title: CRC1566LMO0A04017001R01000, LMO_BASALE, bio rep 2, QC ok

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

value: O

tag: genotype

value: WT


title: human liver sample 200714841

status: Public on Mar 01 2023

type: SRA

city: Durham

first: Anna Mae

last: Diehl

address: 905 S LaSalle St

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: liver cells

extract_protocol:
Total RNAs were isolated from liver tissues or hepatocytes as previously described
Libraries were made with NEBNext Ultra RNA Library Prep Kit from Illumina. Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 2500

tag: cell type

value: liver cells

tag: fibrotic stage


title: CRC1566LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

last: Trusolino

state: Turin

address: Strada Provinciale, 142 -KM 3.95

department: Oncology

country: Italy

institute: IRCCS Istituto Candiolo

molecule: polyA RNA

source_name: Colorectal Cancer

growth_protocol: Please check the linked publication

treatment_protocol: Please check the linked publication

tag: tissue

value: Colorectal Cancer

tag: cell line

value: X

value: LM

tag: treatment


title: LT_CTN_20μM_rep1

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

data_processing:
Fastqc for reads quality check
Cutadapt for adaptor trimming
STAR for alignment to human reference genome
RSeQC for post-alignment quality control
edgeR for normalization to CPM
Assembly: Homo sapiens GRCh38.107
Supplementary files format and content: Tab-delimited TXT file containing raw read counts of each gene for each sample
Supplementary files format and content: CSV file containing log2CPM values of each gene for all the samples

growth_protocol: HEK293 cells were regularly cultured in MEM containing 10% FBS.

extract_protocol:
RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.

treatment_protocol: HEK293 cells were treated with 20 μM CTN for 3 days (short-term, ST) and 30 days (long-term, LT). Colony formation assay was performed at day 30 and the colonies formed were picked up for RNA-seq analysis. HEK293 cells treated with vehicle for 30 days were served as control (CTRL).

value: Embryonic kidney epithelium

value: CTN 20 microM

tag: time point

value: 30 day CTN treatment


title: human liver sample 200713137

value: Control


title: Fast Rep 4

city: Saarbrücken

first: Kathrin

last: Kattler-Lackes

state: non-US Resident

address: Campus A2.4 Raum 0.13

department: Epigenetics

country: Germany

institute: Saarland University

data_processing:
Raw reads were subjected to quality control and then trimmed for library adapters and low-quality tails.
Trimmed reads were mapped to the mouse reference genome (mm10) using STAR (version v2.6.1d).
The quantification of read numbers mapped of each gene was performed by FeatureCounts.
Raw counts were normalized as FPKM values.
Assembly: mm10
Supplementary files format and content: FPKM gene count matrix

organism: Mus musculus

source_name: brain - tanycytes

extract_protocol:
Dissociation was performed using a Papain dissociation system (Worthington) as described previously73. The dissociated cells were then sorted using FACS (Sony SH800). Cells were sorted by fluorescence (endogenously expressed GFP and virally expressed mCherry) with excitation at 488 nm and 560 nm and emission detected at 508 nm and 600/60 nm.
Smart-seq2

treatment_protocol: M5-GFP and M5-DREADD-GFP mice were i.c.v. injected with 2 ml AAV2/1+2-CAGS-mCherry virus three weeks before cell sorting. The basal hypothalamus from adult male M5-GFP mice, which either underwent 14 hours of fasting (8 mice) or normal diet feeding (6 mice) or from 6 adult male M5-DREADD-GFP mice (M5-GFP mice were used as control (6 mice), animals were injected with 2 µg CNO i.c.v. and sacrificed after 3 hours) were dissected and pooled from 2 mice.

value: brain - tanycytes

tag: Sex

value: male

tag: age

value: >12 weeks

value: fasted


title: ST_CTN_20μM_rep2

value: 3 day CTN treatment + 27 day CTN-free


title: human liver sample 200801191


title: Fast Rep 3


title: Total

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

data_processing:
NovaSeqTM 6000 (Illumina, San Diego, CA, USA) running in a 50-bp pair-end mode.
Reads were mapped an counted on human genome using STAR aligner
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath 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 genomic benchwork
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: amniotic fluid stem cells

growth_protocol: hAFSCs were grown in culture medium (αMEM) supplemented with 20% foetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacture's instructions.
RNA Truseq Stranded Total
Bead-based rRNA depletion, cDNA synthesis, and PCR

value: amniotic fluid stem cells

value: no-treatment


title: human liver sample 200711734


title: CRC1563LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: human liver sample 200711733


title: ST_CTN_20μM_rep1


title: CRC1566LMO0A04013001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: CTRL_rep2

value: CTN 0 microM

value: 30 day CTN-free


title: Fast Rep 2


title: human liver sample 200711735

value: liver cells


title: CRC1563LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: WT


title: CRC1562LMX0B04007TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: X

value: LM

value: NT


title: human liver sample A1026828


title: CRC1562LMX0B04005TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: CTRL_rep1

value: Embryonic kidney epithelium


title: human liver sample 200710778

value: Control


title: CRC1562LMX0B02001TUMR01000, LMX_BASALE, bio rep 2, QC ok


title: DREADD Rep 2

value: brain - tanycytes

value: male

value: >12 weeks


title: human liver sample 200711524


title: CRC1562LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC1562LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: EA_SSc30

city: Charleston

first: Carol

last: Feghali-Bostwick

state: SC

address: 96 Jonathan Lucas St room 822

department: Medicine

institute: Medical University of South Carolina

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
Gene-level count data were generated by HTSeq and FeatureCounts. DE analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). Significance criteria q-value<0.1, log2FC>0.6 upregulation, log2FC<-0.6 downregulation
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: raw counts

source_name: lung

growth_protocol: skin fibroblasts were maintained in DMEM media with 10%FBS, 1X ab/am

extract_protocol:
total RNA was extracted with trizol method
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit for Illumina (NEB, USA).

value: lung

value: primary

value: fibroblasts

value: SSc lung EA


title: EA_SSc38

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA


title: SIFK

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

country: China

institute: the First Affiliated Hospital of China Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (Version 6.0.2) was used to demultiplex the reads, which was followed by extraction of the cell barcodes and unique molecular identifiers (UMIs). The cDNA insert sequence was aligned to the human reference genome (GRCh38-2020).
Assembly: GRCh38-2020
Supplementary files format and content: Tab-separated values files and matrix files

source_name: knee joint cartilage

extract_protocol:
The fresh cartilage specimens were subjected to collagenase digestion to isolate the chondrocytes. Then, approximately 20,000 cells were used to acquire a single library of 10,000 cells by a Chromium controller
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: knee joint cartilage

value: Articular chondrocyte

tag: disease state

value: Subchondral insufficiency fracture of the knee (SIFK)


title: EA_SSc27

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA


title: Fast Rep 1

value: fasted


title: CRC1561LMO0A05032001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O

value: LM

value: WT


title: human liver sample 200708685

value: liver cells


title: human liver sample 200709383


title: DREADD Rep 3

value: brain - tanycytes

value: Control


title: CRC1561LMO0A05031001R01000, LMO_BASALE, bio rep 1, QC ok


title: human liver sample 200709495


title: EA_SSc23

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA


title: CRC1523LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: Ground control mouse 3 - G3

city: Loma Linda

first: Lorelei

last: Hughes

state: CA

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

data_processing:
Cutadapt and perl scripts in house were used to remove reads with adaptor contamination, low quality bases and undetermined bases
sequence quality verified using FastQC
HISAT2 was used to map the reads
StringTie was used to assemble mapped reads
StringTie and Ballgown were used to estimate expression levels of transcripts
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: heart

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method

value: heart

value: female

value: 14 weeks

value: ground control

tag: time

value: 30 days


title: EA_SSc19

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA

value: lung

value: primary

value: fibroblasts

value: SSc lung EA


title: AA_SSc85

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt

value: SSc lung AA


title: DREADD Rep 1

value: male

value: >12 weeks


title: CRC1523LMO0A05021001R01000.2, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O

value: LM

value: WT


title: Ground control mouse 1 - G25


title: CRC1523LMO0A05019001R01000.2, LMO_BASALE, bio rep 1, QC ok


title: human liver sample 200708487

value: liver cells


title: human liver sample 200707919

value: Control


title: AA_SSc77

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt


title: CRC1520PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: CRC1516PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: human liver sample 200707904


title: IECs,KO,bio rep 2

city: Wuhan City

first: Keying

last: Yu

state: Hubei Province

address: 299 Bayi Road, Wuchang District

institute: Wuhan University, China

data_processing:
Cutadapt Data filtering At least 10 bp overlap (agatcggaag), allowing a base error rate of 20%
Library quality inspection (2100 detection of library size, fluorescence quantitative detection of total library concentration < quantifluor st fluorometer, Promega, e6090; quant it PicoGreen dsDNA assay kit, Invitrogen, p7589) >, qPCR quantitative detection of effective library concentration < Thermo Scientific steponeplus real time PCR systems >)
All RNA-seq data wrer aligned to Mus musculus GRCm38 genome with Ensembl byTophat2 microexon-search and library-type firststrand
Quantitative gene expression using union scheme in HTSeq
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: excel with FPKM for every gene and every sample

source_name: small intestine

growth_protocol: The intestines of mice were excised and flushed thoroughly with phosphate-buffered saline (PBS). They were turned inside out and cut into 0.5 cm sections. The sections were incubated in epithelial cell isolation buffer (5 mL RPMI 1640, 500 μL FBS, 200 μL 0.5×10-3 m EDTA, 20 μL 1×10-3 m DTT, 20 μL 50 μg mL gentamicin) and shaken at 180 rpm at 37 °C for 30 min. The epithelial cell isolation buffer was filtered through a sterilenylon membrane and the flow-through was centrifuged at 1000 rpm at 4 °C for 5 min and saved as epithelial cells. CD45 magnetic beads were used to remove immune cells and obtain purer epithelial cells.

extract_protocol:
The cells were homogenized in TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis.
TruSeq Stranded mRNA LT Sample Prep Kit was used to synthesized the first strand cDNA through the action of random primers and reverse transcriptase, the second strand cDNA is synthesized with the first strand cDNA as the template, cDNA library construction followed by sequencing on an Illumina NovaSeq 6000 platform.  RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with cutadapt, then aligned to Mus musculus GRCm38 genome with Ensembl. The numbers of counts were summarized at the gene level using HTseq.

treatment_protocol: The mice were given 2.5% DSS in drinking water for 2 d

value: small intestine

value: intestinal epithelial cells


title: AA_SSc59

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt

value: lung


title: IECs,KO,bio rep 1


title: AA_SSc46

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt

value: primary


title: IECs,WT,bio rep 2


title: human liver sample 200708691


title: human liver sample A1025223


title: AA_SSc18

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt

value: fibroblasts


title: CRC1508PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: Ground control mouse 2 - G2

value: heart

value: female

value: 14 weeks

value: ground control

value: 30 days


title: IECs,WT,bio rep 1


title: CRC1507PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: NGP cells, Ulixertinib-3

city: Washington

first: Yang

state: DC

address: 111 Michigan Ave NW

institute: Children's national hospital

data_processing:
RNA-Seq experiments were conducted by using Illumina paired-end sequencing technology.
Raw reads were adaptor removed, and sequencing quality was assessed with the bioinformatics software FastQC (version 0.11.2).
Reads were mapped against the human reference genome (GRCh38.p13 assembly) using the aligner, HISAT2 (v2.1.0).
The mapped reads were subsequently assembled into transcripts or genes using the assembler, StringTie (v1.3.5).
Assembly: Homo_sapiens.GRCh38.dna. primary_assembly.fa.gz
Supplementary files format and content: ReadCounts.xlsx

source_name: NGP

growth_protocol: NGP cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Thermo Fisher). 100 ng 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.

treatment_protocol: NGP cells were treated with ulixertinib at 7.5 µmol/L for 24 hours, same volum DMSO were used as the control.

value: NGP

value: neuroblastoma cells

value: Ulixertinib

value: Day 5


title: CRC1504PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: WT


title: NGP cells, Ulixertinib-2

value: Day 0


title: AA_SSc15

description:
CCCR_counts_SSCL.txt
CCCR_counts_AA.txt

value: SSc lung AA


title: diff 48h bio rep3

city: Nanjing

first: Yan

last: Yuan

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
rRNA of trimmed sequence reads were filtered using sortmerna
Filtered sequence reads were mapped to GRCm38 using hisat2
Numbers of reads assigned to features (or meta-features) was caculated using featureCounts
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: EGFP-SSCs

growth_protocol: EGFP-SSCs were maintained on mitomycin C (Sigma)-exposed mouse embryonic fibro-blasts in a 37℃ incubator with 5% carbon dioxide. The SSC culture medium was StemPro-34 SFM (Invitrogen) with StemPro34 supplement (Invitrogen), along with 25mg/ml insulin, 100 mg/ml transferrin, 60 mM putrescine, 30 nM sodium selenite, 6 mg/ml D-(L)-glucose, 30 mg/ml pyruvic acid, 1 ml/ml DL-lactic acid (Sigma), 5 mg/ml bo-vine albumin (Sigma, A3803), 2mM L-glutamine, 5×10-5 M 2-mercaptoethanol, minimal essential medium vitamin solution (Invitrogen), MEM nonessential amino acid solution (Invitrogen), 10-4 M ascorbic acid, 10 mg/ml D-biotin, 30 ng/ml β-estradiol, 60 ng/ml pro-gesterone (Sigma), 20 ng/ml mouse epidermal growth factor (R&D), 10 ng/ml human basic fibroblast growth factor (R&D), 10 ng/ml recombinant rat glial cell line-derived neu-rotrophic factor (GDNF) (R&D), and 1% FBS (Invitrogen, 16141).

extract_protocol:
RNAs were purified from Trizol(15596018, Thermo Fischer Scientific) extraction
Total RNA was used as input material for the RNA sample preparations. Briefly,mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

treatment_protocol: For the SSCs differentiation, 3-7 day postpartum (dpp) busulfan-exposed murine testes were extracted, followed by a two-step enzymatic digestion, as reported earlier. Cells underwent filtration through a 40 μm cell strainer, then were centrifuged for collection. SSCs were then combined with busulfan-exposed murine testicular somatic cells at a 1:1 ratio, prior to culture in α-MEM containing 10% KSR, BMP-4/7 (20 ng/ml each, R&D Sys-tems), retinoic acid (10-6 M, Sigma), activin A (100 ng/ml, R&D Systems), testosterone (10 mM, Acros Organics), FSH (200 ng/ml, Sigma), and BPE (50 mg/ml, Corning Life Scienc-es). EGFP-positive cells were sorted by flow cytometry after differentiating for 24 and 48 hours

value: EGFP-SSCs

value: spermatogonial stem cells

value: differentiated for 48 hours


title: NGP cells, Ulixertinib-1


title: EA_NL66

description:
CCCR_counts_NL.txt
CCCR_counts_EA

value: lung

value: primary

value: fibroblasts

value: normal lung EA


title: EA_NL59

description:
CCCR_counts_NL.txt
CCCR_counts_EA


title: diff 48h bio rep2


title: CRC1502LMX0A03012TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: LM

value: NT


title: NGP cells, DMSO-2

value: NGP

value: DMSO


title: NGP cells, DMSO-3

value: neuroblastoma cells


title: CRC1502LMX0A03008TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: Colorectal Cancer

value: CET


title: EA_NL45

description:
CCCR_counts_NL.txt
CCCR_counts_EA


title: EA_NL57

description:
CCCR_counts_NL.txt
CCCR_counts_EA


title: CRC1502LMX0A02001TUMR02000, LMX_BASALE, bio rep 1, QC ok

value: X

value: WT


title: CRC1502LMO0A04010001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: diff 24h bio rep3

value: EGFP-SSCs

value: differentiated for 24 hours


title: EA_NL41

description:
CCCR_counts_NL.txt
CCCR_counts_EA


title: diff 24h bio rep2

value: spermatogonial stem cells


title: CRC1502LMO0A03010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1502LMH0000000000R02000, LMH, bio rep 1, QC ok

value: H


title: ALI-Skin org, SA 10⁶ CFU 18 hrs, rep3

city: Seoul

first: Min-Ji

last: Kim

address: Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
The libraries were sequenced on a HiSeq2500 platform to generate paired-end 100 bp sequence reads
The reads were mapped and quantified using the Bowtie2 (version 2.3.4.1) aligner and HISAT2 (version 2.1.0) with the human genome (hg19/GRCh37)
Differentially expressed genes (DEGs) were called using the DESeq2 packages. Of the 46,427 genes identified, 26,458 with at least one zero fragments per kilobase of transcript per million mapped reads were excluded, which left 19,969 genes to be processed for DEGs analysis.
The functional annotation and Gene Ontology Enrichment analysis was performed using g:Profiler.
The gene-set enrichment test and the mapping of KEGG pathways were performed using KEGG Mapper.

source_name: hiPSC-derived skin organoid

growth_protocol: Skin organoids were differentiated using a previously published protocol with modifications (Lee et al., 2020). In short, iPSCs were detached with ReLeSR™ (Stem Cell Technologies) and dissociated into single cells using Accutase (Stem Cell Technologies). Viable cells were counted with a hemocytometer with trypan blue staining. For embryoid body (EB) formation at day 0, approximately 1 x 103 hiPSCs were plated into individual wells of a U-bottom low-attachment 96-well plate (Corning) in Essential 8 (Corning). From day 0 to day 2, 10 μM Y-27632 was added to the media for EB formation. On day 2, the EBs were transferred into individual wells of a new U-bottom low-attachment 96-well plate in E6-based differentiation medium (Thermofisher) containing 2% Matrigel (Corning), 10 µM SB431542 (Tocris), 4 ng/ml FGF (PeproTech), and 15 ng/ml BMP4 (PeproTech). From day 6, 200 ng/ml FGF, 50 µg/ml LDN 193189 (Tocris), and 3 µM Wnt agonist (CHIR99021; Tocris) were added. On days 11 to 12, skin maturation medium (Lee et al., 2020) was added to each well, and to induce self-assembly of the epidermis, all organoids were transferred into 6-well low-attachment plates (Thermo Fisher Scientific) in 3 ml of skin organoid maturation medium and transferred to a shaker (65rpm; Thermo Fisher). The maturation medium was replaced every 2 to 3 days. No changes were made to the composition of the medium compared with the original protocol (Lee et al., 2020). An acellular collagen layer was prepared at a concentration of 2 mg/ml by neutralizing an acidic collagen solution (BD™ Collagen I, rat tail, BD Biosciences). After neutralization, 10X PBS was added to make a 1X PBS solution, and distilled water was added to adjust the collagen concentration. A NaOH solution was carefully added to adjust the pH. A total volume of 150 µl of 2% neutralized collagen was deposited on a high-density translucent membrane cell culture insert (0.4 μm pore size) (Corning, NY, USA) in 12-well plates. After 30 min of polymerization in a humidified incubator at 37°C with 5% CO2, 600 μl of skin maturation medium was added to the bottom of the insert in a tissue culture 12-well plate. After approximately 85 days of skin organoid culture, each cyst-like skin organoid was cut into four evenly sized portions and placed on the polymerized collagen I-coated Transwell culture inserts. The skin organoid pieces were exposed to the ALI in a humidified incubator at 37 °C with 5% CO2 for 3-4 weeks. From this point, skin organoid pieces are referred to as ALI-skin organoids. Skin maturation medium was replaced every 2 to 3 days. To induce epidermal maturation, ALI-skin organoids were transferred to an incubator without humidity at 37 °C with 5% CO2 (dry condition) for 6 more days. The skin medium was replaced daily in dry conditions.

extract_protocol:
The total RNA was extracted from three biological replicates of ALI-skin organoids after treatment with S. aureus (106 CFU) for 18 hrs using the Easy-spin Total RNA Extraction kit (iNtRON Biotechnology, Seoul, Korea)
The cDNA library was performed using the TruSeq Stranded mRNA Sample Prep kit

treatment_protocol: ALI-skin organoids were washed with skin maturation medium without antibiotics once. Prior to inoculation with bacteria, ALI-skin organoids were cultured in skin maturation medium without antibiotics in dry conditions for 6 days. Skin maturation medium was replaced daily. 1 µl of the bacterial suspension was inoculated on top of the ALI-skin organoid and allowed to dry. The control was treated with the PBS vehicle only. The ALI-skin organoid and bacteria were co-cultured in an incubator without humidity at 37°C with 5% CO2 (dry condition) for 18 hrs, 24 hrs, or 48 hrs, depending on the experiment.

value: hiPSC-derived skin organoid

value: Staphylococcus aureus


title: SSC 0h bio rep3

value: normal culture


title: diff 24h bio rep1


title: EA_NL38

description:
CCCR_counts_NL.txt
CCCR_counts_EA

value: lung

value: primary

value: fibroblasts

value: normal lung EA


title: AA_NL78

description:
CCCR_counts_NL.txt
CCCR_counts_AA.txt

value: normal lung AA


title: ALI-Skin org, SA 10⁶ CFU 18 hrs, rep2


title: ALI-Skin org, SA 10⁶ CFU 18 hrs, rep1


title: CRC1501LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: SSC 0h bio rep2


title: diff 48h bio rep1

value: differentiated for 48 hours


title: AA_NL71

description:
CCCR_counts_NL.txt
CCCR_counts_AA.txt


title: ALI-Skin org, control rep3

value: PBS


title: CRC1500LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: WT


title: SSC 0h bio rep1

value: EGFP-SSCs


title: ALI-Skin org, control, rep2


title: CRC1477LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: AA_NL22

description:
CCCR_counts_NL.txt
CCCR_counts_AA.txt


title: ALI-Skin org, control, rep1


title: NGP cells, DMSO-1

value: NGP

value: neuroblastoma cells

value: DMSO

value: Day 0


title: CRC1473LMX0B03012TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: AA_NL131

description:
CCCR_counts_NL.txt
CCCR_counts_AA.txt

value: lung

value: primary


title: TE4 CTL IG CD45 Total

city: St Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St.Louis

description: IgG control, from 6 to 9.5 months

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes.

source_name: Cortex and Hippocampus

extract_protocol:
Mice were perfused with pre-chilled PBS to fully remove blood contamination. Hippocampus and cortex were dissected followed by Dounce homogenization. Cell suspensions were then passed through Percoll density centrifugation to remove myelin and debris. The cell pellets were washed with 0.5% BSA for analysis or collection. For meninges, meninges were peeled intact from the skullcap using fine forceps and prepared for single cell analysis. Briefly, meninges were mashed through a cell strainer, using a sterile syringe plunger and washed in 0.5%BSA.  Single cell suspensions were incubated with anti-CD16/32 (Fc block; Bio legend) for 5 min then fluorescently conjugated CD45 were added for another 15 min. After washing, samples were collected by 300g followed by a 5min spin down and suspended in 5% BSA with PI for live/Dead selection before sorting. Cells were sorted using FACsAria II (BD Bioscience).
After counting and analyzing single cell integrity, 8,000-16,000 individual single cells per sample were loaded onto a 10X Genomics Chromium platform for Gel Beads-in-emulsion (GEM) and cDNA generation carrying cell- and transcript-specific barcodes and sequencing libraries constructed using the Chromium Single Cell 5’library & Gel Bead Kit V2. Libraries were sequenced on the Illumina NovaSeq6000.

value: CD45 positive cell

value: Cortex and Hippocampus

tag: strain

value: 9.5 months


title: TE4 CTL aT CD45 Total

description: CD4 and CD8 antibodies for T cell depletion, from 6 to 9.5 months


title: CRC1473LMX0B03003TUMR01000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: Colorectal Cancer

value: LM

value: NT


title: TE4m CD45 Total  Replicate 2

description: Baseline

source_name: Meninge

value: Meninge


title: HeLa cells, DBL (SETD3+SETD6) KO rep1

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
DBL_KO_1

data_processing:
The sequences were quality trimmed and filtered using Trim Galore (v0.4.5) and cutadapt (v1.15
Alignment of the reads to the human genome (GRCh38) was done using STAR (v2.5.2a)
The number of reads per gene per sample was counted using RSEM (v1.2.28
Quality assessment (QA) of the process was carried out using FASTQC (v0.11.8) and MultiQC (v1.0.dev0)
Assembly: hg38
Supplementary files format and content: GeneMat.results, Processed_RLOG_Normalized_counts.txt

source_name: HeLa

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
mRNA was purified from 500 ng of total input RNA followed by fragmentation and the generation of double-stranded cDNA. After Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent)

value: HeLa

value: Human cervical cancer cells

value: DBL (SETD3+SETD6) KO


title: CRC1473LMX0B02003TUMR01000, LMX_BASALE, bio rep 2, QC ok

value: X

value: WT


title: HeLa cells, SETD3 KO rep2

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
SETD3_KO_2

value: SETD3 KO


title: HeLa cells, DBL (SETD3+SETD6) KO rep2

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
DBL_KO_2


title: TE4m CD45 Total  Replicate 1 TCR

description: Baseline. TCR


title: TE4m CD45 Total  Replicate 1

description: Baseline


title: Lymph node, participant 128 and 129, TCR-derived cDNA

city: San Francisco

first: Matthew

last: Spitzer

address: 513 Parnassus Ave.

institute: University of California, San Francicso

description:
5' TCR library: read1 file contains cell barcode and UMI; read2 file contains transcript
VDJ enriched poly A RNA
IPIPOOL004_IPIPOOL005_comb_TCR_filtered_contig_annotations.csv

data_processing:
Alignment of raw sequencing results to generate count matrices was performed using Cell Ranger (v3.0.2 or v.6.0.2) with default settings and aligning to the hg38 genome build for gene expression or TotalSeq-C Feature Reference for ADT. The raw TCR fastq files for each participant from the lymph node and tumor were aligned to the vdj GRCh38 v.7.0.0 reference jointly in order to call shared clonotypes across the tissues using Cell Ranger v.7.0.0. The GEX BAM alignment files from each of the multiplexed libraries were used as the input for dsc-pileup v.0.1beta to generate pileup files which were then used as input for freemuxlet v.0.1beta for doublet identification, inferred genotypes for individuals in each library, and singlet assignment to those inferred genotypes. The percentage of shared single nucleotide polymorphism (SNP) assignments from the freemuxlet genotypes was used to match samples from the two individuals in the lymph node library and the tumor library to each other. The two samples in each pool were from a male and a female participant so the sex assignment (based on XIST expression and the percentage of total counts based on unique molecular identifiers (UMIs) mapping to Y chromosome genes) was used to match the freemuxlet IDs to the clinical trial participant IDs.
Further processing was done with scanpy v1.7.1 (cell and gene filtering, clustering, shared clones identification, and gene set scoring analysis).
Assembly: hg38
Assembly: TotalSeq-C Feature Reference
Assembly: vdj GRCh38 v.7.0.0
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated from gene expression data from all ten samples
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated gene expression data and TCR assignment from subsetted CD8+ T cells from all ten samples
Supplementary files format and content: h5ad file with raw ADT counts for filtered cells
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Library strategy: TCR-seq

source_name: Lymph Node

extract_protocol:
CD45+ and CD45- cells from paired HNSCC tumor and LN samples from five human participants were purified by flow cytometry. Purified cells were mixed in a 8:2 CD45+:CD45- ratio. For three of the participants, the resulting samples were then stained with a panel of 137 TotalSeq-C antibodes (Antibody Derived Tags) before loading into a Chromium Controller (10X Genomics). The samples from the other two participants were loaded directly on the Chromium Controller.
GEMs were prepared using Chromium Single Cell 5ʹ v1.1 protocol (10x Genomics) following manufacturer’s insturctions. The cDNA libraries for each sample were generated using all or a subset of Chromium Next GEM Single Cell 5' Library Kit (10X Genomics) for gene expression (GEX), Chromium Single Cell V(D)J Enrichment kit (10X Genomics) for T cell receptor (TCR), and Chromium Single Cell 5' Feature Barcode Library kit (10X Genomics) for antibody derived tag (ADT) according to the manufacturer’s instructions.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
OTHER: TCR-seq (V(D)J enrichment for immune profiling of human T cells)
OTHER: scRNA-seq (5' whole transcriptome gene expression of polyadenylated mRNA)

value: Lymph Node

tag: library type

value: VDJ

tag: antibodies/tags


title: Tumor, participant 128 and 129, TCR-derived cDNA

source_name: Tumor

value: Tumor


title: HeLa cells, SETD6 KO rep2

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
SETD6_KO_2

value: SETD6 KO


title: CRC1473LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: Lymph node, participant 128 and 129, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
adata_ADT.h5ad

library_source: other

data_processing:
Alignment of raw sequencing results to generate count matrices was performed using Cell Ranger (v3.0.2 or v.6.0.2) with default settings and aligning to the hg38 genome build for gene expression or TotalSeq-C Feature Reference for ADT. The raw TCR fastq files for each participant from the lymph node and tumor were aligned to the vdj GRCh38 v.7.0.0 reference jointly in order to call shared clonotypes across the tissues using Cell Ranger v.7.0.0. The GEX BAM alignment files from each of the multiplexed libraries were used as the input for dsc-pileup v.0.1beta to generate pileup files which were then used as input for freemuxlet v.0.1beta for doublet identification, inferred genotypes for individuals in each library, and singlet assignment to those inferred genotypes. The percentage of shared single nucleotide polymorphism (SNP) assignments from the freemuxlet genotypes was used to match samples from the two individuals in the lymph node library and the tumor library to each other. The two samples in each pool were from a male and a female participant so the sex assignment (based on XIST expression and the percentage of total counts based on unique molecular identifiers (UMIs) mapping to Y chromosome genes) was used to match the freemuxlet IDs to the clinical trial participant IDs.
Further processing was done with scanpy v1.7.1 (cell and gene filtering, clustering, shared clones identification, and gene set scoring analysis).
Assembly: hg38
Assembly: TotalSeq-C Feature Reference
Assembly: vdj GRCh38 v.7.0.0
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated from gene expression data from all ten samples
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated gene expression data and TCR assignment from subsetted CD8+ T cells from all ten samples
Supplementary files format and content: h5ad file with raw ADT counts for filtered cells
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Library strategy: CITE-seq

molecule: protein

value: ADT

value: 137 TotalSeqC antibodies


title: A-PE4m CD45 Total  TCR

description: Baseline. TCR

value: CD45 positive cell

value: 9.5 months


title: A-PE4m CD45 Total

description: Baseline


title: AA_NL25

description:
CCCR_counts_NL.txt
CCCR_counts_AA.txt

value: lung

value: primary

value: fibroblasts

value: normal lung AA


title: CRC1472LMO0A05013001R01000.2, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O

value: LM


title: E4m CD45 Total  Replicate 2

description: Baseline

value: Meninge


title: Lymph node, participant 128 and 129, mRNA-derived cDNA

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
adata.h5ad
adata_CD8.h5ad

data_processing:
Alignment of raw sequencing results to generate count matrices was performed using Cell Ranger (v3.0.2 or v.6.0.2) with default settings and aligning to the hg38 genome build for gene expression or TotalSeq-C Feature Reference for ADT. The raw TCR fastq files for each participant from the lymph node and tumor were aligned to the vdj GRCh38 v.7.0.0 reference jointly in order to call shared clonotypes across the tissues using Cell Ranger v.7.0.0. The GEX BAM alignment files from each of the multiplexed libraries were used as the input for dsc-pileup v.0.1beta to generate pileup files which were then used as input for freemuxlet v.0.1beta for doublet identification, inferred genotypes for individuals in each library, and singlet assignment to those inferred genotypes. The percentage of shared single nucleotide polymorphism (SNP) assignments from the freemuxlet genotypes was used to match samples from the two individuals in the lymph node library and the tumor library to each other. The two samples in each pool were from a male and a female participant so the sex assignment (based on XIST expression and the percentage of total counts based on unique molecular identifiers (UMIs) mapping to Y chromosome genes) was used to match the freemuxlet IDs to the clinical trial participant IDs.
Further processing was done with scanpy v1.7.1 (cell and gene filtering, clustering, shared clones identification, and gene set scoring analysis).
Assembly: hg38
Assembly: TotalSeq-C Feature Reference
Assembly: vdj GRCh38 v.7.0.0
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated from gene expression data from all ten samples
Supplementary files format and content: h5ad file with filtered, processed, and cluster annotated gene expression data and TCR assignment from subsetted CD8+ T cells from all ten samples
Supplementary files format and content: h5ad file with raw ADT counts for filtered cells
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries
Supplementary files format and content: comma separated text file with clonotype and TCR chain assignment for each cell barcode from the indicated combined libraries

value: Lymph Node

value: mRNA


title: HeLa cells, Control rep2

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
CT_2

value: HeLa

value: Human cervical cancer cells

value: Control


title: CRC1473LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

value: X

value: WT


title: CRC1472LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1472LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: HeLa cells, SETD3 KO rep1

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
SETD3_KO_1

value: SETD3 KO


title: Lymph node, participant 126, ADT-derived cDNA

value: ADT

value: 137 TotalSeqC antibodies


title: EA_SSc25

description:
CCCR_counts_SSCL.txt
CCCR_counts_EA

value: lung

value: primary

value: fibroblasts

value: SSc lung EA


title: E4m CD45 Total  Replicate 1

description: Baseline

value: CD45 positive cell

value: 9.5 months


title: Mutant treated with 50 mg/L Chl 3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli MG1655 reference genome (NC_000913.3) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Assembly: NC_000913.3
Supplementary files format and content: Excel files include FPKM values for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild-type strain E. coli K-12 MG1655 was cultured in triplicate in 50 mg/L of each antidepressant for 2 hours, at 25 °C, with shaking 120 rpm.

value: Mutant

tag: agent

value: 50 mg/L Chl


title: human liver sample 200708496

data_processing:
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver cells

value: liver cells


title: TE4B CD45 High  Replicate 2

description: Baseline

value: CD45 high cell

value: Cortex and Hippocampus


title: CRC1460LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

source_name: Colorectal Cancer

value: Colorectal Cancer

value: X

value: LM


title: CRC1464LMX0B02004TUMR05000, LMX_BASALE, bio rep 1, QC ok

value: WT


title: CRC1472LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: Mutant treated with 50 mg/L Chl 2


title: TE4B CD45 High  Replicate 1 TCR

description: Baseline. TCR


title: HeLa cells, SETD6 KO rep1

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
SETD6_KO_1

value: HeLa

value: Human cervical cancer cells

value: SETD6 KO


title: Mutant treated with 50 mg/L Chl 1


title: TE4B CD45 High  Replicate 1

description: Baseline


title: Lymph node, participant 126, mRNA-derived cDNA

value: Lymph Node

value: mRNA


title: Mutant treated with 1 mg/L Chl 3

value: 1 mg/L Chl


title: CRC1459PRX0A03012TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Tumor, participant 118, TCR-derived cDNA

description:
5' TCR library: read1 file contains cell barcode and UMI; read2 file contains transcript
VDJ enriched poly A RNA
IPIHNSC118_comb_TCR_filtered_contig_annotations.csv

value: Tumor

value: VDJ


title: CRC1460LMO0A04008001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: A-PE4B CD45 High  TCR

description: Baseline. TCR

value: 9.5 months


title: HeLa cells, Control rep1

description:
Processed_RLOG_Normalized_counts.txt
GeneMat.results
CT_1

value: Control


title: Mutant treated with 1 mg/L Chl 2

value: Mutant


title: CRC1451LMO0A04010001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: Mutant treated with 1 mg/L Chl 1


title: E4m CD45 Total  Replicate 1 TCR

description: Baseline. TCR

value: CD45 positive cell

value: Meninge


title: A-PE4B CD45 High

description: Baseline

value: CD45 high cell

value: Cortex and Hippocampus


title: Lymph node, participant 118, mRNA-derived cDNA


title: Tumor, participant 118, mRNA-derived cDNA


title: E4B CD45 High  Replicate 2

description: Baseline


title: Mutant treated with 1 mg/L Amo 3

value: 1 mg/L Amo


title: CRC1451LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H

value: LM

value: WT


title: CRC1451LMO0A04008001R01000.2, LMO_BASALE, bio rep 1, QC ok


title: Tumor, participant 117, TCR-derived cDNA

description:
5' TCR library: read1 file contains cell barcode and UMI; read2 file contains transcript
VDJ enriched poly A RNA
IPIHNSC117_comb_TCR_filtered_contig_annotations.csv


title: Mutant treated with 1 mg/L Amo 2


title: Lymph node, participant 117, TCR-derived cDNA

value: Lymph Node


title: CRC1449LMX0B01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: TE4B CD45 Total  Replicate 2

description: Baseline


title: CRC1449LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok


title: Lymph node, participant 118, TCR-derived cDNA


title: Tumor, participant 117, mRNA-derived cDNA

value: Tumor

value: mRNA


title: Mutant treated with 1 mg/L Amo 1


title: Mutant treated with 1 mg/L Cip 3

value: 1 mg/L Cip


title: Lymph node, participant 117, mRNA-derived cDNA


title: Mutant treated with 1 mg/L Cip 2


title: CRC1448LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: A-PE4B CD45 Total

description: Baseline

value: 9.5 months


title: TE4B CD45 Total  Replicate 1

description: Baseline


title: Mutant treated with 1 mg/L Cip 1


title: TF1 IDH1-R132H Replicate2

city: Boston

first: Julie-Aurore

middle: E

last: Losman

state: MA

address: 450 Brookline Ave MA448

institute: Dana-Farber Cancer Institute

data_processing:
Reads were mapped using STAR (v2.5, mismatch=2).
Reads mapping to each gene were counted using HTSeq (v0.6.1).
DESeq2 was used to normalize the data and calculate log2(fold-change) and p-values (v2_1.6.3).
Supplementary files format and content: Read Counts (HTSeq output)

growth_protocol: Cells were grown in GMCSF-rich media (RPMI, 10%FBS, 1xPenStrep).

extract_protocol: RNA was extracted with Qiagen RNeasy mini kit (Qiagen #74106).

treatment_protocol: Cells were grown for 21 days after infection before collection.

value: growth factor dependent erythroblast

value: Vector expressing IDH1-R132H


title: CRC1446LMO0A04009001R01000, LMO_BASALE, bio rep 1, QC ok

extract_protocol:
total RNA extraction
PolyA enriched
Forward Stranded

value: Colorectal Cancer

value: O


title: E4B CD45 Total  Replicate 2

description: Baseline

value: CD45 positive cell


title: TF1 IDH1-R132H Replicate1


title: E4B CD45 High  Replicate 1 TCR

description: Baseline. TCR

value: CD45 high cell


title: CRC1445LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: E4B CD45 Total  Replicate 1

description: Baseline

value: Cortex and Hippocampus


title: Mutant treated with 1 mg/L Tet 3

value: Mutant

value: 1 mg/L Tet


title: Mutant treated with 1 mg/L Tet 2


title: E4B CD45 High  Replicate 1

description: Baseline


title: CRC1445LMO0B05015001R01000, LMO_BASALE, bio rep 2, QC ok

value: LM


title: TF1-Empty Vector Replicate2

value: Empty vector


title: dPKO_6B69

city: New Haven

first: Stephen

middle: M

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

description: 10x Genomics

data_processing:
Reads where aligned to mm10 mouse genome referemce and masked for low quality sequences using the Cell Ranger Software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Samples under went two rounds snRNA sequencing, to increase sequencing depth, using Illumina NoveSeq 5000/6000 software for basecalling.
Scanpy (Wolf F. et al, 2018) was used to generate a merged anndata objects of all study samples for QC processing and gene filtering.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Data was log-normalized and underwent sample based integration using Scanpy's implementation of Seurat_v3.
mm10 whole genome using 3.0.0_premrna with parameters chemistry=SC3Pv3
Leiden clustering, UMAP embedding, cell type cluster assigments, DEG testing, and read count extraction was performed using Scanpy's data processing pipelin.
Seurat (Butler et al., 2018 was used to generate seurat objects of single nuclei transcriptomic datasets, with pre-processing and quality control analysis
Nuclei doublet idenitification and removal using DoubletFinder (McGinnis CS, et. Al)
Log-normalization and multi-dataset reference-based integration with dimensionally reduced UMAP generation using Seurat
Assembly: mm10-2020-A
Supplementary files format and content: comma separated gene count matrix files.

source_name: Coxtex, Hippocampus

growth_protocol: Mice where ageed for 10 or 20 months

extract_protocol:
Cerebral cortex and hippocampal tissues where disected from the left brain hemisphere. The tissues were pooled together for each mouse and processed for nuclei isolation via sucrose density gradient centrifugation with 8000-1000 nuclei used for 10x Genomics barcode mRNA sequencing.
RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3P' v3.1  Kit following the manufacturer's protocols.
snRNAseq

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI; Prnp-/-

value: AD

value: Male

value: 20 months


title: TF1-Empty Vector Replicate1

value: growth factor dependent erythroblast


title: CRC1446LMX0B02003TUMR05000, LMX_BASALE, bio rep 1, QC ok

city: Candiolo

first: Livio

address: Strada Provinciale, 142 -KM 3.95

institute: IRCCS Istituto Candiolo

value: X

value: WT


title: Mutant treated with 1 mg/L Tet 1


title: dPKO_5A1A

description: 10x Genomics

value: Female


title: CRC1445LMO0B04010002R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O


title: CRC1441PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: Mutant treated with 50 mg/L Amo 2

value: Mutant

value: 50 mg/L Amo


title: dPKO_4B30

description: 10x Genomics


title: Mutant treated with 50 mg/L Amo 3


title: CRC1436PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: dPKO_2662

description: 10x Genomics


title: dPKO_4D7A

description: 10x Genomics


title: Mutant treated with 50 mg/L Amo 1


title: CRC1435PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: UNT2-CPZ-RNA

city: Los Angeles

first: Brent

middle: L

last: Fogel

address: 710 Westwood Plaza

institute: UCLA

data_processing:
Reads were mapped to hg38 using the STAR aligner
BAM files were sorted using samtools
Reads were counted using HTSeq
Read counts were normalized to RPKM in R before downstream analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts values for each Sample

source_name: HOG

extract_protocol:
All cells were collected using the QIAGEN miRNeasy Mini or Micro Kit with on-column DNase digestion.
RNA libraries of 100 bp paired-end reads were prepared using the TruSeq Stranded Total RNA Gold Kit following the manufacturer’s instructions.

value: HOG

value: untreated


title: UNT1-CPZ-RNA


title: UNT3-CPZ-RNA


title: HOG-P2-B2

value: pcDNA1 Flag ATXN1[85Q]

value: DMSO


title: CRC1432LMO0B04013001R01000, LMO_BASALE, bio rep 2, QC ok

last: Trusolino

value: LM


title: Mutant treated with 50 mg/L Cip 3

value: 50 mg/L Cip


title: dPKO_2273

description: 10x Genomics

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI; Prnp-/-

value: AD

value: Male


title: Mutant treated with 50 mg/L Cip 2


title: dKI_4C40

description: 10x Genomics

value: DKI

value: Female

value: 20 months


title: HOG-P2-B1

value: pcDNA1 Flag ATXN1[30Q]


title: Mutant treated with 50 mg/L Cip 1

value: Mutant


title: HOG-P2-A2


title: dKI_4074

description: 10x Genomics


title: CRC1430LMX0A02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: WT


title: CRC1430LMO0B05012001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: Mutant treated with 50 mg/L Tet 3

value: 50 mg/L Tet


title: HOG-P2-A1

value: HOG


title: CRC1429PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: dKI_2977

description: 10x Genomics

value: Coxtex, Hippocampus


title: HOG-P1-B2

value: pcDNA1 Flag ATXN1[85Q]

value: DMSO


title: Mutant treated with 50 mg/L Tet 1


title: dKI_222A

description: 10x Genomics

value: hTau/APPNL-G-F

value: AD


title: dKI_2070

description: 10x Genomics

value: DKI

value: Male


title: Mutant control 3

value: control


title: CRC1432LMO0B04010001R01000, LMO_BASALE, bio rep 1, QC ok

value: LM


title: Mutant control 2

value: Mutant


title: PKO_5D11

description: 10x Genomics

value: Prnp-/-

value: Wildtype

value: Female

value: 20 months


title: HOG-P1-A1

value: pcDNA1 Flag ATXN1[30Q]


title: Mutant treated with 50 mg/L Tet 2

value: 50 mg/L Tet


title: CRC1420PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: PR

value: WT


title: HOG-P1-B1

value: HOG

value: DMSO


title: CRC1426PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: HOG-P1-A2

value: pcDNA1 Flag ATXN1[85Q]


title: CRC1430LMO0B04008001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: Mutant control 1

value: control


title: B3-mir506-48h

value: miR506 ASO 48h


title: PKO_3217

description: 10x Genomics

value: Coxtex, Hippocampus


title: CRC1418PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: PKO_004D

description: 10x Genomics

value: Prnp-/-

value: Male


title: WT treated with 50 mg/L Ago 3

value: 50 mg/L Ago


title: CRC1414PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: WT treated with 50 mg/L Ago 2


title: PKO_6D46

description: 10x Genomics

value: Wildtype

value: Female

value: 20 months


title: PKO_3F11

description: 10x Genomics


title: B3-UNT

value: untreated


title: WT_7413

description: 10x Genomics


title: B3-mir506-24W

value: miR506 ASO 24W


title: WT_704A

description: 10x Genomics


title: B2-mir506-24W


title: CRC1412LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: LM


title: WT treated with 50 mg/L Esc 1

value: WT

value: 50 mg/L Esc


title: WT treated with 50 mg/L Esc 3


title: CRC1419PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: PKO_322A

description: 10x Genomics


title: WT treated with 50 mg/L Ago 1


title: CRC1413PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC1408LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC1409PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: B3-EtOH-HOG-RNA

value: HOG

value: EtOH


title: B2-EtOH-HOG-RNA


title: WT treated with 50 mg/L Esc 2


title: WT_1048

description: 10x Genomics

value: Coxtex, Hippocampus


title: WT treated with 50 mg/L Bup 3

value: 50 mg/L Bup


title: CRC1399LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: B2-mir506-48h

value: miR506 ASO 48h


title: WT_4239

description: 10x Genomics


title: B2-DMSO-85Q-HOG

value: pcDNA1 Flag ATXN1[85Q]

value: DMSO


title: WT treated with 50 mg/L Bup 2


title: B2-UNT


title: WT_0813

description: 10x Genomics

value: Wildtype

value: Male


title: CRC1391PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: WT treated with 50 mg/L Dul 3

value: 50 mg/L Dul


title: WT treated with 50 mg/L Bup 1


title: CRC1390LMO0B04024002R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: B1-mir506-24W

value: miR506 ASO 24W


title: B1-GFP-ASO

value: GFP ASO


title: CRC1390LMO0B03018001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: WT treated with 50 mg/L Dul 2

value: WT


title: CRC1390LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: WT treated with 50 mg/L Ser 3

value: 50 mg/L Ser


title: CRC1389LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: WT_1160

description: 10x Genomics

value: 20 months


title: dPKO_F5E

description: 10x Genomics

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI; Prnp-/-

value: AD

value: 10 months


title: dPKO_879

description: 10x Genomics


title: B1-EtOH-HOG-RNA

value: HOG

value: EtOH


title: B1-DMSO-30Q-HOG

value: pcDNA1 Flag ATXN1[30Q]

value: DMSO


title: WT treated with 50 mg/L Dul 1

value: 50 mg/L Dul


title: CRC1389LMO0A04008001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: WT treated with 50 mg/L Ser 2


title: dKI_434

description: 10x Genomics

value: DKI

value: Female


title: A3-PLP1-ASO-48h

value: PLP1 ASO 48h


title: WT treated with 50 mg/L Ser 1

value: WT


title: dKI_A60

description: 10x Genomics

value: Male


title: B1-mir506-48h

value: miR506 ASO 48h


title: CRC1389LMO0A02004001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: CRC1399LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok


title: dPKO_631

description: 10x Genomics

value: Coxtex, Hippocampus

value: hTau/APPNL-G-F

value: DKI; Prnp-/-


title: WT treated with 1 mg/L Ser 3

value: 1 mg/L Ser


title: dPKO_A4B

description: 10x Genomics

value: AD

value: 10 months


title: A3-PLP1-ASO-24h

value: HOG

value: PLP1 ASO 24h


title: WT treated with 1 mg/L Ser 2


title: A3-mir124-48h

value: miR124 ASO 48h


title: CRC1387PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: X

value: PR


title: A3-miR124-24W

value: miR124 ASO 24W


title: A3-GFP-ASO-48h

value: GFP ASO 48h


title: WTcontrol 3

value: WT

value: control


title: WT treated with 1 mg/L Ser 1


title: dKI_A20

description: 10x Genomics

value: DKI

value: Female


title: CRC1387LMX0A01001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: LM


title: PKO_50C

description: 10x Genomics

value: Coxtex, Hippocampus

value: Prnp-/-

value: Wildtype


title: CRC1382PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: CRC1381PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: WTcontrol 2


title: A3-CPZ-HOG-RNA

value: Cuprizone treated


title: CRC1378PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: WTcontrol 1


title: PKO_00B

description: 10x Genomics

value: Male

value: 10 months


title: B1-GFP-ASO-48h

value: HOG


title: CRC1376LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: A2-PRT4165-85Q-HOG

value: pcDNA1 Flag ATXN1[85Q]


title: dKI_432

description: 10x Genomics

value: hTau/APPNL-G-F

value: AD


title: dKI_75E

description: 10x Genomics


title: WT_C42

description: 10x Genomics

value: WT


title: CRC1376LMO0C05032002R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: WT+LPS 4h, replicate 2

city: Evanston

first: Brian

last: Wray

state: IL

address: 633 Clark Street

department: Feinberg School of Medicine

institute: Northwestern University

description: 10x Genomics

data_processing:
Demultiplexed raw reads were mapped to the mouse genome (Mm10) using Cell Ranger (v6.1.0) with default settings.
Unfiltered count matrices for each library were loaded into R for processing by the Seurat package (V4.1.0, Hao and How et al. 2021) within R (v4.1.3) (Hao et al., 2021). Several filters were applied using Seurat. First, cells were removed if they didn’t have a minimum of 300 features. Then we applied filters to remove cells that had more than 20% mitochondrial genes, or had fewer than 700 features, or had either fewer than 1000 UMIs, or had more than 100,000 UMIs. Applying these filters reduced the number of combined cells from 64,330 to 58,011. Cell cycle stage was estimated using Seurat. All samples were combined into a single Seurat object and then log normalized. Cell cycle stage, percentage of mitochondrial genes, and number of features were regressed out during normalization.
Dimensionality reduction for clustering was done via PCA combined with Jackstraw in the Seurat package. Clustering was performed using the first 50 PCs with a range of resolutions (0.25 – 4, stepping every 0.5) and then used as input to t-SNE for imaging. The t-SNE plots were consulted to select a clustering resolution of 0.75. The Seurat function FindAllMarkers() was used to identify marker genes that differentiate any given cluster from the rest of the cells. Another Seurat function, FindMarkers(), was used to compare individual clusters to each other and to find genes that differentiate the two clusters
SingleR (v1.6.1) was used to identify resident macrophage cells in the dataset (Aran et al., 2019). We based the cell-type classification on the ImmGen database, which has normalized expression values for immune cells from 830 murine microarrays. Macrophage populations were confirmed with UMAP plotting of canonical marker genes
String network was generated using the list of differentially expressed genes in macrophage subclusters (iAM vs rAM), uploaded to Cytoscape 3 against reference species (Mus musculus) with confidence cutoff of 0.4 and zero additional interactions. Gene networks were clustered using MCL algorithm with granularity of 4. String functional enrichment was retrieved for network using the whole genome as background.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
whole lungs were minced and digested with 500 μg/mL Liberase TB (Sigma, # 5401127001), 150 μg/mL DNase I (Sigma #1010459001), and 5 mM MgCl2 in PBS (pH 7.4) for 20 min at 37 oC. Then, single cell suspension was filtered through 70 μm nylon mesh cell strainer and treated with RBC Lysis Buffer (Invitrogen, # 00430054) according to manufacturer’s instructions. Ten million lung cells in suspension were mixed with 5 μL Component A, 5 μL Component B, and 5 μL magnetic RapidSpheresTM provided in the EasySep kit, and incubated for 5 min in ice. CD45+ cells trapped in magnetic beads were isolated using a magnetic platform, and released diluted in EasySepTM Buffer (StemCell #20144).
Sample quality, library complexity, and alignment statistics were checked using an established pipeline at the NUSeq Core Facility at Northwestern University

treatment_protocol: WT or NOS1-/- mice were challenged with intraperitoneal dose of 10 mg/kg LPS or vehicle control for 4 h. CD45+ cells were isolated from lungs using EasySepTM Mouse CD45 Positive Selection Kit

value: hematopoietic (CD45+ enriched)

value: lung

value: mouse


title: A3-GFP-ASO

value: GFP ASO


title: A2-PLP1-ASO-48h

value: PLP1 ASO 48h


title: PKO_420

description: 10x Genomics

value: Coxtex, Hippocampus

value: Prnp-/-


title: CRC1372PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: PR


title: WT_A00

description: 10x Genomics

value: Wildtype

value: Female

value: 10 months


title: WT+LPS 4h, replicate 1

description: 10x Genomics


title: CRC1370PRX0A01001TUMR05000, PRX_BASALE, bio rep 1, QC ok

value: X


title: A2-PLP1-ASO-24h

value: HOG

value: PLP1 ASO 24h


title: WT_513

description: 10x Genomics

value: WT

value: Male


title: A2-mir124-48h

value: miR124 ASO 48h


title: NOS1 KO +LPS 4h, replicate 2

description: 10x Genomics

value: hematopoietic (CD45+ enriched)

value: lung


title: CRC1367LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: WT control

description: 10x Genomics

value: mouse


title: WT_541

description: 10x Genomics

value: Coxtex, Hippocampus


title: A2-GFP-ASO

value: GFP ASO


title: WT_16F

description: 10x Genomics


title: CRC1367LMO0A04012001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: O


title: NOS1 KO +LPS 4h, replicate 1

description: 10x Genomics


title: A2-GFP-ASO-48h

value: GFP ASO 48h


title: AngII heart, rep 2

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: GRCm39
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Heart

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

treatment_protocol: For AngII-induced cardiac hypertrophy model, wild-type C57BL/6J mice were injected with Ang II (1 μg/kg/min) or normal saline via an osmotic pump for four weeks to induce cardiac hypertrophy based on our previous research. An osmotic pump was subcutaneously implanted in the back of each mouse. In the first week after the operation, the incision of the mice was observed daily, while the blood pressure and body weight were measured and recorded every three days. The mice were sacrificed to collect serum and heart tissue samples at four weeks.

value: heart

value: 10 weeks

value: AngII-induced cardiac hypertrophy model


title: NOS1 KO control

description: 10x Genomics


title: Internal_control_Normal_IgG_S2

library_source: genomic

data_processing:
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt
Trimmed reads were aligned to the Mus musculus genome (mm10) using Bowtie2 (version 2.4.1) with default parameters while only reads that mapped uniquely to the genome were used in subsequent analysis.
ChIP-seq analysis was performed largely using Hypergeometric Optimization of Motif EnRichment (HOMER, version 4.11) (Duttke et al., 2019).  HOMER was used to call peaks, identify loci of differential binding, generate UCSC read density tracks, annotate peaks, and detect motif enrichments.
Heatmaps of TSS enrichment of were generated using deepTools2
Assembly: mm10

molecule: genomic DNA

source_name: BMDM

growth_protocol: BMDM were generated from bone marrow prepared for in vitro differentiation for 5 days in complete Roswell Park Memorial Institute (RPMI) 1640 Medium (Gibco, # 22400089) supplemented with 10% (v/v) fetal bovine serum, 20 ng/mL recombinant murine MCSF (Preprotech, # 315-02), 100 U/mL Penicilin-Streptomycin and 2 mM L-Glutamine, at 37 oC and 5% CO2 atmosphere.

extract_protocol:
~1x107 BMDM were briefly fixed with 1% methanol-free formaldehyde solution (Thermo Scientific, # 28908) for 1 min at RT. Then, reaction was quenched with addition of 125 mM glycine for 3 min. Cells were harvested in ice-cold PBS (pH 7.4) and centrifuged at 300 x g for 5 min at 4 oC. Chromatin isolation and immunoprecipitation were carried out using CUTANATM ChIC/CUT&RUN kit (EpiCypher #141048). One hundred thousand cells were resuspended in Wash Buffer (Pre-Wash Buffer supplemented with 1X protease inhibitor cocktail, 460 mM Spermidine, 1% Triton X-100, 0.045% SDS), and incubated with activated ConA beads for 10 min at RT. Then, cells were permeabilized with 0.01% Digitonin in Wash Buffer, and incubated with 0.5 g target antibody at 4 oC overnight with agitation. The antibodies used were anti-p65 (Cell Signaling, # 8242), anti-SOCS1 (Cell Signaling, # 3950), or Normal Rabbit IgG (Cell Signaling, # 2729). Cells were washed twice with cold Wash Buffer supplemented with Digitonin, and chromatin regions around target-DNA complex were digested with pAG-MNase for 10 min at RT, followed by addition of 2 mM CaCl2, and incubation with agitation for 2 h at 4 oC. Digestion was stopped with addition of Stop Buffer, and E. coli Spike-in DNA was added to each sample for normalization. Target-DNA complex fragments were released by heat shock at 37 oC for 10 min, followed by magnetic separation of cells. Cross linking was reversed by digestion of proteins in the supernatant with 20 g Proteinase K at 55 oC overnight. Chromatin fragments were purified by standard protocol using DNA Cleanup Columns provided in the kit. IL).
Sample quality, library complexity, and alignment statistics were checked using an established pipeline at the NUSeq Core Facility at Northwestern University (Chicago,

treatment_protocol: Cells were treated at time points with 100 ng/mL LPS.

value: BMDM

value: bone marrow-derived macrophages


title: AngII heart, rep 3


title: CRC1360LMX0B05010TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: X

value: WT

value: NT


title: A2-CPZ-HOG-RNA

value: HOG

value: Cuprizone treated


title: CRC1360LMX0B05005TUMR01000, LMX_cetux_6w, bio rep 1, QC ok

value: LM

value: CET


title: Internal_control_H3K9me3_S1


title: ChIP_SOCS1_WT_LPS8h_S5

tag: chip antibody

value: SOCS1 (Cell Signaling 3950)


title: A2-miR124-24W

value: miR124 ASO 24W


title: CRC1369LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: AngII heart, rep 1


title: A1-PRT4165-30Q-HOG

value: pcDNA1 Flag ATXN1[30Q]


title: CRC1360LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CON heart, rep 2

value: CON


title: A1-PLP1-ASO-24h

value: PLP1 ASO 24h


title: ChIP_SOCS1_WT_LPS30min_S4


title: A1-PLP1-ASO-48h

value: PLP1 ASO 48h


title: CRC1360LMO0B04012001R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: CRC1359LMX0A02003TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: CRC1360LMH0000000000R09000, LMH, bio rep 1, QC ok

value: H


title: A1-miR124-48h

value: miR124 ASO 48h


title: A1-miR124-24W


title: CON heart, rep 1

value: heart

value: 10 weeks


title: ChIP_SOCS1_KO_LPS30min_S7

value: BMDM

value: bone marrow-derived macrophages


title: CRC1359LMO0B02004001R01000, LMO_BASALE, bio rep 1, QC ok

value: WT


title: CRC1359LMO0B04008001R01000, LMO_BASALE, bio rep 2, QC ok

value: LM


title: WD fed mice PBS treated 2

city: Maywood

first: Gregory

last: Aubert

address: 2160 S 1st Ave

institute: Loyola University Chicago

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw gene counts

source_name: Heart ventricle

extract_protocol:
Total RNA was extracted from mouse heart using RNAeasy (Qiagen).
RNA libraries for RNA-seq were prepared using IDT for Illumina DNA/RNA UD Library Prep Kit following manufacturer's protocols.

value: Heart ventricle

tag: diet

value: western-diet

value: PBS


title: WD fed mice PBS treated 3

tag: genotype


title: ChIP_SOCS1_WT_Control_S3

tag: cell type

value: SOCS1 (Cell Signaling 3950)


title: A1-GFP-ASO

value: HOG

value: GFP ASO


title: A1-CPZ-HOG-RNA

value: Cuprizone treated


title: ChIP_SOCS1_KO_Control_S6


title: A1-GFP-ASO-48h

value: GFP ASO 48h


title: CON heart, rep 3

value: CON


title: CRC1357PRX0B02001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

value: PR


title: ChIP_p65_WT_LPS8h_S11

value: NFkB p65 (Cell Signaling 8242)


title: WD fed mice Tributyrin treated 2

value: Tributyrin


title: WD fed mice Tributyrin treated 3


title: WD fed mice PBS treated 1


title: CRC1353LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: ChIP_SOCS1_KO_LPS8h_S8

value: BMDM

value: bone marrow-derived macrophages


title: ChIP_p65_KO_LPS8h_S14


title: CRC1355LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: ChIP_p65_WT_LPS30min_S10


title: WD fed mice Tributyrin treated 1

value: Heart ventricle

value: western-diet


title: PC3 cells expressing AR-Y764C-2 [YC-2]

city: Hospitalet de Llobregat

first: Alvaro

last: Aytes

state: Barcelona

address: Granvia 199

department: ProCURE

country: Spain

institute: IDIBELL

description: Column R

data_processing:
Read count was performed with the STAR parameter - quantMode GeneCounts
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCh38 using STAR
Assembly: GRCh38
Supplementary files format and content: Count_matrix.txt

source_name: Prostate

growth_protocol: RPMI 10% CSS

extract_protocol:
TOTAL RNA
Stranded RNA

treatment_protocol: 20nM DHT

value: Prostate

value: Cancer-epithelial

value: expressing AR-Y764C-2


title: ChIP_p65_KO_LPS30min_S13


title: CRC1350LMO0B04028003R01000.2, LMO_BASALE, bio rep 2, QC ok

value: O


title: PC3 cells expressing AR-Y764C-3 [YC-3]

description: Column S

value: expressing AR-Y764C-3


title: ChIP_p65_WT_Control_S9


title: p53 AD/- thymus [SC206_5 scRNA-seq]

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: single cell RNA

data_processing:
cellranger V4.0.0 mkfastq
cellranger V4.0.0 count
reads are mapped to GRCm38
UMI counts are summarized are gene expression levels
Assembly: GRCm38
Supplementary files format and content: filtered feature matrix, barcodes, features

source_name: thymus

extract_protocol:
mice with germline p53 alterations were sacrificed for thymus collection at 4 weeks of age
Cells were processed according to the manufactures protocol.

tag: background strain

value: 4 weeks of age

value: thymus

value: Female


title: PC3 cells expressing AR-WILD TYPE [WT-2]

description: Column O

tag: tissue

value: expressing AR-WILD TYPE


title: ChIP_p65_KO_Control_S12

tag: cell line

value: NFkB p65 (Cell Signaling 8242)


title: p53 -/- thymus [SC206_3 scRNA-seq]

description: single cell RNA


title: CRC1350LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X

tag: treatment


title: ChIP_IgG_WT_LPS30min_S16

value: BMDM

value: bone marrow-derived macrophages

value: IgG (Cell Signaling 2729)


title: CRC1344LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM

value: WT


title: RP normal control [JGAme_795_EAR WES]

data_processing:
library strategy: DNA-seq
fastq files were trimmed using trim_galore (0.6.5)
reads were aligned to genome using bwa mem (0.7.17)
cnv analysis carried out using gistic (2.0)
mutation call carried out using gatk (4.1.0.0)
Assembly: GRCm38
Supplementary files format and content: tab-deliminated segment mean

source_name: ear

extract_protocol:
mice with germline p53 alterations were sacrificed and tumors collected at end point
Library preparation followed standard Illumina protocol

value: ear


title: PC3 cells expressing AR-WILD TYPE [WT-1]

description: Column N

value: Prostate

value: Cancer-epithelial


title: RP tumor [JGAme_372_S WES]

source_name: sarcoma

value: sarcoma


title: p53+/- thymus [SC206_1 scRNA-seq]

description: single cell RNA


title: ChIP_IgG_WT_Control_S15


title: CRC1350LMO0B04026002R01000.2, LMO_BASALE, bio rep 1, QC ok

value: O


title: RP tumor [JGAme_442_S WES]


title: PC3 cells expressing AR-V758A-3 [VA-3]

description: Column M

value: expressing AR-V758A-3


title: CRC1344LMO0A04007001R01000, LMO_BASALE, bio rep 1, QC ok


title: RP tumor [JGAme_795_S WES]


title: PC3 cells expressing AR-V758A-2 [VA-2]

description: Column L

value: expressing AR-V758A-2


title: PC3 cells expressing AR-V758A-1 [VA-1]

description: Column K

value: expressing AR-V758A-1


title: CRC1342LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: ChIP_IgG_KO_LPS8h_S20


title: CRC1350LMH0000000000R01000, LMH, bio rep 1, QC ok

value: H


title: ChIP_IgG_KO_LPS30min_S19


title: ChIP_IgG_WT_LPS8h_S17


title: ChIP_IgG_KO_Control_S18


title: RP tumor [JGAme_449_S WES]


title: PC3 cells expressing AR-Q799E-3 [QE-3]

description: Column J

value: expressing AR-Q799E-3


title: CRC1342LMO0A04007001R01000, LMO_BASALE, bio rep 1, QC ok

value: Colorectal Cancer


title: PC3 cells expressing AR-Y764C-1 [YC-1]

description: Column Q

value: expressing AR-Y764C-1


title: PC3 cells expressing AR-Q799E-2 [QE-2]

description: Column I

value: expressing AR-Q799E-2


title: MCWR_2019_000398

data_processing:
none provided
Assembly: mm10
Supplementary files format and content: tab-delimited text files with htseq counts

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN, # 74106) with additional DNase treatment using RNase-free DNase Set (QIAGEN, # 1023460).
Sequencing libraries were generated using Illumina Novaseq platform.

value: BMDM

value: macrophage

value: BMDM NOS1 KO

value: LPS


title: AD tumor [JGAme_724_S WES]


title: AD normal control [JGAme_724_EAR WES]

value: ear


title: PC3 cells expressing AR-Q799E-1 [QE-1]

description: Column H

value: Prostate

value: expressing AR-Q799E-1


title: CRC1337LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X

value: LM

value: WT


title: MCWR_2019_000397


title: CRC1340PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: PC3 cells expressing AR-F755V-3 [FV-3]

description: Column G

value: Cancer-epithelial

value: expressing AR-F755V-3


title: RP tumor [JGAme_379453_S WES]

value: sarcoma


title: MCWR_2019_000396

value: control


title: PC3 cells expressing AR-F755V-2 [FV-2]

description: Column F

value: expressing AR-F755V-2


title: CRC1337LMO0A04008001R01000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer

value: O


title: CRC1337LMO0A04007003R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1336LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: MCWR_2019_000395

value: BMDM

value: macrophage

value: BMDM WT


title: PC3 cells-3 [CNT-3]

description: Column D


title: PC3 cells expressing AR-F755V-1 [FV-1]

description: Column E

value: expressing AR-F755V-1


title: AD tumor [JGAme_383_S WES]


title: AD tumor [JGAme_20121_S WES]


title: AD tumor [JGAme_698_S WES]


title: MCWR_2019_000393


title: PC3 cells-2 [CNT-2]

description: Column C

value: Prostate


title: CRC1331LMX0B04011TUMR01000, LMX_cetux_h_NT, bio rep 2, QC ok

value: NT


title: RP normal control [JGAme_367_EAR WES]

value: ear


title: PC3 cells-1 [CNT-1]

description: Column B


title: MCWR_2019_000391

value: NOS1 KO

value: LPS


title: RP tumor [JGAme_784_TL WES]

source_name: thymic lymphoma

value: thymic lymphoma


title: LAMA84-R cell, siANGPT1 lentiviral transfection, rep3

city: Guiyang

first: Yunsheng

last: Ran

state: Guizhou

address: No. 9 Beijing Road, Guiyang City, Guizhou Province

department: Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D

institute: Guizhou Medical University

description:
iRNA-3
Bone Marrow

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh_38
Supplementary files format and content: all.counts.txt: Tab-delimited text file contains counts for each sample.

growth_protocol: K562R, LAMA84-R cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The siANGPT1 lentivirus, purchased from GenenChem (Shanghai, China), was added to two pairs of CML cell lines (2 × 10^5) seeded in 500 μL RPMI 1640 medium in 24-well plates. Cells were then transduced according to the instructions provided by Genechem.

value: ANGPT1 knockdown

tag: phenotype

value: TKI-resistant

value: Without drug treatment


title: AD tumor [JGAme_465_S WES]

value: sarcoma


title: RP tumor [JGAme_782_TL WES]


title: CRC1331LMX0B04001TUMR05000, LMX_cetux_h, bio rep 2, QC ok

value: X

value: LM

value: WT

value: CET


title: MCWR_2019_000390

value: BMDM

value: macrophage

value: control


title: MCWR_2019_000394

value: BMDM WT


title: CRC1331LMX0A04009TUMR01000, LMX_cetux_h_NT, bio rep 1, QC ok

value: Colorectal Cancer

value: NT


title: LAMA84-R cell, siANGPT1 lentiviral transfection, rep2

description:
iRNA-2
Bone Marrow


title: CRC1334PRX0A01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: MCWR_2019_000389

value: NOS1 KO

value: LPS


title: LAMA84-R cell, siANGPT1 lentiviral transfection, rep1

description:
iRNA-1
Bone Marrow

value: ANGPT1 knockdown


title: RP tumor [JGAme_660_TL WES]

value: thymic lymphoma


title: RP tumor [JGAme_370_TL WES]


title: MCWR_2019_000388


title: CRC1343PRX0A02003TUMR01000, PRX_BASALE, bio rep 1, QC ok


title: LAMA84-R cell, empty vector transfection, rep2

description:
EV-2
Bone Marrow

value: TKI-resistant

value: Without drug treatment


title: MCWR_2019_000392


title: CRC1331LMX0A02005TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: MCWR_2019_000387


title: RP tumor [JGAme_367_TL WES]


title: MCWR_2019_000386


title: CRC1331LMO0A04011001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: LM


title: RP tumor [JGAme_340_TL WES]


title: LAMA84-R cell, empty vector transfection, rep1

description:
EV-1
Bone Marrow

value: WT


title: CRC1331LMO0A02010002R01000, LMO_cetuxi_h, bio rep 2, QC ok

value: CET


title: K562R cell, siANGPT1 lentiviral transfection, rep3

description:
LR-SI3
Bone Marrow


title: CRC1331LMX0A04004TUMR01000, LMX_cetux_h, bio rep 1, QC ok


title: CRC1331LMO0A02010001R01000, LMO_cetuxi_h_NT, bio rep 2, QC ok


title: MCWR_2019_000385

value: BMDM

value: macrophage


title: AD normal control [JGAme_441_EAR WES]

value: ear


title: RP tumor [JGAme_355_TL WES]


title: AD tumor [JGAme_387_TL WES]


title: CRC1331LMO0A04027003R02000, LMO_BASALE, bio rep 2, QC ok

value: Colorectal Cancer


title: CRC1331LMO0A02009002R01000, LMO_cetuxi_h, bio rep 1, QC ok


title: LAMA84-R cell, empty vector transfection, rep3

description:
EV-3
Bone Marrow


title: K562R cell, siANGPT1 lentiviral transfection, rep1

description:
LR-SI1
Bone Marrow


title: CRC1331LMO0A02009001R01000, LMO_cetuxi_h_NT, bio rep 1, QC ok

value: NT


title: MCWR_2019_000380


title: AD tumor [JGAme_954_TL WES]


title: MCWR_2019_000384

value: control


title: MCWR_2019_000381


title: K562R cell, empty vector transfection, rep3

description:
LR-EV3
Bone Marrow

source_name: K562R cell, empty vector transfection


title: K562R cell, siANGPT1 lentiviral transfection, rep2

description:
LR-SI2
Bone Marrow


title: AD tumor [JGAme_711_TL WES]


title: CRC1331LMH0000000000R09000, LMH, bio rep 1, QC failed

value: H


title: CRC1326LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: K562R cell, empty vector transfection, rep1

description:
LR-EV1
Bone Marrow


title: CRC1325PRX0B02003TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: PR


title: MCWR_2019_000379

value: NOS1 KO

value: LPS


title: AD tumor [JGAme_626_TL WES]

value: thymic lymphoma


title: mRNAseq_Str_3

city: Changzhou City

first: kang

last: wen

state: Jiangsu Province

address: Changzhou University, HUTANG Town, Wujin District

department: Institute of Biomedical Engineering and Health Sciences

institute: Changzhou University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: hASMCs,stretch,bioflex plate,72h

growth_protocol: ASMCs were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 units/mL penicillin, and 100 μg/mL streptomycin in an incubator containing 5% CO2 humidified at 37 °C. Prior to the experiment

extract_protocol:
RNA was harvested using RNA isolater Total RNA Extraction Reagent（vazyme）and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: exponential proliferating ASMCs at passage 3-10 were plated on type I collagen-coated Bioflex 6-well plates and were serum-deprived for 24 h. With high stretch treatment, cells grown on Bioflex plates were exposed to a 13% cyclic strain at 0.5 Hz (1 s of deformation alternating with 1 s of relaxation, Flexcell 5000, FlexCell International, Hillsborough, NC, USA) to simulate the strain during MV for 72 h. Without high stretch treatment, cells grown in Bioflex plates were maintained in static conditions for 72 h. The cells without high stretch treatment on Bioflex plates were used as the static group and the cells with high stretch treatment on Bioflex plates were used as the experiment  group. Cells in 6-well plates without high stretch treatment were maintained under static conditions for 72 hours as a control group.

value: airway

value: airway smooth muscle cells


title: AD tumor [JGAme_599_TL WES]


title: AD tumor [JGAme_699_TL WES]


title: mRNAseq_Str_2

value: with high stretch treatment on Bioflex plates


title: MCWR_2019_000378


title: AD tumor [JGAme_441_TL WES]


title: MCWR_2019_000383


title: CRC1321LMO0B04006001R01000, LMO_BASALE, bio rep 1, QC ok

value: O

value: LM


title: MCWR_2019_000377


title: K562R cell, empty vector transfection, rep2

description:
LR-EV2
Bone Marrow

value: WT

value: TKI-resistant

value: Without drug treatment


title: mRNAseq_Str_1


title: PC3 cells expressing AR-WILD TYPE [WT-3]

description: Column P

value: Prostate

value: Cancer-epithelial

value: expressing AR-WILD TYPE


title: JGAmr_701_AD_thymus_basal tissues [RNA-seq]

data_processing:
alignment and gene count by STAR (version 2.6.0b)
gene annotation used GENCODE M19 (Ensembl 94)
differential expression analysis carried out in R (3.5.1) using Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-deliminated data matrix of gene counts

extract_protocol:
mice with germline p53 alterations of 4 weeks of age were exposed to irradiation or not, and were sacrificed (4h post-IR) for organ collection
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thymus

tag: tissue type

value: basal tissues


title: MCWR_2019_000376

value: BMDM

value: macrophage


title: CRC1319PRX0A02004TUMR01000, PRX_BASALE, bio rep 1, QC failed

data_processing:
Align with STAR on hybrid mm/hs genome
Assign counts to genes with FeatureCounts
Consider only human genes to normalize with DESeq2
QC based on evidence of lymphomatous infiltration
https://github.com/molinerisLab/StromaDistiller, https://github.com/vodkatad/RNASeq_biod_metadata
Assembly: GRCh38_GRCm38
Supplementary files format and content: merged_hs_mm.tsv.gz: raw counts for human and murine genes
Supplementary files format and content: vsd.tsv.gz: normalized expression values for human genes

value: Colorectal Cancer

value: X

value: PR


title: mRNAseq_Sta_3

source_name: hASMCs,static,bioflex plate,72h

value: airway

value: airway smooth muscle cells

value: without high stretch treatment on Bioflex plates


title: CRC1318LMX0B02004TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: LM


title: JGAmr_702_AD_thymus_basal tissues [RNA-seq]


title: MCWR_2019_000374

value: NOS1 KO

value: LPS


title: CRC1315PRX0B01001TUMR01000, PRX_BASALE, bio rep 1, QC ok

value: WT


title: MCWR_2019_000375

value: control


title: mRNAseq_Sta_2


title: CRC1321LMX0B02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: JGAmr_700_AD_thymus_basal tissues [RNA-seq]


title: CRC1314LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: mRNAseq_Sta_1


title: MCWR_2019_000373


title: CRC1314LMO0A02074002R01000, LMO_BASALE, bio rep 1, QC ok

value: O


title: mRNAseq_con_2

source_name: hASMCs,control,6-hole plate,72h

value: without high stretch treatment  on 6-well plates


title: JGAmr_703_Het_thymus_basal tissues [RNA-seq]

value: thymus


title: CRC1314LMO0A04016001R01000, LMO_BASALE, bio rep 2, QC ok


title: MCWR_2019_000372


title: MCWR_2019_000371


title: JGAmr_923_Null_thymus_basal tissues [RNA-seq]

value: basal tissues


title: MCWR_2019_000370

value: BMDM


title: MCWR_2019_000369

value: macrophage


title: JGAmr_859_Null_thymus_basal tissues [RNA-seq]


title: mRNAseq_con_1


title: miRNAseq_Str_2

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw single end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )
Then clean reads were separately aligned to reference genome with orientation mode using bowtie software.
the expression level of each miRNA was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify miRNA abundances.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

value: with high stretch treatment on Bioflex plates


title: MCWR_2019_000368


title: CRC1313LMX0B02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: Colorectal Cancer

value: X


title: JGAmr_855_Het_thymus_basal tissues [RNA-seq]


title: MCWR_2019_000367


title: miRNAseq_Str_1

value: airway


title: mRNAseq_con_3

value: airway smooth muscle cells


title: JGAmr_656_RP_IR_thymus_irradiated tissues [RNA-seq]

value: irradiated tissues


title: CRC1313LMH0000000000R05000, LMH, bio rep 1, QC ok

value: H

value: LM


title: CRC1309PRX0A02002TUMR01000, PRX_BASALE, bio rep 1, QC failed

value: PR


title: JGAmr_654_RP_IR_thymus_irradiated tissues [RNA-seq]


title: JGAmr_697_Het_thymus_basal tissues [RNA-seq]


title: JGAmr_653_RP_IR_thymus_irradiated tissues [RNA-seq]


title: miRNAseq_Sta_3

value: without high stretch treatment on Bioflex plates


title: JGAmr_649_RP_IR_thymus_irradiated tissues [RNA-seq]


title: miRNAseq_Sta_2


title: MCWR_2019_000366

value: WT

value: control


title: CRC1307LMX0A02002TUMR01000, LMX_BASALE, bio rep 1, QC ok


title: miRNAseq_Sta_1


title: CRC1313LMX0B03001TUMR05000, LMX_cetux_6w, bio rep 1, QC ok

value: CET


title: JGAmr_727_AD_IR_thymus_irradiated tissues [RNA-seq]

value: thymus


title: CRC1307LMO0A04012001R01000, LMO_BASALE, bio rep 2, QC ok

value: O


title: miRNAseq_Str_3


title: MCWR_2019_000364

value: BMDM

value: LPS


title: miRNAseq_con_3

value: without high stretch treatment  on 6-well plates


title: CRC1313LMX0B03005TUMR05000, LMX_cetux_6w_NT, bio rep 1, QC ok

value: Colorectal Cancer

value: NT


title: MCWR_2019_000363

value: macrophage


title: JGAmr_726_AD_IR_thymus_irradiated tissues [RNA-seq]


title: CRC1307LMO0A03010001R01000, LMO_BASALE, bio rep 1, QC ok


title: CRC1306LMX0A02001TUMR01000, LMX_BASALE, bio rep 1, QC ok

value: X


title: JGAmr_633_AD_IR_thymus_irradiated tissues [RNA-seq]

value: irradiated tissues