title: SMC_diff

city: Córdoba

first: Melina

middle: Mara

last: Musri

state: Córdoba

address: Friuli 2434

country: Argentina

institute: Instituto de Investigación Médica Mercedes y Martín Ferreyra

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality reads using Trim Galore version 0.6.7 and cutadapt version 3.5. (parameters- Trimming mode: single end, Quality Phred score cutoff: 20, Maximum trimming error rate: 0.1 (default), Minimum required adapter overlap (stringency): 1 bp
Quality control was performed before and after adapter trimming using FASTQC version 0.12.0
Reads were aligned to human genome (GRCh38) using bowtie2 version 2.4.2 on default settings, single end.
Counts were generated from alignment files using featureCounts version 2.0.1 (parameters-  Level : meta-feature level, Paired-end : no, Multimapping reads : not counted, Multi-overlapping reads : not counted, Min overlapping bases : 1
Assembly: GRCh38
Supplementary files format and content: tab delimited file includes raw counts for each sample

source_name: Pulmonary artery

growth_protocol: Human Pulmonary Artery Smooth Muscle Cells (hPASMC)  were grown in Sm-bullet medium (Lonza) for hPASMC supplemented with 10% FBS in a mammalian cell incubator in standard conditions (95% humidity 5% Carbon Dioxide at 37°C)

extract_protocol:
Extraction was performed using TRIZOL followed by Chloroform / Isopropanol extraction. Total RNA was used for library preparation.
RNA libraries were prepared using the TruSeq RNA Library Prep Kit by Illumina following manufacturer's instructions

treatment_protocol: Undifferentiated cells (D0) were harvested 24 hours after plating, at a confluency of 70-80%. For cells at the beginning of differentiation (D2), cells were mantained for extra 48 hours and were allowed to reach full plate confluency prior to harvesting.

value: Pulmonary artery

value: hPASMC (Lonza)

value: Smooth muscle cell

value: Normal

value: Confluent


title: 3wAIR_F3_RNAseq

status: Public on Sep 18 2024

type: SRA

city: Minneapolis

first: Natalia

last: Tretyakova

state: Minnesota

address: 2231 6th St SE Room 2-147

department: Medicinal Chemistry

country: USA

institute: University of Minnesota

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3S-FC3_S6

library_source: transcriptomic

data_processing:
Trimmomatic to remove low quality bases and adapter contamination
HISAT2 to map read pairs to the mm10 genome
Samtools to sort mapped reads by query name and filter by mapping quality
featureCounts to quantify gene expression
edgeR to analyze gene expression data
Assembly: mm10
Supplementary files format and content: CSV with the test results for differential gene expression. Contains Ensembl ID, base mean expression, log2(fold change), nominal P-values, and FDR values

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples from 9 mice were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS) by the University Flow Cytometry Resource at the University of Minnesota using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was saved for downstream analyses. A portion of the cell pellet (1.25 x 105 – 5 x 105 cells) was set aside to isolate protein. The remaining sample was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.
Total RNA samples were converted to Illumina sequencing libraries using SMARTer Stranded Total RNA-Seq Kit – Pico Mammalian Input (Takara Bio USA, Mountain View CA).
Alveolar type II epithelial cells (Type II pneumocytes) were isolated according to published procedures. Briefly, the lungs were perfused with 10 mL cold phosphate buffered saline (PBS) before enzymatic digestion with 2 mL of dispase infused into the lung, after which they were removed and incubated in an additional 2 mL of dispase for one hour. The lungs were then manually disintegrated and the resulting cell suspension labeled with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32 (Thermo Fisher Scientific). Samples from 9 mice were pooled to include three sets of lungs per sample for a total of three samples for FACS separation. Type II pneumocytes were isolated by negative selection and thus identified as the unlabeled cell population. Type II pneumocytes were also gated as sideward scatter high (SSChigh) cell population which minimizes contamination with lymphoid cells by selecting cells with a higher granularity. The cells were separated by fluorescence activated cell sorting (FACS) by the University Flow Cytometry Resource at the University of Minnesota using a BD FACS Aria II P07800142 (BSL2) (BD Biosciences, San Jose, CA). Following isolation via FACS, Type II pneumocytes were pelleted by centrifugation. The samples were first centrifuged for 12 min at 200 x g and 4°C and the supernatant was removed, except for the bottom 1 mL, which was transferred to a 1.7 mL Eppendorf tube. To this tube, 500 µL of PBS was added, and the tube was centrifuged for 12 min at 200 x g at 4°C. The supernatant was removed while the bottom 100 μL was saved. One mL of PBS was added to the tube, and the sample was centrifuged for 12 min at 800 x g and 4°C. After this final centrifugation, all supernatant is removed, and the cell pellet was saved for downstream analyses. A portion of the cell pellet (1.25 x 105 – 5 x 105 cells) was set aside to isolate protein. The remaining sample was used to isolate DNA and RNA using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Hilden Germany) according to the man-ufacturer’s instructions.

tag: tissue

value: Lung

tag: Sex

value: female

tag: cell type

value: Alveolar type II epithelial cells

tag: treatment

value: 3 weeks filtered air


title: SMC_undiff

organism: Homo sapiens

tag: cell line

tag: genotype

value: Proliferative


title: post 10wCS_F2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_FS_DEG_Test.csv.gz
14-f-cs-2_S110

value: 10 weeks cigarette smoke folowed by 4 weeks filtered air


title: 3wAIR_F1_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3S-FC1_S4


title: BlisterFluid36, SCAR, rep1

city: Perth

first: Andrew

last: Gibson

state: Western Australia

address: Building 390, Discovery Way, Murdoch University

country: Australia

institute: Murdoch University

library_source: transcriptomic single cell

data_processing:
Single-cell sequencing data were processed using CellRanger v6.1.2 to demultiplex individual cell barcodes, remove PCR duplicates, and align reads to the reference GRCh38 human transcriptome. The individual hashes within each 10x run were further demultiplexed using Souporcell to cluster samples based on SNPs in the RNA-seq reads. The hashtag negatives or doublets, as well as cells with >50% mitochondrial content were removed to filter low quality, dead, or dying populations for initial QC, with a second pass filter excluding apoptotic populations characterized by a low percentage of ribosomal genes and a high percentage of mitochondrial genes, using a defined mitochondrial-ribosomal RNA ratio of >0.47. A standardized mitochondrial DNA threshold of 10% is recommended for human tissue, which was met by 98% of ‘live’ cells identified. The remaining 2% of cells were excluded. Downstream transcriptome-based graph clustering and PCA with cell phenotype calling were performed using R Seurat v4.1.1 package, without input of TCR, BCR, mitochondrial, ribosomal, or sex-linked genes to avoid bias due to known expression variability. Batch correction for 10x run, sample type (skin or blister fluid), and cell cycle phase were performed using harmony. Experimental doublets were identified and removed using a majority consensus benchmark of three independent bioinformatic algorithms (DoubletFinder, scDBLfinder, scDS).
Assembly: GRCh38
Supplementary files format and content: Normalized_Counts.csv : This is the normalized count matrix derived from Seurat's normalize method for all the single-cells included in the project.
Supplementary files format and content: Metadata_CITESeq+TCR.tsv : This tab-delimited text file contains for each cell barcode - sample meta-data  (such as age, sex, etc.) , CITESeq antibody counts and TCR alpha/beta chains.

molecule: polyA RNA

source_name: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 23, blister fluid

extract_protocol:
Cryopreserved skin biopsies were thawed and digested using published methods optimized for lymphoid cell recovery and single-cell sequencing (RPMI 1640 medium with 10% FBS, 1mg/ml collagenase P and 40ug/ml DNAase I with agitation for 90 minutes). Tissue lysates were washed and passed through a 70µm Flowmi™ Cell Strainer. Single-cell suspensions of enzymatically-digested skin or thawed unprocessed blister fluid were then subject to surface antibody staining for a panel of up to 137 functional and surface lineage markers in the TotalSeq™-C Human Universal Cocktail, V1.0 (Biolegend) as per manufacturer’s protocol. 1µl of the appropriate hashtag antibody was also added, with subsequent incubation for 30mins at 4°C. Each cell-antibody cocktail was then resuspended in 3.5ml cell staining buffer and washed three times in PBS before cells were passed through a 70µm Flowmi™ Cell Strainer. Cell count and viability were recorded and cells were diluted as per the manufacturer’s instruction for loading onto the 10X Chromium Next GEM chip K.
Cells were loaded onto the chromium Next GEM chip K chip at the manufacturer (10x Genomics) recommended concentration and single-cell libraries made using a chromium controller and Chromium Next GEM Single Cell 5' Reagent Kit, Version 2.0 (10x Genomics) as per manufacturer instruction (https://www.10xgenomics.com/support/single-cell-immune-profiling/documentation/steps/library-prep/chromium-single-cell-5-reagent-kits-user-guide-v-2-chemistry-dual-index-with-feature-barcoding-technology-for-cell-surface-protein-and- immune-receptor-mapping), with a target of 1,000-20,000 cells. 5’ libraries were then sequenced using the Illumina NovaSeq 6000 platform.

value: Female


title: post 10wCS_F1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_FS_DEG_Test.csv.gz
14-f-cs-1_S109


title: BlisterFluid35, SCAR, rep1

value: Hash 1_SCAR patient 18, blister fluid / Hash 2_SCAR patient 23, blister fluid


title: 3wCS_F2_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-FS2_S11

value: 3 weeks cigarette smoke


title: post 10wAIR_M3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-air-3_S114

value: male

value: 14 weeks filtered air


title: BlisterFluid34, SCAR, rep1


title: 3wCS_F3_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-FS3_S12


title: agshEV71-h1#1-Input

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

country: China

institute: Wuhan institue of virology, CAS

data_processing:
Fo small RNAs, libraries of small RNAs were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s protocols, and then sequenced by Illumina HiSeq 2000 at Bioacme (Wuhan, China). Quality control and adapter trimming process were performed using Trim Galore (v0.6.4) with default parameters, and reads length between 17 and 70 were used for subsequent analyses. The sequenced reads were aligned to the human genome (GRCh38) by using Bowtie2 (v2.3.5.1). Reads that cannot be aligned to the human genome were then aligned to agshRNA. The sequences and lengths of reads aligned to agshRNA were then determined using an in-house script. Reads mapped to genome were further categorized as miRNA, tRNA, snoRNA etc. by using htseq-count (v0.11.2).
For total RNAs, libraries of total RNAs were constructed using MGIEasy RNA Library Preparation Kits (BGI) according to manufacturer’s protocols, and then sequenced by MGISEQ2000 (BGI) at Wuhan Institute of Virology, CAS. Quality control and adapter trimming were performed using Trim Galore (v0.6.4) with default parameter. All reads were mapped to the human genome (GRCh38) using Hisat2(v2.1.0) and then annotated using htseq-count(v0.11.2)
Assembly: Human genome (GRCh38)
Supplementary files format and content: small RNA sequencing: bed format
Supplementary files format and content: Transcriptome sequencing: expression matrix counted by htseq-count

source_name: Human  HEK293T cells

extract_protocol:
For small RNA sequencing, Total RNA was extrated using Trizol regent accounding to the manufacturer's instructions. For transcriptome sequencing, RNA was extracted using Total RNA kit according to the manufacturer's instuctions
TruSeq Small RNA Library Preparation Kits (Illumina) (for small RNAs); MGIEasy RNA Library Preparation Kits (BGI) (for total RNAs)
Illumina HiSeq 2000 (for small RNAs); MGISEQ2000 (BGI) (for total RNAs)

value: Human  HEK293T cells


title: post 10wAIR_M2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-air-2_S113


title: BlisterFluid33, SCAR, rep1

source_name: Hash 1_SCAR patient 10, blister fluid / Hash 2_SCAR patient 12, blister fluid

value: Pooled Male and Female


title: post 10wAIR_M1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-air-1_S112


title: 3wCS_M3_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-MS3_S9


title: 3wCS_M2_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-MS2_S8


title: 3wAIR_M1_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3S-MC1_S1


title: post 10wCS_M3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-cs-3_S117


title: b16_shS_wts_IFNg-2

city: Shanghai

first: Liu

last: Yongzhong

institute: Shanghai Cancer Institute

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low qulity base with Trimmomatic
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The processed count data is provided as a tab-delimited text file (.txt) containing gene IDs as rows, sample names as columns, and the corresponding gene expression values. The counts were generated using featureCounts and normalized using DESeq2
Assembly: GRCm39
Supplementary files format and content: count.matrix.txt

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by TRIzol and subjected to RNA-seq analysis. 1ug of total RNA was used for the construction of sequencing libraries.
Total RNA samples in each experiment were submitted to Tiangen Inc. for sequencing. Standard mRNA library preparation kit was used for library preparation. Paired-end sequencing was performed on Illumina HiSeq 2500.

treatment_protocol: Tumor cells were treated with or without IFNγ (10ng ml-1) for 24h.

value: sdc1 knockdown+sdc1 wt

value: stimulated with IFNr (10ng/ml)


title: 3wAIR_M2_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3S-MC2_S2


title: 3wAIR_M3_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3S-MC3_S3


title: post 10wCS_M2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-cs-2_S116


title: BlisterFluid30, SCAR, rep1

source_name: Hash 1_SCAR patient 2, blister fluid / Hash 2_SCAR patient 17, blister fluid


title: b16_shS_wts_IFNg-1


title: BlisterFluid31, SCAR, rep1

value: Hash 1_SCAR patient 10, blister fluid / Hash 2_SCAR patient 12, blister fluid


title: b16_shS_IFNg-2

value: sdc1 knockdown


title: 3wCS_F1_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-FS1_S10

value: Lung


title: post 10wCS_M1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_14w_MS_DEG_Test.csv.gz
14-m-cs-1_S115


title: mc38_shS_ect_IFNg-2

value: sdc1 knockdown+ect mutant


title: 10wAIR_F3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_FS_DEG_Test.csv.gz
10-f-air-3_S98

value: female

value: Alveolar type II epithelial cells

value: 10 weeks filtered air


title: agshEV71-h1#1-IP


title: mc38_shS_ect_IFNg-1


title: mc38_shS_c30_IFNg-2

value: sdc1 knockdown+c30 mutant


title: 10wAIR_F2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_FS_DEG_Test.csv.gz
10-f-air-2_S97


title: mc38_shS_c30_IFNg-1


title: BlisterFluid28, SCAR, rep1

value: Hash 1_SCAR patient 2, blister fluid / Hash 2_SCAR patient 17, blister fluid

value: Female


title: BlisterFluid32, SCAR, rep1


title: 3wCS_M1_RNAseq

description:
Project_011_Raw_Counts.txt.gz
Project_011_DEG_Test.csv.gz
3-MS1_S7

value: 3 weeks cigarette smoke


title: BlisterFluid27, SCAR, rep1

source_name: Hash 1_SCAR patient 24, blister fluid / Hash 2_SCAR patient 25, blister fluid


title: mc38_shS_IFNg-2


title: mc38_shS_IFNg-1


title: BlisterFluid26, SCAR, rep1

value: Hash 1_SCAR patient 24, blister fluid / Hash 2_SCAR patient 25, blister fluid


title: 10wAIR_F1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_FS_DEG_Test.csv.gz
10-f-air-1_S96


title: 10wCS_F3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_FS_DEG_Test.csv.gz
10-f-cs-3_S101

value: 10 weeks cigarette smoke


title: SHSdc1IFNr-3

first: Yun

last: Liu

address: No. 2200, Xietu Road, Xuhui District, Shanghai, China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and trimming low quality base with Trimmomatic.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Htseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: count.matrix.txt: Tab-delimited text file includes counts for each Sample.

source_name: B16 melanoma

growth_protocol: B16 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics with 5% CO2 at 37C.

treatment_protocol: Shsdc1 or control shRNA-transfected B16 tumor cells were treated with or without IFNγ (10ng ml-1) for 24h.

value: B16 melanoma


title: SHSdc1IFNr-2


title: 10wCS_F2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_FS_DEG_Test.csv.gz
10-f-cs-2_S100


title: SHSdc1IFNr-1


title: SHRFPIFNr-3

value: RFP control knockdown


title: b16_shS_IFNg-1


title: SHRFPIFNr-2


title: 10wCS_F1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-f-cs-1_S99


title: SHSdc1-3

value: unstimulated


title: Skin5, SCAR, rep1

source_name: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, skin biopsy


title: SHRFPIFNr-1

value: stimulated with IFNr (10ng/ml)


title: 10wAIR_M3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-air-3_S103

value: male


title: SHSdc1-2

value: sdc1 knockdown


title: Skin4, SCAR, rep1

value: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, skin biopsy


title: SHSdc1-1


title: 10wAIR_M2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-air-2_S102

value: Lung


title: SHRFP-2


title: SHRFP-3


title: Skin3, SCAR, rep1

source_name: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, PBMC


title: 10wAIR_M1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-air-1_S118


title: SHRFP-1


title: Skin2, SCAR, rep1

value: Hash 1_SCAR patient 26, skin biopsy / Hash 2_SCAR patient 26, PBMC


title: 10wCS_M3_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-cs-3_S106

value: Alveolar type II epithelial cells


title: BlisterFluid25, SCAR, rep1

value: Pooled Male and Female


title: Skin1, SCAR, rep1


title: Trip_30min_A12_H2AZ_CnT

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

library_source: genomic

data_processing:
ChIP-seq analysis. Reads were trimmed using Cutadapt and aligned to both hg19 and dm6 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Scale factors were calculated for each sample by dividing the minimum number of dm6 reads for a given antibody by number of dm6 reads for each sample using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Reads were trimmed using Cutadapt and aligned to both hg19 and mm10 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Deduplicated read counts were used to calculate the human:mouse ratio, which was then used to calculate scaling factors for samples performed side by side with the same antibody. The scale factor was calculated by dividing the human:mouse read ratio for each sample using a given antibody by the maximum human:mouse read ratio from samples using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Assembly: hg19
Supplementary files format and content: bigwig coverage files
Library strategy: CUT&TAG

molecule: genomic DNA

growth_protocol: Human T47D A1-2 (Archer et al., 1994) and MCF-7 cell were grown in MEM (Gibco 10370) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  HeLa, SW-13, U2OS, primary human fibroblast and mouse C127 cells were grown DMEM (Gibco 11965-092) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  K562 cells were grown in suspension in RPMI Medium 1640 (Gibco 11875-093) supplemented with 10% fetal bovine serum (Gibco 26140-079), GlutaMAX (Gibco 3505), HEPES (Sigma H0887), and Penicillin/Streptomycin (Sigma P0781).  All cells were cultured in a humidified incubator at 37°C with 5% CO2 in the indicated growth medium with media changed every 2-3 days.  Cells were seeded in new tissue culture treated dishes when 80% confluency reached.

extract_protocol:
Cells were fixed in PBS with 1% methanol-free formaldehyde (ThermoFisher Scientific 28906) at 37C for 10 min and quenched with glycine (0.125M) for 5 min at room temperature.  After glycine quench, cells were washed three times and scraped into ice-cold PBS and pelleted by centrifugations at 500g for 5 min.  Compact cell pellets were resuspended in MNase swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 0.5 mM PMSF, and 1x cOmplete EDTA-free protease inhibitors (PIC)) (Roche), incubated on ice for 10 min then subjected to Dounce homogenization using 20-strokes with “tight” pestle (Duran Wheaton Kimble, 357542).  Nuclei were sedimented through digestion buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose, 0.5 mM PMSF, and PIC) by centrifugation for 930g for 7 min at 4C. Nuclei pellets were fully resuspended in digestion buffer containing 3.3 mM CaCl2 and digested with MNase (0.75U/1x10ˆ6 cells, Worthington, cat#) at 37C for 15min. MNase fragmentation was stopped by addition of 10 mM EGTA and incubation for 5 min on ice.  Digested nuclei were centrifuged at 930g for 7 min at 4C and compact nuclei pellets resuspended in 20 volumes (v/v) ChIP Shearing buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS containing spermidine, PIC and PMSF) and incubated on ice for 10 min.  Samples were subjected to sonication using PIXUL Multi-Sample Sonicator (Active Motif) at 12C using the following parameters: Pulse [N]: 50; PRF [kHz]: 1.00; Process Time: 10 min; Burst Rate [Hz]: 20.00.  After sonication, fragmented chromatin was recovered in supernatant after centrifugation at 18,000g for 10 min with extent of fragmentation determined by agarose gel electrophorese prior to immunoprecipitation.  The concentration of fragmentated chromatin determined by Bradford assay.  Fragmentated chromatin was diluted in two-fold in 2xIP buffer (20 mM Tris-HCl pH 8.0, 300 mM NaCl, 2 mM EDTA, 20% Glycerol, 1% Triton X-100, 0.5 mM PMSF and PIC) and immunoprecipitation performed with the indicated antibodies at a ratio of 1 ug antibody per 200 ug chromatin.  Equal amounts of Spike-IN antibody and Drosophila chromatin (Active Motif 61686 and 53083) added to each immunoprecipitation for normalization.  Immune complexes were captured using protein G dynabeads (Invitrogen 10004D), washed once each with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (same as low salt buffer, except 500 mM NaCl), and LiCl buffer (Tris-HCl pH 8.0, 250 mM LiCl, 2 mM EDTA, 1 % NP-40, 1% (wt/vol) sodium deoxycholate), and twice with TE.  Immunoprecipitated DNA recovered from beads by incubation in ChIP Elution Buffer (1% SDS, 0.1M Sodium Bicarbonate) for 30 min at room temperature.  Eluted DNA was treated with RNaseA (Roche 10109169001) and Proteinase K (Invitrogen #25530015) and purified using Qiagen PCR purification columns.  ChIP-seq in K562 cells with milder cross-linking and fragmentation performed using a SimpleChIP Plus Enzymatic Chromatin IP Kit with Magnetic Beads (Cell Signaling Technologies #9005S) according to manufacturer’s protocol.
Cells were treated, harvested, and subjected to CUT&TAG analysis using a modified published protocol [Kaya-Okur et al., 2019].  Trypsinized cells were washed once with PBS and incubated with NE nuclear extraction buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitors (Roche cOmplete) for 30 min on ice followed by Dounce homogenization using 20-strokes from Dounce Tissue Grinder (Wheaton 357542) tight pestle.  Following homogenization, samples were centrifuged for 3 min at 600g, nuclei pellet resuspended in NE buffer supplemented with 0.1 % formaldehyde and incubated at room temperature for 2 minutes followed by quench with 0.125 M glycine.  Following formaldehyde cross-link, nuclei were re-centrifuged, resuspended in fresh NE buffer and counted with trypan blue dye using Bio-Rad TC20 Automated Cell Counter.   After isolation, 150,000 total nuclei [135,000 nuclei from experimental sample with 15,000 mouse spike-in nuclei] were incubated with activated concanavalin A-coated (ConA) magnetic beads (EpiCypher) in 0.2 ml thin-walled tubes for 10 min at room temperature.  Nuclei-bound ConA beads were resuspended in antibody incubation buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.01% Digitonin, 2 mM EDTA, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor), 0.75 ug indicated primary antibody (see Table S2) added and samples incubated overnight at 4C with gently rotation.  Primary antibody removed from ConA bead solution by placing samples on magnetic stand until clear followed by supernatant removal.  Samples were incubated with 0.75 ug species specific secondary antibody for 30 min at room temperature with gentle rotation followed by two washes with Digitonin150 wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor) then incubation with pAG-Tn5 in Digitonin300-wash buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine, 100 uM PMSF, and 1x EDTA-free protease inhibitor) for 1h at room temperature.   After pAG-Tn5 incubation, bound ConA beads were washed twice with Digitonin300-wash buffer then resuspended in Tagmentation buffer (Digitonin300 wash buffer containing 10 mM MgCl2) and incubated for 1h at 37C.  Beads were then pelleted, resuspended in TAPS buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA).  TAPS buffer removed and beads carefully resuspended in SDS Release buffer (10 mM TAPS pH 8.5, 0.1% SDS) and incubated for 1 h at 58 C.  Following incubation, SDS Quench buffer (0.67% Triton X-100) was added to each sample along with 2 μl of a universal i5 and a uniquely barcoded i7 primers (from 10 μM stocks).  Equal volume (25 ul) NEBNext High-Fidelity 2x PCR Master mix (M0541, New England Biolabs) was added to each sample and mixed by gentle pipetting.  Samples subjected to DNA amplification using a thermocycler and the CUT&TAG-specific PCR cycling parameters: 58C for 5 min; 72C for 5 min; 98C for 45 sec; with 19 cycles of 98C for 15 sec and 60C for 10 sec; final extension at 72 °C for 1 min; and hold at 4C.  DNA clean-up performed by adding 1.3x AMPure XP beads (A63880, Beckman Coulter) to each sample, allowing libraries to incubated with beads for 10 min at room temperature, followed by two washes with 80% ethanol, then elution in 15 μl of 10 mM Tris pH 8.0.  While on magnetic stand, supernatant was carefully taken and transferred to a fresh tube.  Library size distribution determined by Agilent TapeStation 4200 (Agilent Technologies) and libraries mixed to yield equal representation prior to paired-end (2 x 50 bp) Illumina sequencing by NIEHS The Epigenomics and DNA Sequencing Core Facility.
Two replicates were used for each treatment condition. Cells were collected and subjected to the ATAC-seq protocol described by Buenrostro et al (2013).  Isolated cells were treated in 10 mM PIPES, pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, and 0.1% Triton X-100 and then treated with the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits for 30 min followed by mixing every 10 min. Libraries were sequenced at the NIEHS Epigenomics Core Facility on a NovaSeq instrument
ChIP-seq libraries were generated using the xGen ssDNA & Low-Input DNA Library Prep Kit and xGen CDI Primers (IDT 10009817 and 10009815) according to manufacturer’s protocol and sequenced on the Illumina NextSeq platforms.

treatment_protocol: Cells were treated for the indicated time individually, or in combination, with 100 nM Dexamethasone (Sigma D4902) or vehicle (equal volume EtOH or DMSO), 0.5 uM Triptolide (Tocris 3253), 0.5 uM Flavopiridol (Tocris 3094), 0.5 uM A485 (Tocris 6387), 0.1 uM Trichostatin A (Sigma T8552), 10 ug/ml Doxycycline (Sigma D9891), or 1 uM 5-Ph-IAA (AID) ligand (Sigma SML3574).

value: breast cancer

tag: spike-in control

value: Mouse nuclei

tag: chip antibody

value: H2AZ (Diagenode C15410201)

tag: treatment 1

value: 0.5uM Triptolide


title: Trip_5min_A12_H2AZ_CnT


title: BlisterFluid18, SCAR, rep1

source_name: Hash 1_SCAR patient 4, blister fluid / Hash 2_SCAR patient 18, blister fluid / Hash 3_SCAR patient 8, blister fluid / Hash 4_SCAR patient 3; blister fluid


title: Skin6, SCAR, rep1

value: Female


title: Trip_120min_A12_H3K4me3_CnT

value: H3K4me3 (Diagenode C15410003)


title: MnUS_3

first: Wanbo

last: Zhu

state: None Selected

address: No600, Yishan road, Shanghai, China

institute: Shanghai Sixth Peoples Hospital Affiliated to Shanghai Jiao Tong University

data_processing:
1. Data preprocessing and genomic alignment: Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads need to be filtered by quality. Trimmomatic [1] software was first used for quality control and linker removal, and then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using Rockhooper2 [2] to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment
2. Genetic assembly and structural 2.1 UTR and novel gene prediction: Identify the sequence of genes in an annotated gene or an unannotated area. Seeds gene sequence is a sequence area at genome that contains 10 bases at least and each one in this area are covered at least T sequence (T means a function of the2.2 Operator prediction Prokaryotes function on several related genes in are arranged in series with the often constitute manipulation substructure expression as a unit, is regulated by the common upstream area and the downstream transcription termination signal control. When transcribed, multiple structural genes are transcribed onto one mRNA strand and then translated into proteins. Rockhopper2 was used to develop the operon prediction algorithm from pure sequence features to combine experimental data of RNA-seq (ie, the gene expression quantity), that is to use bayesian classifier model to predict operons by combine the inter-genic distance and gene expression quantity, the sensitivity and specificity of the prediction algorithm are as high as 95%. Calculate and visualize 5 the predicted length distribution of operons, the number of structural genes involved, and the operon chain distribution count of genome-wide base average coverage sequence ). Through the bayesian model to judge whether the seed, seed each gene sequences repeatedly extended again after merging adjacent sequence of seeds or overlapping genes ultimately get the genetic map is obtained based on sequence alignment data reference gene annotation to the map and comparison, identification of boundary and the new genes.
3. Gene expression analysis: The direct expression of a gene expression level is its abundance. The higher the degree of gene abundance, the higher the gene expression level. In transcriptome sequencing analysis, the expression level of genes was estimated by locating the count of sequencing sequence (reads) in the genome area or the exon region of the gene. The Reads count is positively correlated with the length of the gene and the depth of the sequencing, in addition to the true expression level of the gene. We used the known reference gene sequences as the database, and the expression abundance of each gene in each sample was identified by sequence similarity comparison.Rockhooper2 was used to obtain the number of reads aligned to the gene in each sample and then to calculate RPKM[3].The calculated transcript expression levels can be directly used to compare transcript expression differences between different samples, and this method can eliminate the effect of differences in transcriptional length and sequencing amount on the expression of transcripts. Visualize quantitative data to obtain box plots, density plots, expression plots, etc. to determine differences in expression across all sample
4. Difference analysis and functional analysis: Using the estimateSizeFactors function of the R package of DESeq [4] (2012) to standardize counts, and use the nbinomTest function to calculate the pvalue and foldchange of difference comparison. Pick out the difference transcripts that p-value less than 0.05 and Difference of multiples more than two, and the GO and KEGG enrichment analysis of the differential genes was performed by hypergeometric distribution tests to determine the biological functions or pathways that are mainly affected by differential genes
Assembly: GCF_003052445.1_ASM305244v1

source_name: Mice tissue (ICR)

growth_protocol: Infected mice were executed on the tenth day and the tissue surrounding the implant was collected.

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times.  Leave the mixture on ice for 10 min.  B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate  the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the  lower phase, and transfer it to a fresh tube.  C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass  the mixture through the filter. Discard the flow-through. E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into  the same Collection Tube.  F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min.  G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into  the same Collection Tube.  H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the  center of the filter. Leave it at the room temperature for 2 min. Spin for 20–30 sec at maximum speed  to recover the RNA. Collect the eluate (which contains the RNA) and store it at -70°C.
a. Add 5 μL rRNA Binding Buffer and 5 μL rRNA Removal Mix-Gold to each well with 10 μL total RNA (1 μg). Gently pipette the entire volume up anddown 6 times to mix thoroughly.  b. Incubate the PCR plate at 68°C for 5 min, and then place at room temperature for 1 min. c. Add 35 μL of rRNA Removal Beads to each well of the new PCR plate. Adjust the pipette to 45 μL, then with the tip of the pipette at the bottom of the well, pipette quickly up and down 20 times to mix thoroughly. Incubate at room temperature for 1 min. Place the PCR plate on the magnetic stand at room temperature for 1 min. Transfer all of the supernatant from each well to the corresponding well of the new PCR plate. d. Add 99 μL of RNAClean XP beads (If starting with degraded total RNA, add 193 μL of RNAClean XP beads to each well) to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min. e. Place the PCR plate on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well of the PCR plate. f. Add 200 μL freshly prepared 70% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. Let the PCR plate stand at room temperature for 15 min to dry. g. Add 11 μL Elution Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min. Transfer 8.5 μL supernatant from the PCR plate to the new 0.2 ml tube. h. Add 8.5 μL Elute, Prime, Fragment High Mix to each well of the plate. Gently pipette the entire volume up and down 6 times to mix thoroughly. i. Incubate at 94°C for 8 min, hold at 4°C, and then centrifuge shortlya. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well of the PCR plate. Gently pipette the entire volume up and down 6 times to mix thoroughly.  b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C.
2.3 Synthesize Second Strand cDNA  a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well of the PCR plate. b. Add 20 μL Second Strand Marking Master Mix. Gently pipette the entire volume up and down 6 times to mix thoroughly. c. Incubate at 16°C for 60 min. Remove the plate from the thermal cycler2.3.1 Purification  a. Add 90 μL mixed AMPure XP beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard 135 μL supernatant from each well of the plate. d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time. f. Let the plate stand at room temperature for 15 min to dry, and then remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. h. Incubate the plate at room temperature for 2 min. Then place the plate on the magnetic stand at room temperature for 5 min. i. Transfer 15 μL supernatant from the plate to the new PCR plate. 2.4 Adenylate 3’ Ends a. Add 2.5 μL of diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL 9  Resuspension Buffer) to each well of the plate.  b. Add 12.5 μL of A-Tailing Mix to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 2.5 Ligate Adapters  a. Add 2.5 μL of diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) to each well of the plate. b. Add 2.5 μL of Ligation Mix to each well of the plate. c. Add 2.5 μL of RNA Adapter Index to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. d. Incubate at 30°C for 10 min. e. Add 5 μL of Stop Ligation Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. 2.5.1 Purification  a. Add 42 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. c. Remove and discard 79.5 μL supernatant from each well of the plate. d. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time for a total of two 80% EtOH washes. f. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. 10 h. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 minutes or until the liquid is clear. i. Transfer 50 μL supernatant from each well of the plate to the corresponding well of the new PCR plate. j. Add 50 μL of mixed AMPure XP Beads to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the plate at room temperature for 15 min. k. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. l. Remove and discard 95 μL supernatant from each well of the plate. m. With the plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. n. Repeat step m one time for a total of two 80% EtOH washes. o. With the plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer to each well of the plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. q. Incubate the plate at room temperature for 2 min. Place the plate on the magnetic stand at room temperature for 5 min or until the liquid is clear. r. Transfer 20 μL supernatant from each well of the plate to the corresponding well of the new PCR plate. 2.6 Enrich DNA Fragments  a. Add 5 μL of PCR Primer Cocktail to each well of the PCR plate. b. Add 25 μL of PCR Master Mix to each well of the PCR plate. Gently pipette the entire volume up and down to mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 s; 15 cycles 98°C for 10 s, 60°C for 30 s, 72°C for 30 s; 1 cycle 72°C for 5 min; hold at 10°C. 11 2.7.1 Purification  a. Add 50 μL of the mixed AMPure XP Beads to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. Incubate the PCR plate at room temperature for 15 min. b. Place the plate on the magnetic stand at room temperature for 15 min or until the liquid is clear. c. Remove and discard 95 μL supernatant from each well of the PCR plate. d. With the PCR plate on the magnetic stand, add 200 μL freshly prepared 80% EtOH to each well. Incubate the PCR plate at room temperature for 30 s, and then remove and discard all of the supernatant from each well. e. Repeat step d one time for a total of two 80% EtOH washes. f. With the PCR plate on the magnetic stand, let the samples air-dry at room temperature for 15 min, and then remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer to each well of the PCR plate. Gently pipette the entire volume up and down 10 times to mix thoroughly. h. Incubate the PCR plate at room temperature for 2 min. Place the PCR plate on the magnetic stand at room temperature for 5 min or until the liquid is clear. i. Transfer 30 μL supernatant from each well of the PCR plate to the corresponding well of the new PCR plate. 2.8 Validate library  a. Load 1 μL sample on an Agilent Technologies 2100 Bioanalyze. b. Check the size and purity of the sample

treatment_protocol: The collected tissues were sheared and excess red blood cells were removed from the tissues using erythrocyte lysate and digested using collagenase I, II, and IV to obtain single cell suspensions.

value: peri-implant tissue

tag: strain

value: ICR

value: WT

value: Treated by MnPM+US


title: Trip_30min_A12_H3K4me3_CnT


title: Trip_15min_A12_H3K4me3_CnT


title: BlisterFluid17, SCAR, rep1

value: Hash 1_SCAR patient 4, blister fluid / Hash 2_SCAR patient 18, blister fluid / Hash 3_SCAR patient 8, blister fluid / Hash 4_SCAR patient 3; blister fluid


title: BlisterFluid16, SCAR, rep1


title: Trip_5min_A12_H3K4me3_CnT


title: MnUS_2


title: BlisterFluid15, SCAR, rep1

source_name: Hash 2_SCAR patient 15, blister fluid / Hash 3_SCAR patient 2, blister fluid / Hash 4_SCAR patient 14, blister fluid / Hash 5_SCAR patient 27; blister fluid


title: Trip_120min_A12_K27ac_CnT

value: K27ac (Abcam ab4729)


title: MnUS_1


title: Trip_0min_A12_H3K4me3_CnT


title: Trip_120min_A12_H2AZ_CnT


title: Control_3

value: Non treatment


title: Trip_15min_A12_K27ac_CnT


title: Trip_5min_A12_K27ac_CnT


title: 10wCS_M2_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-cs-2_S105

value: Lung

value: male

value: 10 weeks cigarette smoke


title: Trip_15min_A12_H2AZ_CnT


title: Control_2


title: Trip_TSA_A12_H2AZ_CnT

value: 0.1 uM TSA

tag: treatment 2


title: Trip_0min_A12_K27ac_CnT

value: breast cancer


title: 10wCS_M1_RNAseq

description:
Project_017_Raw_Counts.txt.gz
Project_017_10w_MS_DEG_Test.csv.gz
10-m-cs-1_S104

value: Alveolar type II epithelial cells


title: Trip_0min_A12_H2AZ_CnT

value: Mouse nuclei

value: H2AZ (Diagenode C15410201)


title: BlisterFluid29, SCAR, rep1

value: Hash 1_SCAR patient 2, blister fluid / Hash 2_SCAR patient 17, blister fluid

value: Female


title: TSA_A12_H2AZ_CnT

value: DMSO


title: BlisterFluid12, SCAR, rep1

source_name: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 1, blister fluid / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16; blister fluid

value: Pooled Male and Female


title: Control_1

value: peri-implant tissue

value: ICR

value: WT


title: Trip_A485_A12_H2AZ_CnT

value: 0.5uM Triptolide


title: BlisterFluid10, SCAR, rep1

value: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 1, blister fluid / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16; blister fluid


title: iMac rep2

first: Guoyu

last: Chen

address: Xuhui District Yueyang Road 320

institute: PICB

data_processing:
raw sequencing reads were mapped to mm10/gencode vM25 using STAR
raw read counts were quantified using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: induced macrophage

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using VAHTS mRNA-seq v3 Library Prep Kit (VAHTS，NR611).

value: induced macrophage

value: wild type


title: iMac rep1


title: BlisterFluid11, SCAR, rep1


title: Trip_30min_A12_K27ac_CnT

value: K27ac (Abcam ab4729)


title: BlisterFluid14, SCAR, rep1

value: Hash 2_SCAR patient 15, blister fluid / Hash 3_SCAR patient 2, blister fluid / Hash 4_SCAR patient 14, blister fluid / Hash 5_SCAR patient 27; blister fluid


title: A485_A12_H2AZ_CnT

value: breast cancer


title: BlisterFluid13, SCAR, rep1


title: Untr_A12_H2AZ_CnT_rep2


title: TSA_A12_H3K4me3_CnT

value: H3K4me3 (Diagenode C15410003)

value: 0.1 uM TSA


title: MCC rep1

source_name: myeloid-like cell complex

value: myeloid-like cell complex


title: Trip_A485_A12_H3K4me3_CnT

value: Mouse nuclei


title: Trip_A12_H3K4me3_CnT_rep2


title: A485_A12_H3K4me3_CnT


title: BlisterFluid8, SCAR, rep1

source_name: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 28, skin biopsy / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16, blister fluid


title: BlisterFluid7, SCAR, rep1

value: Hash 1_SCAR patient 5, blister fluid / Hash 2_SCAR patient 28, skin biopsy / Hash 3_SCAR patient 9, blister fluid / Hash 4_SCAR patient 16, blister fluid


title: Untr_HCTaidRPB1_H3K18ac_CnT_rep1

value: colorectal carcinoma

value: H3K18ac (Diagenode C15410139)

value: DMSO

value: 10 ug/ml Doxycycline


title: MEF rep2

source_name: Mouse embryonic fibroblasts (MEF)

value: Mouse embryonic fibroblasts (MEF)


title: Aux_HCTaidRPB1_H3K18ac_CnT_rep1

value: 1 uM 5-Ph-IAA


title: MEF rep1


title: MCC rep2


title: Untr_HCTaidRPB1_H3K9ac_CnT_rep1

value: H3K9ac (Diagenode C15410004)


title: BlisterFluid6, SCAR, rep1

source_name: Hash 1_SCAR patient 29, skin biopsy / Hash 2_SCAR patient 9, skin biopsy / Hash 3_SCAR patient 7, blister fluid

value: Pooled Male and Female


title: BlisterFluid5, SCAR, rep1

value: Hash 1_SCAR patient 29, skin biopsy / Hash 2_SCAR patient 9, skin biopsy / Hash 3_SCAR patient 7, blister fluid


title: Aux_HCTaidRPB1_H3K9ac_CnT_rep1


title: BlisterFluid9, SCAR, rep1


title: Trip_TSA_A12_H3K4me3_CnT

value: 0.5uM Triptolide


title: BlisterFluid4, SCAR, rep1


title: fat-diestrus-5

city: shanghai

first: baiyier

middle: yier

last: bai

state: shanghai

address: shanghai huangpuqu

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description:
SAMC3366167
CRX958652
CRR1050701

data_processing:
Illumina adapter sequences were trimmed using Skewer (v0.2.2)
The quality checking was performed using FastQC (v0.11.5)
Then clean reads were mapped to human genome version hg38 using STAR (v2.5.3a)
StringTie (v1.3.1c) was used to generate gene expression data.
Assembly: GRCm38
Supplementary files format and content: Tab-excel file includes FPKM Values from Transcriptome Profiling of Adipose Tissues Across Estrous Cycles in Mice

source_name: fat

extract_protocol:
Total RNA was extracted from 20 adipose tissue samples using TRIzol reagent (Invitrogen, California, USA) following the manufacturer's instructions.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme).

value: fat


title: Untr_HCTaidRPB1_H4K5ac_CnT_rep1

value: H4K5ac (Diagenode C15410025)


title: Untr_HCTaidRPB1_H2AZ_CnT_rep1

value: H2AZ (Diagenode C15410201)


title: Aux_HCTaidRPB1_H4K5ac_CnT_rep1


title: fat-diestrus-4

description:
SAMC3366166
CRX958651
CRR1050700


title: BlisterFluid3, SCAR, rep1

source_name: Hash 1_SCAR patient 30, blister fluid / Hash 2_SCAR patient 31, skin biopsy / Hash 3_SCAR patient 27, blister fluid / Hash 4_SCAR patient 32; skin biopsy


title: fat-diestrus-3

description:
SAMC3366165
CRX958650
CRR1050699


title: Aux_HCTaidRPB1_H2AZ_CnT_rep1


title: Untr_A12_H3K4me3_CnT_rep2

value: breast cancer

value: H3K4me3 (Diagenode C15410003)


title: Untr_HCTaidRPB1_H3K4me3_CnT_rep3

value: Mouse nuclei


title: Untr_HCTaidRPB1_K27ac_CnT_rep5

value: K27ac (Abcam ab4729)


title: Aux_HCTaidRPB1_H3K4me3_CnT_rep3

value: colorectal carcinoma


title: BlisterFluid2, SCAR, rep1

value: Hash 1_SCAR patient 30, blister fluid / Hash 2_SCAR patient 31, skin biopsy / Hash 3_SCAR patient 27, blister fluid / Hash 4_SCAR patient 32; skin biopsy


title: Aux_HCTaidRPB1_K27ac_CnT_rep5


title: BlisterFluid1, SCAR, rep1


title: fat-diestrus-2

description:
SAMC3366164
CRX958649
CRR1050698


title: fat-diestrus-1

description:
SAMC3366163
CRX958648
CRR1050697


title: Trip_SW13_H2AZ_CnT

value: adrenal carcinoma


title: kd_ASCC3_4EHP_RNAseq_rep2

city: Saitama

first: Peixun

last: Han

address: Hirosawa Wako

country: Japan

institute: Riken

data_processing:
RNA-seq
Quality filtering and 3′ adaptor trimming by Fastp 0.21.0
Demultiplex according to the barcodes by Fastx
Alignment to non-coding RNA with STAR v2.7.0a
Alignment to hg38 genome with STAR v2.7.0a
Suppressing duplicated reads by UMI-tools 1.1.1
Read quantification
Assembly: hg38
Supplementary files format and content: text files contain three columns, transcript ID, CDS length (nt), read counts.

source_name: HEK293 Flp-In T-REx

growth_protocol: HEK293 Flp-In T-REx cells were grown in DMEM with high glucose and GlutaMAX containing 10% fetal bovine serum at 5% CO2 37℃.

extract_protocol:
Cells were lysed with lysis buffer and treated with DNase.
For ribosome profiling, RNase I digestion, ribosome pelleting, size seletion, linker ligation, rRNA depletion, T7 reverse transcription, cDNA synthesis. For RNA-seq, TruSeq Stranded Total RNA Library Prep Kit (Illumina).

treatment_protocol: eRF1-overexpression in stable cell lines was induced using 0.2 μg/ml tetracycline for 48 h before harvest. siRNA knockdown was conducted first by transfection of  75 nM siRNA and incubation for 72 h, followed by transfection of 30 nM siRNA and incubation for 24 h.

value: HEK293 Flp-In T-REx

value: Human embryonic kidney

value: ASCC3, 4EHP double knockdown


title: Untr_SW13_H2AZ_CnT

value: DMSO


title: Trip_HCT116_H2AZ_CnT


title: fat-metestrus-5

description:
SAMC3366162
CRX958647
CRR1050696


title: Untr_A549_H2AZ_CnT

value: lung carcinoma


title: kd_4EHP_RNAseq_rep2

value: 4EHP knockdown


title: kd_ASCC3_4EHP_RNAseq_rep1


title: Untr_K562_H2AZ_CnT

value: lymphoblast


title: Trip_A549_H2AZ_CnT

value: 0.5uM Triptolide


title: fat-metestrus-3

description:
SAMC3366160
CRX958645
CRR1050694

value: fat


title: fat-metestrus-2

description:
SAMC3366159
CRX958644
CRR1050693


title: Untr_A549_H3K4me3_CnT


title: Trip_K562_H2AZ_CnT

value: H2AZ (Diagenode C15410201)


title: Trip_A549_H3K4me3_CnT


title: kd_4EHP_RNAseq_rep1


title: kd_ASCC3_RNAseq_rep2

value: ASCC3 knockdown


title: fat-metestrus-1

description:
SAMC3366158
CRX958643
CRR1050692


title: Untr_K562_H3K4me3_CnT

value: H3K4me3 (Diagenode C15410003)


title: Trip_K562_H3K4me3_CnT

value: Mouse nuclei


title: fat-estrus-5

description:
SAMC3366157
CRX958642
CRR1050691


title: Trip_A549_K27ac_CnT

value: K27ac (Abcam ab4729)


title: Untr_A549_K27ac_CnT


title: kd_ASCC3_RNAseq_rep1


title: Untr_K562_K27ac_CnT


title: fat-estrus-3

description:
SAMC3366155
CRX958640
CRR1050689


title: Trip_K562_K27ac_CnT


title: fat-estrus-4

description:
SAMC3366156
CRX958641
CRR1050690


title: m_kd_ASCC3_4EHP_rep2

data_processing:
*library strategy: Ribosome profiling (Monosome)
Quality filtering and 3′ adaptor trimming by Fastp 0.21.0
Demultiplex according to the barcodes by Fastx
Alignment to non-coding RNA with STAR v2.7.0a
Alignment to hg38 genome with STAR v2.7.0a
Suppressing duplicated reads by UMI-tools 1.1.1
Read quantification
Assembly: hg38
Supplementary files format and content: text files contain three columns, transcript ID, CDS length (nt), read counts.


title: fat-metestrus-4

description:
SAMC3366161
CRX958646
CRR1050695


title: kd_CTRL_RNAseq_rep1

value: Knockdown control


title: Trip_A12_H4K12ac_CnT

value: breast cancer

value: H4K12ac (Diagenode C15410331)


title: kd_CTRL_RNAseq_rep2

value: HEK293 Flp-In T-REx


title: Untr_A12_H4K12ac_CnT


title: Untr_A12_H4K5ac_CnT

value: H4K5ac (Diagenode C15410025)


title: m_kd_ASCC3_4EHP_rep1

value: Human embryonic kidney

value: ASCC3, 4EHP double knockdown


title: Untr_A12_K27ac_CnT_rep8

value: DMSO


title: fat-estrus-1

description:
SAMC3366153
CRX958638
CRR1050687


title: Trip_A12_K27ac_CnT_rep8


title: Untr_A12_K27ac_CnT_rep7


title: m_kd_4EHP_rep2

value: 4EHP knockdown


title: Trip_A12_K27ac_CnT_rep7


title: m_kd_4EHP_rep1


title: Untr_A12_K27ac_CnT_rep6


title: Trip_A12_K27ac_CnT_rep6


title: Trip_A12_H4K5ac_CnT


title: fat-proestrus-4

description:
SAMC3366151
CRX958636
CRR1050685


title: fat-proestrus-3

description:
SAMC3366150
CRX958635
CRR1050684


title: m_kd_ASCC3_rep2


title: fat-estrus-2

description:
SAMC3366154
CRX958639
CRR1050688


title: Trip_A12_K27ac_CnT_rep5


title: Untr_A12_K27ac_CnT_rep5


title: Untr_A12_K27ac_CHIP_rep5

data_processing:
ChIP-seq analysis. Reads were trimmed using Cutadapt and aligned to both hg19 and dm6 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Scale factors were calculated for each sample by dividing the minimum number of dm6 reads for a given antibody by number of dm6 reads for each sample using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Reads were trimmed using Cutadapt and aligned to both hg19 and mm10 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Deduplicated read counts were used to calculate the human:mouse ratio, which was then used to calculate scaling factors for samples performed side by side with the same antibody. The scale factor was calculated by dividing the human:mouse read ratio for each sample using a given antibody by the maximum human:mouse read ratio from samples using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Assembly: hg19
Supplementary files format and content: bigwig coverage files

value: Drosophila chromatin


title: DexTrip_A12_RNAP2_CHIP

value: RNAP2 (ActiveMotif 39097)

value: 100nM Dexamethasone

value: 0.5uM Triptolide


title: fat-proestrus-1

description:
SAMC3366148
CRX958633
CRR1050682

value: fat


title: m_kd_ASCC3_rep1

value: ASCC3 knockdown


title: Trip_A12_K27ac_CHIP_rep5


title: fat-proestrus-2

description:
SAMC3366149
CRX958634
CRR1050683


title: Dex_A12_RNAP2_CHIP


title: VehTrip_A12_RNAP2_CHIP

value: EtOH Vehicle


title: fat-proestrus-5

description:
SAMC3366152
CRX958637
CRR1050686


title: m_kd_ABCE1_rep1

value: ABCE1 knockdown


title: Veh_A12_RNAP2_CHIP


title: m_kd_CTRL_rep2

value: Knockdown control


title: PHF6_KO_THP1_RNA-Seq_Rep4

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: clonally expanded and sequence verified

data_processing:
Sequence reads were trimmed for low quality/adapter sequence using Trimmomatic.
Trimmed reads were mapped to hg19 genome using STAR.
read quantification and feature annotation were performed using featureCounts.
Differential expression analysis was performed using DESeq2.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw read counts on all samples

source_name: Hematopoietic

growth_protocol: Cells were transduced with lentiviral vector expressing Cas9 and PHF6 gRNAs or non-targeting gRNAs. Resultant pools was sorted and selected for individual KO and CTRL clones. Cells were grown in complete media (RPMI1640 +FBS) and used for RNA-extraction.

extract_protocol:
1 million cells from each clone were used for total RNA extraction using RNeasy mini kit (Qiagen 74106) following the manufacturer recommended protocol. RNA concentration was determined by using Agilent 2200 TapeStation and a high sensitivity RNA Screentape (Agilent 5067-5579). Samples with RIN greater than 8 were used to construct RNA-Seq libraries. RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530L) using the manufacturer recomended protocol. Concentrations and sizes of libraries were determined using Agilent 2200 TapeStation and KAPA library quantification kit (Roche KK4824).
RNA libraries were prepared using  NEBNext Ultra RNA Library Prep Kit for Illumina (NEB E7530L) using the manufacturer recomended protoco. Concentration and the size of the libraries were detremined using Agilent 2200 Tapestation and KAPA library quantification kit (Roche KK4824).
Libraries from all samples were pooled in equimolar concentrations and denatured for paired-end sequencing. Pooled libraries were quantified using KAPA library quantification kit (Roche KK4824).

value: Hematopoietic

value: AML cell line

value: PHF6 knockout


title: PHF6_KO_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified


title: PHF6_KO_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified


title: m_kd_CTRL_rep1

value: HEK293 Flp-In T-REx


title: PN0296_RES_0006

city: Belfast

first: Deborah

middle: Y.

last: Moss

address: 97 Lisburn Road

department: Patrick G. Johnston Centre for Cancer Research

country: United Kingdom

institute: Queen's University Belfast

data_processing:
RNA-seq reads were aligned to the human genome (hg37) using STAR aligner and the number of reads mapping to genes annotated in Gencode build 37 (v22) were calculated using HTseq.
Assembly: The indexes used for these libraries were from the KAPA Unique Dual-Indexed Adapter kit.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Colon adenocarcinoma

growth_protocol: Organoids were resuspended in Matrigel and supplemented with Advanced DMEM/F-12 medium with 2mM L-glutamine, 10mM HEPES, 100U/ml penicillin and 100µg/ml streptomycin, 1x B27, 1x N-2, 50ng/ml EGF ad 100ng/ml Noggin

extract_protocol:
RNA was isolated using the KAPA RNA HyperPrep kit with RiboErase and processed as per manufacturer's protocols
NGS library construction from 25 ng–1 μg of total RNA and depletes both cytoplasmic (5S, 5.8S, 18S and 28S) and mitochondrial (12S and16S) ribosomal RNA species
The libraries were sequenced using the Illumina NovaSeq 6000 sequencing system.

treatment_protocol: 5FU resistant organoids were generated through chronic exposure to 5FU

value: Colon adenocarcinoma

value: AKP organoids

value: murine colorectal cancer organoids


title: PHF6_KO_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified


title: PC, sample 2

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: 10X genomics

data_processing:
demultiplex, mapping and read counting was done with the cellranger v 7.1.0 pipeline from 10 X genomics
Cellranger outpus were further processed using seurat v4.3
Assembly: mm39
Supplementary files format and content: tab separated value files (featurs and barcodes) and matrix file

source_name: small intestine

extract_protocol:
The small intestine was taken and crypts were isolated  from the material. The crypts were porcessed to a single cell suspension and PCs were purfied from the mixture using FACS
Library construction was done by the VIB single cell core accoring to the manufacturers instructions (10X genomics, singl cell 3' v3)

value: small intestine

value: WT

tag: age

value: 10 weeks

value: purified paneth cells


title: PN0296_RES_0005


title: CTRL_THP1_RNA-Seq_Rep5

description: clonally expanded and sequence verified

value: Wildtype


title: d_kd_ASCC3_4EHP_rep2

data_processing:
*library strategy: Ribosome profiling (Disome)
Quality filtering and 3′ adaptor trimming by Fastp 0.21.0
Demultiplex according to the barcodes by Fastx
Alignment to non-coding RNA with STAR v2.7.0a
Alignment to hg38 genome with STAR v2.7.0a
Suppressing duplicated reads by UMI-tools 1.1.1
Read quantification
Assembly: hg38
Supplementary files format and content: text files contain three columns, transcript ID, CDS length (nt), read counts.

value: Human embryonic kidney

value: ASCC3, 4EHP double knockdown


title: d_kd_ASCC3_4EHP_rep1


title: CTRL_THP1_RNA-Seq_Rep3

description: clonally expanded and sequence verified


title: m_kd_ABCE1_rep2


title: CTRL_THP1_RNA-Seq_Rep4

description: clonally expanded and sequence verified


title: FICZ 2

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

data_processing:
Demultiplexing using a custom R-script (available on request)
count files produced by standard pipeline of Scdiscoveries
Assembly: GRCh38

source_name: Small intestine

growth_protocol: N39 APOA1-tdTomato organoids were used. These were cultured under standard conditions as described.

extract_protocol:
RNEasy kit
Cell-seq2 protocol (performed by Scdiscoveries)

treatment_protocol: Different stimuli were used, added to AdvDMEM-F12

value: Small intestine

value: Various

value: FICZ


title: CTRL_THP1_RNA-Seq_Rep1

description: clonally expanded and sequence verified

value: Hematopoietic


title: PN0296_PAR_0003


title: FICZ 1


title: Clofibric acid 2

value: Clofibric acid


title: PC, sample 1

description: 10X genomics


title: Clofibric acid 1


title: PN0296_PAR_0002


title: d_kd_4EHP_rep1

value: 4EHP knockdown


title: SR12813 1


title: d_kd_ABCE1

value: HEK293 Flp-In T-REx

value: ABCE1 knockdown


title: d_kd_CTRL_rep2

value: Knockdown control


title: d_kd_ASCC3

value: ASCC3 knockdown


title: GW4064 2


title: PN0296_RES_0004

value: Colon adenocarcinoma

value: AKP organoids

value: murine colorectal cancer organoids


title: SR12813 2


title: GW3965 2


title: CTRL_THP1_RNA-Seq_Rep2

description: clonally expanded and sequence verified

value: AML cell line


title: GW3965 1


title: RGD-Alg/Laponite@1IL-12 co-culture, 48h, rep1

city: Chongqing

first: chuanchuan

last: lin

state: China

address: Shayang Road, Shapingba distract,

institute: Chongqing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

growth_protocol: C57BL/6 mouse BM-MSCs and BM-MSCs complete medium were procured from Cyagen (Guangzhou, China). Cells were passaged when they reached 70-80% confluence, and cells from the 3rd to 5th passages were utilized for subsequent experiments.

extract_protocol:
qRT-PCR was employed to quantify the mRNA expression of cells. First, BM-MSCs under different treatment conditions were collected and lysed by Trizol, and a total RNA extraction kit was used to extract the total RNA of BM-MSCs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 5 Gy irradiation, the BM-MSCs were co-cultured with various biomaterials for 48 h.

value: bone marrow

value: Primary cells

value: mesenchymal stem cells


title: d_kd_CTRL_rep1

value: Human embryonic kidney


title: m_erf1_IP_AAQ2

value: SBP-eRF1-AAQ overexpression


title: ER+BMP 2

value: Small intestine

value: Various

value: ER+BMP


title: GW4064 1


title: PN0296_PAR_0001


title: Calcitriol 1

value: Calcitriol


title: RGD-Alg/Laponite co-culture, 48h, rep3

value: RGD-Alg/Laponite


title: m_erf1_IP_AAQ1

value: HEK293 Flp-In T-REx


title: Calcitriol 2


title: RGD-Alg/Laponite co-culture, 48h, rep2


title: ER+BMP 1


title: HUVECS_CCM2_scRNAseq

city: Leuven

first: Apeksha

last: Shapeti

address: Celestijnelaan 300C

department: Mechanical Engineering

institute: KU Leuven

description: 10x Genomics

data_processing:
Image analyses and base calling were performed using the Nextseq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using cellranger mkfastq v6.1.2. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
cellranger count v6.1.2 was used to align reads to the reference genome (refdata-gex-GRCh38-2020-A) and generate the raw and filtered gene-barcodes matrices.
cellranger aggr v6.1.2 was used to combine the results of the two samples.
Assembly: GRCh38 (CellRanger version: refdata-gex-GRCh38-2020-A)
Supplementary files format and content: MEX file format: the matrix.mtx file contains the filtered gene-barcode matrix (total UMI count per cell and gene combination); the .tsv files contain all annotated genes and cell barcodes represented in the mtx file.
Supplementary files format and content: Supplementary file : processed_data csv file was generated from the Seurat object on R, and contains the raw count of each gene for every cell that remained after the QC step
Supplementary files format and content: Supplementary file : metadata text file was generated from the Seurat object on R, and contains the metadata of each cell that remained after the QC step

source_name: Mosaic of WT+siCCM2 HUVECs invading PEG hydrogels

growth_protocol: Wild type (WT) human umbilical vein endothelial cells (HUVECs) were labeled with Lifeact-RFP, while control (CT) or CCM2 siRNA silenced HUVECs were labeled with Lifeact-GFP. Red wild type HUVECs were combined in a 1:1 ratio with either siCT or siCCM2 HUVECs and allowed to invade overnight as mosaics into a PEG based hydrogel using our 3D-in vitro model of angiogenic sprouting

extract_protocol:
Hydrogels were then collected using a spatula into a falcon tube and dissociated into single cells using an incubation period of 15 min in trypsin at 37°C to dissociate endothelial cells. Dissociated cells were then filtered in EGM2 growth medium and then centrifuged (1200 rpm for 5 min). The solutions were neutralized with a 1:10 volume of EGM-2 without antibiotics  and centrifuged for 5 min at 300 RCF, followed by 10 min at 500 RCF. After decanting the supernatant, the cell pellets were resuspended in 200 μL of EGM-2 and put on ice. Cells were isolated by fluorescence activated cell sorting (FACS) by flow cytometry on a Aria IIu (BD Biosciences). Discrimination of cell populations was based on fluorescence at 530/30 nm from 488 nm excitation and 610/20 nm from 561 nm excitation to identify respectively cells expressing Lifeact-GFP or Lifeact-RFP. Cells were run through a 100 um nozzle under 20 psi at a flow rate of 1 and recovered simultaneously in tubes in a 4-way purity mode. The sorted cells were labeled as WT, WT-CCM2, siCCM2 and frozen in EGM-2 + 40% FCS + 10% DMSO. After thawing the cells, their viability (>80%) and aggregation were tested before starting the single-cell library preparation. The concentration of freshly dissociated cells was adjusted to 1000 cells/μL in HBSS/0.05% BSA, and then the 10x Chromium Controller and the Chromium Single Cell 3′ Reagent kit V3.1 were used to perform the scRNAseq experiments.
Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.

treatment_protocol: Four independent trials of mosaic invasion samples were prepared for control (WT-RFP + siCT-GFP HUVECs) and siCCM2 (WT-RFP + siCCM2-GFP HUVECs) conditions and allowed to sprout for 24h into degradable PEG 1.5% hydrogels with a high concentration of S1P (400nM) to allow for significant hydrogel invasion by both cell populations.

value: Human umbilical vein endothelial cells

value: siRNA silencing of CCM2


title: RGD-Alg/Laponite co-culture, 48h, rep1


title: m_erf1_IP_WT2

value: SBP-eRF1 overexpression


title: RGD-Alg/Laponite@1IL-12 co-culture, 48h, rep3


title: HUVECs_WTinCT_scRNAseq

description: 10x Genomics

source_name: Mosaic of WT+siCT HUVECs invading PEG hydrogels

value: untreated, wild type


title: RGD-Alg/Laponite@1IL-12 co-culture, 48h, rep2


title: U2OS_Nutlin-3a_2_QuantSeq

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic 66 v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10 67.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4 68.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v102, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option disabled. Mappings were filtered for uniqueness and properly aligned reads by Samtools v1.12.
Pre-processed data was split into strand-specific subsets using Samtools. PEAKachu v0.2.0 was used over all replicates including both conditions to call cell and strand-specific peaks. When the distance between peaks was within 50 bp, Bedtools v2.30.0 was used to merge the peaks.
Assembly: hg38
Supplementary files format and content: PEAKachu peak files

source_name: bone

growth_protocol: MCF-7 and U2OS cells were grown in high glucose DMEM with pyruvate. RPE-1 hTERT cells were cultured in DMEM:F12 media. Culture media were supplemented with 10% FBS and penicillin/streptomycin. In addition, DMEM was supplemented with non-essential amino acids for culturing MCF-7 cells.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. Total RNA was quantified and quality checked using a 2100 Bioanalyzer in combination with RNA 6000 assay or a 4200 Tapestation instrument in combination with RNA ScreenTape
QuantSeq libraries were prepared from 500 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit REV (Lexogen, Vienna, Austria) following the manufacturer's instructions. Quantification and quality check of libraries was done using a 2100 Bioanalyzer instrument and DNA 7500 kit or a 4200 Tapestation instrument and a DNA 1000 kit (Agilent Technologies).
Libraries were pooled and sequenced on a HiSeq 2500 using 50 cycle high-output reagents or a NextSeq 500 using 75 cycle high-output v2.5 reagents

treatment_protocol: Cells were treated with Nutlin-3a 10 µM or DMSO control for 24 h

value: bone

value: epithelial cells

value: wild-type

value: Nutlin-3a 10 uM 24 h


title: m_erf1_IP_WT1


title: U2OS_Nutlin-3a_3_QuantSeq


title: m_erf1_IP_trex

value: Naive


title: RGD-Alg/IL-12 co-culture, 48h, rep3

value: bone marrow

value: Primary cells

value: mesenchymal stem cells


title: U2OS_Nutlin-3a_1_QuantSeq


title: RGD-Alg/IL-12 co-culture, 48h, rep2


title: RGD-Alg/IL-12 co-culture, 48h, rep1


title: U2OS_DMSO_3_QuantSeq

value: DMSO 24 h


title: U2OS_DMSO_2_QuantSeq


title: U2OS_DMSO_1_QuantSeq


title: m_erf1_input_AAQ2

value: Human embryonic kidney

value: SBP-eRF1-AAQ overexpression


title: RPE-1_Nutlin-3a_3_QuantSeq

source_name: retina

value: retina

value: hTERT immortalized


title: m_erf1_input_AAQ1

value: HEK293 Flp-In T-REx


title: HUVECS_WTinCCM2_scRNAseq

description: 10x Genomics

value: Mosaic of WT+siCCM2 HUVECs invading PEG hydrogels

value: Human umbilical vein endothelial cells


title: RPE-1_Nutlin-3a_2_QuantSeq


title: m_erf1_input_WT2

value: SBP-eRF1 overexpression


title: RGD-Alg co-culture, 48h, rep3

value: RGD-Alg


title: RGD-Alg co-culture, 48h, rep2


title: RPE-1_Nutlin-3a_1_QuantSeq

value: epithelial cells


title: m_erf1_input_WT1


title: RPE-1_DMSO_3_QuantSeq


title: RGD-Alg co-culture, 48h, rep1


title: U2OS_Nutlin-3a_3_CAGE-seq

description: m7-cap-filtered 5'RNA

data_processing:
Informed by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports, we used Trimmomatic 66 v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v2.10 67.
Potential sequencing errors were detected and corrected using Rcorrector v1.0.4 68. In addition, Cutadapt was used with adapter parameter ‘XG’ to clip the first position of CAGE-seq reads if that was a guanin base to correct for CAGE-seq’s 5’-end guanin addition bias.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v102, using the mapping software segemehl v0.3.4 with adjusted accuracy (95%) and split-read option disabled. Mappings were filtered for uniqueness and properly aligned reads by Samtools v1.12.
Pre-processed data was split into strand-specific subsets using Samtools. PEAKachu v0.2.0 was used over all replicates including both conditions to call cell and strand-specific peaks. When the distance between peaks was within 50 bp, Bedtools v2.30.0 was used to merge the peaks.
Assembly: hg38
Supplementary files format and content: PEAKachu peak files

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol. Total RNA was quantified and quality checked using a 2100 Bioanalyzer in combination with RNA 6000 assay or a 4200 Tapestation instrument in combination with RNA ScreenTape
CAGE-seq libraries were prepared from 5000 ng of total RNA using the CAGE Preparation Kit (Kabushiki Kaisha DNAFORM, Yokohama, Japan) following the manufacturer's instructions. Quantification and quality check of libraries was done using a 2100 Bioanalyzer instrument and DNA 7500 kit or a 4200 Tapestation instrument and a DNA 1000 kit (Agilent Technologies).
Libraries were pooled and sequenced on a NextSeq 500 v2 300 cycles runs. System run in 151 cycle/paired-end mode.

value: bone

value: wild-type


title: d_kd_4EHP_rep2

value: 4EHP knockdown


title: IR-Control, 48h,rep3

value: bone marrow


title: d_erf1_IP_AAQ2


title: m_erf1_input_trex

value: Naive


title: RPE-1_DMSO_1_QuantSeq


title: RPE-1_DMSO_2_QuantSeq


title: U2OS_Nutlin-3a_1_CAGE-seq

description: m7-cap-filtered 5'RNA

value: Nutlin-3a 10 uM 24 h


title: d_erf1_IP_AAQ1


title: U2OS_DMSO_2_CAGE-seq

description: m7-cap-filtered 5'RNA

value: DMSO 24 h


title: U2OS_DMSO_3_CAGE-seq

description: m7-cap-filtered 5'RNA


title: U2OS_Nutlin-3a_2_CAGE-seq

description: m7-cap-filtered 5'RNA


title: IR-Control, 48h,rep2

value: Primary cells

value: mesenchymal stem cells


title: U2OS_DMSO_1_CAGE-seq

description: m7-cap-filtered 5'RNA


title: RPE-1_Nutlin-3a_3_CAGE-seq

description: m7-cap-filtered 5'RNA

value: retina


title: maleWTTCR

city: Manhasset

first: Zarina

last: Brune

state: New York

address: 350 Community Drive

institute: The Feinstein Institutes for Medical Research

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Spleen

extract_protocol:
Freshly collected splenocytes were sorted for CD3+CD4+ T cells. Sorted CD4+ T cells were stimulated for 6 hours in RPMI + 10% FBS (v/v) + 1x Pen/Strep with anti-CD3/anti-CD28 Dynabeads for 6 hours in 37°C incubator.
Library construction was performed according to the manufacturers instructions (Single Cell 3' v3.1 Protocol, 10x Genomics). Briefly, CD4+ T cells were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate the gel beads-in-emulsion (GEM). The poly-A-RNA from the cell lysate was then retrotranscribed to cDNA. The pooled barcoded cDNA was cleaned with Silane Dynabeads and amplified by PCR. SPRIselect reagent was used to select appropriately sized fragments for library construction. During library construction, Ilumina TruSeq Read 2 primer sequence, paired-end constructions with P5 and P7 sequences and a sample index were added.

value: Spleen

tag: gender

value: male

value: Splenic CD4 T cells

value: WT

value: anti-CD3/CD28 stimulated


title: RPE-1_Nutlin-3a_1_CAGE-seq

description: m7-cap-filtered 5'RNA

value: hTERT immortalized


title: d_erf1_IP_WT1

value: HEK293 Flp-In T-REx

value: Human embryonic kidney

value: SBP-eRF1 overexpression


title: d_erf1_IP_trex


title: IR-Control, 48h,rep1


title: Trip_A12_H2AZ_CnT_rep2

data_processing:
ChIP-seq analysis. Reads were trimmed using Cutadapt and aligned to both hg19 and dm6 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Scale factors were calculated for each sample by dividing the minimum number of dm6 reads for a given antibody by number of dm6 reads for each sample using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Reads were trimmed using Cutadapt and aligned to both hg19 and mm10 genomes using bowtie2. Aligned reads were deduplicated with picardtools. Deduplicated read counts were used to calculate the human:mouse ratio, which was then used to calculate scaling factors for samples performed side by side with the same antibody. The scale factor was calculated by dividing the human:mouse read ratio for each sample using a given antibody by the maximum human:mouse read ratio from samples using the same antibody. Scaled and normalized coverage files were generated using deeptools with calculated scale factors and rpkm normalization.
Assembly: hg19
Supplementary files format and content: bigwig coverage files
Library strategy: CUT&TAG

value: breast cancer

value: Mouse nuclei

value: H2AZ (Diagenode C15410201)

value: DMSO

value: 0.5uM Triptolide


title: RPE-1_DMSO_1_CAGE-seq

description: m7-cap-filtered 5'RNA

value: epithelial cells

value: DMSO 24 h


title: maleKOTCR

description: 10X Genomics


title: d_erf1_input_AAQ2

value: SBP-eRF1-AAQ overexpression


title: femaleWTTCR

description: 10X Genomics

value: Spleen

value: female


title: RPE-1_DMSO_2_CAGE-seq

description: m7-cap-filtered 5'RNA

value: retina


title: femaleKOTCR

description: 10X Genomics

value: Splenic CD4 T cells


title: MCF-7_Nutlin-3a_4

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.19.1.403.
We used Trimmomatic v0.39 (5nt sliding window approach, mean quality cutoff 22) for read quality trimming according to inspections made from FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) v0.11.9 reports.
Illumina universal adapter as well as mono- and di-nucleotide content was clipped using Cutadapt v3.3. Potential sequencing errors were detected and corrected using Rcorrector v1.0.4. Ribosomal RNA (rRNA) transcripts were artificially depleted by read alignment against rRNA databases through SortMeRNA v2.1 for uniqueness and properly aligned mate pairs.
The preprocessed data was aligned to the reference genome hg38, retrieved along with its gene annotation from Ensembl v.102 (46), using the mapping software segemehl (47, 48) v0.3.4 with adjusted accuracy (95%) and split-read option enabled. Mappings were filtered by Samtools v1.12 (49) for uniqueness.
Following pre-processing of the data, read quantification was performed on exon level using featureCounts v2.0.1, parametrized according to the strand specificity inferred through RSeQC v4.0.0. Differential gene expression and its statistical significance was identified using DESeq2 v1.32.0.
Assembly: hg38
Supplementary files format and content: DESeq2 results table
Supplementary files format and content: TPM values table

source_name: breast

growth_protocol: MCF-7 cells were grown in high glucose DMEM with pyruvate. Culture media were supplemented with 10% fetal bovine serum, penicillin/streptomycin, and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s protocol.
Libraries were prepared from 800 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1/2/3/4) following the manufacturer's instructions (New England Biolabs) including size-selection at around 500 bp. Quantification and quality checked of libraries was done using a 2100 Bioanalyzer instrument and DNA 7500 kit (Agilent Technologies).
Libraries were pooled and sequenced on a NextSeq 500 v2 300 cycles runs. System run in 151 cycle/paired-end mode.

treatment_protocol: MCF-7 cells were treated with Nutlin-3a 10 µM or DMSO control for 24 h

value: breast

value: wild-type

value: Nutlin-3a 10 µM 24 h


title: RPE-1_DMSO_3_CAGE-seq

description: m7-cap-filtered 5'RNA

value: hTERT immortalized


title: d_erf1_input_AAQ1

value: HEK293 Flp-In T-REx

value: Human embryonic kidney


title: MCF-7_Nutlin-3a_3


title: MCF-7_Nutlin-3a_1


title: MCF-7_DMSO_4


title: d_erf1_input_WT2

value: SBP-eRF1 overexpression


title: GF_AFD, replicate1, scRNA-seq

city: Yokohama

first: Takaharu

last: Sasaki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Thurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

description: 10x Genomics

data_processing:
FASTQ raw files were processed by Cell Ranger v3.0.2 software and aligned to the mouse reference genome mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peyer's patches

extract_protocol:
Peyer's patches dissected from mice were minced with scissors and then stirred in a 20-mL conical flask containing 10 mL of RPMI medium supplemented with 2% (v/v) FCS, 1 mg/mL Collagenase (WAKO), and 50 μg/mL DNase, using a stir bar at 37°C and 500 rpm for 15 minutes. The suspension was then passed through an 18 G needle 10 times and stirred at 37°C and 500 rpm for an additional 15 minutes. Samples were filtered through a 100-μm Cell Strainer, centrifuged at 4°C and 500 g for 5 minutes, and CD19-negative PI-negative cells were sorted by FACS for subsequent scRNA-seq analysis.
Library was prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacter's instructions.

value: Peyer's patches

value: 10-12 weeks old

value: wild-type (germ-free)

value: AFD


title: GF_AFD, replicate2, scRNA-seq

description: 10x Genomics


title: MCF-7_DMSO_2

value: epithelial cells

value: DMSO 24 h


title: d_erf1_IP_WT2


title: MCF-7_DMSO_1


title: d_erf1_input_WT1


title: MCF-7_DMSO_3


title: GF_NCD, replicate2, scRNA-seq

description: 10x Genomics

value: NCD


title: RPE-1_Nutlin-3a_2_CAGE-seq

description: m7-cap-filtered 5'RNA

value: Nutlin-3a 10 uM 24 h


title: mouse kidney_sham_24h_5

city: Berlin

first: Robert

last: Labes

address: Charitéplatz 1

department: Institute of Translational Physiology

institute: Charité - Universitätsmedizin Berlin

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.). The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 20.0.4 was used to demultiplex the raw sequencing reads according to the sample indices. The “Quantify QIAseq UPX 3’ workflow” was used to process the demultiplexed sequencing reads with default settings. The reads were then mapped to the mMouse genome GRCm38 v. 80 and annotated using the ENSEMBL GRCm38 v. 86 mRNA annotation.
Assembly: GRCm38 v. 80
Supplementary files format and content: xlsx file, includes counts

source_name: kidney

extract_protocol:
RNA extraction from frozen kidney samples was performed using RNA-STAT-60 (Tel-Test, Inc. USA) according to the manufacturer's instructions followed by cDNA synthesis with random primers and Superscript II reverse transcriptase (Thermo Fisher Scientific Inc., USA).
QIAseq UPX 3’ Transcriptome Kit (QIAGEN) according to the manufacturers instruction

treatment_protocol: In order to induce RIAKI, drinking water was withheld for 19 hours, followed by IM injection of either 50% glycerol (0.05 ml per 10 g body weight; N= 10) or saline (sham controls; N= 10) into the left hind limb under isoflurane anesthesia. For pain management, Rimadyl© (5 mg/kg body weight i.p.) was administered at 0 h and 3 h. At 24 h, blood was obtained from the mandibular venous plexus. Mice were euthanized by cervical dislocation, and kidneys were snap frozen or immersion-fixed in 4 % paraformaldehyde for 24 hours.

value: kidney

value: WT

value: sham


title: mouse kidney_sham_24h_6


title: mouse kidney_rhabdomyolysis_24h_6

value: rhabdomyolysis


title: mouse kidney_sham_24h_4


title: SPF_AFD, replicate2, scRNA-seq

description: 10x Genomics

value: wild-type (SPF)


title: I-BET 762-SK-UT-1 24 RNA

city: San Antonio

first: Azad

last: Khosh

state: TX

address: 7703 Floyd Curl Dr

institute: UTHSCSA

data_processing:
The quality of reads controlled using FastQC, version 0.73 then reads were processed  using Trimmomatic, and parameters were chosen to trim the reads  according to FastQC results. The reads were mapped to the human reference genome,  version hg38 using Hisat2, version 2.2.1. Next, raw reads were mapped to the  human reference transcriptome using featurecounts, version 2.0.3 and annotation  file of Gencode, version V41. Gene counts pre-processed and normalized using  the DESeq2 package in R, version 1.36.0. quality of samples examined using  comparative boxplot and PCA and outlier samples excluded from the analysis.  Differentially expressed genes identify using DESeq2.
Assembly: HG38
Supplementary files format and content: csv format

source_name: uterine leiomyosarcoma cell line

extract_protocol:
We performed whole transcriptome analysis to determine the mechanism  underlying the inhibitory effect of BET protein inhibition on the uLMS. The SK-UT-1 cells  were treated with BET protein inhibitors JQ1 and I-BET 762 at a concentration of 5 µM  for 48 h. RNA was isolated using Trizol. RNA quality and quantity were assessed using  the Agilent bio-analyzer.
Strand-specific RNA-Seq libraries were prepared using a  TruSeq total RNA-Seq library protocol (Illumina provided). Library quality and quantity  were assessed using the Agilent bio-analyzer, and libraries were sequenced using an  Illumina NovaSEQ6000 (illumine provided reagents and protocols).

value: uterine leiomyosarcoma cell line

value: human uterine leiomyosarcoma

value: I-BET 762


title: I-BET 762-SK-UT-1 23 RNA


title: mouse kidney_rhabdomyolysis_24h_5


title: MCF-7_Nutlin-3a_2

value: breast

value: wild-type

value: Nutlin-3a 10 µM 24 h


title: mouse kidney_sham_24h_2


title: I-BET 762-SK-UT-1 21 RNA


title: mouse kidney_rhabdomyolysis_24h_4


title: mouse kidney_sham_24h_3


title: GF_NCD, replicate1, scRNA-seq

description: 10x Genomics

value: Peyer's patches

value: 10-12 weeks old

value: wild-type (germ-free)


title: SPF_AFD, replicate1, scRNA-seq

description: 10x Genomics

value: AFD


title: JQ1 -SK-UT-1 20 RNA


title: SPF_NCD, replicate1, scRNA-seq

description: 10x Genomics

value: NCD


title: mouse kidney_rhabdomyolysis_24h_1


title: JQ1 -SK-UT-1 19 RNA


title: mouse kidney_rhabdomyolysis_24h_2


title: mouse kidney_sham_24h_1


title: Aorta_30mo_4

city: Osaka-shi

first: Masaki

last: Takasugi

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

institute: Osaka Metropolitan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC.
Trimmed sequence reads were mapped to GRCm39 using STAR.
Read count extraction was performed using RSEM.
Count data were normalized using DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Aorta

extract_protocol:
Mice were euthanized and tissues were collected and immediately frozen pulverized in liquid nitrogen. Pulverized tissues were homogenized in RNAiso Plus (Takara) reagent using pestle and then RNA was isolated following the manufacturer's instructions.
The sequencing libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina) following the manufacturer's instructions.

value: Aorta

value: Wild-type


title: Aorta_30mo_3


title: Proximal, Group 4, scRNAseq

city: Ithaca

first: Coulter

last: Ralston

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

description:
mP4
10X Genomics (Single Cell 3' v2)

data_processing:
The raw sequencing reads were aligned to the mm39 reference genome and quantified using the cellranger (v6.1.2, 10x Genomics) count function. The outputs are barcode, feature, and matrix files for further analysis involving gene counts
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Uterine Tube (Oviduct)

extract_protocol:
Each uterine tube was placed in sterile PBS containing 100 IU ml-1 of penicillin and 100 µg ml-1 streptomycin (Corning, 30-002-Cl), and separated in distal and proximal regions. Tissues from the same region were combined in a 40 µl drop of the same PBS solution, cut open lengthwise, and minced into 1.5-2.5 mm pieces with 25G needles. Minced tissues were transferred with help of a sterile wide bore 200 µl pipette tip into a 1.8 ml cryo vial containing 1.2 ml A-mTE-D1 (300 IU ml-1 collagenase IV mixed with 100 IU ml-1 hyaluronidase; Stem Cell Technologies, 07912, in DMEM Ham’s F12, Hyclone, SH30023.FS). Tissues were incubated with loose cap for 1 h at 37°C in a 5% CO2 incubator. During the incubation tubes were taken out 4 times and tissues suspended with a wide bore 200 µl pipette tip. At the end of incubation, the tissue-cell suspension from each tube was transferred into 1 ml TrypLE (Invitrogen, 12604013) pre-warmed to 37°C, suspended 70 times with a 1000 µl pipette tip, 5 ml A-SM [DMEM Ham’s F12 containing 2% fetal bovine serum (FBS)] were added to the mix, and TE cells were pelleted by centrifugation 300x g for 10 minutes at 25°C. Pellets were then suspended with 1 ml pre-warmed to 37°C A-mTE-D2 (7 mg ml-1 Dispase II, Worthington NPRO2, and 10 µg ml-1 Deoxyribonuclease I, Stem Cell Technologies, 07900), and mixed 70 times with a 1000 µl pipette tip. 5 ml A-mTE-D2 was added and samples were passed through a 40 µm cell strainer, and pelleted by centrifugation at 300x g for 7 minutes at +4°C. Pellets were suspended in 100 µl microbeads per 107 total cells or fewer, and dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) according to the manufacturer’s protocol. Pelleted live cell fractions were collected in 1.5 ml low binding centrifuge tubes, kept on ice, and suspended in ice cold 50 µl A-Ri-Buffer (5% FBS, 1% GlutaMAX-I, Invitrogen, 35050-079, 9 µM Y-27632, Millipore, 688000, and 100 IU ml-1 penicillin 100 μg ml-1 streptomycin in DMEM Ham’s F12). Cell aliquots were stained with trypan blue for live and dead cell calculation. Live cell preparations with a target cell recovery of 5,000-6,000 were loaded on Chromium controller (10X Genomics, Single Cell 3' v2 chemistry) to perform single cell partitioning and barcoding using the microfluidic platform device. After preparation of barcoded, next-generation sequencing cDNA libraries samples were sequenced on Illumina NextSeq500 System.
The libraries were prepared with the chromium Single Cell 3' reagent kit (10X Genomics, Single Cell 3' v2 chemistry) following the maunfacturer's instructions. Live cell preparations were loaded with a target cell recovery of 5,000-6,000.

value: Uterine Tube (Oviduct)

tag: tissue section

value: proximal section


title: Proximal, Group 3, scRNAseq

description:
mP3
10X Genomics (Single Cell 3' v2)


title: Proximal, Group 2, scRNAseq

description:
mP2
10X Genomics (Single Cell 3' v2)


title: Aorta_30mo_2


title: Distal, Group 3, scRNAseq

description:
mD4
10X Genomics (Single Cell 3' v2)

value: distal section


title: JQ1 -SK-UT-1 17 RNA


title: Aorta_30mo_1


title: d_erf1_input_trex

source_name: HEK293 Flp-In T-REx

value: HEK293 Flp-In T-REx

value: Human embryonic kidney

value: Naive


title: VEH-SK-UT-1 15 RNA

value: uterine leiomyosarcoma cell line

value: human uterine leiomyosarcoma

value: VEH


title: I-BET 762-SK-UT-1 22 RNA

value: I-BET 762