mice in the untreated control and salbutamol treated group received 60% of their chow as individually assessed under ad libitum conditions, just before the dark phase, at 17.00 PM. Mice were terminated on day 14 by cervical dislocation and blood was immediately collected from the heart. Quadriceps and gastrocnemius muscles were isolated and snap-frozen in liquid nitrogen. Soleus muscles were fixated in formalin.

value: quadriceps (leg muscle)

value: CR

value: I

value: S

value: R


title: HS_Plac_20


title: CR+Immob-Salbutamol-right-104


title: HS_Plac_15


title: CR+Immob-Salbutamol-right-102


title: CR+Immob-Salbutamol-right-103


title: CR+Immob-Salbutamol-right-101


title: CR+Immob-Salbutamol-right-099


title: CR+Immob-Salbutamol-right-100


title: HS_Plac_13


title: CR+Immob-Salbutamol-right-095


title: CR+Immob-Salbutamol-right-097


title: CR+Immob-Salbutamol-right-094


title: CR+Immob-Salbutamol-right-098


title: HS_Plac_11


title: CR+Immob-Salbutamol-right-092


title: CR+Immob-Salbutamol-right-093


title: CR+Immob-Salbutamol-right-091


title: CR+Immob-Untreated-right-088


title: CR+Immob-Untreated-right-087


title: CR+Immob-Untreated-right-090


title: CR+Immob-Untreated-right-086


title: CR+Immob-Untreated-right-085


title: HS_Plac_1


title: HS_Plac_3


title: CR+Immob-Untreated-right-084


title: CR+Immob-Untreated-right-083


title: CR+Immob-Untreated-right-081


title: CR+Immob-Untreated-right-082


title: CR+Immob-Untreated-right-080


title: CR+Immob-Salbutamol-right-096


title: CR+Immob-Untreated-right-078


title: CR+Immob-Untreated-right-076


title: CR-Salbutamol-left-043

value: L


title: CR+Immob-Untreated-right-077


title: CR-Salbutamol-left-041


title: CR-Salbutamol-left-045


title: CR-Salbutamol-left-044


title: CR-Salbutamol-left-040


title: CR-Salbutamol-left-042


title: CR-Salbutamol-left-038


title: CR+Immob-Untreated-right-089


title: CR-Salbutamol-left-035


title: CR-Salbutamol-left-037


title: CR-Salbutamol-left-039


title: CR-Salbutamol-left-034


title: CR-Salbutamol-left-033


title: CR-Salbutamol-left-032


title: CR-Untreated-left-030


title: CR-Untreated-left-029


title: CR-Salbutamol-left-031


title: CR-Untreated-left-028


title: CR-Untreated-left-027


title: CR-Untreated-left-026


title: CR-Untreated-left-025


title: CR+Immob-Untreated-right-079


title: CR-Untreated-left-023


title: CR-Untreated-left-024


title: CR-Untreated-left-022


title: CR-Untreated-left-019


title: CR-Untreated-left-016


title: CR-Untreated-left-017


title: Healthy-right-075

value: H


title: CR-Untreated-left-021


title: CR-Untreated-left-020


title: Healthy-right-074


title: Healthy-right-072


title: CR-Salbutamol-left-036


title: Healthy-right-073


title: CR-Untreated-left-018


title: Healthy-right-069


title: Healthy-right-068


title: Healthy-right-067


title: Healthy-right-070


title: Healthy-right-065


title: Healthy-right-071


title: Healthy-right-063


title: Healthy-right-066


title: Healthy-right-062


title: AML980

type: genomic

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Human MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Illumina iScan System with default settings

data_processing: R package minfi ((version 1.50.0)

label: Cy3 and Cy5

source_name: AML PDX line

label_protocol: Standard Illumina protocol

growth_protocol: PDX cells were amplified in NSG mice and reisolated from bone marrow

extract_protocol: DNA was extracted using the standard protocol recommended for the Illumina Infiniumm MethylationEPIC BeadChip array

treatment_protocol: mice were not treated

tag: mutations panel

value: DNMT3A, TET2, NPM1, FLT3-TKD, ASXL1, FLT3-ITD

tag: karyotype

value: CN with NPM1 and FLT3-ITD

tag: disease status

value: ID

tag: age group

value: older adults

value: patient derived xenograft cells

tag: disease

value: acute myeloid leukemia


title: AML979

value: DNMT3A, NPM1, FLT3-ITD, IDH2, WT1

value: CN w/o FLT3-ITD


title: AML955

value: DNMT3A, NPM1, WT1

value: adults (unspecified)


title: AML896

value: DNMT3A, IDH2, FLT3-ITD, NPM1, ASXL2

value: CN

value: adults


title: AML842

value: NPM1, FLT3-ITD, DCLK1, DNMT3A

value: Trisomie 8, komplex aberranter Karyotyp

value: young adults


title: AML788

value: DNMT3A, NPM1, FLT3-ITD


title: AML579

value: DNMT3A, IDH1, NPM1, FLT3-ITD

value: R


title: AML415

value: FLT3-ITD, NPM1, DNMT3A, IDH1

value: CN with NPM1 and FLT3-ITD


title: AML959

value: NPM1, FLT3-ITD, DNMT3A, TET2

value: ND

value: patient derived xenograft cells


title: AML640

value: IDH1, NPM1, FLT3-ITD

value: older adults

value: acute myeloid leukemia


title: AML491

value: DNMT3A, BCOR, NRAS, KRAS, ETV6, PTPN11, RUNX1


title: AML573

value: DNMT3A, IDH2, FLT3-ITD, WT1, MLL-PTD


title: AML393

value: BCOR, KRAS

value: adults


title: AML981

value: DNMT3A, TET2, NPM1, FLT3-ITD, FLT3-TKD, WT1, ASXL1


title: garlic-derived exosomes

city: ChongqingPR China

first: Li

last: Yin

address: 69 Hongguang Road Huaxi Street, Banan District

department: College of Pharmacy and Biological Engineering

institute: Chongqing University of Technology

data_processing:
Quality control:Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
Reads mapping to the reference sequence:The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to   analyze their expression and distribution on the reference.
Known miRNA alignment:Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified   software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the   secondary structures.
Remove tags from these sources: To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, TRNA, snRNA, and snoRNA,   small RNA tags were mapped to Repeat Masker, Rfam database or those types of data from the specified species itself.
Small RNA annotation summary:Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA   tags may be mapped to more than one category.
Assembly: miRBase20.0
Supplementary files format and content: tab-delimited text files include readcount and tpm values for each Sample

organism: Allium sativum

source_name: bulb

extract_protocol:
After total RNAs were extracted from GDE  by the exoRNeasy Maxi Kit (Qiagen), and the quality and concentration of the RNAs were checked using an Agilent 2200 UV spectrophotometer.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing   libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.)   following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Ultracentrifugation combined with PEG precipitation was used to isolate exosomes from garlic purchased from a local market.

tag: rna population

value: exosomal miRNA

value: bulb


title: AML669

value: KRAS

value: MLL-AF9 (KMT3A/MLLT3)


title: Healthy-right-064

value: quadriceps (leg muscle)

value: H

value: R


title: AML664

value: ND

value: pediatric


title: Healthy-right-061


title: 16-20 h embryo, ft-GFP[C], Replicate 3, NovaSeq X Plus (ChIP)

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 3 (ChIP)

data_processing:
ChIP-seq reads were trimmed using Trimmomatic v0.33 with default settings.  ChIP-seq reads were algined to dm6 genome using Burrows-Wheeler Aligner v0.7.16a with default settings. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequnced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format using HOMER 4.11.1.
Peaks were called using MACS v2.1.2 with the significance cut-off q-value <= 0.01 and were annotated with ChIPseeker and motifs identified with HOMER v4.11.1.
Assembly: dm6
Supplementary files format and content: bigWig

organism: Drosophila melanogaster

source_name: 16-20 h embryo

growth_protocol: Drosophila were reared at 25C on standard fly food.  Embryos were collected and aged at 25C on grape juice agar plates.

extract_protocol:
Embryos were collected for 4 hrs, aged for 16 hrs at 25C, and dechorionated in 50% bleach.  Eye-brain complexes were dissected from 3rd instar larvae in ice-cold PBS.  Tissues were crosslinked in 2 mM EGS for 45 min, followed by paraformaldehyde for 15 min, quenched, washed, flash frozen in liquid nitrogen and stored at -80C until use.  50 ml settled embryos or 100 eye-brain complexes were used per sample.  Crosslinked tissues were homogenized by douncing, followed by nuclear lysis and sonication of the genomic DNA using a Bioruptor or Qsonica Q700 sonicator.  Fragmented chromatin was incubated with anti-GFP or anti-FLAG antibodies and precipitated using MagnaChIP A+G beads or Dynabeads G.
ChIP-seq libraries were prepared from 10 ng DNA.  DNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends.  Size selection was performed with AMPure beads to limit the fragment size to 150-700 bp.  Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags.

value: 16-20 h embryo

value: Ft-GFP[C]

tag: chip antibody

value: a-GFP (ab290)


title: Gcn4_MOT1AA SM_induced_with Rapamycin_Replicate 4

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 49 Convent Drive Bldg49/Rm 6A30

institute: NIH, NICHD

description:
Library name: PM166_106
Biological replicate 4

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of TBP, Rpb1, Gcn4, and TFIIB were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Assembly: SacCer3
Supplementary files format and content: Bigwig files

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.3 to 0.4) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), cells were treated with rapamycin  at 1µg/ml for 90 min before adding SM at 1µg/ml or no SMsulfometuron (SM) for 25 min to induce Gcn4.

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-TBP (from Joseph Reese's lab), anti-Rpb1 (Biolegend, Cat#664906), anti-Gcn4 (in-house),and anti-TFIIB (from Stephen Buratowski's lab). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

value: Whole cells

tag: cell line

value: Gcn4 (lab generated)

tag: genotype

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4

value: Formaldehyde-fixed and sonicated


title: AML538

value: DNMT3A, IDH1

value: CN w/o FLT3-ITD

value: adults (unspecified)

tag: tissue

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML388

value: KRAS

value: ID

value: older adults


title: Gcn4_MOT1AA SM_induced_with Rapamycin_Replicate 3

description:
Library name: PM166_105
Biological replicate 3

tag: cell type

tag: treatment


title: AML663

value: FLT3-ITD, WT1

value: ND

value: R


title: Gcn4_MOT1AA SM_induced_with Rapamycin_Replicate 2

description:
Library name: PM166_104
Biological replicate 2


title: 16-20 h embryo, ft-GFP[C], Replicate 2, NovaSeq X Plus (Input)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 2 (Input)

value: 16-20 h embryo

value: Ft-GFP[C]


title: AML372

value: TP53, KRAS

value: complex including Monosomie 17, Monosmie 7, ETV-Deletion, ATM-Deletion

value: adults


title: 16-20 h embryo, ft-GFP[C], Replicate 2, NovaSeq X Plus (ChIP)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 2 (ChIP)

value: a-GFP (ab290)


title: AML661

value: DNMT3A, BCOR, NRAS, ETV6, PTPN11, RUNX1, JAK1, EZH2


title: AML356

value: pediatric


title: Gcn4_MOT1AA SM_induced_with Rapamycin_Replicate 1

description:
Library name: PM166_103
Biological replicate 1

value: Whole cells

value: Gcn4 (lab generated)

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4

value: Formaldehyde-fixed and sonicated


title: AML346

value: interstitielle 5q Del / interstitielle 13q Del

value: patient derived xenograft cells

value: acute myeloid leukemia


title: 16-20 h embryo, ft-GFP[C], Replicate 3, NovaSeq X Plus (Input)

description: Library name: 16-20 h embryo, ft-GFP[C], Replicate 3 (Input)


title: Gcn4_WTAA SM_induced_with Rapamycin_Replicate 4

description:
Library name: PM166_98
Biological replicate 4

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6


title: Gcn4_WTAA SM_induced_with Rapamycin_Replicate 3

description:
Library name: PM166_97
Biological replicate 3


title: AML358

value: ND

value: R


title: Gcn4_WTAA SM_induced_with Rapamycin_Replicate 2

description:
Library name: PM166_96
Biological replicate 2


title: Gcn4_WTAA SM_induced_with Rapamycin_Replicate 1

description:
Library name: PM166_95
Biological replicate 1


title: 16-20 h embryo, ft^fd5-5/ft^X13, Rep4, NovaSeq X Plus

description:
Library name: ftfd_R4
Column name in McNeill_Ft_raw_gene_counts.txt: ftfd_R4

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

growth_protocol: Embryos were collected at aged at 25 C on grape agar plates.

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds.  cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases

value: 16-20 h embryo


title: 16-20 h embryo, w^1118, Rep1, NovaSeq X Plus

description:
Library name: w1118_R1
Column name in McNeill_Ft_raw_gene_counts.txt: w1118_R1


title: 16-20 h embryo, ft^fd5-5/ft^X13, Rep2, NovaSeq X Plus

description:
Library name: ftfd_R2
Column name in McNeill_Ft_raw_gene_counts.txt: ftfd_R2


title: 16-20 h embryo, ft^fd5-5/ft^X13, Rep3, NovaSeq X Plus

description:
Library name: ftfd_R3
Column name in McNeill_Ft_raw_gene_counts.txt: ftfd_R3


title: Gcn4_WTAA uninduced_with Rapamycin_Replicate 4

description:
Library name: PM166_94
Biological replicate 4


title: 16-20 h embryo, ft^fd5-5/ft^X13, Rep1, NovaSeq X Plus

description:
Library name: ftfd_R1
Column name in McNeill_Ft_raw_gene_counts.txt: ftfd_R1


title: 16-20 h embryo, w^1118, Rep2, NovaSeq X Plus

description:
Library name: w1118_R2
Column name in McNeill_Ft_raw_gene_counts.txt: w1118_R2


title: PBMCs_HC_rep4

type: RNA

last: Zhou

address: 61 Middle University Road，Huxi Street

department: College of Public Health

description: PBMCs at 4, HC group

hyb_protocol: 5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 25× Fragmentation Buffer and 10× Gene Expression Blocking following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Gex Hybridization buffer was added to the fragmentation mixture and hybridized to Sino Human ceRNA array V3.0 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G5761A) using one color scan setting for 1x44k array slides.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The Processed_data.txt contains fold-change data.

source_name: PBMCs from the healthy individual

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using RNA 6000 Nano Assay Kit (RNA Series II Kit, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The peripheral blood mononuclear cells (PBMCs)

extract_protocol: Total RNA was isolated using RNeasy Total RNA Isolation Kit (Qiagen,  GmBH, Germany) according to the manufacturer’s instructions.

value: PBMCs

tag: gender

value: male

tag: age

tag: subject status

value: healthy individual


title: FXYD3 knockout LS174T_1

city: Hangzhou

first: Qingqing

last: Wang

state: Zhejiang

address: 866 Yu Hang Tang Road

department: Institute of Immunology

institute: Zhejiang University

description: Library name: KO1

data_processing:
Raw RNA sequencing fastq format data were processed through in-house perl scripts and clean data were obtained by removing reads containing adapter or poly-N and low-quality reads from raw data. Reads were then mapped to mm10 RefSeq genes downloaded from the UCSC Table Browser using Hisat2(v2.0.5). FeatureCounts(v1.5.0-p3) was used to count the reads numbers mapped to each gene. And FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length and reads count mapped to the gene.
Assembly: mm10
Supplementary files format and content: csv file inculde raw counts for each sample

source_name: Colon

extract_protocol:
Approximately 2000000 cells per sample were pelleted and lysed in TRIzol reagent and cryopreserved at -80 °C, followed by RNA extraction.
RNA libraries for Rna-seq were prepared uding NEBNext UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations.

value: Colon

value: Human Colorectal Adenocarcinoma cells;goblet-like cell

value: FXYD3 knockout


title: FXYD3 knockout LS174T_3

description: Library name: KO3


title: Gcn4_WTAA uninduced_with Rapamycin_Replicate 3

description:
Library name: PM166_93
Biological replicate 3

value: Whole cells


title: FXYD3 knockout LS174T_2

description: Library name: KO2


title: PBMCs_HC_rep1

description: PBMCs at 1, HC group

value: female


title: Rpb1_MOT1AA DA_induced_with Rapamycin_Replicate 4

description:
Library name: PM162_122
Biological replicate 4

source_name: Whole yeast cells

value: Whole yeast cells

tag: strain

value: anti-Rpb1 (Biolegend, Cat#664906)

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4


title: PBMCs_HC_rep3

description: PBMCs at 3, HC group


title: AML602

value: DNMT3A, TET2, NPM1, FLT3-ITD, CEBPA, JAK3

value: complex

value: adults

value: patient derived xenograft cells


title: PBMCs_CHB_rep4

description: PBMCs at 4, CHB group

source_name: PBMCs from the CHB patient

value: patient with chronic hepatitis B


title: PBMCs_HC_rep5

description: PBMCs at 5, HC group


title: Gcn4_WTAA uninduced_with Rapamycin_Replicate 2

description:
Library name: PM166_92
Biological replicate 2

value: Gcn4 (lab generated)

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6

value: Formaldehyde-fixed and sonicated


title: PBMCs_CHB_rep1

description: PBMCs at 1, CHB group

value: PBMCs


title: PBMCs_CHB_rep3

description: PBMCs at 3, CHB group

value: male


title: LS174T_2

description: Library name: WT2

value: Colon

value: Human Colorectal Adenocarcinoma cells;goblet-like cell

value: WT


title: Gcn4_WTAA uninduced_with Rapamycin_Replicate 1

description:
Library name: PM166_91
Biological replicate 1

value: Whole cells


title: Rpb1_MOT1AA DA_induced_with Rapamycin_Replicate 2

description:
Library name: PM162_120
Biological replicate 2

value: Whole yeast cells


title: PBMCs_CHB_rep2

description: PBMCs at 2, CHB group


title: Rpb1_MOT1AA SM_induced_with Rapamycin_Replicate 3

description:
Library name: AGH151_9
Biological replicate 3

value: anti-Rpb1 (Biolegend, Cat#664906)


title: Monocyte, LPS stimulated, high inflammation risk, patient6

city: Wuhan

first: Jiyu

last: Zhang

state: Hubei

address: 1277 Jiefang Road, Jianghan District, Wuhan 430022, Hubei, China

institute: Huazhong University of Science and Technology

description: Library name: H6L

data_processing:
Raw sequencing data were first filtered by Trimmomatic (version 0.39). Low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed using fastp (version 0.23.1).
Clean reads were mapped back to the human genome Homo_sapiens. GRCh38 using STAR software (version 2.5.3a).
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then FPKMs were calculated.
Assembly: GRCh38
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

source_name: blood

growth_protocol: Monocytes were cultured in 96-well flat plates with RPMI 1640 basic  at 37°C and 5% CO2. 10% fetal bovine serum and 10 μg/mL gentamicin were added to the culture.

extract_protocol:
Total RNA was extracted from cell pellets using TRIzol Reagent (Invitrogen, 15596026) according to the manufacturer's instructions. A total of 1 μg RNA per sample was used for stranded RNA-sequencing library construction.
RNA-sequencing library using the KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog no. DR08402) following the manufacturer’s instructions.

treatment_protocol: After purification with magnetic cell sorting, monocytes were either processed immediately as fresh samples or stimulated with LPS (10 ng/mL) for 6 hours before processing.

value: blood

value: monocyte

value: After isolating with magnetic cell sorting, monocytes were stimulated with 10 ng/ml LPS for 6 hours


title: PBMCs_HC_rep2

institute: Chongqing Medical University

description: PBMCs at 2, HC group

value: healthy individual


title: LS174T_1

description: Library name: WT1


title: Mouselungs_Bleo_Vehicle_3

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

description:
Library name: Mouselungs_Bleo_Vehicle_3
10X Genomics

data_processing:
The demultiplexing, gene counting and alignment processes were performed using CellRanger software (v 7.0).
Doublets were removed for each sample. Normalization was performed with help of Seurat (v4.4.1) R package and integration of all sequenced samples was performed using Harmony (v0.1) R package.
Each cell cluster identified was annotated by canonical cell surface markers.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Lungs

extract_protocol:
Nuclei were isolated from frozen mouse lungs (n=12, weighing approximately 50 mg) by physical dissociation using a glass dounce homogenizer and were sorted using fluorescence-activated cell sorting (FACS) based on DAPI-positive fluorescence to obtain a single nuclei population. Nuclei concentration was manually determined using DAPI staining and hemocytometer and adjusted to 1000 nuclei/uL.
Single nuclei RNA sequencing libraries were generated using the 10X Genomics Chromium Instrument and Chromium Next GEM Single Cell 3’ Reagent Kits (v3.1) from approximately 4000 nuclei. Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).

treatment_protocol: Lungs were extracted with mice instilled with PBS or bleo treated with/without EphB4 Inhibitor (NVP-BHG712) and stored in liquid nitrogen until use. Total 12 mouse lungs (n=3 PBS+vehicle, n=3 PBS+ NVP-BHG712, n=3 bleomycin+vehicle and n=3 bleomycin+NVP-BHG712) were subjected to single nuclei RNA sequencing.

value: Lungs

tag: batch


title: Rpb1_MOT1AA SM_induced_with Rapamycin_Replicate 2

description:
Library name: AGH151_8
Biological replicate 2

value: MATa his3-del1 leu2-del0 met15-del0 ura3-del0 fpr1del::kanMX4 tor1-1 RPL13A-2xFKBP12::his3MX6 MOT1-FRB-GFP ::hphMX4


title: Mouselungs_Bleo_Vehicle_2

description:
Library name: Mouselungs_Bleo_Vehicle_2
10X Genomics


title: Rpb1_MOT1AA DA_induced_with Rapamycin_Replicate 3

description:
Library name: PM162_121
Biological replicate 3


title: Rpb1_MOT1AA DA_induced_with Rapamycin_Replicate 1

description:
Library name: PM162_119
Biological replicate 1


title: Rpb1_MOT1AA uninduced_with Rapamycin_Replicate 4

description:
Library name: PM162_118
Biological replicate 4


title: Monocyte, LPS stimulated, high inflammation risk, patient5

description: Library name: H5L