title: Mixed SOD1 early-stage and control, sample 4

city: Stanford

first: Olivia

last: Gautier

state: CA

address: 279 Campus Dr

institute: Stanford University

description: Library name: sod1_mn_nuclei_2_9

data_processing:
Sequencing reads were demultiplexed and aligned to a custom mouse pre-mRNA reference transcriptome containing mutant hSOD1 (10x Genomics) using the cellranger mkfastq and cellranger count pipelines (Cell Ranger v3.1.0, 10x Genomics).
Subsequent analyses were performed in R (v4.1.1) using the Seurat package (v4.0.4) to produce the .rds files.
Assembly: mm10
Supplementary files format and content: h5 files

molecule: nuclear RNA

source_name: Spinal cord

extract_protocol:
Nuclei were isolated from mouse spinal cords and sorted using FANS.
Libraries were constructed according to the manufacturer's protocol (Chromium Single Cell 3′ Reagent Kit v3, 10x Genomics).

value: Spinal cord


title: siGATA6, +DEX, BT549 cells, Biorep1

status: Public on Aug 27 2025

type: SRA

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: transcriptomic

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove low quality read.
FeatureCounts were used to quantify raw read coverage before further analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Raw FeatureCounts

molecule: total RNA

organism: Homo sapiens

growth_protocol: BT549 and MDA-MB-231 cells were maintained in RPMI supplemented with 10% FBS and antibiotics and culutred at 37 degress and 5% CO2

extract_protocol:
Total RNA was harvested from cells with Tri-reagent (Sigma-Aldrich, 93289) and purified with chloroform on EconoSpin Columns (EconoSpin, 1910). Ribosomal RNA was depleted using the NEBNext rRNA depletion kit (Biolabs, E6310) before the library was prepared with the NEBNext RNA Library Prep kit (Biolabs, E7540).
Samples were sequenced on a NovaSeq 6000 (Illumina) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 500nM DEX (dissolved in water) for 2h or 4h, 10μM BRM014 (dissolved in DMSO) for 4h, SMARTpool siRNA used for 72h knock-down of GATA6

tag: sirna

tag: cell line

tag: cell type

value: TNBC

tag: genotype

value: WT

tag: treatment

value: 2h Dex (500nM)


title: Mixed SOD1 early-stage and control, sample 3

country: USA

description: Library name: sod1_mn_nuclei_2_1

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue


title: Mixed SOD1 early-stage and control, sample 2

description: Library name: sod1_mn_nuclei_1_16b


title: SK_4VID_F05, calcifediol, time 0

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: SK_4VID_F05

data_processing:
Bulk RNA data were processed using  WARDEN workflow for the analysis of RNA-Seq differential expression (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: expression_matrix.txt

source_name: Blood

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Blood

value: CD14 Monocyte

value: calcifediol

tag: time (day)


title: prostate_cancer_primary_79 (STAMPEDE)

type: RNA

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was normalized uisng SCAN (SCAN.UPC package from Bioconductor)
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg38.core.mps

label: biotin

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by an expert pathologist, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the FFPE block with the biopsy core containing the highest pathologic Gleason grade and the greatest linear length of tumor. At least 0.5 mm of linear tumor was required. Tissue sections were macrodissected to enrich for tumor used for RNA extraction.

treatment_protocol: Not Applicable

tag: gleason score

tag: age at randomization

tag: psa at randomization (ng/ml)

value: FFPE prostate cancer


title: siGATA6, Veh, BT549 cells, Biorep3

value: Veh


title: Mixed SOD1 early-stage and control, sample 1

description: Library name: sod1_mn_nuclei_1_15


title: SK_4VID_F03, calcitriol, time 0

description: Library name: SK_4VID_F03

value: calcitriol


title: prostate_cancer_primary_77 (STAMPEDE)


title: siGATA6, Veh, BT549 cells, Biorep2


title: Mixed SOD1 mid-stage and control, sample 2

description: Library name: sod1_mn_nuclei_3_5


title: siGATA6, Veh, BT549 cells, Biorep1


title: SK_4VID_F01, placebo, time 0

description: Library name: SK_4VID_F01

value: placebo


title: SK_4VID_E12, placebo, time 2

description: Library name: SK_4VID_E12


title: Mixed SOD1 mid-stage and control, sample 1

description: Library name: sod1_mn_nuclei_2_20


title: siCtl, +DEX, BT549 cells, Biorep3

value: siCtl


title: SOD1 mid-stage, sample 2

description: Library name: SI-GA-G8


title: SK_4VID_E11, placebo, time 0

description: Library name: SK_4VID_E11


title: SK_4VID_F04, calcitriol, time 2

description: Library name: SK_4VID_F04


title: prostate_cancer_primary_76 (STAMPEDE)


title: SOD1 mid-stage, sample 1

description: Library name: SI-GA-H7


title: prostate_cancer_primary_78 (STAMPEDE)


title: prostate_cancer_primary_75 (STAMPEDE)


title: SK_4VID_E10, calcifediol, time 2

description: Library name: SK_4VID_E10


title: siCtl, +DEX, BT549 cells, Biorep2


title: CHIP005, LMNB1, siControl, Rep3

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

institute: University of Pennsylvania

description: Library name: CHIP005

library_source: genomic

data_processing:
Basecalling was performed with bcl2fastq v2.20. Reads were deduplicated, trimmed, and filtered for low complexity using fastp v0.23.2. High-quality reads (MAPQ >20) were aligned to the UCSC hg38 genome with Bowtie2 v2.5.1, and only uniquely mapped reads were retained using sambamba v1.0.0.
ChIP-seq coverage plots were generated by extending mapped reads to 120 bp to approximate fragment sizes, normalizing to counts per million (CPM), computing log₂ ratios over input, and z-scaling the resulting signal. The resulting bigwig files were generated using deeptools v3.1.3. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
Broad domains for LB1, H3K9me3, H3K9me3, and H3K27me3 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed files with domain calls per condition as described above.

molecule: genomic DNA

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml-1 penicillin, and 100 µg ml-1 streptomycin at 37°C with 5% CO2.

extract_protocol:
ChIP-seq was performed as previously described(Shah et al. 2023; 2021). HCT116 cells were crosslinked in culture by addition of methanol-free formaldehyde (Pierce, final 1% v/v) for 10minutesat room temperature with gentle rotation. Crosslinking was quenched by addition of glycine (final 125 mM) for 5minuteswith gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (1500 rpm, 3 minutes at room temperature). Resulting pellets were flash frozen in liquid nitrogen and stored at −80°C. For ChIP, 30μL protein G magnetic beads (per ChIP sample; ThermoFisher) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250μL blocking buffer and 2μg antibody (Lamin B1, Abcam, ab16048; H3K9me2, Abcam, ab1220; H3K9me3, Abcam, ab8898; H3K27me3, Cell Signaling Technology, #9733) and rotated at 4°C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate or equivalent cell number) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors), and rotated at 4°C for 10 minutes, followed by centrifugation (1500 rpm at 4°C for 3 minutes). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (1500 rpm at 4°C for 3 minutes). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris). Samples were sonicated using a Covaris S220 sonicator (High Cell Chromatin Shearing: PIP 140W, CPB 200, Duty Factor 5%, 15 minutes). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4°C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bio-Rad Protein Assay Kit (Bio-Rad, Protein Assay Kit #5000002). Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50μL blocking buffer and added to 500μg input protein for overnight incubation with rotation at 4°C. 50μg lysate was stored at −20°C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) with inversion to mix followed by 2-minute incubation on ice for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes at room temperature before final resuspension in 210μL elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65°C for 30 minutes. 200μL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65°C with agitation for a minimum of 12 hours, but not more than 18 hours. 200μL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were treated with RNaseA (final 0.2mg/mL RNase; 37°C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55°C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
ChIP and input DNA were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit according to manufacturer’s instructions (NEB). Samples were indexed for multiplex sequencing with dual unique indices (NEBNext Multiplex Oligos for Illumina). Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (NEBNext Library Quant Kit). Libraries were pooled for multiplex sequencing, re-quantified, and sequenced on the Illumina NextSeq1000 platform (121bp single-end sequencing).

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium and pipetted onto siRNA (nontargeting control or HNRNPK). The mixture was incubated at room temperature for 20 minutes. HCT116 cells were harvested by trypsinization, resuspended in antibiotic-free medium, and plated onto siRNA duplexes for a final siRNA concentration of 25 nM. Cells were collected for extraction after 72 hours of RNAi treatment.

value: Human colon cancer

tag: chip antibody

value: LMNB1 (abcam, #ab16048)

value: Nontargeting control siRNA


title: SK_4VID_E09, calcifediol, time 0

description: Library name: SK_4VID_E09


title: siCtl, +DEX, BT549 cells, Biorep1


title: SOD1 end-stage, sample 2

description: Library name: SI-GA-F7


title: prostate_cancer_primary_73 (STAMPEDE)


title: prostate_cancer_primary_74 (STAMPEDE)


title: SK_4VID_F02, placebo, time 2

description: Library name: SK_4VID_F02


title: siCtl, Veh, BT549 cells, Biorep3


title: SK_4VID_E08, placebo, time 2

description: Library name: SK_4VID_E08


title: prostate_cancer_primary_72 (STAMPEDE)


title: SOD1 end-stage, sample 1

description: Library name: SI-GA-G7


title: siCtl, Veh, BT549 cells, Biorep2


title: siCtl, Veh, BT549 cells, Biorep1


title: SK_4VID_E07, placebo, time 0

description: Library name: SK_4VID_E07


title: Input, +DEX, BT549 cells_2

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove PCR duplicates and low quality reads, before MACS2 was used to call peaks using defult settings, except summits were set to 300
Homer was used to generate files for plotting the data of the regions of interest.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files the ChIP-seq data or MACS2 called peaks in narrowPeak format

growth_protocol: BT549 cells were maintained in RPMI supplemented with 10% HI FBS and antibiotics and culutred at 37 degrees and 5% CO2

extract_protocol:
For each chromatin immunoprecipitation, cells from two 15cm plates were crosslinked at RT using 2mM disuccinimidyl glutarate (DSG) for 20min followed by 1% formaldehyde for 10min, which was quenched in 0.1M glycine for 10min. Cells were washed twice in cold PBS and scraped off in cold PBS containing protease inhibitors (Roche, Complete 11836170001 and Halt, Thermo Scientific, 78438). Crosslinked material was resuspended in lysis buffer 1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10min followed by 5min in lysis buffer 2 (10mM Tris-HCL pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) before resuspending in lysis buffer 3 (10mM Tris-HCL pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0,5% N-lauroylsarcosine). Samples were sonicated using Covaris Ultrasonicator ME220 until DNA fragments had a size between 150-500bp. Chromatin was immunoprecipitated overnight using protein A coated dynabeads (Dynabeads, 10002D) with specific antibodies. After washing the beads, chromatin was eluted and decrosslinked by incubating at 65 degrees over-night in elution buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS). Samples were treated with RNase A (20ng/mL) for 1h followed by proteinase K (200ng/mL) for 2h before DNA was purified by standard phenol-chloroform purification.
Purified DNA was submitted to library preparation using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E765). The samples were sequenced on a NovaSeq 6000 (Illumi-na) to reach approximately 25M paired-end reads per sample.

tag: antibody

value: 4h DEX (500nM)


title: prostate_cancer_primary_70 (STAMPEDE)


title: Newborn_keratinocytes_KLF3_Rep1

city: Ithaca

first: Tudorita

last: Tumbar

state: NY

address: 526 Campus Rd

department: Molecular biology and genetics

institute: Cornell University

description: Library name: Sample 7

data_processing:
Sequencing was performed on a NovaSeq 6000 platform (NovoGene Inc, CA, USA) with 2×150 bp paired-end reads. Raw sequencing data quality was checked using FastQC, followed by adapter trimming using Cutadapt (minimum read length: 20 bp; minimum adapter overlap: 10 bp). Trimmed reads were aligned to the mouse genome (mm39) with Bowtie2 in end-to-end very-sensitive mode. IP samples were normalized against background (input) controls using bamCompare (deepTools) with CPM normalization, followed by subtracting background from IP signals (bin size: 10 bp; minimum mapping quality: 30). Cleaned bedGraph files were sorted and converted to bigWig format using bedGraphToBigWig, and the resulting bigWig files were used for further analyses. Mean CUT&RUN signals of select regions were calculated using bedtools map (-o mean) on cleaned bedGraph files.
Assembly: mm39
Supplementary files format and content: Sample specific bigwig files.
Library strategy: CUT&Run

source_name: Skin

growth_protocol: For the CUT&RUN experiments, newborn skin samples were incubated in Dispase at 4°C for 30 minutes, epidermis was separated from the dermis and incubated with trypsin for 10 minutes at RT.

extract_protocol:
CUT&RUN experiments for H3K27ac, NRF1, KLF3, and BRD4 were performed on freshly isolated newborn keratinocytes using the CUTANA™ CUT&RUN Kit Version 4 (EpiCypher) according to the manufacturer’s protocol. Antibodies used for CUT&RUN include: H3K27ac (Active Motif, 39134), and Atlas Antibodies for NRF1 (HPA029329), KLF3 (HPA065054), BRD4 (HPA061646).
Libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) and multiplexed using NEBNext® Multiplex Oligos for Illumina (Index Primers Set 1).

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre


title: Newborn_keratinocytes_KLF3_Rep2

description: Library name: Sample 8


title: Newborn_keratinocytes_NRF1_Rep2

description: Library name: Sample 6


title: prostate_cancer_primary_71 (STAMPEDE)


title: SK_4VID_E05, calcifediol, time 0

description: Library name: SK_4VID_E05


title: prostate_cancer_primary_68 (STAMPEDE)


title: BRG1 ChIP, +DEX, BT549 cells, Biorep3

value: TNBC


title: prostate_cancer_primary_67 (STAMPEDE)


title: SK_4VID_E04, calcifediol, time 2

description: Library name: SK_4VID_E04


title: Newborn_keratinocytes_NRF1_Rep1

description: Library name: Sample 5


title: SK_4VID_E03, calcifediol, time 0

description: Library name: SK_4VID_E03


title: SK_4VID_E02, calcitriol, time 2

description: Library name: SK_4VID_E02


title: Newborn_keratinocytes_BRD4_Rep2

description: Library name: Sample 4


title: Input, Veh, BT549  cells


title: BRG1 ChIP, +DEX, BT549 cells, Biorep1


title: prostate_cancer_primary_69 (STAMPEDE)


title: prostate_cancer_primary_66 (STAMPEDE)


title: prostate_cancer_primary_65 (STAMPEDE)


title: SK_4VID_E06, calcifediol, time 2

description: Library name: SK_4VID_E06


title: SK_4VID_E01, calcitriol, time 0

description: Library name: SK_4VID_E01


title: prostate_cancer_primary_64 (STAMPEDE)


title: BRG1 ChIP, Veh, BT549 cells, Biorep2


title: prostate_cancer_primary_62 (STAMPEDE)


title: SK_4VID_D12, calcitriol, time 2

description: Library name: SK_4VID_D12


title: Newborn_keratinocytes_H3K27ac_Rep1

description: Library name: Sample 1


title: prostate_cancer_primary_61 (STAMPEDE)


title: BRG1 ChIP, Veh, BT549 cells, Biorep1


title: prostate_cancer_primary_63 (STAMPEDE)


title: SK_4VID_D11, calcitriol, time 0

description: Library name: SK_4VID_D11


title: KCT3266:mCAFs cells, C57BL6, EC359+Gem-3

city: Omaha

first: Sushil

last: Kumar

state: NE

address: 985870 Nebraska Medical Center, DRC1

institute: UNMC

description:
Library name: GE3
Column name: GE-3

data_processing:
Arraystar RNA sequnceing workflow was used for the analysis. Raw sequences were processed for quality control using FastQC.
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software.
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown.
Differentially expressed gene and transcript analyses were performed with R package ballgown.
Assembly: GRCm38 Mus musculus from GenCode
Supplementary files format and content: tab-delimited text file includes raw counts (FPKM_counts_C_E_G_GE.txt)

growth_protocol: The PDAC cell lines from  mice (KCT3266 derived from KPC tumors), and CAFs were cultured at 370C with 5% carbon dioxide in a humidified chamber in DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
RNA isolated from orthotopic tumors treated with vehicle, EC359, Gem, and EC359+Gem was analyzed by RNA sequencing (Novogene Co. Ltd., CA) using the Arraystar RNA Sequencing service, which includes library preparation, sequencing, quality control, and mapping (mapping statistic summary, transcript coverage)
Briefly, mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module. Alternatively, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched mRNA or rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina).

treatment_protocol: For the orthotopic model, PDAC cells were mixed with CAFs (viability>95%) in a 1:1 ratio and implanted into mice pancreas at 2.5x105 cells in 50 µl phosphate buffer saline (PBS) in 6-8-weeks-old C57BL/6 (murine cells), mice (male and female). As the tumors were palpable (~10 days), the animals were randomly divided into four groups and treated with vehicle (PBS), EC359 (E, 5 mg/kg body weight), Gem (G, 25 mg/kg body weight, IP), and a combination of EC359 and Gem (E+G). After the therapy, animals were euthanized, and organs were harvested for further analysis.

value: Orthotopic tumor cells

value: EC359 + Gemcitabine


title: BRG1 ChIP, +DEX, BT549 cells, Biorep2


title: Newborn_keratinocytes_H3K27ac_Rep2

description: Library name: Sample 2


title: KCT3266:mCAFs cells, C57BL6, EC359+Gem-2

description:
Library name: GE2
Column name: GE-2


title: SK_4VID_D10, calcifediol, time 2

description: Library name: SK_4VID_D10

value: Blood

value: CD14 Monocyte


title: Input, +DEX +BRM014, BT549 cells


title: MED1 ChIP, +DEX +BRM014, BT549 cells, Biorep2

value: Bethyl laboratories A300-793A lot:10


title: KCT3266:mCAFs cells, C57BL6, EC359+Gem-1

description:
Library name: GE1
Column name: GE-1


title: prostate_cancer_primary_60 (STAMPEDE)

value: FFPE prostate cancer


title: SK_4VID_D09, calcifediol, time 0

description: Library name: SK_4VID_D09

value: calcifediol


title: SK_4VID_D08, calcitriol, time 2

description: Library name: SK_4VID_D08

value: calcitriol


title: KCT3266:mCAFs cells, C57BL6, Gem-3

description:
Library name: G3
Column name: G-3

value: Gemcitabine 25 mg/kg body weight


title: MED1 ChIP, +DEX +BRM014, BT549 cells, Biorep1


title: KCT3266:mCAFs cells, C57BL6, Gem-2

description:
Library name: G2
Column name: G-2


title: prostate_cancer_primary_58 (STAMPEDE)


title: MYC ChIP, +DEX +BRM014, BT549 cells, Biorep2

value: Cell Signaling (D3N8F) 13987 lot:5


title: SK_4VID_D07, calcitriol, time 0

description: Library name: SK_4VID_D07


title: MYC ChIP, +DEX +BRM014, BT549 cells, Biorep1


title: KCT3266:mCAFs cells, C57BL6, Gem-1

description:
Library name: G1
Column name: G-1


title: prostate_cancer_primary_57 (STAMPEDE)


title: SK_4VID_D06, placebo, time 2

description: Library name: SK_4VID_D06

value: placebo


title: GR ChIP, +DEX +BRM014, BT549 cells, Biorep3

value: Cell Signaling (D6H2L) 12041 lot:3


title: SK_4VID_D05, placebo, time 0

description: Library name: SK_4VID_D05


title: KCT3266:mCAFs cells, C57BL6, EC359-3

description:
Library name: E3
Column name: E-3

value: EC359 5 mg/kg body weight


title: prostate_cancer_primary_55 (STAMPEDE)


title: GR ChIP, +DEX +BRM014, BT549 cells, Biorep2


title: KCT3266:mCAFs cells, C57BL6, EC359-2

description:
Library name: E2
Column name: E-2


title: prostate_cancer_primary_56 (STAMPEDE)


title: GR ChIP, +DEX +BRM014, BT549 cells, Biorep1


title: SK_4VID_D04, calcitriol, time 2

description: Library name: SK_4VID_D04


title: KCT3266:mCAFs cells, C57BL6, EC359-1

description:
Library name: E1
Column name: E-1


title: KCT3266:mCAFs cells, C57BL6, Control3

description:
Library name: C3
Column name: C-3

value: Vehicle Control


title: prostate_cancer_primary_59 (STAMPEDE)


title: SK_4VID_D02, calcitriol, time 2

description: Library name: SK_4VID_D02


title: Input, +DEX, BT549 cells_1

value: 4h DEX (500nM) +DMSO


title: prostate_cancer_primary_54 (STAMPEDE)


title: MED1 ChIP, +DEX, BT549 cells, Biorep2


title: SK_4VID_D01, calcitriol, time 0

description: Library name: SK_4VID_D01


title: MED1 ChIP, +DEX, BT549 cells, Biorep1


title: KCT3266:mCAFs cells, C57BL6, Control2

description:
Library name: C2
Column name: C-2


title: KCT3266:mCAFs cells, C57BL6, Control1

description:
Library name: C1
Column name: C-1


title: MYC ChIP, +DEX, BT549 cells, Biorep2


title: prostate_cancer_primary_51 (STAMPEDE)


title: SK_4VID_C12, calcifediol, time 2

description: Library name: SK_4VID_C12


title: Macrophage_U18666A_rep 3

city: Sioux Falls

first: Kevin

middle: R

last: Francis

state: SD

department: Cellular Therapies

institute: Sanford Research

description:
Library name: Sample 19
Column name in raw_counts: M3 U18

data_processing:
Read mapping to the reference genome used HISAT2 and identification of differentially expressed genes utilized DESeq2. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Mus musculus GRCm39/mm39
Supplementary files format and content: tab-delimited text file provides raw counts for each sample

source_name: Bone marrow isolation

growth_protocol: Bone marrow derived macrophages isolated from the femur of C57/Bl6J mice were maintained at 37 degrees celsium in a humidified incubator in DMEM, 20% (v/v) fetal bovine serum, 0.1% (v/v) penicillin/streptomycin, 50 ng/mL colony-stimulating factor 1, and 57.6 nM β-mercaptoethanol.  Media was equilibrated to pH 7.4 by placing it in an incubator set to 37 degree C and 5% CO2 prior to use.

extract_protocol:
RNA was extracted with on-column DNase digestion performed using the RNeasy mini kit following manufacturer’s instructions.
cDNA library preparation from mRNA utilized the Abclonal mRNA-seq Lib Prep Kit for Illumina.

treatment_protocol: Cells were washed gently with PBS and cultured in media containing 20% (v/v) lipoprotein-deficient serum (LPDS) for 48 h or media containing LPDS and simvastatin (1 uM), AY9944 (1 uM), or U18666A (20 nM).

value: Bone marrow isolation

value: Bone marrow derived macrophages

value: Macrophage

value: Wild-type

tag: batch


title: prostate_cancer_primary_50 (STAMPEDE)


title: Macrophage_U18666A_rep 4

description:
Library name: Sample 20
Column name in raw_counts: M4 U18


title: SK_4VID_C10, placebo, time 2

description: Library name: SK_4VID_C10

value: Blood


title: SK_4VID_C11, calcifediol, time 0

description: Library name: SK_4VID_C11

value: CD14 Monocyte


title: GR ChIP, +DEX, BT549 cells, Biorep3

value: TNBC


title: prostate_cancer_primary_49 (STAMPEDE)

value: FFPE prostate cancer


title: SK_4VID_C09, placebo, time 0

description: Library name: SK_4VID_C09


title: SK_4VID_D03, calcitriol, time 0

description: Library name: SK_4VID_D03


title: Macrophage_U18666A_rep 2

description:
Library name: Sample 18
Column name in raw_counts: M2 U18


title: MYC ChIP, +DEX, BT549 cells, Biorep1


title: prostate_cancer_primary_53 (STAMPEDE)


title: prostate_cancer_primary_48 (STAMPEDE)


title: GR ChIP, +DEX, BT549 cells, Biorep2


title: SK_4VID_C08, calcitriol, time 2

description: Library name: SK_4VID_C08


title: Macrophage_U18666A_rep 1

description:
Library name: Sample 17
Column name in raw_counts: M1 U18


title: GR ChIP, +DEX, BT549 cells, Biorep1


title: prostate_cancer_primary_52 (STAMPEDE)


title: SK_4VID_C07, calcitriol, time 0

description: Library name: SK_4VID_C07


title: Input, siGATA6, +DEX, BT549 cells

value: 2h DEX (500nM)


title: Macrophage_AY9944_rep 4

description:
Library name: Sample 16
Column name in raw_counts: M4 AY


title: prostate_cancer_primary_47 (STAMPEDE)


title: prostate_cancer_primary_45 (STAMPEDE)


title: Macrophage_AY9944_rep 3

description:
Library name: Sample 15
Column name in raw_counts: M3 AY


title: prostate_cancer_primary_44 (STAMPEDE)


title: prostate_cancer_primary_46 (STAMPEDE)


title: GR ChIP, siGATA6, +DEX, BT549, Biorep3

value: Cell Signaling (D6H2L) 12041 lot:09/2020


title: SK_4VID_C06, calcifediol, time 2

description: Library name: SK_4VID_C06

value: calcifediol


title: GR ChIP, siGATA6, +DEX, BT549, Biorep2


title: SK_4VID_C05, calcifediol, time 0

description: Library name: SK_4VID_C05


title: Macrophage_AY9944_rep 1

description:
Library name: Sample 13
Column name in raw_counts: M1 AY


title: SK_4VID_C04, placebo, time 2

description: Library name: SK_4VID_C04


title: prostate_cancer_primary_43 (STAMPEDE)


title: GR ChIP, siGATA6, +DEX, BT549, Biorep1


title: SK_4VID_C03, placebo, time 0

description: Library name: SK_4VID_C03


title: Macrophage_Simvastatin_rep 4

description:
Library name: Sample 12
Column name in raw_counts: M4 Simv

value: Simvastatin


title: MED1 ChIP, siGATA6, +DEX, BT549, Biorep3

value: Bethyl laboratories A300-793A lot:10


title: prostate_cancer_primary_42 (STAMPEDE)


title: SK_4VID_C02, calcifediol, time 2

description: Library name: SK_4VID_C02


title: prostate_cancer_primary_41 (STAMPEDE)


title: Macrophage_Simvastatin_rep 3

description:
Library name: Sample 11
Column name in raw_counts: M3 Simv


title: MED1 ChIP, siGATA6, +DEX, BT549, Biorep2


title: Macrophage_Simvastatin_rep 2

description:
Library name: Sample 10
Column name in raw_counts: M2 Simv


title: prostate_cancer_primary_40 (STAMPEDE)


title: SK_4VID_C01, calcifediol, time 0

description: Library name: SK_4VID_C01


title: MED1 ChIP, siGATA6, +DEX, BT549, Biorep1


title: SK_4VID_B12, placebo, time 2

description: Library name: SK_4VID_B12

value: placebo


title: Newborn_keratinocytes_BRD4_Rep1

description: Library name: Sample 3

value: Skin

value: Keratinocytes

value: Polr2b.fl.fl.GFP; K14Cre


title: Input, siGATA6, Veh, BT549 cells

value: Veh


title: Macrophage_AY9944_rep 2

description:
Library name: Sample 14
Column name in raw_counts: M2 AY

value: Bone marrow isolation

value: Bone marrow derived macrophages


title: Macrophage_LPDS_rep 3

description:
Library name: Sample 7
Column name in raw_counts: M3 LPDS

value: Macrophage

value: Wild-type

value: LPDS culture


title: SK_4VID_B11, placebo, time 0

description: Library name: SK_4VID_B11

value: Blood

value: CD14 Monocyte


title: prostate_cancer_primary_37 (STAMPEDE)

value: FFPE prostate cancer


title: SK_4VID_B10, placebo, time 2

description: Library name: SK_4VID_B10


title: prostate_cancer_primary_39 (STAMPEDE)


title: MED1 ChIP, siGATA6, Veh, BT549, Biorep2

value: TNBC


title: Macrophage_LPDS_rep 2

description:
Library name: Sample 6
Column name in raw_counts: M2 LPDS


title: SK_4VID_B09, placebo, time 0

description: Library name: SK_4VID_B09


title: Macrophage_LPDS_rep 1

description:
Library name: Sample 5
Column name in raw_counts: M1 LPDS


title: prostate_cancer_primary_36 (STAMPEDE)


title: Macrophage_FBS_rep 4

description:
Library name: Sample 4
Column name in raw_counts: M4 FBS

value: FBS culture


title: Macrophage_Simvastatin_rep 1

description:
Library name: Sample 9
Column name in raw_counts: M1 Simv

value: Simvastatin


title: SK_4VID_B08, calcifediol, time 2

description: Library name: SK_4VID_B08

value: calcifediol


title: prostate_cancer_primary_34 (STAMPEDE)


title: prostate_cancer_primary_35 (STAMPEDE)


title: SK_4VID_B07, calcifediol, time 0

description: Library name: SK_4VID_B07


title: GR ChIP, siCtl, +DEX, BT549, Biorep3

value: siCtl

value: Cell Signaling (D6H2L) 12041 lot:09/2020

value: 2h DEX (500nM)


title: Macrophage_FBS_rep 3

description:
Library name: Sample 3
Column name in raw_counts: M3 FBS


title: Macrophage_LPDS_rep 4

description:
Library name: Sample 8
Column name in raw_counts: M4 LPDS


title: SK_4VID_B06, placebo, time 2

description: Library name: SK_4VID_B06

value: placebo


title: GR ChIP, siCtl, +DEX, BT549, Biorep2


title: MED1 ChIP, siGATA6, Veh, BT549, Biorep3

value: Bethyl laboratories A300-793A lot:10

value: Veh


title: Macrophage_FBS_rep 2

description:
Library name: Sample 2
Column name in raw_counts: M2 FBS

value: Bone marrow isolation

value: Bone marrow derived macrophages


title: prostate_cancer_primary_33 (STAMPEDE)


title: SK_4VID_B05, placebo, time 0

description: Library name: SK_4VID_B05


title: prostate_cancer_primary_32 (STAMPEDE)


title: prostate_cancer_primary_38 (STAMPEDE)


title: prostate_cancer_primary_31 (STAMPEDE)


title: GR ChIP, siCtl, +DEX, BT549, Biorep1


title: Macrophage_FBS_rep 1

description:
Library name: Sample 1
Column name in raw_counts: M1 FBS

value: Macrophage

value: Wild-type


title: SK_4VID_B04, calcitriol, time 2

description: Library name: SK_4VID_B04

value: Blood

value: calcitriol


title: MED1 ChIP, siCtl, +DEX, BT549, Biorep3


title: MED1 ChIP, siGATA6, Veh, BT549, Biorep1


title: Input, siCtl, +DEX, BT549 cells


title: prostate_cancer_primary_30 (STAMPEDE)

value: FFPE prostate cancer


title: BMDM, stearic acid, 100 uM, 24 hours, rep 3

first: Sam

middle: J

last: McCright

address: 3615 Civic Center Blvd.

department: Division of Allergy and Immunology

institute: Children's Hospital of Philadelphia

description: Library name: SA_24h_3

data_processing:
Samples were demultiplexed using DRAGEN
Further processing was performed using CLC Genomics Workbench Version 21.0.4
Sequence reads were mapped to GRCm38 / mm10 using parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: mm10
Supplementary files format and content: csv files contain TPM and RPKM values for each sample

molecule: polyA RNA

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages were generated by culturing bone marrow with 10 ng/mL of M-CSF (PeproTech) in complete media for 7 days in 10 cm non-tissue treated polystyrene plates. Additional media containing M-CSF was added on day 3. Differentiated cells were harvested by brief incubation on ice followed by gentle scraping. Cells were plated at a density of 250,000 cells / well in 24 well plates for gene expression studies.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and RNeasy Plus Mini kits (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared using an Illumina TruSeq Stranded mRNA library preparation kit according to manufacturer's protocol.

treatment_protocol: One day after replating, media was removed, cells were washed with PBS, and treatment media with 100 uM stearic acid (or an equivalent volume of vehicle) was added. Cells were treated for 24 hours.

value: bone marrow derived macrophages

value: stearic acid, 100 uM, 24 hr


title: SK_4VID_B03, calcitriol, time 0

description: Library name: SK_4VID_B03

value: CD14 Monocyte


title: prostate_cancer_primary_29 (STAMPEDE)


title: BMDM, stearic acid, 100 uM, 24 hours, rep 2

description: Library name: SA_24h_2


title: SK_4VID_B02, calcitriol, time 2

description: Library name: SK_4VID_B02


title: BMDM, stearic acid, 100 uM, 24 hours, rep 1

description: Library name: SA_24h_1


title: SK_4VID_B01, calcitriol, time 0

description: Library name: SK_4VID_B01


title: MED1 ChIP, siCtl, +DEX, BT549, Biorep1

value: TNBC


title: Input, siCtl, Veh, BT549 cells

value: siCtl


title: MED1 ChIP, siCtl, Veh, BT549, Biorep3


title: prostate_cancer_primary_28 (STAMPEDE)


title: BMDM, vehicle, 24 hours, rep 3

description: Library name: EtOH_24h_3

value: vehicle


title: SK_4VID_A12, calcitriol, time 2

description: Library name: SK_4VID_A12


title: BMDM, vehicle, 24 hours, rep 2

description: Library name: EtOH_24h_2


title: prostate_cancer_primary_26 (STAMPEDE)


title: BMDM, vehicle, 24 hours, rep 1

description: Library name: EtOH_24h_1


title: prostate_cancer_primary_27 (STAMPEDE)


title: MED1 ChIP, siCtl, Veh, BT549, Biorep1_2


title: prostate_cancer_primary_25 (STAMPEDE)


title: 3T3-L1 differentiated day 7, biol rep 3, mRNA seq

first: April

middle: Elizabeth

last: Williams

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: Library name: 479-18-mRNA

data_processing:
Raw single-end FASTQ reads were trimmed using FASTX Toolkit 0.0.14 to remove library adapters and low-quality bases.
The trimmed reads were then first aligned (using STAR 2.7.11a) to a list of tRNA/rRNA sequences to filter out tRNA/rRNA contaminants.
Remaining unmapped reads were aligned to the mm10 reference genome.
These aligned reads were used to annotate smORFs generated from Ribo-seq.
Assembly: mm10
Supplementary files format and content: excel file with identified smORFs

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with 10% Bovine Calf Serum.

extract_protocol:
For collection of RNAseq samples, cells were washed with PBS followed by addition of 500uL TRIZOL (Invitrogen Cat# 15596018) to each well and RNA is extracted following manufacturer’s protocol. The RNA samples were stored at -80°C until library prep and sequencing.
For each 3T3-L1 cell condition,  both total RNA  and polyA enriched mRNA library construction  was processed using TruSeq Stranded Total RNA Ribo-Zero Gold and Illumina Truseq mRNA kits according to manufacturor's instructions,The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on NovaSeq6000, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on a NovaSeq6000 and paired-end reads were generated.

treatment_protocol: For differentiating 3T3-L1 cells into adipocytes, cells are grown to confluency before changing into fresh maintenance media. After 24 hours, media is removed and replaced with differentiation media: DMEM + 10% FBS (Gibco, A5670701), 500uM 3-Isobutyl-1-methylxanthine (IBMX, Sigma, I5879), 5ug/ml Insulin (Sigma, I0516), and 1uM dexamethasone (Sigma, D1756). After 72 hours with differentiation media, cells are maintained in differentiation media without IBMX and dexamethasone for an additional 4-7 days with fresh media replaced every 48 hours.

value: Fibroblast

value: WT

value: Adipogenic Differentiation

tag: time

value: Day 7


title: SK_4VID_A09, calcifediol, time 0

description: Library name: SK_4VID_A09

value: calcifediol


title: MED1 ChIP, siCtl, +DEX, BT549, Biorep2

value: Bethyl laboratories A300-793A lot:10

value: 2h DEX (500nM)


title: Input, +DEX, BT549 cells, Biorep3_2


title: prostate_cancer_primary_24 (STAMPEDE)


title: SK_4VID_A08, calcifediol, time 2

description: Library name: SK_4VID_A08


title: prostate_cancer_primary_23 (STAMPEDE)


title: SK_4VID_A07, calcifediol, time 0

description: Library name: SK_4VID_A07


title: Input, +DEX, BT549 cells, Biorep1_2


title: SK_4VID_A11, calcitriol, time 0

description: Library name: SK_4VID_A11


title: prostate_cancer_primary_21 (STAMPEDE)


title: MED1 ChIP, siCtl, Veh, BT549, Biorep2

value: Veh


title: 3T3-L1 differentiated day 7, biol rep 1, mRNA seq

description: Library name: 479-6-mRNA


title: SK_4VID_A10, calcifediol, time 2

description: Library name: SK_4VID_A10

value: Blood


title: 3T3-L1 differentiated day 7, biol rep 2, total RNA seq

description: Library name: 479-12-TotalRNA


title: SK_4VID_A05, placebo, time 0

description: Library name: SK_4VID_A05

value: placebo


title: SK_4VID_A06, placebo, time 2

description: Library name: SK_4VID_A06


title: GATA6 ChIP, +DEX, BT549 cells, Biorep2

value: Cell Signaling (D61E4) 5851 lot:5


title: 3T3-L1 differentiated day 7, biol rep 1, total RNA seq

description: Library name: 479-6-TotalRNA


title: 3T3-L1 differentiated day 7, biol rep 3, total RNA seq

description: Library name: 479-18-TotalRNA


title: SK_4VID_A03, calcifediol, time 0

description: Library name: SK_4VID_A03


title: GATA6 ChIP, +DEX, BT549 cells, Biorep1


title: 3T3-L1 differentiated day 3, biol rep 3, mRNA seq

description: Library name: 479-16-mRNA

value: Day 3


title: prostate_cancer_primary_20 (STAMPEDE)

value: FFPE prostate cancer


title: Input, +DEX, BT549 cells, Biorep2_2


title: Input, Veh, BT549 cells, Biorep3_2


title: 3T3-L1 differentiated day 7, biol rep 2, mRNA seq

description: Library name: 479-12-mRNA


title: prostate_cancer_primary_22 (STAMPEDE)


title: prostate_cancer_primary_18 (STAMPEDE)


title: SK_4VID_A02, placebo, time 2

description: Library name: SK_4VID_A02

value: CD14 Monocyte


title: prostate_cancer_primary_17 (STAMPEDE)


title: 3T3-L1 differentiated day 3, biol rep 3, total RNA seq

description: Library name: 479-16-TotalRNA


title: prostate_cancer_primary_16 (STAMPEDE)


title: Input, Veh, BT549 cells, Biorep2_2

value: TNBC


title: GATA6 ChIP, +DEX, BT549 cells, Biorep3


title: 3T3-L1 differentiated day 3, biol rep 2, mRNA seq

description: Library name: 479-10-mRNA


title: prostate_cancer_primary_15 (STAMPEDE)


title: Input, Veh, BT549 cells, Biorep1_2


title: 3T3-L1 differentiated day 3, biol rep 2, total RNA seq

description: Library name: 479-10-TotalRNA


title: SK_4VIC_H10, calcitriol, time 2

description: Library name: SK_4VIC_H10

value: calcitriol


title: SK_4VID_A04, calcifediol, time 2

description: Library name: SK_4VID_A04


title: SK_4VID_A01, placebo, time 0

description: Library name: SK_4VID_A01


title: 3T3-L1 differentiated day 3, biol rep 1, mRNA seq

description: Library name: 479-4-mRNA


title: prostate_cancer_primary_19 (STAMPEDE)


title: GATA6 ChIP, Veh, BT549 cells, Biorep3


title: prostate_cancer_primary_14 (STAMPEDE)


title: GATA6 ChIP, Veh, BT549 cells, Biorep2


title: SK_4VIC_H08, placebo, time 2

description: Library name: SK_4VIC_H08


title: prostate_cancer_primary_12 (STAMPEDE)


title: 3T3-L1 differentiated day 3, biol rep 1, total RNA seq

description: Library name: 479-4-TotalRNA


title: prostate_cancer_primary_13 (STAMPEDE)


title: GATA6 ChIP, Veh, BT549 cells, Biorep1


title: 3T3-L1 undifferentiated, biol rep 3, mRNA seq

description: Library name: 479-14-mRNA

value: Day 0


title: SK_4VIC_H07, placebo, time 0

description: Library name: SK_4VIC_H07


title: Input, Veh, BT549 cells, Biorep3_1


title: 3T3-L1 undifferentiated, biol rep 3, total RNA seq

description: Library name: 479-14-TotalRNA

value: Fibroblast


title: SK_4VIC_H06, placebo, time 2

description: Library name: SK_4VIC_H06


title: 3T3-L1 undifferentiated, biol rep 2, mRNA seq

description: Library name: 479-8-mRNA

value: WT


title: prostate_cancer_primary_11 (STAMPEDE)


title: SK_4VIC_H05, placebo, time 0

description: Library name: SK_4VIC_H05


title: Input, Veh, BT549 cells, Biorep1_1


title: prostate_cancer_primary_10 (STAMPEDE)


title: SK_4VIC_H09, calcitriol, time 0

description: Library name: SK_4VIC_H09


title: Input, +DEX, BT549 cells, Biorep3_1


title: 3T3-L1 undifferentiated, biol rep 2, total RNA seq

description: Library name: 479-8-TotalRNA

value: Adipogenic Differentiation


title: SK_4VIC_H04, calcifediol, time 2

description: Library name: SK_4VIC_H04


title: SK_4VIC_H03, calcifediol, time 0

description: Library name: SK_4VIC_H03


title: Input, +DEX, BT549 cells, Biorep2_1


title: prostate_cancer_primary_9 (STAMPEDE)


title: 3T3-L1 undifferentiated, biol rep 1, total RNA seq

description: Library name: 479-2-TotalRNA


title: SK_4VIC_H02, calcitriol, time 2

description: Library name: SK_4VIC_H02


title: Input, +DEX, BT549 cells, Biorep1_1


title: SK_4VIC_H01, calcitriol, time 0

description: Library name: SK_4VIC_H01


title: prostate_cancer_primary_7 (STAMPEDE)


title: U20S cells siCtrl +4OHT rep3

city: Oxford

first: Monika

last: Gullerova

address: S Parks Rd

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: nascent RNA

data_processing:
ChromRNASeq adapters were trimmed using Cutadapt (version 4.4)  in paired end mode and the quality of the resulting fastq files were assessed using FastQC
The trimmed reads were then aligned to human hg19 reference genome using STAR aligner
Each alignment file was then split using Samtools into two alignment files containing positively stranded and negatively stranded reads
Strand specific coverage files containing CPM normalized read count per nucleotide position was generated for each alignment using deeptools bamCoverage
ComputeMatrix operation of deepTools was then performed on the strand separated bigwig files to calculate the CPM coverage in the 2.5kb flanking region of AsiSI site with bin size set at one
Assembly: hg19
Supplementary files format and content: bigwig containing CPM coverage at each nucleotide position (non-strand separated coverage)
Library strategy: chrRNA-Seq

source_name: Bone

extract_protocol:
RNA was extracted by Trizol/chloroform RNA extraction, and further cleaning (to get rid of DNA contamination) with Monarch® Total RNA Miniprep Kit (NEB,T2010S) by following manufacturer's protocol.
Sequencing libraries preparation was performed with the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) followed by paired-end sequencing on HiSeq6000 (Illumina).

treatment_protocol: The wild-type U2OS orAsiSI-ER U2OS cells with proper RNAi reaching 50%-70% confluency in 15cm dish (~4-8 million cells) before starting of work. Following DSB induction, cells were washed and harvested by gently scrapping into 5mL PBS and pelleted by centrifuge (400g, 5min, 4°C). The cell pellets were lysed with 4 mL HLB+N buffer [10mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40], and underlaid with 1 mL HLB+NS buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40, 10% sucrose] before spin at 400g for 5min (4°C) to collect the nuclear pellets. Cytoplasmic fragment was collected for western blot to confirm the successful breakage of cells. Next, nuclear pellets were lysed and resuspended in 125µLNUN1 buffer [20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, 50% glycerol], and chromatin was extracted by incubating in 1.2 mL NUN2 buffer [20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% NP-40, 1M urea] on ice for 15min with interval vortex in every 3-4 min. The chromatin samples were then collected by full speed spin at 4°C for 15min. To digest DNA and chromatin-associated proteins, 2µL/sample Proteinase K(20ug/uL)(NEB,P8107S) and 1µL/sample Turbo DNase in 1X Turbo DNase Buffer (100µL/sample)(Thermo fisher,AM2238) was added to digest chromatin pellets at37°Cwith 1000rpm shake until pellets were dissolved.

value: Bone

value: osteosarcoma

value: AsiSI

value: siCtrl +4OHT


title: Input, Veh, BT549 cells, Biorep2_1

value: Veh


title: SK_4VIC_G12, calcitriol, time 2

description: Library name: SK_4VIC_G12

value: Blood


title: 210KO_type_MacrophagesM2_S11

city: Bucharest

first: Laudy

last: Cherry

state: Sector 5

address: Strada B.P.Hasdeu nr.8, sector 5, Bucuresti

department: Biology

country: Romania

institute: Institute of cellular biology and pathology

description: Library name: S210KOM2_S11

data_processing:
Data processing was performed in-house; adaptor trimming and PCR duplicate removal were done with Trimmomatic and Picard, respectively.
Trimmed reads were mapped to mouse genome GRCm39 P110 using STAR
Stranded quantification was performed with featureCounts.
Details are provided in the materials and methods section
Assembly: Mouse genome GRCm39 P110
Supplementary files format and content: csv file contains normalized counts from Deseq2 M0.WT_vs_M2.WT
Supplementary files format and content: csv file contains normalized counts from Deseq2 M0.KO_vs_M2.KO
Supplementary files format and content: csv file contains normalized counts from Deseq2 M0.KO_vs_M0.WT
Supplementary files format and content: csv file contains normalized counts from Deseq2 M2.KO_vs_M2.WT
Supplementary files format and content: csv file contains raw_counts_M0.WT_vs_M2.WT
Supplementary files format and content: csv file contains raw_counts M0.KO_vs_M2.KO
Supplementary files format and content: csv file contains raw_counts M0.KO_vs_M0.WT
Supplementary files format and content: csv file contains raw_counts M2.KO_vs_M2.WT

source_name: Bone Marrow

extract_protocol:
Long bones were extracted from the hind limbs of mice under sterile conditions. Bone marrow aspirate was obtained using the protocol previously described (Marinescu et al, 2021). Briefly, medullary channels were flushed with 5 ml of medium (high glucose DMEM supplemented with 10% foetal fetal bovine serum) using a 25-G needle connected to a 5-ml syringe. Subsequently, the single-cell suspension obtained by passing the bone marrow aspirate through needles of decreasing sizes (18G, 21G, 23G, 25G) was resuspended to a concentration of 106 cells/ml and used for further experiments.
Monocytes were obtained using EasySep™ Mouse Monocyte Isolation Kit (STEMCELL Technologies, #19761) following the manufacturer's instructions.  Briefly, around 60x106 bone marrow aspirate was resuspended in 1 ml of EasySep buffer (STEMCELL Technologies, #20144) and incubated with an antibody cocktail targeting non-monocyte cells, including erythrocytes, lymphocytes, neutrophils, and dendritic cells. Afterward, EasySep™ Dextran RapidSpheres™ were added to the cell suspension to bind the antibody-labelled cells. The suspension was then placed into an EasySep™ magnet, which selectively retains the magnetically labelled cells while allowing the untouched monocytes to be transferred into a new tube. The isolated monocytes were washed, counted, and either used for flow cytometry analysis or cultured in vitro to differentiate into macrophages for further experiments.                                                                                Isolated monocytes were seeded in culture-treated plates at a density of 40,000 cells/cm² in a differentiation medium i.e., high glucose DMEM supplemented with 20% FBS and 30% L929 conditioned medium (L929-CM), as the source of M-CSF. A medium refresh was done after three days of culture. After seven days of differentiation, the cells (M0 macrophages) were polarized towards M1 or M2 phenotypes, by incubating with 100 ng/ml LPS and 20 ng/ml IFN-γ for M1 polarization, or with 20 ng/ml IL-4 for M2 polarization, for the next three days. Cells maintained cultured in the differentiation medium without cytokines served as control.
Total RNA was isolated from cells using the standard protocol of TRIzol reagent (Thermo Fisher Scientific, #15596026). One µg of total RNA was used for reverse transcription, using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific, MA, USA#4387406). The RT-PCR was performed on the ViiA™ 7 Real-Time PCR System using SYBR™ Select Master Mix (ThermoFisher ScientificApplied Biosystems, #4472918). Relative expression level was determined using the comparative CT method, with RPL32 used for normalization. miR-210 expression levels were measured using TaqMan™ MicroRNA Assays (ThermoFisher Scientific, #A25576) in combination with the TaqMan™ MicroRNA Reverse Transcription Kit (ThermoFisher Scientific, #4366596). The expression of U6 snRNA was used as an endogenous control for normalization.
Details are provided in the materials and methods section

value: Bone Marrow

value: Macrophages

value: Hematopoietic

value: C57Bl/6J mice

tag: genetic modification

value: MiR-210- KO


title: 210KO_type_MacrophagesM2_S12

description: Library name: S210KOM2_S12

growth_protocol: Details are provided in the materials and methods section


title: U20S cells siCtrl +4OHT rep2

description: nascent RNA


title: prostate_cancer_primary_6 (STAMPEDE)

value: FFPE prostate cancer


title: prostate_cancer_primary_5 (STAMPEDE)


title: prostate_cancer_primary_4 (STAMPEDE)


title: 210KO_type_MacrophagesM2_S10

description: Library name: S210KOM2_S10

treatment_protocol: Details are provided in the materials and methods section


title: U20S cells siCtrl +4OHT rep1

description: nascent RNA


title: 3T3-L1 undifferentiated, biol rep 1, mRNA seq

description: Library name: 479-2-mRNA


title: SK_4VIC_G11, calcitriol, time 0

description: Library name: SK_4VIC_G11

value: CD14 Monocyte

value: calcitriol


title: 210KO_type_MacrophagesM0_S9

description: Library name: S210KOM0_S9


title: U20S cells siNSUN2 +4OHT rep3

description: nascent RNA

value: siNSUN2 + 4OHT


title: SK_4VIC_G09, calcifediol, time 0

description: Library name: SK_4VIC_G09

value: calcifediol


title: SK_4VIC_G10, calcifediol, time 2

description: Library name: SK_4VIC_G10


title: 210KO_type_MacrophagesM0_S8

description: Library name: S210KOM0_S8


title: U20S cells siNSUN2 +4OHT rep2

description: nascent RNA


title: Head_Control_biol rep 3

city: Madison

first: Grace

last: Boekhoff-Falk

state: WI

address: 1111 Highland Ave.

department: Cell and Regenerative Biology

institute: UW-Madison

description:
Library name: U
4hr_PTBI_DE_Genes.xlsx

data_processing:
Fast QC program was used to verify raw data quality of the Illumina reads
The Drosophila melanogaster genome and gene annotations were downloaded from FlyBase and used for mapping.
The raw sequence reads were mapped to the genome using Subjunc aligner from Subread, with the majority of the reads (over 98% for all samples) aligned to the genome.
The alignment bam files were compared against the gene annotation GFF file, and raw counts for each gene were normalized using the voom method from the R Limma package.
Assembly: Drosophila 1.0
Supplementary files format and content: Each column is a sample, and each row represents the scaled expression values for one gene (blue is low, red is high). In this clustering there were 367 genes with differential expression of 2-fold or greater between the two groups. 259 of those were upregulated, and 108 were downregulated with a false discovery rate (FDR) <0.05.

organism: Drosophila melanogaster

source_name: whole head

growth_protocol: All flies were reared at 25°C on a standard cornmeal-sugar medium.

extract_protocol:
RNA-Seq samples were isolated from heads of males four hours after PTBI to both hemispheres of the central brain and from the heads of age- and sex-matched controls without injury.
Libraries were prepared using the TruSeq strand-specific mRNA sample preparation system (Illumina). Libraries were sequenced (single end 50 bp reads) using the Illumina HiSeq2500, with six samples (three control and three injured) per lane, for a total of over twenty million reads per sample.

treatment_protocol: PTBI was induced using thin metal needles (~12.5 μm diameter tip, 100 μm rod; Fine Science Tools) sterilized in 70% ethanol to penetrate the head capsule of CO2-anesthetized adult flies. Injured flies were transferred back to our standard sugar food for recovery and aging.

value: whole head

value: adult

tag: Sex

value: male

value: w; UAS-mCD8-GFP;; OK107-GAL4 X yw

value: Uninjured

value: total RNA


title: prostate_cancer_primary_8 (STAMPEDE)


title: prostate_cancer_primary_2 (STAMPEDE)


title: Head_Control_biol rep 2

description:
Library name: S
4hr_PTBI_DE_Genes.xlsx


title: prostate_cancer_primary_3 (STAMPEDE)


title: prostate_cancer_primary_1 (STAMPEDE)


title: 210KO_type_MacrophagesM0_S7

description: Library name: S210KOM0_S7


title: SK_4VIC_G08, placebo, time 2

description: Library name: SK_4VIC_G08

value: Blood

value: placebo


title: Wild_type_MacrophagesM2_S6

description: Library name: SWTM2_S6

value: Bone Marrow

value: Macrophages

value: wild-type (WT)


title: Head_Control_biol rep 1

description:
Library name: R
4hr_PTBI_DE_Genes.xlsx


title: U20S cells siNSUN2 +4OHT rep1

description: nascent RNA

value: Bone

value: osteosarcoma

value: AsiSI


title: SK_4VIC_G07, placebo, time 0

description: Library name: SK_4VIC_G07

value: CD14 Monocyte


title: Head_4hr_PTBI_biol rep 3

description:
Library name: P
4hr_PTBI_DE_Genes.xlsx

value: PTBI


title: SK_4VIC_G06, calcitriol, time 2

description: Library name: SK_4VIC_G06

value: calcitriol


title: Wild_type_MacrophagesM2_S5

description: Library name: SWTM2_S5

value: Hematopoietic

value: C57Bl/6J mice


title: Wild_type_MacrophagesM2_S4

description: Library name: SWTM2_S4


title: LA_AF_03

city: Beijing

first: Xiaoyi

last: Wang

address: No.167, Beilishi Road, Xicheng District, 100037

department: Department of Cardiovascular Surgery, Fuwai Hospital

country: China

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

description: one sample from human left atrial appendage

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters (Cell Ranger software v6.0.1)
Assembly: GRCh38 for human data;
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Left atrial appendage

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy

value: Left atrial appendage

tag: age


title: LA_AF_02


title: Head_4hr_PTBI_biol rep 2

description:
Library name: O
4hr_PTBI_DE_Genes.xlsx

value: whole head

value: adult

value: male

value: w; UAS-mCD8-GFP;; OK107-GAL4 X yw


title: SK_4VIC_G05, calcitriol, time 0

description: Library name: SK_4VIC_G05

value: Blood


title: Head_4hr_PTBI_biol rep 1

description:
Library name: N
4hr_PTBI_DE_Genes.xlsx

value: total RNA


title: Wild_type_MacrophagesM0_S3

description: Library name: SWTM0_S3

value: Bone Marrow

value: Macrophages


title: LA_SR_03


title: SK_4VIC_G04, placebo, time 2

description: Library name: SK_4VIC_G04

value: placebo


title: patient14 relapse

city: Shanghai

first: Jie

last: Zheng

address: No.197, Rui Jin Er Road

department: Department of Dermatology

institute: Ruijin Hospital, School of Medicine, Shang Jiao Tong University

description: with urticaria

data_processing:
Bcl2fastq (v2.17.1.14) were used for base calling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v 1.9.1)
Trimmed sequence reads were mapped to hg19 usingHisat2(v2.0.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skin


title: Wild_type_MacrophagesM0_S2

description: Library name: SWTM0_S2

value: wild-type (WT)


title: SK_4VIC_G03, placebo, time 0

description: Library name: SK_4VIC_G03

value: CD14 Monocyte


title: DU145, CCS1477-2

city: lexington

first: Jinghui

last: Liu

state: KY

address: Room 352, HEALTHY KENTUCKY RESEARCH BUILDING, 760 Press Avenue

institute: University of Kentucky

description: Library name: D2

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads. The trimmed reads were then mapped to Ensembl [GRCh38r98] transcripts annotation for human samples.
Assembly: GRCh38r98
Supplementary files format and content: The processed data include expected counts data and TPM-normalized data, both in tsv format.

source_name: prostate

growth_protocol: DU145  cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum, incubated at 37 °C with 5% CO₂ in a humidified atmosphere.

extract_protocol:
Total RNA was extracted from DU145 cells using the RNeasy Mini Kit (QIAGEN, 74104).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

treatment_protocol: cells were treated with either DMSO (control) or 1 μM CCS1477 for 24 hours

value: prostate

value: cancer cell line

value: WT


title: DU145, CCS1477-1

description: Library name: D1


title: Wild_type_MacrophagesM0_S1

description: Library name: SWTM0_S1

value: Hematopoietic

value: C57Bl/6J mice


title: patient14 remission

description: with urticaria


title: SK_4VIC_G02, placebo, time 2

description: Library name: SK_4VIC_G02


title: TA_muscle, Nrip1KO, rep2

first: Daniel

last: Kelly

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

description:
Library name: sample_5
TA-5

data_processing:
Reads are quantified using Salmon v1.10.2
Differential gene expression analysis is performed using DESeq2 v1.44.0
Assembly: mm10
Supplementary files format and content: Tab-separated table with FPKM values for all samples and DESeq2-generated adjusted p-values and log2 fold changes for relevant comparisons

source_name: muscle

extract_protocol:
RNA was extracted utilizing the Rneasy mini kit plus (Qiagen) treated with Dnase.
Library construction was performed utilizing the NEBNext Ultra RNA Library Prep Kit for Illumina by NEB.

value: muscle


title: SK_4VIC_G01, placebo, time 0

description: Library name: SK_4VIC_G01


title: DU145, Ctrl3

description: Library name: C3

value: DMSO


title: patient13 relapse

description: with urticaria


title: SK_4VIC_F12, calcitriol, time 2

description: Library name: SK_4VIC_F12

value: calcitriol


title: TA_muscle, Nrip1KO, rep1

description:
Library name: sample_4
TA-4


title: DU145, Ctrl2

description: Library name: C2


title: patient13 remission

description: with urticaria


title: TA_muscle, Ctrl, rep3

description:
Library name: sample_3
TA-3

value: Ctrl


title: SK_4VIC_F11, calcitriol, time 0

description: Library name: SK_4VIC_F11

value: Blood


title: patient13 baseline

description: with urticaria


title: TA_muscle, Ctrl, rep2

description:
Library name: sample_2
TA-2


title: SK_4VIC_F10, calcitriol, time 2

description: Library name: SK_4VIC_F10


title: SK_4VIC_F09, calcitriol, time 0

description: Library name: SK_4VIC_F09


title: SMC19, whole slide

city: Seoul

first: Sang-Won

last: Um

address: 81 Irwon-ro

department: Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Library name: SMC19
FFPE Spatial transcriptomes (Visium)

data_processing:
For bulk RNA sequencing, reads were trimmed for adapter sequences and aligned to the hg38 genome using STAR aligner. Gene quantification was performed using RSEM.
For single-cell RNA sequencing, raw data were processed using Cell Ranger, including demultiplexing, barcode processing, and gene counting. Reads were aligned to the hg38 genome.
For spatial transcriptomics, raw sequencing data were processed using Space Ranger, aligned to hg38, and gene expression matrices were generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples
Supplementary files format and content: tab-delimited text files of barcodes, features and matrix files
Supplementary files format and content: tab-delimited text files of barcodes, features, matrix and coordinate spot files, hi-/low resolution image file, cropped image file
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Total RNA were extracted from FFPE tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. For scRNA seq, fresh tumor and  normal lung tissues were enzymatically dissociated using Miltenyi Tumor Dissociation Kit in combination with the GentleMACS Dissociator (Miltenyi Biotec). Single-cell suspensions were filtered through a 40 μm cell strainer, and cell viability (>85%) was confirmed using Trypan Blue staining and the Countess II Automated Cell Counter (Thermo Fisher). Live cells were enriched using Dead Cell Removal Kit (Miltenyi Biotec).
Total RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina). Sequencing was performed on an Illumina HiSeq 4000 system in 150-bp paired-end mode. Single-cell libraries were constructed using the 10X Genomics Chromium Single Cell 3’ v2 Kit. Following cell capture and cDNA synthesis, cDNA amplification and library preparation were performed according to the 10X Genomics protocol. For spatial transcriptomic analysis, 10X Genomics Visium Spatial Gene Expression Slides & Reagent Kit was used according to the manufacturer’s protocol

tag: individuals

value: Lung


title: DU145, CCS1477-3

description: Library name: D3

tag: cell line


title: patient12 remission

description: with urticaria


title: DU145, Ctrl1

description: Library name: C1

tag: cell type


title: patient12 baseline

description: with urticaria


title: TA_muscle, Ctrl, rep1

description:
Library name: sample_1
TA-1

tag: genotype


title: SMC30, Solid (S) component

description:
Library name: SMC30_S
10x Genomics

data_processing:
For bulk RNA sequencing, reads were trimmed for adapter sequences and aligned to the hg38 genome using STAR aligner. Gene quantification was performed using RSEM.
For single-cell RNA sequencing, raw data were processed using Cell Ranger, including demultiplexing, barcode processing, and gene counting. Reads were aligned to the hg38 genome.
For spatial transcriptomics, raw sequencing data were processed using Space Ranger, aligned to hg38, and gene expression matrices were generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples
Supplementary files format and content: tab-delimited text files of barcodes, features and matrix files
Supplementary files format and content: tab-delimited text files of barcodes, features, matrix and coordinate spot files, hi-/low resolution image file, cropped image file


title: SMC30, Ground-glass (GG) component

description:
Library name: SMC30_GG
10x Genomics


title: patient11 relapse

description: with urticaria


title: SMC30, Adjacent normal (AN) lung region

description:
Library name: SMC30_AN
10x Genomics


title: EDL_muscle, Nrip1KO, Trained, rep2

description: Library name: sample_11

tag: training

value: Trained


title: EDL_muscle, Nrip1KO, Trained, rep3

description: Library name: sample_12

tag: tissue


title: patient11 remission

description: with urticaria


title: SK_4VIC_F07, calcifediol, time 0

description: Library name: SK_4VIC_F07

data_processing:
Bulk RNA data were processed using  WARDEN workflow for the analysis of RNA-Seq differential expression (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: expression_matrix.txt

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

tag: treatment

value: calcifediol

tag: time (day)


title: patient14 baseline

description: with urticaria


title: EDL_muscle, Nrip1KO, Trained, rep1

description: Library name: sample_10


title: SK_4VIC_F06, calcifediol, time 2

description: Library name: SK_4VIC_F06


title: patient11 baseline

description: with urticaria


title: SMC30, Distant normal (DN) lung region

description:
Library name: SMC30_DN
10x Genomics


title: EDL_muscle, Ctrl, Trained, rep3

description: Library name: sample_9


title: SK_4VIC_F05, calcifediol, time 0

description: Library name: SK_4VIC_F05


title: EDL_muscle, Ctrl, Trained, rep2

description: Library name: sample_8


title: SMC29, Solid (S) component

description:
Library name: SMC29_S
10x Genomics


title: patient10 relapse

description: with urticaria


title: patient10 remission

description: with urticaria


title: SK_4VIC_F04, calcitriol, time 2

description: Library name: SK_4VIC_F04


title: SMC29, Ground-glass (GG) component

description:
Library name: SMC29_GG
10x Genomics


title: EDL_muscle, Ctrl, Trained, rep1

description: Library name: sample_7


title: SK_4VIC_F03, calcitriol, time 0

description: Library name: SK_4VIC_F03


title: SMC29, Distant normal (DN) lung region

description:
Library name: SMC29_DN
10x Genomics


title: EDL_muscle, Nrip1KO, Sedentary, rep3

description: Library name: sample_6

value: Sedentary


title: SMC29, Adjacent normal (AN) lung region

description:
Library name: SMC29_AN
10x Genomics


title: patient9 remission

description: with urticaria

value: skin


title: EDL_muscle, Nrip1KO, Sedentary, rep2

description: Library name: sample_5


title: SK_4VIC_F08, calcifediol, time 2

description: Library name: SK_4VIC_F08


title: patient10 baseline

description: with urticaria


title: SK_4VIC_F01, placebo, time 0

description: Library name: SK_4VIC_F01

value: placebo


title: SK_4VIC_F02, placebo, time 2

description: Library name: SK_4VIC_F02

value: CD14 Monocyte


title: SMC27, Solid (S) component

description:
Library name: SMC27_S
10x Genomics


title: SMC27, Ground-glass (GG) component

description:
Library name: SMC27_GG
10x Genomics


title: SK_4VIC_E12, calcitriol, time 2

description: Library name: SK_4VIC_E12


title: EDL_muscle, Ctrl, Sedentary, rep3

description: Library name: sample_3


title: EDL_muscle, Nrip1KO, Sedentary, rep1

description: Library name: sample_4


title: patient9 baseline

description: with urticaria


title: SK_4VIC_E11, calcitriol, time 0

description: Library name: SK_4VIC_E11


title: patient8 relapse

description: non urticaria


title: SMC27, Adjacent normal (AN) lung region

description:
Library name: SMC27_AN
10x Genomics


title: patient8 remission

description: non urticaria


title: EDL_muscle, Ctrl, Sedentary, rep2

description: Library name: sample_2


title: SK_4VIC_E10, calcifediol, time 2

description: Library name: SK_4VIC_E10


title: SMC27, Distant normal (DN) lung region

description:
Library name: SMC27_DN
10x Genomics


title: EDL_muscle, Ctrl, Sedentary, rep1

description: Library name: sample_1


title: SK_4VIC_E09, calcifediol, time 0

description: Library name: SK_4VIC_E09


title: patient8 baseline

description: non urticaria


title: patient7 relapse

description: non urticaria


title: SMC26, Solid (S) component

description:
Library name: SMC26_S
10x Genomics


title: EPS, rep3

city: Houston

first: Yuxiang

last: Sun

state: Texas

address: One Baylor Plaza, Houston, TX, 77030, United States

institute: Baylor College of Medicine

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: peritoneum

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer  (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: peritoneum

value: intraperitoneal injection of PD fluid + SHS +LPS


title: SK_4VIC_E08, placebo, time 2

first: Changde

last: Cheng

description: Library name: SK_4VIC_E08


title: patient7 remission

description: non urticaria


title: SK_4VIC_E07, placebo, time 0

description: Library name: SK_4VIC_E07


title: SMC26, Ground-glass (GG) component

description:
Library name: SMC26_GG
10x Genomics


title: EPS, rep2

description: Library name: Sample 5

value: WT


title: SMC26, Adjacent normal (AN) lung region

description:
Library name: SMC26_AN
10x Genomics


title: SMC26, Distant normal (DN) lung region

description:
Library name: SMC26_DN
10x Genomics


title: patient6 relapse

description: non urticaria


title: SK_4VIC_E06, calcifediol, time 2

description: Library name: SK_4VIC_E06


title: SK_4VIC_E05, calcifediol, time 0

description: Library name: SK_4VIC_E05


title: patient6 baseline

description: non urticaria


title: control, rep3

description: Library name: Sample 3

value: intraperitoneal injection of saline


title: SK_4VIC_E03, calcitriol, time 0

description: Library name: SK_4VIC_E03


title: S21-19188-1

city: Goyang-si

first: Sehwa

last: Hong

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

department: Research Institute

institute: National cancer center

description: Formalin-fixed, paraffin-embedded (FFPE) blocks

data_processing:
To extract gene expression profile, we used Space Ranger v2.1.1 (10X Genomics) pipeline for FASTQ file generation from raw sequencing data. Visium spatial expression libraries were analyzed with the ‘count’ command.
Raw gene expression matrices were converted to Seurat objects and further analyses were performed using the Seurat R package (v4.3.0)
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: tissue-associated barcodes in HDF5 format
Supplementary files format and content: detected_tissue_image.jpg, tissue_hires_image.png, tissue_lowres_image.png: tissue H&E image in each resolution
Supplementary files format and content: scalefactors_json.json: scaling factor that converts pixel positions in the original, full-resolution image to pixel positions
Supplementary files format and content: tissue_positions.csv: spot barcodes and position to image pixel coordinates
Library strategy: Spatial Transcriptomics

extract_protocol:
We followed manufacturer Visium protocol for each step. Visium CytAssist spatial gene expression workflow for formalin fixed & paraffin embedded (FFPE) were performed for sectioning, and RNA quality assessment (DV200 >= 30%). Tissue slides were deparaffinized, hematxylin & eosin (H&E) stained, imaged, and decross-linked. Probe hybridization should be immediately performed according to Visium Spatial Gene Expression for FFPE reagent kit (10X Genomics). These probe pairs hybridize to their gene target and are then ligated to one another. The single stranded ligation products are released from the tissue to a capture area on the Visium slide within the CytAssist instrument. Once ligation products were captured, the slides can be removed from the instrument. Probes were extended by the addition of UMI, spatial barcode and partial read.
Library was constructed according to 10X Genomics Visium Spatial pipeline.

tag: disease

value: Lung cancer

tag: histopathology

value: Adenocarcinoma

tag: developmental stage

value: IV

value: Osimertinib


title: S20-12254-L9


title: EPS, rep1

description: Library name: Sample 4


title: MED15 T604A C57 mouse hippocamous tissue, RNA-seq, rep3

first: Yuanming

address: 220 Handan Rd., Shanghai

institute: fudan university

description: Library name: Hippocampus_T604A_rep3

data_processing:
Raw reads were trimmed for adptor sequence/low quality sequence using Trim Galore (parameter -q 20 --phred33 --stringency 3 --length 20 -e 0.1 )
The filtered clean reads were mapped to the human reference genome hg19 or mm10 with HISAT2
Raw counts were count by HTSeq count
Gene quantification and the differential expression analysis were performed with DEseq2
Assembly: Hg19/mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes CPM values for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from cells lysed with TRIzol
We used a commercial RNA library kit to prepare the RNAseq library according to the manufacturer’s specifications (VAHTS® Universal V8 RNA-seq LibraryPrep Kit) for Illumina. Briefly, mRNA was captured with mRNA capture beads before fragmentation

value: Hippocampus

value: Neuron

value: Med15 T604A

value: untreated


title: control, rep1

description: Library name: Sample 1


title: patient5 remission

description: non urticaria


title: 3T3-L1 differentiated Day 3 biol rep 3, Riboseq

description: Library name: 479-15

library_source: other

data_processing:
Raw single-end FASTQ reads were trimmed using FASTX Toolkit 0.0.14 to remove library adapters and low-quality bases. The trimmed reads were then first aligned (using STAR 2.7.11a) to a list of tRNA/rRNA sequences to filter out tRNA/rRNA contaminants, and the remaining unmapped reads were aligned to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: excel file with identified smORFs

molecule: other

extract_protocol:
Cells were washed twice after treatment with ice cold PBS supplemented with 100ug/mL cycloheximide (CHX; Fisher Scientific, AAJ66004X) and snap frozen in liquid nitrogen and stored at -80°C. After thawing briefly on ice, the cells were lysed with 300uL of ice-cold lysis buffer (20mM Tris-HCl, pH 7.4, 150mM NaCl, 5mM MgCl2, 1% Triton X-100, 1mM DTT, 25U Turbo DNase (Thermofisher Cat# AM2238), and 100ug/mL CHX – added fresh) for 10 minutes with periodic vortexing and pipetting through an 18G needle to ensure the cells are dispersed. Cell lysates were clarified by centrifugation for 15,000g for 10 minutes at 4°C, flash frozen in liquid nitrogen, and stored in -80°C for up to 1 week.
For each 3T3-L1 cell condition, ribosome footprinting was carried out by digesting 50 ug of RNA in 300 uL lysate with 0.375 U/ug RNase I (Lucigen, N6901K) for 45 min at room temperature. Digestion reactions were quenched with 200 U Superase-In RNase I inhibitor (Thermo Fisher, AM2694) on ice. Following digestion, monosomes were purified from small RNA fragments using Micro-Spin S-400 HR columns (GE Life Sciences), and ribosome protected RNA fragments (RPFs) were extracted by acid phenol chloroform and isopropanol precipitation. Sequencing libraries were prepared as in McGlincy and Ingolia with some modifications. First, the RiboZero Mammalian Kit (Illumina) was used to deplete rRNA after RPF extraction and just prior to RPF size selection by gel extraction. Second, the Zymo clean & concentrator step after adaptor ligation is omitted and the reaction was carried over straight into reverse transcription. For the reverse transcription step to form cDNA, Episcript RT (Lucigen, ERT12910K) was used. Following reverse transcription, excess primer was degraded using Exonuclease I (Lucigen, X40520K) and the RNA templates were degraded using Hybridase (Lucigen, H39500). For the cDNA circularization step, CircLigase I (Lucigen, CL4111K) was used. PCR amplification was then carried out using Phusion Hot Start II High-Fidelity Master Mix (Thermo Fisher, F565L) for 9–12 cycles.

value: Fibroblast

value: Adipogenic Differentiation

value: Day 3


title: SK_4VIC_E01, placebo, time 0

address: 1824 6th Ave S, Wallace Tumor Institute 520A

institute: University of Alabama at Birmingham

description: Library name: SK_4VIC_E01

value: Blood

value: placebo


title: MED15 T604A C57 mouse hippocamous tissue, RNA-seq, rep2

description: Library name: Hippocampus_T604A_rep2


title: SK_4VIC_E02, placebo, time 2

description: Library name: SK_4VIC_E02

value: CD14 Monocyte


title: patient5 baseline

description: non urticaria

value: skin


title: patient6 remission

description: non urticaria


title: 3T3-L1 undifferentiated, biol rep 3, Riboseq

description: Library name: 479-13

value: WT

value: Day 0


title: patient7 baseline

description: non urticaria


title: MED15 T604A C57 mouse hippocamous tissue, RNA-seq, rep1

description: Library name: Hippocampus_T604A_rep1


title: SK_4VIC_D12, calcifediol, time 2

description: Library name: SK_4VIC_D12

value: calcifediol


title: patient4 relapse

description: non urticaria


title: control, rep2

description: Library name: Sample 2

value: peritoneum

value: intraperitoneal injection of saline


title: 3T3-L1 differentiated Day 7, biol rep 2, Riboseq

description: Library name: 479-11

value: Day 7


title: 3T3-L1 differentiated Day 3, biol rep 2, Riboseq

description: Library name: 479-9


title: patient4 remission

description: non urticaria


title: WT C57 mouse hippocamous tissue, RNA-seq, rep3

description: Library name: Hippocampus_WT_rep3

value: Hippocampus


title: WT C57 mouse hippocamous tissue, RNA-seq, rep2

description: Library name: Hippocampus_WT_rep2

value: Neuron


title: patient5 relapse

description: non urticaria


title: 3T3-L1 differentiated Day 7, biol rep 3, Riboseq

description: Library name: 479-17


title: SK_4VIC_D10, placebo, time 2

description: Library name: SK_4VIC_D10


title: patient4 baseline

description: non urticaria


title: 3T3-L1 undifferentiated, biol rep 2, Riboseq

description: Library name: 479-7


title: WT C57 mouse hippocamous tissue, RNA-seq, rep1

description: Library name: Hippocampus_WT_rep1


title: SK_4VIC_D09, placebo, time 0

description: Library name: SK_4VIC_D09


title: patient3 relapse

description: non urticaria


title: 3T3-L1 differentiated Day 7, biol rep 1, Riboseq

description: Library name: 479-5


title: SK_4VIC_D08, calcifediol, time 2

description: Library name: SK_4VIC_D08


title: con6

first: Rongjiao

last: Shao

state: Shanghai

address: Department of Critical Care Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.23.0. (parameter:-l 50; -n 5; -q 20;-W 4;-M 20) ；  Trimmed sequencereads were mapped to GRCh38 usng hisat2 v2-2.1.0 (paramtrer:-p 8;-5 5;-3 5;--min-intronlen 20;--max-intronlen 500000;-k 3;--phred33)  ；Read count extraction and normaliation were performed using Htseq v2.0.1 (paramtrer:-s no;-a 10;-m union;-i gene_name;--nonunique none)
Assembly: GRCm38_93_year_2012
Supplementary files format and content: raw counts for each Sample

source_name: Heart

extract_protocol:
About 30mg of liquid nitrogen samples were ground and total RNA was extracted using TRIzol™ Reagent. According to the Total amount of Total RNA, 0.1-1ug of total RNA was taken. mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit.
The mRNA Library was then constructed using the NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® Library Construction Kit.Library sequencing was performed using a NovaSeq 6000 instrument with a matching NovaSeq S4 reagent kit

value: Heart

value: Sham


title: patient3 remission

description: non urticaria


title: 3T3-L1 differentiated Day 3, biol rep 1, Riboseq

description: Library name: 479-3

value: Fibroblast


title: con5

department: Department of Critical Care Medicine, Shanghai Chest Hospital


title: SK_4VIC_D07, calcifediol, time 0

description: Library name: SK_4VIC_D07


title: patient3 baseline

description: non urticaria


title: 3T3-L1 undifferentiated, biol rep 1, Riboseq

description: Library name: 479-1

value: Adipogenic Differentiation


title: SK_4VIC_D06, placebo, time 2

description: Library name: SK_4VIC_D06


title: con4


title: patient2 relapse

description: non urticaria


title: SK_4VIC_D11, calcifediol, time 0

description: Library name: SK_4VIC_D11


title: R162-H-008

city: CARDIFF

first: Neil

last: Rodrigues

address: Maindy Road

department: The European Cancer Stem Cell Research Institute

institute: Cardiff University

description:
Library name: Gata2; Asxl1-DH-8
Gata2; Asxl1-Double heterozygote HSC 4 (LSK CD48- CD150+)

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCm38 v17 gene annotation.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

source_name: bone marrow

extract_protocol:
HSC cells were resuspended in RLT buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB).
Sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). The steps included RNA fragmentation and priming, 1st strand cDNA synthesis, 2nd strand cDNA synthesis, adenylation of 3’ ends, adapter ligation, PCR amplification (11-cycles) and validation. The manufacturer’s instructions were followed. The libraries were validated using the Agilent 2100 Bioanalyser and a high-sensitivity kit (Agilent Technologies) to ascertain the insert size, and the Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 10nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

value: bone marrow

value: HSCs

value: Gata2; Asxl1-Double heterozygote


title: SK_4VIC_D05, placebo, time 0

description: Library name: SK_4VIC_D05

value: Blood

value: CD14 Monocyte

value: placebo


title: patient2 remission

description: non urticaria

value: skin


title: SK_4VIC_D04, calcifediol, time 2

description: Library name: SK_4VIC_D04

value: calcifediol


title: R162-H-007

description:
Library name: Gata2; Asxl1-DH-7
Gata2; Asxl1-Double heterozygote HSC 3 (LSK CD48- CD150+)


title: con3

value: WT


title: con2


title: patient2 baseline

description: non urticaria


title: R162-H-005

description:
Library name: Gata2; Asxl1-DH-5
Gata2; Asxl1-Double heterozygote HSC 1 (LSK CD48- CD150+)


title: R162-H-006

description:
Library name: Gata2; Asxl1-DH-6
Gata2; Asxl1-Double heterozygote HSC 2 (LSK CD48- CD150+)


title: SK_4VIC_D03, calcifediol, time 0

description: Library name: SK_4VIC_D03


title: CLP-IL-4-e

value: cecal ligation and puncture with IL-4 treatment


title: SK_4VIC_D02, placebo, time 2

description: Library name: SK_4VIC_D02


title: CLP-IL-4-d


title: patient1 relapse

description: non urticaria


title: R128-H-004 [re-used]

description:
Library name: Gata2; Asxl1 WT-4
Wild Type HSC 4 (LSK CD48- CD150+)

value: Gata2; Asxl1 WT


title: patient1 remission

description: non urticaria


title: R128-H-002 [re-used]

description:
Library name: Gata2; Asxl1 WT-2
Wild Type HSC 2 (LSK CD48- CD150+)


title: SK_4VIC_D01, placebo, time 0

description: Library name: SK_4VIC_D01


title: LA_AF

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters (Cell Ranger software v6.0.1)
Assembly: GRCh38 for human data; mm10 for mice data
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

treatment_protocol: C57BL/6 C57BL/6 J Cdh5-CreERT2/RFP  mice were performed transverse aortic constriction or sham surgery at 10-12 weeks

value: Left atrial appendage


title: CLP-f

value: cecal ligation and puncture


title: LA_SR_02


title: R128-H-001 [re-used]

description:
Library name: Gata2; Asxl1 WT-1
Wild Type HSC 1 (LSK CD48- CD150+)


title: CLP-IL-4-b

value: Heart


title: CLP-e


title: R162-H-004

description:
Library name: Asxl1-Het-4
Asxl1 heterozygote HSC 4 (LSK CD48- CD150+)

value: Asxl1 heterozygote


title: SK_4VIC_C10, calcifediol, time 2

description: Library name: SK_4VIC_C10


title: LA_SR_01


title: R162-H-003

description:
Library name: Asxl1-Het-3
Asxl1 heterozygote HSC 3 (LSK CD48- CD150+)


title: SK_4VIC_C09, calcifediol, time 0

description: Library name: SK_4VIC_C09


title: R3 injury peripheral tissue

city: Tianjin

first: Jianhao

address: Anshan Road No.154

institute: Tianjin Medical University General Hospital

description: mRNA

data_processing:
The raw sequence reads were analyzed by Cell Ranger v.4.0.0 with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tar: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: Brain

extract_protocol:
CD45-CD31+ selection for endothelial cell enrichment was performed using microbeads (130-045-801, 130-091-935, Miltenyi Biotec).
scRNAseq libraries were prepared using Chromium Single Cell V3.1 Reagent Kit (10X Genomics) according to the manufacturer’s protocol.

tag: brain region

value: Injury peripheral tissue

value: CD45-CD31+ cells

value: adult

tag: patient


title: SK_4VIC_C08, calcifediol, time 2

city: Birmingham

description: Library name: SK_4VIC_C08

source_name: Blood


title: CLP-c


title: R162-H-002

description:
Library name: Asxl1-Het-2
Asxl1 heterozygote HSC 2 (LSK CD48- CD150+)

value: bone marrow

value: HSCs


title: R162-H-001

description:
Library name: Asxl1-Het-1
Asxl1 heterozygote HSC 1 (LSK CD48- CD150+)


title: CLP-IL-4-c


title: SK_4VIC_C07, calcifediol, time 0

description: Library name: SK_4VIC_C07

value: Blood


title: patient1 baseline

description: non urticaria


title: R2 injury peripheral tissue

description: mRNA


title: R128-H-003 [re-used]

description:
Library name: Gata2; Asxl1 WT-3
Wild Type HSC 3 (LSK CD48- CD150+)


title: Duodenum,Zeb2 mutation,rep4

first: Yang

middle: yang

last: Ge

state: Beijing

address: No. 2 Yabao Road

department: Department of Medical Genetics

institute: Capital Institute of Pediatrics

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 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: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab delimited text file includes FPKM values for each sample

source_name: Duodenum

extract_protocol:
RNA was extracted from duodenal tissues of Zeb2+/+ and Zeb2+/- mice
Messenger RNA was purified from total RNA using poly-T oligo attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Duodenum

value: Zeb2 Mutation


title: Duodenum,Zeb2 mutation,rep3


title: SK_4VIC_C12, calcitriol, time 2

description: Library name: SK_4VIC_C12

value: CD14 Monocyte

value: calcitriol


title: R128-H-004

value: Asxl1 WT


title: SK_4VIC_C11, calcitriol, time 0

description: Library name: SK_4VIC_C11


title: R2 injury center tissue

description: mRNA

value: Injury center tissue


title: SK_4VIC_C06, placebo, time 2

description: Library name: SK_4VIC_C06

value: placebo


title: SK_4VIC_C05, placebo, time 0

description: Library name: SK_4VIC_C05


title: R128-H-003


title: Duodenum,Zeb2 mutation,rep2


title: R1 injury peripheral tissue

description: mRNA


title: R128-H-002


title: Duodenum,Zeb2 mutation,rep1


title: CLP-d

value: WT


title: R1 injury center tissue

description: mRNA


title: R3 injury center tissue

description: mRNA


title: IC-21-siSMIM30-3

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The original FASTQ read files were trimmed and cleaned using fastp, then quality analysis was performed using FastQC
The trimmed fastq files were aligned by HISAT2 to human GENCODE v38 genome reference.
The aligned reads were calculated by featureCounts and differential expression genes (DEGs) were analyzed by R package DESeq2/3.1.0
Assembly: GENCODE v38
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

source_name: IC-21 cell line

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

tag: strain

value: LPS

value: IC-21 cell line


title: SK_4VIC_C03, calcitriol, time 0

department: Medicine

description: Library name: SK_4VIC_C03


title: R128-H-001


title: SK_4VIC_C02, calcitriol, time 2

description: Library name: SK_4VIC_C02


title: SMC20, Solid (S) component

description:
Library name: SMC20_S
Column name in raw counts in all_Samples.txt : SMC20_S_counts

value: Lung


title: SMC20, Ground-glass (GG) component

description:
Library name: SMC20_GG
Column name in raw counts in all_Samples.txt : SMC20_GG_counts


title: SK_4VIC_C01, calcitriol, time 0

description: Library name: SK_4VIC_C01


title: Duodenum,wide type,rep2


title: IC-21-siSMIM30-1


title: SK_4VIC_B12, calcifediol, time 2

description: Library name: SK_4VIC_B12

value: calcifediol


title: SMC20, Distant normal (DN) lung region

description:
Library name: SMC20_DN
Column name in raw counts in all_Samples.txt : SMC20_DN_counts


title: IC-21-siControl-3


title: AD4

city: xiamen

first: zuoxing

last: wu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen

institute: xiamen university

data_processing:
CLC Genomics Workbench y 11 .0.1
Assembly: GRCm39.107
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: Dorsal root ganglion

extract_protocol:
Total RNA was extracted from cultured cells or tissues using Trizol (Invitrogen, 15596026), as directed by the manufacturer.
RNA was harvested using Rneasy mini plus kit (Qiagen)1.5 ug of total RNA was used for the construction of sequencing libraries

value: Dorsal root ganglion

value: neruro

value: sensory neruro