title: MALE ischemic mice #5 - IP

description: Gene expression data from mouse brain


title: MALE sham mice #3 - IP

status: Public on Nov 14 2022

type: RNA

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

country: Spain

institute: Vall d'Hebron Institute of Research

description: Gene expression data from mouse brain

hyb_protocol: cDNA was hybridizated in GeneChip Mouse Clariom S Affymetrix microarrays for 16 hours with rotation at 45 ºC with rotation

scan_protocol: Microarrays were scanned in Affymetrix GeneChip Scanner 3000

data_processing: the images were processed with the Affymetrix GeneChip Command Console software for CEL file generation. To check the array image quality, Affymetrix Expression Console was used. Samples that demonstrated good quality results (pm mean, bgrd mean, pos vs neg auc,...) were subjected to subsequent analysis

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse brain, ipsilateral hemisphere (IP)

label_protocol: Samples were amplified and labeled using GeneChip WT Plus Reagent Kit

growth_protocol: Saline-perfused mouse brain samples were isolated; IP and CL hemispheres were separated and flash frozen with liquid N2 until RNA isolation.

extract_protocol: RNA was isolated from frozen brain samples with the MirVana™ Paris™ (Thermo Fisher Scientific Inc., USA) and kept at -80ºC until the array was performed.

treatment_protocol: flash frozen at -80ºC

tag: strain

tag: age

value: 8-12 weeks

tag: condition

value: young

tag: Sex

value: male

tag: treatment

value: sham

tag: tissue

value: brain

tag: brain hemisphere

value: IP


title: MALE sham mice #4 - CL

description: Gene expression data from mouse brain

source_name: mouse brain, contralateral hemisphere (CL)

value: CL


title: MALE sham mice #4 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #8 - IP

description: Gene expression data from mouse brain

source_name: mouse brain, ischemic hemisphere (IP)

value: ischemic


title: MALE sham mice #1 - CL

description: Gene expression data from mouse brain


title: MALE sham mice #2 - CL

description: Gene expression data from mouse brain


title: ino80_repeat2

type: SRA

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

library_source: transcriptomic

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 version 2.2.0 with the default parameters.
The differentially expressed genes and transposable elements were identified with |log2FC| >1 and P value<0.01 using edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Total RNA was isolated from 11-day-old seedlings in LD using Trizol reagent.
Sequencing libraries were built for RNA-seq (the 150 bp paired-end or the single-ended 50-bp strategy).

value: Arabidopsis seedlings

tag: growth conditions

value: long day (16 h light, 8 h dark)

tag: genotype


title: ino80_repeat1


title: FEMALE ischemic mice #1 - IP

description: Gene expression data from mouse brain

value: female


title: MALE ischemic mice #8 - CL

description: Gene expression data from mouse brain

source_name: mouse brain, healthy hemisphere (CL)


title: MALE ischemic mice #5 - CL

description: Gene expression data from mouse brain


title: FEMALE ischemic mice #2 - IP

description: Gene expression data from mouse brain


title: MALE sham mice #2 - IP

description: Gene expression data from mouse brain


title: Col-0_repeat6

value: wild type


title: MALE ischemic mice #4 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #2 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #1 - CL

description: Gene expression data from mouse brain


title: MALE ischemic mice #3 - CL

description: Gene expression data from mouse brain


title: MALE ischemic mice #6 - CL

description: Gene expression data from mouse brain


title: MALE ischemic mice #1 - IP

description: Gene expression data from mouse brain


title: MALE ischemic mice #3 - IP

description: Gene expression data from mouse brain


title: SCLC, RB1 IHC negative rep1

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

country: USA

institute: Case Western Reserve University

data_processing:
Base calling and generation of FASTQ files were performed using standard CASAVA pipeline.
RNA-seq quality was checked by running FastQC, and TrimGalore was used for adapter and quality trimming. RNA-seq reads were mapped against hg38 using STAR aligner with default parameters.
TPM values were generated using RSEM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include PTM values for each sample.

organism: Homo sapiens

source_name: Lung

extract_protocol:
The Tempus xT-RNA Assay employs TNA extraction methods for FFPE biopsy (tumor) from which total RNA is isolated through the digestion of DNA.
RNA-seq library was prepared using IDT unique dual-index adapters, followed by hybrid capture with custom the IDT xGen Lockdown probes.

value: Lung

value: RB1 WT


title: SCLC, RB1 IHC positive rep1


title: SCLC, RB1 IHC negative rep3


title: SCLC, RB1 IHC negative rep2


title: SCLC, RB1 IHC positive rep2


title: MALE ischemic mice #2 - CL

description: Gene expression data from mouse brain


title: Stool small RNA-Seq CMa009

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Stool

extract_protocol:
Stool RNA was extracted from 200µl aliquots using stool total RNA purification kit (Norgen Biotek Corp.) following manufacturer’s protocol. RNA quality and quantity were verified following the MIQE guidelines (http://miqe.gene-quantification.info/). The RNA concentration was quantified with the Qubit microRNA assay kit (Invitrogen). The DNA was extracted with the DNeasy PowerSoil Pro Kit (Qiagen) following manufacturer's instructions with a higher final elution buffer volume (50µl) to increase DNA concentration which was quantified with Qubit DNA high sensitivity assay kit (Invitrogen).
Small RNA (sRNA) transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA).

value: Female

tag: class

value: Untreated CD


title: Stool small RNA-Seq Cii074

value: tCD-TG+


title: Stool small RNA-Seq CMa010b


title: Stool small RNA-Seq Cii044


title: Stool small RNA-Seq 442GB

value: Male


title: Stool small RNA-Seq CMa010


title: Stool small RNA-Seq Cii044b


title: Stool small RNA-Seq CMa006

value: tCD-TG-


title: Stool small RNA-Seq 421FR


title: Col-0_repeat5


title: Stool small RNA-Seq 424MM


title: Stool small RNA-Seq 415PM


title: Stool small RNA-Seq Cii097

value: Healthy


title: Stool small RNA-Seq 380BR


title: Stool small RNA-Seq Cii094


title: Stool small RNA-Seq 388SB


title: Stool small RNA-Seq Cii090


title: Stool small RNA-Seq Cii088


title: Stool small RNA-Seq Cii089


title: Stool small RNA-Seq Cii083


title: Stool small RNA-Seq Cii080


title: Stool small RNA-Seq Cii081


title: Stool small RNA-Seq Cii070


title: Stool small RNA-Seq Cii078


title: Stool small RNA-Seq Cii077


title: Stool small RNA-Seq 438SA


title: Stool small RNA-Seq 389GM


title: Stool small RNA-Seq Cii041


title: Stool small RNA-Seq Cii091


title: Stool small RNA-Seq Cii082


title: Stool small RNA-Seq Cii075


title: Stool small RNA-Seq Cii068


title: Stool small RNA-Seq Cii076


title: Stool small RNA-Seq Cii065


title: Stool small RNA-Seq Cii079


title: Stool small RNA-Seq Cii064


title: Stool small RNA-Seq Cii066


title: Stool small RNA-Seq Cii063


title: Stool small RNA-Seq Cii067


title: Stool small RNA-Seq Cii062


title: Stool small RNA-Seq Cii060


title: Stool small RNA-Seq Cii061


title: Stool small RNA-Seq Cii055


title: Stool small RNA-Seq Cii056


title: Stool small RNA-Seq Cii054


title: Stool small RNA-Seq Cii053


title: Stool small RNA-Seq Cii052


title: Stool small RNA-Seq Cii050


title: Stool small RNA-Seq Cii051


title: Stool small RNA-Seq Cii047


title: Stool small RNA-Seq Cii046


title: Stool small RNA-Seq Cii043


title: Stool small RNA-Seq Cii039


title: Stool small RNA-Seq Cii040


title: Stool small RNA-Seq Cii034


title: Stool small RNA-Seq Cii038


title: Stool small RNA-Seq Cii028


title: Stool small RNA-Seq Cii033


title: Stool small RNA-Seq Cii035


title: Stool small RNA-Seq Cii032


title: Stool small RNA-Seq Cii059


title: Stool small RNA-Seq Cii027


title: Stool small RNA-Seq Cii026


title: Stool small RNA-Seq Cii057


title: Stool small RNA-Seq Cii029


title: Stool small RNA-Seq Cii025


title: Stool small RNA-Seq Cii023


title: Stool small RNA-Seq Cii049


title: 19P2873 | 005 | Tumour

type: protein

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description: GeoMx DSP Ncounter

hyb_protocol: DSP eluates were hybridised as per manufacturers instructions in nCounter Readout User Manual.

scan_protocol: Hybridised samples were loaded into Nanostring prep station and processed as per DSP Slide Prep User Manual. N counter was performed with default parameters, and counts from Ncounter uploaded back to DSP instrument

data_processing: Counts were aligned and ERCC corrected automatically on the DSP instrument. This QC data was exported for analysis.

label: DNA barcode

molecule: protein

source_name: FFPE Resected Tumour

label_protocol: DSP experiments were performed as per manufacturers DSP Slide Prep User Manual instructions. Slides were deparafinised, antigen retrieval by HIER, and overnight staining with antibody cocktail as per DSP Slide Prep User Manual. Slides were images and samples collected on DSP instrument

extract_protocol: Clinical FFPE samples on individual slides were obtained with appropriate ethics approval

tag: patient

tag: roi

value: Tumour

value: Progression

value: N/A (oral tongue, not oropharynx)


title: 19P2873 | 006 | TME

description: GeoMx DSP Ncounter

value: TME


title: 19P2873 | 001 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii021


title: Stool small RNA-Seq Cii020


title: Stool small RNA-Seq Cii036


title: Stool small RNA-Seq Cii019


title: Stool small RNA-Seq Cii015


title: 19P2873 | 003 | Tumour

description: GeoMx DSP Ncounter


title: 19P2873 | 004 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii018


title: 19P2873 | 002 | Tumour

description: GeoMx DSP Ncounter


title: 19P2873 | 002 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii010


title: Stool small RNA-Seq Cii008


title: Stool small RNA-Seq Cii012


title: Stool small RNA-Seq Cii013


title: Stool small RNA-Seq Cii011


title: Stool small RNA-Seq Cii014


title: Stool small RNA-Seq 409IG


title: Stool small RNA-Seq 436BC


title: Stool small RNA-Seq Cii024


title: Stool small RNA-Seq Cii022


title: 19P2873 | 006 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 412VL


title: Stool small RNA-Seq Cii031


title: Stool small RNA-Seq Cii084


title: 196P2747 | 001 | TME

description: GeoMx DSP Ncounter

value: Partial response

value: N/A (oral cavity, not oropharynx)


title: Stool small RNA-Seq CMa002


title: Stool small RNA-Seq Cii030


title: Stool small RNA-Seq CMa001


title: 196P2747 | 004 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii085


title: 196P2747 | 005 | TME

description: GeoMx DSP Ncounter


title: 196P2747 | 002 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq CMa007


title: 196P2747 | 006 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq CMa003


title: Stool small RNA-Seq CMa005


title: Stool small RNA-Seq CMa004


title: Stool small RNA-Seq CMa012


title: Stool small RNA-Seq CMa011


title: 15P21530 | 010 | TME

description: GeoMx DSP Ncounter

value: Positive


title: 15P21530 | 011 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii073


title: 196P2747 | 003 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii072


title: Stool small RNA-Seq Cii044c


title: 15P21530 | 008 | Tumour

description: GeoMx DSP Ncounter


title: 15P21530 | 009 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii071


title: Stool small RNA-Seq Cii045


title: Stool small RNA-Seq Cii042


title: MALE ischemic mice #4 - CL

description: Gene expression data from mouse brain

value: 8-12 weeks

value: young

value: male

value: ischemic

value: brain

value: CL


title: 15P21530 | 001 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii037

value: Female


title: 15P21530 | 007 | TME

description: GeoMx DSP Ncounter


title: 15P21530 | 005 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii016

value: Male


title: Stool small RNA-Seq Cii007

value: tCD-TG-


title: 15P21530 | 004 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 383MP


title: Stool small RNA-Seq Cii017


title: 15P21530 | 003 | Tumour

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii004


title: Stool small RNA-Seq Cii006


title: Stool small RNA-Seq Cii005


title: Stool small RNA-Seq 437BCM


title: Stool small RNA-Seq Cii003


title: Stool small RNA-Seq Cii002


title: Stool small RNA-Seq 442GM


title: 15P21530 | 006 | Tumour

description: GeoMx DSP Ncounter


title: 15P21530 | 002 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 406BR


title: 16P10175 | 001 | TME

description: GeoMx DSP Ncounter


title: 15P21530 | 003 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 402BRA


title: 16P10175 | 006 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 405GA


title: Stool small RNA-Seq 403LR


title: Stool small RNA-Seq 401IA


title: 16P10175 | 005 | TUMOUR

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq Cii009


title: Stool small RNA-Seq 399CE


title: Stool small RNA-Seq 398AG


title: Stool small RNA-Seq 397TE


title: 16P10175 | 005 | TME

description: GeoMx DSP Ncounter


title: 16P10175 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 390CG


title: Stool small RNA-Seq 387DCF


title: Stool small RNA-Seq 427AE


title: Stool small RNA-Seq 416ST


title: 16P10175 | 004 | TME

description: GeoMx DSP Ncounter


title: 16P10175 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 351DLEM


title: Stool small RNA-Seq 381NB


title: Stool small RNA-Seq 352LGE


title: Stool small RNA-Seq 378PF


title: 19P2873 | 001 | Tumour

description: GeoMx DSP Ncounter


title: 16P10175 | 002 | TME

description: GeoMx DSP Ncounter


title: 16P10175 | 003 | TME

description: GeoMx DSP Ncounter


title: Stool small RNA-Seq 392AB


title: 16P10175 | 002 | TUMOUR

description: GeoMx DSP Ncounter


title: 16P10175 | 001 | TUMOUR

description: GeoMx DSP Ncounter


title: SNB19 cells, EV_CTBP2 Chip-seq 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

library_source: genomic

data_processing:
Basecalls performed using HiSeq Control Software version 3.4.0.38
ChIP-seq reads were aligned to the hg19 genome assembly using BWA-MEM (v 0.7.5a) with default parameters. Reads were filtered for blacklisted regions, de-  duplicated to remove PCR duplicates and filtered to remove multimapping reads, using SAMtools (v 2.17).
peaks were called using MACS2 with the default settings.
Genome_build: hg19
Supplementary_files_format_and_content: peak files were generated using MACS2; colums represent chromosome; start; end; name; score

molecule: genomic DNA

source_name: Glioblastoma cell line

growth_protocol: 5x10^6 cells were seeded in 15 cm dishes and grown for 24h in DMEM + 10%FBS

extract_protocol:
Chromatin preparation and immunoprecipittaion was performed using the iDeal ChIP-seq kit for Transcription Factors (Diagenode Cat#C01010055) following the manual's instruction.
DNA libraries were prepared for 50 bp single-end sequencing on an Illumina HiSeq3000/4000 system using standard Illumina protocols.

treatment_protocol: Cells were transduced with lentiviral particles (pCHMWS-eGFP (Empty vector, EV), pCHMWS-eGFP FLAG-ZBTB18 or pCHMWS-eGFP FLAG-ZBTB18-mut. Cells were fixed and processed using iDeal ChIP-seq kit for Transcription Factors (Diagenode Cat#C01010055) according to the manufacturer's instruction. During crosslinking an additional step with ChIP Cross-link Gold (Diagenode Cat# C01019027) was included.

tag: cell type

value: glioblastoma cells

value: Transduced with pCHMWS-eGFP (Empty vector, EV)

tag: chip antibody

value: Active Motif anti-CTBP2 (ChIP grade) Cat#61262


title: SNB19 cells, ZBTB18_FLAG ChIP-seq 3

value: Transduced with pCHMWS-eGFP FLAG-ZBTB18

value: Sigma anti-FLAG M2 Cat#F1804-200UG


title: SNB19 cells, EV_FLAG ChIP-seq 1


title: SNB19 cells, ZBTB18_CTBP2 Chip-seq 2


title: SNB19 cells, EV_CTBP2 Chip-seq 3


title: SNB19 cells, ZBTB18_FLAG ChIP-seq 2


title: SNB19 cells, EV_FLAG ChIP-seq 2


title: 20P18553 | 006 | Tumour

description: GeoMx DSP Ncounter

value: Tumour

value: Stable Disease


title: Diclo2

city: Kolkata

first: Uday

last: Bandyopadhyay

state: WB

address: EN 80, Salt Lake, College More, EN Block, Sector V, Kolkata,

department: Division of Molecular Medicine

country: India

institute: Bose Institute

data_processing:
Bcl files were converted to Fastq files using Bcl2fastq tool and the data were subjected to quality check using FastQC v.0.11.7.
This was followed by adapter trimming with Cutadapt v1.16 using Illumina Universal Adapter.
Hisat2 2.1.0. was used to align the trimmed reads with Rat Rno6 reference genome .
Sorting of Bam files were performed with Samtools v1.19.
Next, gene count was performed with FeatureCounts followed by differential analysis with DESeq2.Differentially expressed genes with ≥  or ≤ 1.5-fold expression change and p value ≤ 0.05 and FDR ≤ 0.05 were filtered.
Assembly: rno6
Supplementary files format and content: tab-delimited text files include Count values for each Sample

organism: Rattus norvegicus

source_name: Gastric mucosa

extract_protocol:
Total RNA sequencing library preparation using TruSeq Stranded Total RNA Library preparation kit from Illumina. Briefly, total RNA was isolated from the tissue or cell samples using PureLink RNA Mini Kit (Thermo) following manufacturer’s guidelines. 45 mg of tissue or 107 cells per sample were used as the starting material. Quality and concentration of the isolated RNA samples were checked in Nanodrop 2000 (Thermo) and Agilent 2100 Bioanalyzer. Samples with RIN ≥ 7.0 were subsequently used for library preparation. Equal amount (200 ng) of RNA from each sample was first subjected to ribosomal RNA depletion using the Ribo-Zero Human/Mouse/Rat depletion module of the kit followed by purification and divalent cation-based fragmentation. The resulting fragments were purified and subjected to cDNA synthesis, A-tailing and dual index adapter ligation. The products were subsequently purified and PCR enriched. The resulting RNA libraries were checked in Agilent 2200 TapeStation (Agilent Technologies), quantified, normalized and subjected to equimolar pooling. The pooled libraries were finally loaded on sequencing run flow cell (Illumina) and subjected to 100 bp paired-end massively parallel sequencing in Novaseq 6000 sequencer (Illumina).
RNA libraries for RNA-seq were prepared using Illumina TrueSeq strand Library Prep Kit following manufacturer's protocols.

treatment_protocol: Gastric mucosal injury was developed by oral administration of typical NSAIDs including indomethacin (48 mg/kg), ibuprofen (400 mg/kg), diclofenac (75 mg/kg), aspirin (400 mg/kg) as required. Gastric injury was allowed to develop and after 4 hrs, the rats were subjected to terminal euthanasia followed by sacrifice and collection of mucosal tissue samples for transcriptome analysis and subsequent experiments. For HKL induced protection, rats were pre-treated with HKL (40 mg/kg), intraperitoneally, followed by oral administration of indomethacin after 30 minutes.

value: Gastric mucosa

value: Epithelial cells

value: Sprague Dawley

value: Diclofenac (75mg/kg)

tag: time

value: 4 hrs


title: Asp1

value: Aspirin (400mg/kg)


title: HKL+Indo2

value: Honokiol (40mg/kg) treatment was given 30 minutes prior to indomethacin treatment

value: 0.5 hrs


title: Diclo1


title: Asp2


title: 20P18553 | 004 | Tumour

description: GeoMx DSP Ncounter

value: N/A (oral cavity, not oropharynx)


title: 20P18553 | 005 | TME

description: GeoMx DSP Ncounter

value: TME


title: SNB19 cells, ZBTB18_CTBP2 Chip-seq 1

value: glioblastoma cells


title: Con2


title: 20P18553 | 003 | Tumour

description: GeoMx DSP Ncounter


title: Indo1

value: Indomethacin (48mg/kg)


title: Con1


title: Indo2


title: cardiomyocytes, LPS_SI_R3

city: Shanghai

first: Cheng wu

last: Gong

address: No. 639, Shanghai Manufacturing Bureau Road

department: Department of Thoracic Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

description: small interference siMETTL3 was transfected for 24 h and then treated with LPS for 6 h

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rat101
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: primary myocardial cells

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Sprague-Dawley

value: ventricular muscle

value: primary myocardial cells

value: post natal day 1-3

value: siMETTL3, LPS


title: 20P18553 | 004 | TME

description: GeoMx DSP Ncounter

value: Stable Disease


title: cardiomyocytes, LPS_R2

description: treated with LPS for 6 hours

value: siNC, LPS


title: cardiomyocytes, LPS_SI_R2


title: 20P18553 | 005 | Tumour

description: GeoMx DSP Ncounter

value: Tumour


title: 20P18553 | 003 | TME

description: GeoMx DSP Ncounter


title: cardiomyocytes, LPS_R3

description: treated with LPS for 6 hours


title: CD45+ cells, RNA, 9D9 + Epacadostat Rep_2

city: San Diego

first: Richard

last: Virgen-Slane

state: CA

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

library_source: transcriptomic single cell

data_processing:
libraries were sequenced by UCSD IGM Center on an Illumina NGS HiSeq 4000, with 2x 75 paired-end kits.
scRNAseq data were processed using the Cell Ranger v3.0.2 (10x Genomics) to generate count-level data for further analysis. Each lane of cells was processed independently using the Cell Ranger count. The unique molecular identifier (UMI) counts for each sample were then merged using Seurat v3.0.1, requiring that the 6 number of expressed genes for each cell was > 200. Genes expressed in at least three cells were kept and then normalized and scaled using the default setting in Seurat.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: liver

extract_protocol:
Livers (> 0.5g) were chopped in cold DMEM (Gibco) and digested with the liver dissociation kit, mouse (Miltenyi Biotec) in DMEM according to the manufacturer’s instructions. Samples were dissociated with the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) as per the default manufacturers protocol for murine liver digestion. The single cell suspension was filtered through a 70 µM mesh strainer and washed with cold DMEM, resuspended in RBC lysis buffer (eBioscience) then washed twice in autoMACs buffer with BSA (Miltenyi Biotec). CD45+ cells were isolated with CD45 microbeads (Miltenyi Biotec) according to the manufacturer’s protocol with the autoMACs separator.  The single cell suspension was prepared according to the 10X Genomics single cell sample prep protocol. 6000-8000 cells per sample were loaded onto the 10X Chromium Controller
RNA-seq libraries were prepared using Chromium Single Cell 5’ v2 Reagent Kits (10X Genomics).

value: liver

value: CD45+ cells

value: 9D9 + Epacadostat


title: cardiomyocytes, LPS_R1

description: treated with LPS for 6 hours


title: 20P18553 | 001 | Tumour

description: GeoMx DSP Ncounter


title: HKL+Indo1

value: Gastric mucosa

value: Epithelial cells

value: Sprague Dawley

value: Honokiol (40mg/kg) treatment was given 30 minutes prior to indomethacin treatment


title: 20P18553 | 002 | Tumour

description: GeoMx DSP Ncounter

value: N/A (oral cavity, not oropharynx)


title: CD45+ cells, RNA, 9D9 + Epacadostat Rep_1


title: 20P18553 | 002 | TME

description: GeoMx DSP Ncounter

value: TME


title: 20P18553 | 001 | TME

description: GeoMx DSP Ncounter


title: CD45+ cells, RNA, Veh Rep_3


title: CD45+ cells, RNA, 41BB Rep_3


title: CD45+ cells, RNA, Veh Rep_2


title: 15P25322 | 006 | TUMOUR

description: GeoMx DSP Ncounter

value: N/A (hypopharynx, not oropharynx)


title: CD45+ cells, RNA, 41BB Rep_1


title: 15P25322 | 006 | TME

description: GeoMx DSP Ncounter


title: cardiomyocytes, LPS_SI_R1

value: Sprague-Dawley

value: ventricular muscle


title: CD45+ cells, RNA, Veh Rep_1


title: 15P25322 | 005 | TUMOUR

description: GeoMx DSP Ncounter


title: Flox/Flox Treated 5

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

data_processing:
Reads were mapped to the genome with STAR (parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts in gene loci or exon only were calculated using htseq-count (parameters for genes: --stranded=reverse --order=name --type=gene --idattr=gene_id --mode=union; exon counts specific parameters: --type=exon --mode=intersection-strict).
Assembly: GRCm38
Supplementary files format and content: *.dat: Tab-delimited files containing raw read counts.

source_name: tail fibroblasts

extract_protocol:
Cells were cultured for at least 3-4 days after seeding to ensure desynchronisation of circadian oscillators; medium was removed and cells were directly lysed on the plate with Trizol reagent, followed by RNA extraction according to standard protocols.
RNA-seq libraries were prepared from triplicates/condition according to standard protocols (TruSeq® Stranded Total RNA Library Prep Gold, Illumina) using 1 µg starting material.

value: tail fibroblasts

value: flox/flox

tag: replicate


title: Flox/Flox Treated 6


title: WT Treated 2


title: CD45+ cells, RNA, 9D9 + Epacadostat Rep_3


title: 15P25322 | 005 | TME

description: GeoMx DSP Ncounter

value: Stable Disease


title: Flox/Flox Treated 4


title: Flox/Flox Untreated 6

value: vehicle


title: Flox/Flox Untreated 5


title: WT Treated 1


title: WT untreated 2


title: Flox/Flox Untreated 4


title: Flox/Flox Treated 3


title: Flox/Flox Treated 2


title: 15P25322 | 003 | TME

description: GeoMx DSP Ncounter


title: Flox/Flox Treated 1


title: CD45+ cells, RNA, 41BB Rep_2


title: 15P25322 | 002 | TME

description: GeoMx DSP Ncounter


title: 15P25322 | 002 | TUMOUR

description: GeoMx DSP Ncounter

value: Tumour


title: WT untreated 1


title: Flox/Flox Untreated 2


title: 15P25322 | 001 | TUMOUR

description: GeoMx DSP Ncounter


title: Flox/Flox Untreated 1


title: 15P25322 | 001 | TME

description: GeoMx DSP Ncounter


title: 18P51506 | 001 | TUMOUR

description: GeoMx DSP Ncounter

value: Partial response

value: Negative


title: 18P51506 | 002 | TME

description: GeoMx DSP Ncounter


title: 15P25322 | 004 | TME

description: GeoMx DSP Ncounter


title: 18P51506 | 002 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51506 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51506 | 003 | TME

description: GeoMx DSP Ncounter


title: MALE ischemic mice #7 - CL

description: Gene expression data from mouse brain

value: 8-12 weeks

value: young

value: male

value: ischemic

value: brain

value: CL


title: 18P51506 | 004 | TME

description: GeoMx DSP Ncounter

value: TME


title: Flox/Flox Untreated 3


title: 18P51506 | 006 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51506 | 001 | TME

description: GeoMx DSP Ncounter


title: 19P31908 | 002 | TME

description: GeoMx DSP Ncounter

value: Positive


title: 19P31908 | 002 | TUMOUR

description: GeoMx DSP Ncounter


title: 19P31908 | 001 | TUMOUR

description: GeoMx DSP Ncounter


title: 19P31908 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51506 | 005 | TME

description: GeoMx DSP Ncounter


title: 18P51506 | 006 | TME

description: GeoMx DSP Ncounter


title: 18P51506 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: 19P31908 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: 19P31908 | 004 | TME

description: GeoMx DSP Ncounter


title: 18P51506 | 005 | TUMOUR

description: GeoMx DSP Ncounter


title: VRP MSN09-04R-CM Rep 2 (DGE)

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Preparing required software packages (README.pdf for details)
Compiling UMI extraction program (README.pdf for details)
Preparing required input data files (README.pdf for details)
Aligning 3'-DGE mRNA sequence reads (README.pdf for details)
Mapping aligned sequence reads to reference genes (README.pdf for details)
Identifying differentially expressed genes under drug treatments (README.pdf for details)
Assembly: Reference-Library.tar.gz: a compressed file containing the UCSC human genome reference library (version hg38)
Supplementary files format and content: DGE-RNAseq-Experiment-Design.tsv.gz: a compressed file containing the experiment design table of all the samples from the 3'-DGE dataset to be used by the DEG-comparison pipeline
Supplementary files format and content: DGE-RNAseq-Read-Counts.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 3'-DGE dataset
Supplementary files format and content: DGE-RNAseq-Configs.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 3'-DGE dataset
Supplementary files format and content: DGE-RNAseq-Params.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 3'-DGE dataset
Supplementary files format and content: DGE-DEG-Calc-FDR-0.1.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 3'-DGE dataset
Supplementary files format and content: Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.
Supplementary files format and content: README.pdf.gz: a compressed PDF file containing detailed instructions for running the pipeline

source_name: induced pluripotent stem cell

growth_protocol: Cultured under growth conditions with E8 media and differentiated for 20 days with differentiation media,start Lactate Metabolic Selection for one week,Plate 240k cells into each well of 24-well plate for one week for drug treatment. (see DToxS SOP CE)

extract_protocol:
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Library was prepared using 200 ng of total RNA using HiSeq SBS v4 50 Cycle Kit (Illumina, Cat: FC-401-4002) per manufacturer’s instructions.(See DToxS SOP A - 7.0: Sequencing 3'-end Broad-Prepared mRNA Libraries)

treatment_protocol: Fully confluent and differentiated cells were treated with drugs or vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)

value: skin

value: cardiac myocytes

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

value: VRP

tag: drug name

value: Verapamil

tag: concentration

tag: well

tag: investigative unit

tag: sample id

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)

tag: h2o volume (ul)


title: VRP MSN02-04R-CM Rep 3 (DGE)

tag: tissue

tag: cell type


title: VRP MSN09-04R-CM Rep 1 (DGE)


title: VRP MSN02-04R-CM Rep 2 (DGE)


title: VEM MSN09-04R-CM Rep 4 (DGE)

value: VEM

value: Vemurafenib


title: VRP MSN02-04R-CM Rep 4 (DGE)


title: VRP MSN09-04R-CM Rep 3 (DGE)


title: VEM MSN09-04R-CM Rep 3 (DGE)


title: VRP MSN02-04R-CM Rep 1 (DGE)


title: VRP MSN09-04R-CM Rep 4 (DGE)


title: VEM MSN09-04R-CM Rep 1 (DGE)


title: VEM MSN09-04R-CM Rep 2 (DGE)


title: VEM MSN02-04R-CM Rep 4 (DGE)


title: VEM MSN02-04R-CM Rep 3 (DGE)


title: VEM MSN02-04R-CM Rep 2 (DGE)


title: 19P31908 | 005 | TME

description: GeoMx DSP Ncounter

tag: patient

tag: roi

value: Stable Disease


title: 19P31908 | 008 | TME

description: GeoMx DSP Ncounter


title: VEM MSN02-04R-CM Rep 1 (DGE)

tag: cell line


title: VAN MSN09-04R-CM Rep 2 (DGE)

tag: treatment time (hrs)

value: VAN

value: Vandetanib


title: VAN MSN09-04R-CM Rep 3 (DGE)

tag: treatment condition


title: 19P31908 | 010 | TME

description: GeoMx DSP Ncounter


title: VAN MSN09-04R-CM Rep 1 (DGE)

tag: drug name


title: VAN MSN02-04R-CM Rep 4 (DGE)

tag: concentration


title: 19P31908 | 010 | TUMOUR

description: GeoMx DSP Ncounter

value: Tumour


title: 19P31908 | 001 | TME

description: GeoMx DSP Ncounter


title: VAN MSN02-04R-CM Rep 3 (DGE)

tag: well


title: VAN MSN02-04R-CM Rep 2 (DGE)

tag: investigative unit


title: TRS MSN09-04R-CM Rep 3 (DGE)

value: TRS

value: Trastuzumab

value: 3uM /10uM

tag: sample id


title: VAN MSN02-04R-CM Rep 1 (DGE)

tag: rna amount (ng)


title: TRS MSN09-04R-CM Rep 1 (DGE)

tag: rin


title: TRS MSN09-04R-CM Rep 4 (DGE)

tag: rna conc (ng/ul)


title: TRS MSN09-04R-CM Rep 2 (DGE)

tag: rna volume (ul)


title: TRA MSN09-04R-CM Rep 4 (DGE)

value: TRA

value: Trametinib

tag: h2o volume (ul)


title: TRS MSN02-04R-CM Rep 3 (DGE)

tag: tissue


title: TRS MSN02-04R-CM Rep 4 (DGE)

tag: cell type


title: TRS MSN02-04R-CM Rep 2 (DGE)


title: 19P605767 | 002 | TUMOUR

description: GeoMx DSP Ncounter

tag: patient

value: Partial response


title: TRA MSN09-04R-CM Rep 3 (DGE)


title: VAN MSN09-04R-CM Rep 4 (DGE)


title: 19P605767 | 003 | TME

description: GeoMx DSP Ncounter

tag: roi

value: TME

value: Positive


title: 19P605767 | 002 | TME

description: GeoMx DSP Ncounter


title: TRA MSN09-04R-CM Rep 2 (DGE)

value: skin

value: cardiac myocytes

tag: cell line


title: 19P605767 | 004 | TME

description: GeoMx DSP Ncounter


title: 19P605767 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: TRA MSN02-04R-CM Rep 4 (DGE)

tag: treatment time (hrs)


title: TRA MSN02-04R-CM Rep 3 (DGE)

tag: treatment condition


title: TRA MSN02-04R-CM Rep 2 (DGE)

tag: drug name


title: TRA MSN02-04R-CM Rep 1 (DGE)

tag: concentration


title: TRS MSN02-04R-CM Rep 1 (DGE)

tag: well


title: 19P605767 | 005 | TUMOUR

description: GeoMx DSP Ncounter


title: TOF MSN09-04R-CM Rep 4 (DGE)

value: TOF

value: Tofacitinib

tag: investigative unit


title: 19P605767 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: TOF MSN02-04R-CM Rep 4 (DGE)

tag: sample id


title: 19P605767 | 006 | TME

description: GeoMx DSP Ncounter


title: TOF MSN02-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: TOF MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: TOF MSN09-04R-CM Rep 1 (DGE)

tag: rna conc (ng/ul)


title: TOF MSN09-04R-CM Rep 2 (DGE)

tag: rna volume (ul)


title: 19P605767 | 006 | TUMOUR

description: GeoMx DSP Ncounter


title: TOF MSN02-04R-CM Rep 1 (DGE)

tag: h2o volume (ul)


title: SUN MSN09-04R-CM Rep 3 (DGE)

tag: tissue

value: SUN

value: Sunitinib


title: SUN MSN09-04R-CM Rep 1 (DGE)

tag: cell type


title: 19P6037200 | 006 | Tumour

description: GeoMx DSP Ncounter

tag: patient

value: Progression

value: N/A (oral tongue, not oropharynx)


title: SUN MSN09-04R-CM Rep 4 (DGE)


title: 19P605767 | 001 | TUMOUR

description: GeoMx DSP Ncounter

tag: roi

value: Tumour


title: SUN MSN09-04R-CM Rep 2 (DGE)

tag: cell line


title: TRA MSN09-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: 19P605767 | 001 | TME

description: GeoMx DSP Ncounter


title: 19P605767 | 005 | TME

description: GeoMx DSP Ncounter


title: 19P6037200 | 006 | TME

description: GeoMx DSP Ncounter


title: SUN MSN02-04R-CM Rep 4 (DGE)

tag: treatment condition


title: 19P6037200 | 005 | TME

description: GeoMx DSP Ncounter


title: 19P6037200 | 004 | Tumour

description: GeoMx DSP Ncounter


title: SUN MSN02-04R-CM Rep 3 (DGE)

tag: drug name


title: SUN MSN02-04R-CM Rep 2 (DGE)

tag: concentration


title: SUN MSN02-04R-CM Rep 1 (DGE)

tag: well


title: TOF MSN09-04R-CM Rep 3 (DGE)

tag: investigative unit


title: SOR MSN09-04R-CM Rep 4 (DGE)

value: SOR

value: Sorafenib

tag: sample id


title: 19P6037200 | 004 | TME

description: GeoMx DSP Ncounter


title: SOR MSN09-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: 19P6037200 | 003 | Tumour

description: GeoMx DSP Ncounter


title: SOR MSN02-04R-CM Rep 4 (DGE)

tag: rin


title: SOR MSN09-04R-CM Rep 1 (DGE)

tag: rna conc (ng/ul)


title: 19P6037200 | 002 | Tumour

description: GeoMx DSP Ncounter


title: 19P6037200 | 001 | TME

description: GeoMx DSP Ncounter


title: SOR MSN09-04R-CM Rep 2 (DGE)

tag: rna volume (ul)


title: SOR MSN02-04R-CM Rep 3 (DGE)

tag: h2o volume (ul)


title: RTX MSN09-04R-CM Rep 4 (DGE)

tag: tissue

value: RTX

value: Rituximab


title: RTX MSN09-04R-CM Rep 3 (DGE)

tag: cell type


title: RTX MSN09-04R-CM Rep 1 (DGE)


title: SOR MSN02-04R-CM Rep 1 (DGE)


title: RTX MSN02-04R-CM Rep 3 (DGE)


title: SOR MSN02-04R-CM Rep 2 (DGE)


title: RTX MSN02-04R-CM Rep 4 (DGE)


title: RTX MSN09-04R-CM Rep 2 (DGE)


title: REG MSN09-04R-CM Rep 4 (DGE)

value: REG

value: Regorafenib


title: 19P6037200 | 002 | TME

description: GeoMx DSP Ncounter

tag: patient

value: TME


title: RTX MSN02-04R-CM Rep 2 (DGE)


title: REG MSN09-04R-CM Rep 3 (DGE)


title: 19P6037200 | 005 | Tumour

description: GeoMx DSP Ncounter

tag: roi


title: REG MSN09-04R-CM Rep 2 (DGE)

tag: cell line


title: 19P15105 | 010 | Tumour

description: GeoMx DSP Ncounter


title: REG MSN09-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: 19P15105 | 010 | TME

description: GeoMx DSP Ncounter


title: 19P6037200 | 001 | Tumour

description: GeoMx DSP Ncounter


title: 19P6037200 | 003 | TME

description: GeoMx DSP Ncounter


title: REG MSN02-04R-CM Rep 4 (DGE)

tag: treatment condition


title: 19P15105 | 009 | TME

description: GeoMx DSP Ncounter


title: PRE MSN09-04R-CM Rep 4 (DGE)

value: PRE

tag: drug name

value: Prednisolone


title: REG MSN02-04R-CM Rep 3 (DGE)

value: skin

value: cardiac myocytes

tag: concentration


title: REG MSN02-04R-CM Rep 2 (DGE)

tag: well


title: 19P15105 | 008 | Tumour

description: GeoMx DSP Ncounter


title: RTX MSN02-04R-CM Rep 1 (DGE)

tag: investigative unit


title: PRE MSN09-04R-CM Rep 3 (DGE)

tag: sample id


title: PRE MSN09-04R-CM Rep 2 (DGE)

tag: rna amount (ng)


title: PRE MSN02-04R-CM Rep 3 (DGE)

tag: rin


title: PRE MSN09-04R-CM Rep 1 (DGE)

tag: rna conc (ng/ul)


title: PON MSN09-04R-CM Rep 4 (DGE)

value: PON

value: Ponatinib

tag: rna volume (ul)


title: PRE MSN02-04R-CM Rep 1 (DGE)

tag: h2o volume (ul)


title: 19P15105 | 003 | Tumour

description: GeoMx DSP Ncounter


title: PRE MSN02-04R-CM Rep 2 (DGE)

tag: tissue


title: 19P15105 | 004 | TME

description: GeoMx DSP Ncounter


title: 19P15105 | 006 | Full ROI

description: GeoMx DSP Ncounter


title: PON MSN09-04R-CM Rep 2 (DGE)

tag: cell type


title: PON MSN09-04R-CM Rep 3 (DGE)


title: 19P15105 | 009 | Tumour

description: GeoMx DSP Ncounter

tag: patient


title: 19P15105 | 002 | Tumour

description: GeoMx DSP Ncounter

tag: roi


title: PON MSN02-04R-CM Rep 4 (DGE)

tag: cell line


title: PON MSN02-04R-CM Rep 3 (DGE)

tag: treatment time (hrs)


title: PON MSN09-04R-CM Rep 1 (DGE)

tag: treatment condition


title: 19P15105 | 001 | Tumour

description: GeoMx DSP Ncounter


title: PON MSN02-04R-CM Rep 2 (DGE)

tag: drug name


title: REG MSN02-04R-CM Rep 1 (DGE)

tag: concentration


title: 19P15105 | 007 | Full ROI

description: GeoMx DSP Ncounter


title: 19P15105 | 005 | TME

description: GeoMx DSP Ncounter


title: 20P47599 | 001 | Tumour

description: GeoMx DSP Ncounter

value: Positive


title: PHP MSN09-04R-CM Rep 4 (DGE)

value: PHP

value: Phenylephrine

tag: well


title: PHP MSN09-04R-CM Rep 3 (DGE)

tag: investigative unit


title: 20P47599 | 002 | TME

description: GeoMx DSP Ncounter

value: Progression


title: PON MSN02-04R-CM Rep 1 (DGE)

tag: sample id


title: PRE MSN02-04R-CM Rep 4 (DGE)

tag: rna amount (ng)


title: 20P47599 | 002 | Tumour

description: GeoMx DSP Ncounter

value: Tumour


title: 20P47599 | 003 | TME

description: GeoMx DSP Ncounter


title: PHP MSN09-04R-CM Rep 1 (DGE)

tag: rin


title: PHP MSN09-04R-CM Rep 2 (DGE)

tag: rna conc (ng/ul)


title: PHP MSN02-04R-CM Rep 4 (DGE)

tag: rna volume (ul)


title: PHP MSN02-04R-CM Rep 2 (DGE)

tag: h2o volume (ul)


title: PHP MSN02-04R-CM Rep 1 (DGE)

tag: tissue


title: PAZ MSN09-04R-CM Rep 4 (DGE)

tag: cell type

value: PAZ

value: Pazopanib


title: 20P47599 | 003 | Tumour

description: GeoMx DSP Ncounter

tag: patient


title: PAZ MSN09-04R-CM Rep 3 (DGE)


title: PAZ MSN09-04R-CM Rep 1 (DGE)


title: PAZ MSN02-04R-CM Rep 3 (DGE)


title: PAZ MSN09-04R-CM Rep 2 (DGE)


title: PAZ MSN02-04R-CM Rep 4 (DGE)


title: 20P47599 | 004 | Tumour

description: GeoMx DSP Ncounter

tag: roi


title: 20P47599 | 004 | TME

description: GeoMx DSP Ncounter


title: 20P47599 | 005 | Tumour

description: GeoMx DSP Ncounter


title: 20P47599 | 005 | TME

description: GeoMx DSP Ncounter


title: PAZ MSN02-04R-CM Rep 2 (DGE)

tag: cell line


title: PAZ MSN02-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: OLM MSN09-04R-CM Rep 1 (DGE)

tag: treatment condition

value: OLM

value: Olmesartan


title: OLM MSN09-04R-CM Rep 2 (DGE)

tag: drug name


title: OLM MSN09-04R-CM Rep 4 (DGE)

tag: concentration


title: OLM MSN09-04R-CM Rep 3 (DGE)

tag: well


title: OLM MSN02-04R-CM Rep 3 (DGE)

tag: investigative unit


title: 20P47599 | 001 | TME

description: GeoMx DSP Ncounter


title: OLM MSN02-04R-CM Rep 4 (DGE)

tag: sample id


title: PHP MSN02-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: 20P47599 | 006 | TME

description: GeoMx DSP Ncounter


title: 20P47599 | 006 | Tumour

description: GeoMx DSP Ncounter


title: 15P48811 | 005 | Tumour

description: GeoMx DSP Ncounter

value: Partial response


title: OLM MSN02-04R-CM Rep 1 (DGE)

tag: rin


title: 15P48811 | 005 | TME

description: GeoMx DSP Ncounter

value: TME


title: OLM MSN02-04R-CM Rep 2 (DGE)

tag: rna conc (ng/ul)


title: NIL MSN09-04R-CM Rep 3 (DGE)

value: Nilotinib

tag: rna volume (ul)


title: NIL MSN09-04R-CM Rep 2 (DGE)

tag: h2o volume (ul)


title: NIL MSN09-04R-CM Rep 4 (DGE)

tag: tissue


title: NIL MSN09-04R-CM Rep 1 (DGE)

tag: cell type


title: NIL MSN02-04R-CM Rep 3 (DGE)


title: 15P48811 | 004 | Tumour

description: GeoMx DSP Ncounter

tag: patient


title: NIL MSN02-04R-CM Rep 4 (DGE)


title: 15P48811 | 004 | TME

description: GeoMx DSP Ncounter

tag: roi


title: 15P48811 | 003 | Tumour

description: GeoMx DSP Ncounter


title: 15P48811 | 002 | TME

description: GeoMx DSP Ncounter


title: MIL MSN09-04R-CM Rep 3 (DGE)

tag: cell line

value: MIL

value: Milrinone


title: NIL MSN02-04R-CM Rep 2 (DGE)

value: skin

value: cardiac myocytes

tag: treatment time (hrs)


title: MIL MSN09-04R-CM Rep 2 (DGE)

tag: treatment condition


title: MIL MSN09-04R-CM Rep 1 (DGE)

tag: drug name


title: NIL MSN02-04R-CM Rep 1 (DGE)

tag: concentration


title: MIL MSN09-04R-CM Rep 4 (DGE)

tag: well


title: 15P48811 | 001 | Tumour

description: GeoMx DSP Ncounter


title: MIL MSN02-04R-CM Rep 4 (DGE)

tag: investigative unit


title: 15P48811 | 001 | TME

description: GeoMx DSP Ncounter


title: MIL MSN02-04R-CM Rep 1 (DGE)

tag: sample id


title: MIL MSN02-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: MIL MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: LAP MSN09-04R-CM Rep 4 (DGE)

value: LAP

value: Lapatinib

tag: rna conc (ng/ul)


title: LAP MSN09-04R-CM Rep 2 (DGE)

tag: rna volume (ul)


title: LAP MSN09-04R-CM Rep 3 (DGE)

tag: h2o volume (ul)


title: LAP MSN09-04R-CM Rep 1 (DGE)

tag: tissue


title: 15P48811 | 006 | TME

description: GeoMx DSP Ncounter

value: Positive


title: 17P45086 | 001 | Tumour

description: GeoMx DSP Ncounter

value: Negative


title: LAP MSN02-04R-CM Rep 4 (DGE)

tag: cell type


title: LAP MSN02-04R-CM Rep 3 (DGE)


title: LAP MSN02-04R-CM Rep 2 (DGE)


title: ISO MSN09-04R-CM Rep 4 (DGE)

value: ISO

value: Isoproterenol

value: 2 uM


title: 17P45086 | 002 | TME

description: GeoMx DSP Ncounter

tag: patient

value: Progression


title: ISO MSN09-04R-CM Rep 3 (DGE)


title: 15P48811 | 003 | TME

description: GeoMx DSP Ncounter

tag: roi


title: ISO MSN09-04R-CM Rep 2 (DGE)

tag: cell line


title: ISO MSN09-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: ISO MSN02-04R-CM Rep 2 (DGE)

tag: treatment condition


title: ISO MSN02-04R-CM Rep 4 (DGE)

tag: drug name


title: 17P45086 | 002 | Tumour

description: GeoMx DSP Ncounter

value: Tumour


title: ISO MSN02-04R-CM Rep 1 (DGE)

tag: concentration


title: 17P45086 | 003 | TME

description: GeoMx DSP Ncounter


title: 15P48811 | 006 | Tumour

description: GeoMx DSP Ncounter


title: IMA MSN09-04R-CM Rep 4 (DGE)

value: IMA

value: Imatinib

tag: well


title: IMA MSN09-04R-CM Rep 2 (DGE)

tag: investigative unit


title: 17P45086 | 004 | Tumour

description: GeoMx DSP Ncounter


title: IMA MSN02-04R-CM Rep 4 (DGE)

tag: sample id


title: IMA MSN09-04R-CM Rep 1 (DGE)

tag: rna amount (ng)


title: IMA MSN02-04R-CM Rep 3 (DGE)

tag: rin


title: 17P45086 | 003 | Tumour

description: GeoMx DSP Ncounter


title: IMA MSN02-04R-CM Rep 2 (DGE)

tag: rna conc (ng/ul)


title: 17P45086 | 005 | Tumour

description: GeoMx DSP Ncounter


title: IMA MSN02-04R-CM Rep 1 (DGE)

tag: rna volume (ul)


title: LAP MSN02-04R-CM Rep 1 (DGE)

tag: h2o volume (ul)


title: IDA MSN09-04R-CM Rep 4 (DGE)

tag: tissue

value: IDA

value: Idarubicin


title: 17P45086 | 006 | TME

description: GeoMx DSP Ncounter

value: TME


title: 17P45086 | 005 | TME

description: GeoMx DSP Ncounter


title: ISO MSN02-04R-CM Rep 3 (DGE)

tag: cell type


title: IDA MSN09-04R-CM Rep 3 (DGE)


title: 17P45086 | 004 | TME

description: GeoMx DSP Ncounter

tag: patient


title: IDA MSN09-04R-CM Rep 1 (DGE)


title: 17P45086 | 006 | Tumour

description: GeoMx DSP Ncounter

tag: roi


title: IDA MSN02-04R-CM Rep 4 (DGE)

tag: cell line


title: IDA MSN02-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: 17P45086 | 001 | TME

description: GeoMx DSP Ncounter


title: IMA MSN09-04R-CM Rep 3 (DGE)

tag: treatment condition


title: IDA MSN02-04R-CM Rep 2 (DGE)

tag: drug name


title: GEF MSN09-04R-CM Rep 4 (DGE)

value: GEF

value: Gefitinib

tag: concentration


title: 13P44561 | 001 | TME

description: GeoMx DSP Ncounter

value: Complete response


title: IDA MSN02-04R-CM Rep 3 (DGE)

value: skin

value: cardiac myocytes

tag: well


title: GEF MSN09-04R-CM Rep 2 (DGE)

tag: investigative unit


title: 13P44561 | 002 | Tumour

description: GeoMx DSP Ncounter

value: Positive


title: 13P44561 | 002 | TME

description: GeoMx DSP Ncounter


title: GEF MSN09-04R-CM Rep 1 (DGE)

tag: sample id


title: 13P44561 | 003 | Tumour

description: GeoMx DSP Ncounter


title: GEF MSN02-04R-CM Rep 4 (DGE)

tag: rna amount (ng)


title: GEF MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: 13P44561 | 004 | TME

description: GeoMx DSP Ncounter


title: FLE MSN09-04R-CM Rep 4 (DGE)

value: FLE

value: Flecainide

tag: rna conc (ng/ul)


title: GEF MSN02-04R-CM Rep 3 (DGE)

tag: rna volume (ul)


title: IDA MSN09-04R-CM Rep 2 (DGE)

tag: h2o volume (ul)


title: GEF MSN02-04R-CM Rep 1 (DGE)

tag: tissue


title: FLE MSN09-04R-CM Rep 3 (DGE)

tag: cell type


title: FLE MSN09-04R-CM Rep 2 (DGE)


title: FLE MSN02-04R-CM Rep 4 (DGE)


title: 13P44561 | 004 | Tumour

description: GeoMx DSP Ncounter

tag: patient


title: FLE MSN09-04R-CM Rep 1 (DGE)


title: FLE MSN02-04R-CM Rep 2 (DGE)


title: FLE MSN02-04R-CM Rep 3 (DGE)


title: FLE MSN02-04R-CM Rep 1 (DGE)


title: EST MSN09-04R-CM Rep 4 (DGE)

value: EST

value: Estradiol


title: GEF MSN09-04R-CM Rep 3 (DGE)


title: 13P44561 | 006 | TME

description: GeoMx DSP Ncounter

tag: roi


title: 13P44561 | 003 | TME

description: GeoMx DSP Ncounter


title: 13P44561 | 005 | Tumour

description: GeoMx DSP Ncounter


title: EST MSN09-04R-CM Rep 3 (DGE)

tag: cell line


title: 13P44561 | 001 | Tumour

description: GeoMx DSP Ncounter


title: EST MSN09-04R-CM Rep 2 (DGE)

tag: treatment time (hrs)


title: EST MSN02-04R-CM Rep 4 (DGE)

tag: treatment condition


title: EST MSN09-04R-CM Rep 1 (DGE)

tag: drug name


title: 19P13033 | 001 | TUMOUR

description: GeoMx DSP Ncounter

value: Progression

value: Unknown


title: 19P13033 | 002 | TME

description: GeoMx DSP Ncounter


title: EST MSN02-04R-CM Rep 3 (DGE)

tag: concentration


title: EST MSN02-04R-CM Rep 1 (DGE)

tag: well


title: EST MSN02-04R-CM Rep 2 (DGE)

tag: investigative unit


title: 19P13033 | 002 | TUMOUR

description: GeoMx DSP Ncounter

value: Tumour


title: 13P44561 | 005 | TME

description: GeoMx DSP Ncounter


title: ERL MSN09-04R-CM Rep 4 (DGE)

value: ERL

value: Erlotinib

tag: sample id


title: ERL MSN09-04R-CM Rep 2 (DGE)

tag: rna amount (ng)


title: ERL MSN09-04R-CM Rep 1 (DGE)

tag: rin


title: ERL MSN09-04R-CM Rep 3 (DGE)

tag: rna conc (ng/ul)


title: 19P13033 | 004 | TME

description: GeoMx DSP Ncounter


title: ERL MSN02-04R-CM Rep 3 (DGE)

tag: rna volume (ul)


title: ERL MSN02-04R-CM Rep 4 (DGE)

tag: h2o volume (ul)


title: 13P44561 | 006 | Tumour

description: GeoMx DSP Ncounter


title: ERL MSN02-04R-CM Rep 1 (DGE)

tag: tissue


title: 19P13033 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: EPI MSN09-04R-CM Rep 4 (DGE)

tag: cell type

value: EPI

value: Epirubicin


title: EPI MSN09-04R-CM Rep 3 (DGE)


title: EPI MSN09-04R-CM Rep 2 (DGE)


title: EPI MSN09-04R-CM Rep 1 (DGE)


title: 19P13033 | 005 | TUMOUR

description: GeoMx DSP Ncounter

tag: patient


title: EPI MSN02-04R-CM Rep 4 (DGE)


title: EPI MSN02-04R-CM Rep 3 (DGE)


title: EPI MSN02-04R-CM Rep 2 (DGE)


title: 19P13033 | 001 | TME

description: GeoMx DSP Ncounter

tag: roi

value: TME


title: 19P13033 | 006 | TUMOUR

description: GeoMx DSP Ncounter


title: 19P13033 | 006 | TME

description: GeoMx DSP Ncounter


title: EPI MSN02-04R-CM Rep 1 (DGE)

tag: cell line


title: DOX MSN09-04R-CM Rep 4 (DGE)

tag: treatment time (hrs)

value: DOX

value: Doxorubicin


title: DOX MSN09-04R-CM Rep 2 (DGE)

value: skin

tag: treatment condition


title: DOX MSN09-04R-CM Rep 1 (DGE)

value: cardiac myocytes

tag: drug name


title: 19P13033 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51428 | 005 | TME

description: GeoMx DSP Ncounter

value: Negative


title: 18P51428 | 005 | TUMOUR

description: GeoMx DSP Ncounter


title: ERL MSN02-04R-CM Rep 2 (DGE)

tag: concentration


title: DOX MSN02-04R-CM Rep 4 (DGE)

tag: well


title: DOX MSN02-04R-CM Rep 2 (DGE)

tag: investigative unit


title: DOX MSN09-04R-CM Rep 3 (DGE)

tag: sample id


title: DOX MSN02-04R-CM Rep 1 (DGE)

tag: rna amount (ng)


title: DOB MSN09-04R-CM Rep 4 (DGE)

value: DOB

value: Dobutamine

value: 1 uM

tag: rin


title: DOX MSN02-04R-CM Rep 3 (DGE)

tag: rna conc (ng/ul)


title: DOB MSN09-04R-CM Rep 3 (DGE)

tag: rna volume (ul)


title: DOB MSN02-04R-CM Rep 4 (DGE)

tag: h2o volume (ul)


title: 18P51428 | 004 | TUMOUR

description: GeoMx DSP Ncounter


title: 18P51428 | 004 | TME

description: GeoMx DSP Ncounter


title: DOB MSN02-04R-CM Rep 3 (DGE)

tag: tissue


title: DOB MSN02-04R-CM Rep 2 (DGE)

tag: cell type


title: DOB MSN09-04R-CM Rep 1 (DGE)


title: 18P51428 | 002 | TME

description: GeoMx DSP Ncounter

tag: patient


title: 18P51428 | 003 | TME

description: GeoMx DSP Ncounter

tag: roi


title: DOB MSN02-04R-CM Rep 1 (DGE)

tag: cell line


title: 18P51428 | 006 | TUMOUR

description: GeoMx DSP Ncounter


title: DAU MSN09-04R-CM Rep 3 (DGE)

tag: treatment time (hrs)

value: DAU

value: Daunorubicin


title: DAU MSN09-04R-CM Rep 4 (DGE)

tag: treatment condition


title: DAU MSN09-04R-CM Rep 2 (DGE)

tag: drug name


title: DAU MSN09-04R-CM Rep 1 (DGE)

tag: concentration


title: DAU MSN02-04R-CM Rep 4 (DGE)

tag: well


title: 18P51428 | 002 | TUMOUR

description: GeoMx DSP Ncounter

value: Progression


title: 18P51428 | 001 | TUMOUR

description: GeoMx DSP Ncounter

value: Tumour


title: 18P51428 | 001 | TME

description: GeoMx DSP Ncounter


title: DAU MSN02-04R-CM Rep 1 (DGE)

tag: investigative unit


title: DOB MSN09-04R-CM Rep 2 (DGE)

tag: sample id


title: DAU MSN02-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: DAU MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: DAS MSN09-04R-CM Rep 4 (DGE)

value: DAS

value: Dasatinib

tag: rna conc (ng/ul)


title: 18P51428 | 006 | TME

description: GeoMx DSP Ncounter


title: DAS MSN09-04R-CM Rep 2 (DGE)

tag: rna volume (ul)


title: DAS MSN09-04R-CM Rep 3 (DGE)

tag: h2o volume (ul)


title: 18P51428 | 003 | TUMOUR

description: GeoMx DSP Ncounter


title: DAS MSN09-04R-CM Rep 1 (DGE)

tag: tissue


title: DAS MSN02-04R-CM Rep 4 (DGE)

tag: cell type


title: DAS MSN02-04R-CM Rep 3 (DGE)


title: XY12 male

city: Montreal

first: Anna

middle: K.

last: Naumova

state: Quebec

address: 2155 rue Guy

department: Departments of Obstetrics and Gynecology and Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw reads were trimmed for quality (quality score ≥30) using trimmomatic (v 0.36)
Aligned to the Mus musculus GRCm38 reference genome using the bisulfate read aligner Bismark (v 0.18.1)
Duplicate reads were then removed using Picard (v 2.9.0)
Methylation calls were extracted Bismark (v 0.18.1) methylation caller
CpGs were filtered to remove any sites that overlapped with loci from the NCBI reference SNP database for GRCm38 (dbSNP version 142)
Assembly: GRCm38
Supplementary files format and content: Coverage track file (BigWig format) with the aligned reads
Supplementary files format and content: Methylation track file (BigWig format) with the CpG methylation calls

source_name: Liver

extract_protocol:
Standard proteinase K phenol/chloroform procedure or by QIAamp Fast DNA Tissue Kit (Qiagen, NL)
WGBS libraries were prepared from the extracted genomic DNA using the NEBNext Enzymatic Methyl-seq Kit

value: Liver

tag: strain

tag: sex chromosomes

value: XY

tag: Sex

value: Male

tag: age

value: 8 weeks


title: XY3 female

value: Female


title: DAS MSN02-04R-CM Rep 2 (DGE)

value: skin

tag: cell line

tag: treatment time (hrs)

tag: treatment condition


title: XY2 female


title: DAB MSN09-04R-CM Rep 4 (DGE)

value: cardiac myocytes

value: DAB

tag: drug name

value: Dabrafenib

tag: concentration

tag: well


title: DAB MSN09-04R-CM Rep 3 (DGE)

tag: investigative unit

tag: sample id

tag: rna amount (ng)


title: XY10 male


title: DAB MSN09-04R-CM Rep 2 (DGE)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: XY11 male

tag: tissue


title: XX9 female

tag: strain

value: XX


title: DAB MSN09-04R-CM Rep 1 (DGE)

tag: cell type

tag: h2o volume (ul)


title: XX8 female

tag: sex chromosomes

tag: Sex

tag: age


title: XX7 female


title: XXPaf6 female


title: XY1 female


title: CYC MSN09-04R-CM Rep 4 (DGE)

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

value: CYC

value: Cyclosporine


title: DAB MSN02-04R-CM Rep 3 (DGE)

tag: drug name

tag: concentration

tag: well


title: DAB MSN02-04R-CM Rep 1 (DGE)

tag: investigative unit

tag: sample id

tag: rna amount (ng)


title: CYC MSN09-04R-CM Rep 3 (DGE)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: CYC MSN09-04R-CM Rep 2 (DGE)

tag: tissue

tag: cell type


title: CYC MSN02-04R-CM Rep 4 (DGE)

tag: h2o volume (ul)


title: CYC MSN09-04R-CM Rep 1 (DGE)


title: CYC MSN02-04R-CM Rep 3 (DGE)


title: XO3 female

tag: strain

tag: sex chromosomes

value: X

tag: Sex


title: XO2 female

tag: age


title: CYC MSN02-04R-CM Rep 2 (DGE)

tag: cell line

tag: treatment time (hrs)

tag: treatment condition


title: DAS MSN02-04R-CM Rep 1 (DGE)

tag: drug name

tag: concentration

tag: well


title: CTX MSN09-04R-CM Rep 4 (DGE)

value: CTX

value: Cetuximab

tag: investigative unit

tag: sample id

tag: rna amount (ng)


title: CYC MSN02-04R-CM Rep 1 (DGE)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: XO1 female

tag: tissue


title: CTX MSN09-04R-CM Rep 2 (DGE)

tag: cell type

tag: h2o volume (ul)


title: DAB MSN02-04R-CM Rep 4 (DGE)


title: CTX MSN09-04R-CM Rep 3 (DGE)


title: CTX MSN09-04R-CM Rep 1 (DGE)


title: CTX MSN02-04R-CM Rep 2 (DGE)


title: CTX MSN02-04R-CM Rep 4 (DGE)


title: DAB MSN02-04R-CM Rep 2 (DGE)


title: CTX MSN02-04R-CM Rep 1 (DGE)


title: mice,  tac2_Snai1_KD, 2 weeks

city: Guangzhou

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

data_processing:
limma package on R program
Assembly: mm10
Supplementary files format and content: tab-delimited text files include filtered and normalized gene expression  for each Sample

source_name: mice,  tac2_Snai1_KD, 2 weeks

extract_protocol:
Total RNA from heart tissues and cultured cells was extracted using the TRIzol method (Life Technologies, US).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: heart

tag: genotype

value: Snai1 knockdown

tag: treatment

value: TAC

tag: time

value: 2 weeks


title: mice, tac1_Snai1_KD, 2 weeks

source_name: mice, tac1_Snai1_KD, 2 weeks


title: mice, tac2, 2 weeks

source_name: mice, tac2, 2 weeks

value: WT


title: CTRL MSN09-04R-CM Rep 8 (DGE)

tag: cell line

tag: treatment time (hrs)

value: CTRL

value: Dimethyl sulfoxide


title: mice, tac1, 2 weeks

source_name: mice, tac1, 2 weeks


title: mice, con2, 2 weeks

source_name: mice, con2, 2 weeks

value: sham


title: XXPaf4 female

value: Liver

tag: strain

tag: sex chromosomes

tag: Sex

value: Female

tag: age

value: 8 weeks


title: CTRL MSN09-04R-CM Rep 5 (DGE)

value: skin

value: cardiac myocytes

tag: treatment condition

tag: drug name

tag: concentration

tag: well

tag: investigative unit

tag: sample id


title: CTRL MSN09-04R-CM Rep 6 (DGE)

tag: tissue

tag: cell type

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: mice, con1, 2 weeks

source_name: mice, con1, 2 weeks

tag: genotype

tag: treatment

tag: time


title: CTRL MSN09-04R-CM Rep 7 (DGE)

tag: cell line

tag: treatment time (hrs)

tag: h2o volume (ul)


title: CTRL MSN09-04R-CM Rep 2 (DGE)

tag: treatment condition

tag: drug name


title: CTRL MSN02-04R-CM Rep 8 (DGE)

tag: concentration

tag: well


title: CTRL MSN09-04R-CM Rep 3 (DGE)

tag: investigative unit

tag: sample id


title: CTRL MSN09-04R-CM Rep 1 (DGE)

tag: tissue

tag: cell type


title: FVB/NJ mouse rep2 - Ventral Lobe

city: Chicago

first: Mindy

middle: Kim

last: Graham

state: IL

address: 303 E. Superior Street Chicago

department: Urology

institute: Northwestern University Feinberg School of Medicine

description: single cell RNA-seq

data_processing:
The cDNA libraries were sequenced (150 bp paired-end) on the Illumina HiSeqX platform.
Each sequenced library was demultiplexed to FASTQ files using Cell Ranger (10x Genomics).
Cell Ranger (version 2.2.0) count pipeline was used to align reads to the mm10 mouse transcriptome and create a gene by cell count matrix.
Cell Ranger (version 2.2.0) aggr pipeline was used to aggregate the counts across all the cDNA libraries generated for each mouse prostate lobe.
Genome_build: mm10
Supplementary_files_format_and_content: For each library preparation includes the following files: matrix.mtx, barcodes.tsv, genes.tsv

source_name: prostate

extract_protocol:
Individual prostate lobes were dissected from 6 month old mice and single-cell RNA-sequencing libraries for each lobe were prepared separately.
Libraries for scRNA-seq were prepared using the 10x Genomics Chromium Single Cell 3’ Library and Gel bead Kit V2 (CG00052_RevF).
single-cell RNA-sequencing 10X Genomics platform

tag: strain

value: FVB/NJ

value: prostate

tag: prostate lobe

value: ventral


title: CTRL MSN02-04R-CM Rep 7 (DGE)

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: CTX MSN02-04R-CM Rep 3 (DGE)

tag: cell line

value: CTX

value: Cetuximab


title: FVB/NJ mouse rep1 - Ventral Lobe

description: single cell RNA-seq


title: CTRL MSN02-04R-CM Rep 4 (DGE)

tag: treatment time (hrs)


title: CTRL MSN02-04R-CM Rep 6 (DGE)

tag: h2o volume (ul)


title: CTRL MSN02-04R-CM Rep 5 (DGE)

tag: treatment condition


title: CTRL MSN02-04R-CM Rep 3 (DGE)

tag: drug name


title: CTRL MSN02-04R-CM Rep 2 (DGE)

tag: concentration


title: FVB/NJ mouse rep1 - Lateral Lobe

description: single cell RNA-seq

value: lateral


title: CTRL MSN02-04R-CM Rep 1 (DGE)

tag: well


title: CRI MSN09-04R-CM Rep 4 (DGE)

value: CRI

value: Crizotinib

tag: investigative unit


title: CRI MSN09-04R-CM Rep 3 (DGE)

tag: sample id


title: FVB/NJ mouse rep1 - Dorsal Lobe

description: single cell RNA-seq

tag: tissue

value: dorsal


title: CTRL MSN09-04R-CM Rep 4 (DGE)

tag: cell type

value: CTRL


title: CRI MSN09-04R-CM Rep 2 (DGE)


title: FVB/NJ mouse rep2 - Anterior Lobe

description: single cell RNA-seq

tag: strain

value: anterior


title: CRI MSN09-04R-CM Rep 1 (DGE)


title: FVB/NJ mouse rep1 - Anterior Lobe

description: single cell RNA-seq

tag: prostate lobe


title: CRI MSN02-04R-CM Rep 4 (DGE)

tag: rna amount (ng)


title: CRI MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: CRI MSN02-04R-CM Rep 3 (DGE)

tag: rna conc (ng/ul)


title: C57BL/6J mouse rep3 - Ventral Lobe

description: single cell RNA-seq


title: CRI MSN02-04R-CM Rep 1 (DGE)

tag: rna volume (ul)


title: CER MSN09-04R-CM Rep 4 (DGE)

tag: cell line

value: CER

value: Ceritinib


title: CER MSN09-04R-CM Rep 3 (DGE)

tag: treatment time (hrs)


title: C57BL/6J mouse rep2 - Ventral Lobe

description: single cell RNA-seq


title: CER MSN09-04R-CM Rep 2 (DGE)

tag: h2o volume (ul)


title: C57BL/6J mouse rep1 - Ventral Lobe

description: single cell RNA-seq


title: CER MSN09-04R-CM Rep 1 (DGE)

tag: treatment condition


title: FVB/NJ mouse rep2 - Lateral Lobe

description: single cell RNA-seq


title: CER MSN02-04R-CM Rep 3 (DGE)

tag: drug name


title: CER MSN02-04R-CM Rep 4 (DGE)

tag: concentration


title: CER MSN02-04R-CM Rep 2 (DGE)

tag: well


title: C57BL/6J mouse rep3 - Lateral Lobe

description: single cell RNA-seq


title: FVB/NJ mouse rep2 - Dorsal Lobe

description: single cell RNA-seq


title: C57BL/6J mouse rep2 - Lateral Lobe

description: single cell RNA-seq


title: CAB MSN09-04R-CM Rep 3 (DGE)

value: CAB

value: Cabozantinib

tag: investigative unit


title: CAB MSN02-04R-CM Rep 4 (DGE)

value: skin

tag: sample id


title: CAB MSN09-04R-CM Rep 2 (DGE)

tag: tissue

value: cardiac myocytes


title: CAB MSN09-04R-CM Rep 1 (DGE)

tag: cell type


title: C57BL/6J mouse rep2 - Dorsal Lobe

description: single cell RNA-seq

tag: strain


title: C57BL/6J mouse rep1 - Dorsal Lobe

description: single cell RNA-seq

tag: prostate lobe


title: CAB MSN02-04R-CM Rep 3 (DGE)

tag: rna amount (ng)


title: CAB MSN02-04R-CM Rep 2 (DGE)

tag: rin


title: C57BL/6J mouse rep3 - Anterior Lobe

description: single cell RNA-seq


title: CAB MSN02-04R-CM Rep 1 (DGE)

tag: rna conc (ng/ul)


title: BOS MSN09-04R-CM Rep 2 (DGE)

value: BOS

value: Bosutinib

tag: rna volume (ul)


title: BOS MSN09-04R-CM Rep 3 (DGE)

tag: cell line


title: C57BL/6J mouse rep2 - Anterior Lobe

description: single cell RNA-seq

value: prostate


title: CER MSN02-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)


title: C57BL/6J mouse rep1 - Anterior Lobe

description: single cell RNA-seq


title: BOS MSN09-04R-CM Rep 1 (DGE)

tag: h2o volume (ul)


title: CAB MSN09-04R-CM Rep 4 (DGE)

tag: treatment condition


title: BOS MSN02-04R-CM Rep 3 (DGE)

tag: drug name


title: BEV MSN09-04R-CM Rep 3 (DGE)

value: BEV

value: Bevacizmab

tag: concentration


title: BOS MSN02-04R-CM Rep 4 (DGE)

tag: well


title: C57BL/6J mouse rep1 - Lateral Lobe

description: single cell RNA-seq

value: lateral


title: BOS MSN02-04R-CM Rep 2 (DGE)

tag: investigative unit


title: BEV MSN09-04R-CM Rep 4 (DGE)

tag: sample id


title: BOS MSN02-04R-CM Rep 1 (DGE)

tag: tissue


title: Hemocytes, Bacterial Infection, rep5

city: Kiel

first: Vaibhvi

last: Vaibhvi

state: Germany (DEU)

address: Am Botanischen Garten 3-9

department: Zoology

institute: University of Kiel

description: TPM_values.txt - Column X

data_processing:
CLC Genomics Workbench v 9.5.2
Adaptor and low-quality reads were trimmed using CLC genomic workbench (parameter- Quality limit: 0.05)
Clean reads were mapped to the Drosophila reference genome using CLC genomic workbench (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read counts were extracted using CLC genomic workbench
Differential expression of genes in the different treatments w.r.t their respective tissue controls was calculated using DESeq2
Assembly: Drosophila melanogaster BDGP6 Release 6 plus ISO1 MT
Supplementary files format and content: TPM_values.csv file contains TPM values for each library with the library name as the column name
Supplementary files format and content: log2fc.csv file contains the log2fc values of each gene for the bacteria infected(I)/sterile injury(S) treated fat body (fb) or hemocytes (hemo) w.r.t the respective control untreated values for each cell type. Corresponding adjusted p-values are also provided. basemean values provided by DESeq2 are also provided for each cell type calculations.

organism: Drosophila melanogaster

source_name: circulating hemocytes

extract_protocol:
RNA was extracted using the standard phenol-isopropanol-chloroform protocol. cDNA synthesis was done by the two-step Smart-seq3 protocol (Hagemann-Jensen et al., 2020). Amplification was done by their provided protocol as well but using LATaq Polymerase.
Library preparation was done using an adaptation of the protocol from Picelli et al., 2014

treatment_protocol: Control - Unhandled control adults; Sterile Injury - Thorax injury using a sterile minutin needle dipped in PBS; Bacterial Infection - Systemic infection using Bacillus subtilis bacteria, by pricking the thorax with a needle dipped in the bacterial solution in PBS

value: circulating hemocytes

tag: age

value: Adult

tag: Sex

value: female

tag: genotype

value: WT

tag: treatment

value: Bacterial Infection


title: C57BL/6J mouse rep3 - Dorsal Lobe

description: single cell RNA-seq

tag: strain

tag: prostate lobe

value: dorsal


title: Hemocytes, Bacterial Infection, rep4

description: TPM_values.txt - Column W


title: BEV MSN09-04R-CM Rep 2 (DGE)

tag: cell type

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: Hemocytes, Bacterial Infection, rep3

description: TPM_values.txt - Column V


title: BEV MSN09-04R-CM Rep 1 (DGE)

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

tag: drug name

tag: h2o volume (ul)


title: BEV MSN02-04R-CM Rep 4 (DGE)

tag: tissue

tag: concentration

tag: well

tag: investigative unit

tag: sample id


title: BEV MSN02-04R-CM Rep 3 (DGE)


title: BOS MSN09-04R-CM Rep 4 (DGE)


title: Hemocytes, Bacterial Infection, rep2

description: TPM_values.txt - Column U

tag: age

tag: Sex

tag: genotype

tag: treatment


title: BEV MSN02-04R-CM Rep 1 (DGE)

tag: cell type

tag: rna amount (ng)

tag: rin


title: Hemocytes, Bacterial Infection, rep1

description: TPM_values.txt - Column T


title: AXI MSN09-04R-CM Rep 4 (DGE)

tag: cell line

value: AXI

value: Axitinib

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: BEV MSN02-04R-CM Rep 2 (DGE)

tag: treatment time (hrs)

tag: treatment condition

tag: drug name


title: Hemocytes, Sterile Injury, rep5

description: TPM_values.txt - Column S

tag: tissue

value: Sterile Injury


title: Hemocytes, Sterile Injury, rep4

description: TPM_values.txt - Column R


title: AXI MSN09-04R-CM Rep 2 (DGE)

value: skin

tag: concentration

tag: well

tag: h2o volume (ul)


title: ∆ArAceA_Cu_rep3

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (v1.4.0) (parameter– l 15 -q 0.2 -n 0.1)
Clear reads were mapped to Acidomyces richmondensis BFW genome (version 1.0) using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.2.8) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped fragments per kilobase of transcript per million mapped reads (FPKM) and differential gene expression was determined by DESeq2 package.
Assembly: GCA_001592465.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Acidomyces sp. 'richmondensis'

source_name: Mycelia

growth_protocol: Arthroconidia from 10-day-old agar culture were collected and counted by haemocytometer, then inoculated into 100 mL liquid MMC medium and grown at 28˚C and 200 rpm 4 d. The mycelial biomass was washed with sterilized water at least two times and then transferred to 100 mL MMC medium with or without 15 mM CuCl2 for 6 h before RNA extraction.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: strain

value: Mycelia

tag: cucl2 treatment

value: 15 mM

tag: time

value: 6 h


title: AXI MSN09-04R-CM Rep 1 (DGE)

value: cardiac myocytes

tag: investigative unit

tag: sample id


title: Hemocytes, Sterile Injury, rep2

description: TPM_values.txt - Column P

tag: age

tag: Sex

tag: genotype

tag: treatment


title: ∆ArAceA_Cu_rep1


title: Hemocytes, Sterile Injury, rep1

description: TPM_values.txt - Column O


title: Hemocytes, Sterile Injury, rep3

description: TPM_values.txt - Column Q


title: AXI MSN02-04R-CM Rep 4 (DGE)

tag: cell type

tag: cell line

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)

tag: rna volume (ul)


title: ∆ArAceA_rep2

tag: tissue

value: 0 mM


title: ∆ArAceA_Cu_rep2


title: Hemocytes, Control, rep3

description: TPM_values.txt - Column M

value: Control


title: ∆ArAceA_rep1


title: ∆ArAceA_rep3


title: Hemocytes, Control, rep4

description: TPM_values.txt - Column N


title: AXI MSN02-04R-CM Rep 1 (DGE)

tag: treatment time (hrs)

tag: treatment condition

tag: drug name

tag: concentration

tag: well

tag: h2o volume (ul)


title: AXI MSN02-04R-CM Rep 2 (DGE)

tag: investigative unit

tag: sample id


title: AMI MSN09-04R-CM Rep 4 (DGE)

value: AMI

value: Amiodarone


title: AXI MSN02-04R-CM Rep 3 (DGE)


title: Hemocytes, Control, rep2

description: TPM_values.txt - Column L

value: circulating hemocytes

tag: age

value: Adult

tag: Sex

tag: genotype


title: WT_Cu_rep3

tag: strain

value: WT

tag: cucl2 treatment

tag: time


title: AXI MSN09-04R-CM Rep 3 (DGE)

tag: cell type

tag: cell line

tag: rna amount (ng)

tag: rin

tag: rna conc (ng/ul)


title: WT_Cu_rep2

tag: tissue


title: AMI MSN09-04R-CM Rep 2 (DGE)

tag: treatment time (hrs)

tag: treatment condition

tag: drug name

tag: concentration

tag: rna volume (ul)


title: WT_Cu_rep1


title: AMI MSN09-04R-CM Rep 3 (DGE)

tag: well

tag: investigative unit

tag: sample id

tag: h2o volume (ul)


title: AMI MSN09-04R-CM Rep 1 (DGE)


title: Fat body, Bacterial infection, rep3

description: TPM_values.txt - Column J

source_name: fat body

value: fat body

tag: age

tag: Sex

value: female

tag: genotype

tag: treatment

value: Bacterial Infection


title: Hemocytes, Control, rep1

description: TPM_values.txt - Column K


title: Fat body, Bacterial infection, rep2

description: TPM_values.txt - Column I


title: AMI MSN02-04R-CM Rep 4 (DGE)

tag: cell type

tag: cell line

tag: rna amount (ng)


title: WT_rep2

tag: strain

tag: tissue

tag: cucl2 treatment

tag: time


title: AMI MSN02-04R-CM Rep 3 (DGE)

tag: treatment time (hrs)

tag: treatment condition

tag: drug name

tag: concentration

tag: rin

tag: rna conc (ng/ul)


title: Fat body, Sterile Injury, rep3

description: TPM_values.txt - Column G

tag: age


title: Fat body, Sterile Injury, rep2

description: TPM_values.txt - Column F

tag: Sex


title: AMI MSN02-04R-CM Rep 1 (DGE)

tag: well

tag: investigative unit

tag: sample id

tag: rna volume (ul)

tag: h2o volume (ul)


title: Fat body, Sterile Injury, rep1

description: TPM_values.txt - Column E

tag: genotype

tag: treatment


title: WT_rep1

tag: strain

tag: tissue

tag: cucl2 treatment


title: Fat body, Control, rep2

description: TPM_values.txt - Column C


title: AFA MSN09-04R-CM Rep 4 (DGE)

tag: cell type

tag: cell line

tag: treatment time (hrs)

tag: treatment condition

value: AFA

value: Afatinib

tag: rna amount (ng)


title: AFA MSN09-04R-CM Rep 2 (DGE)

value: skin

tag: drug name

tag: concentration

tag: rin

tag: rna conc (ng/ul)


title: F1_94_2: mutant94_inf_rep2

city: Tampere

first: Anni

last: Saralahti

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

data_processing:
Read alignment to reference genome was done using STAR
Raw expression estimates (raw read counts) for genes (Danio_rerio.GRCz10.91) were counted using FeatureCounts
Raw expression estimates were normalized using median of rations implemented in R-packages DESeq2
Genome_build: Danio_rerio.GRCz10
Supplementary_files_format_and_content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab-delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample.

organism: Danio rerio

source_name: whole zebrafish embryos

growth_protocol: Wild type zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene-breaking transposon based mutagenesis using the RP2 construct.

extract_protocol:
Total RNA was extracted from the pools of 5 embryos using the Qiagen RNeasy Mini Kit (ID: 74104) according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit (K2981).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 days old zebrafish embryos were infected with 100 cfu of TIGR4 strain Streptococcus pneumoniae and the RNA was collected at 18 hours post infection. Control embryos were injected with 0.2 M KCl and the RNA was collected at 18 hpi.

value: whole zebrafish embryos


title: F1_94_1: mutant94_inf_rep1


title: AFA MSN09-04R-CM Rep 3 (DGE)

tag: well

tag: investigative unit

tag: sample id


title: Fat body, Control, rep3

description: TPM_values.txt - Column D

tag: age

tag: Sex

tag: genotype


title: F1_94_3: mutant94_inf_rep3

tag: tissue


title: AB_KCl_3: WT_control_rep3

value: wild type AB


title: AFA MSN09-04R-CM Rep 1 (DGE)

tag: rna volume (ul)

tag: h2o volume (ul)


title: AB_KCl_2: WT_control_rep2


title: Fat body, Control, rep1

description: TPM_values.txt - Column B

tag: treatment


title: AB_18_3: WT_inf_rep3


title: AB_KCl_1: WT_control_rep1


title: AFA MSN02-04R-CM Rep 4 (DGE)

tag: cell type

tag: cell line

tag: treatment time (hrs)


title: AFA MSN02-04R-CM Rep 3 (DGE)

tag: treatment condition

tag: drug name

tag: rna amount (ng)


title: SNI/R-HNK 1

city: 沙田

first: JIN

last: TINGTING

state: 沙田區

address: Prince of wales hospital

country: Hong Kong

institute: Chinese University of Hongkong

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to perform quality control.
Reads mapping to the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: normalized counts values for each Sample

source_name: mouse brain

growth_protocol: PrL tissues were collected and snap-frozen in liquid nitrogen. Total RNA was isolated from the PrL using TRIzol Reagent

extract_protocol:
RNA was purified with RNeasy Micro Kit 50 (74004, Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Library construction and sequencing services were provided by Novogene using the Illumina Novaseq 6000 system (Novogene, Tianjin, China) following a standard protocol.

treatment_protocol: Sham/saline group and SNI/saline group mice treaedt with saline, SNI/R-HNK group treated with R-HNK (10 mg/kg).

tag: mouse model

value: spared nerve injury (SNI)

value: prelimbic cortex

value: R-HNK


title: SNI/R-HNK 2


title: SNI/R-HNK 3


title: Fat body, Bacterial infection, rep1

description: TPM_values.txt - Column H


title: AB_18_2: WT_inf_rep2


title: AFA MSN02-04R-CM Rep 2 (DGE)

value: cardiac myocytes

tag: concentration

tag: well

tag: rin

tag: rna conc (ng/ul)


title: AMI MSN02-04R-CM Rep 2 (DGE)

value: AMI

tag: investigative unit

tag: sample id


title: SNI/saline 3

tag: tissue

value: saline


title: AB_18_1: WT_inf_rep1

tag: genotype


title: SNI/saline 2


title: CML460-UT

city: London

first: Eduardo

last: Gomez Castaneda

address: 30 Guilford Street

department: Institute of Child Health

country: United Kingdom

institute: UCL

data_processing:
Base calling
Trimming with cutadapt 2.10 (parametres -j 12 -m 20 -u -1 -U -1)
Alignment with STAR 2.7.3a
Count matrix generation with featureCounts (subread 2.0)
Assembly: Gencode v31 (Human GRCh38.primary_assembly)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: CML CD34+ cells

growth_protocol: Cells were resuspended at a density of 2x105cells/mL in SFM + physiological growth factors (0.2ng/mL SCF, 1ng/mL G-CSF, 0.2ng/mL GM-CSF, 1ng/mL IL6, 0.05ng/mL LIF, 0.2ng/mL MIP1α) and cultured at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Arcturus PicoPure kit for patients CML423 and CML460 and using the RNAeasy Micro kit for patient CML441. RNA was reverse transcribed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, Saint-Germain-en-Laye). cDNA library preparation was performed using Nextera library preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: NDC

tag: patient

value: PicoPure


title: AFA MSN02-04R-CM Rep 1 (DGE)

tag: rna volume (ul)

tag: h2o volume (ul)


title: CML460-IM0

tag: treatment

value: IM


title: Sham/saline 3

value: Sham (control)


title: MCF7 cells grown in medium from TAMs 3-1

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

data_processing:
Collected reads were trimmed by Trimmomatic28, and clean reads were aligned by HISAT2 (version 2.2.1.0)29. The count values for each genes were calculated by Ballgown
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include FPKM for each Sample

growth_protocol: MCF7 and MDA-MB-231 breast cancer cells cells were maintained using standard conditions. Peripheral blood mononuclear cells (PBMCs) from healthy donors were isolated using CD14 Microbeads(Miltenyi Biotec) according to the manufacturer’s instructions. MDMs (monocyte-derived macrophages) were grown in DMEM medium (Gibco) supplemented with 10% fetal bovine serum, 50U ml-1 penicillin(Gibco) and 50ul ml-1 streptomycin (Gibco). For the polarization of TAMs, MDMs were treated for 6 days with 30% culture medium from MDA-MB-231 cells。Both MDMs and TAMs were washed with PBS and cultured for an additional 48 hours in fresh DMEM 10%FBS, then the medium were collected, filtered through a 0.22mm filter to remove cell debris and named as MDMs CM and TAMs CM respectively.

extract_protocol:
Total RNA was purified from cells using the standard TRIzol method(Life Technologies) and the quality was determined by Bioanalyzer 4200(Agilent, Santa Clara, CA, USA)
For RNA sequencing, the libraries were for all samples were simultaneously constructed using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The libraries were also analyzed by Bioanalyzer 4200 for quality control

treatment_protocol: For induction of MCF7 cells, MCF7 cells were cultured with 30% either MDMs CM or TAMs CM for 6 days.

tag: cell line

tag: cell type

value: breast cancer cell

value: medium from TAMs


title: WT_rep3

tag: strain

value: Mycelia

value: WT

tag: cucl2 treatment

value: 0 mM

tag: time

value: 6 h


title: Sham/saline 2

tag: mouse model


title: CML460-CsA-3

value: CsA


title: MCF7 cells grown in medium from MDMs 2-2

value: medium from MDMs


title: MCF7 cells grown in medium from MDMs 2-3


title: MCF7 cells grown in medium from MDMs 2-1


title: CML460-IM100

value: Combo


title: Sham/saline 1

value: prelimbic cortex


title: CML441-72h-UT

value: RNAeasy


title: CML441-72h-im100


title: Sample2_Negative, scRNAseq

city: Denver

first: Jennifer

middle: R.

last: Knapp

state: Colorado

address: 1400 Jackson St

department: Center for Genes Envionment and Health

institute: National Jewish Health

description: 10x Genomics

data_processing:
Single cell RNA fastq files were mapped and counted using 10X Cell ranger software generating cell/gene counts. CITE-Seq fastq files were counted using CITE-Seq-count  . Tables were imported into R  with Seurat  for filtering, integration, and analysis.
Supplementary files format and content: sparce data frame of gene X cell number counts

source_name: Tumor Infiltrating lymphocytes

extract_protocol:
CT26 tumors were harvested from BALB/c mice, minced using a razor blade, and treated for 25 min at 37°C with 0.1 mg/ml Liberase (Research Grade, Dispase Low) in 5mL serum-free RPMI 1640 medium according to the manufacturer’s instructions (Roche Life Science). Tumors were filtered through a 100-μm cell strainer and washed in complete medium [RPMI with L-glutamine, 10% FBS, 100 U/ml each penicillin and streptomycin, 1 mmol sodium pyruvate, 10 mmol HEPES, and 1× MEM nonessential amino acids]. Splenocytes were harvested from mice, mechanically dissociated, filtered through a 100 μm cell strainer, treated for ∼5 min with ammonium chloride-potassium lysis buffer, and washed in complete medium. For scRNAseq experiments, tumors from 15 mice were pooled together to make a single sample. Before FACS, CD8+ T cells were enriched using a Mouse CD8 Negative Selection Kit (Stemcell Technologies) according to the manufacturer’s instructions. CITE-seq antibodies were added during the final 30 minutes of tetramer staining and added to samples before staining with fluorophore conjugated antibodies for flow sorting. After the 30-minute incubation samples were washed twice with FACS buffer. CD8-enriched TIL were sorted based on tetramer binding into Tet-High, Tet-Low and Tet-Negative groups then were immediately processed for scRNAseq.
Using the Biolegend TotalSeq-A antibodies and protocol along with the Chromium Single Cell 3’ Reagent Kits v3, and CITE-seq were performed. Cells were received in the Genomics Core, viability was assessed using TC20 (Biorad), cells were diluted to an appropriate volume to target 5000 cells. The samples then went onto the 10x Chromium machine for GEM generation and barcoding. Briefly, 10x Barcoded Gel Beads are mixed with the surface protein labeled cells in a master mix and partitioning oil to obtain single cell GEMs. Gel beads are dissolved allowing for incubation of both the poly A RNA and cell surface proteins within each GEM resulting in full length cDNA and DNA from the cell surface protein. GEMs are then cleaned following step 2.1 in the Chromium Single Cell 3’ Reagent Kits v3 protocol. Once done with the clean-up, Protocol – TotalSeq-A Antibodies with 10x Single Cell 3’ Reagent Kit v3 3.1 was followed at Step II. cDNA amplification mix was prepared according to this protocol to allow for Antibody Derived Tag (ADT) libraries. The libraries were finished with the Protocol – TotalSeq-A Antibodies with 10x Single Cell 3’ Reagent Kit v3 3.1. Sequencing was performed at the University of Colorado Genomics Shared Resource lab on the Illumina NovaSeq 6000.

value: Tumor Infiltrating lymphocytes

value: CD8+ T-cells

value: BALB/cAnNCr

tag: group

value: non-tetramer binders


title: CML441-72h-im0

value: IM


title: Sample2_High, scRNAseq

description: 10x Genomics

value: high tetramer binders


title: Sample2_Low, scRNAseq

description: 10x Genomics

value: low tetramer binders


title: MCF7 cells grown in medium from TAMs 3-3

value: breast cancer cell

value: medium from TAMs


title: Sample1_Negative, scRNAseq

description: 10x Genomics


title: CML441-72h-GO100

value: GO


title: Sample1_Low, scRNAseq

description: 10x Genomics


title: SNI/saline 1

value: spared nerve injury (SNI)

value: saline


title: MCF7 cells grown in medium from TAMs 3-2


title: COUPOE, replicate 1

city: Stanford

first: Menglan

last: Xiang

address: 450 Serra Mall

institute: Stanford University

description: 10x Genomics

data_processing:
The Cell Ranger package (v3.0.2) was used to align high quality reads to the mm10 transcriptome (quality control reports available: https://stanford.io/37sXZV3). Quality control and data analysis was carried out as described. Briefly, normalized log expression values were calculated using the scran package. Imputed expression values were calculated using a customized implementation (https://github.com/kbrulois/magicBatch) of the MAGIC (Markov Affinity-based Graph Imputation of Cells) algorithm and optimized parameters (t = 2, k = 9, ka = 3). Supervised cell selection was used to remove cells with non-blood endothelial cell gene signatures: lymphatic endothelial cells (Prox1, Lyve1, Pdpn); Pericytes (Itga7, Pdgfrb); fibroblastic reticular cells (Pdpn, Ccl19, Pdgfra); lymphocytes (Ptprc, Cd52). The Arterial (Gkn3+), HEC, PCV and CRP clusters were defined based on canonical marker expression. Batch effects from technical replicates were removed using the MNN algorithm as implemented in the batchelor package’s (v1.0.1) fastMNN function.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peyer's patches

extract_protocol:
Endothelial cells from the Peyer’s patches of EC-iCOUPOE and control mice were isolated 14-19 days post tamoxifen treatment, dissociated and sorted. Male and female cohorts were processed together and resolved post-sequencing.
Single cell gene expression was assayed using the 10x Chromium v3 platform using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics, PN-120237) according to 10X Genomics guidelines.

value: Blood endothelial cells

value: Peyer's patches

tag: age

value: 6-10 weeks


title: WT

description: 10x Genomics


title: COUPOE, replicate 2

description: 10x Genomics


title: CML460-GO100

value: PicoPure


title: CML441-72h-CsA-3

value: CsA

value: RNAeasy


title: CML423-UT

value: NDC


title: Sample1_High, scRNAseq

description: 10x Genomics

value: Tumor Infiltrating lymphocytes

value: CD8+ T-cells

value: BALB/cAnNCr


title: CML423-IM100

value: Combo


title: Incisor H3K4me2

city: Farmington

first: Emma

middle: Wentworth

last: Winchester

state: Connecticut

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
Align to genome using bowtie 2.2.5 bowtie2 -p 6 -N 1 -X 2000 -t -x $sample.sam
Generate bam format and normalize with samtools 1.3 samtools view -@ 6 -b -F 4 -q 10 -o $sample_norm.bam $sample.sam
Sort bam with samtools 1.3 samtools sort -@ 6 -T $sample -o $sample.bam $sample_norm.bam
Index bam with samtools 1.3 samtools index $sample.bam
Convert to tagAlign format for size estimation samtools view -F 0x0204 -o - $sample.bam  | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c >  $sample.tagAlign.gz
Estimate fragment size using phantompeakqualtools Rscript ~/TOOLS/phantompeakqualtools/run_spp.R -c=../align/$sample.tagAlign.gz -i=../align$sample.tagAlign.gz -savp -rf -s=-500:5:500 -p=16 -out=$sample_fragment.txt -tmpdir=~ANALYSIS/ChIP/macs/tmp -filtchr=M -filtchr=Y
Call peaks with MACS2 2.1.1.20160309 macs2 callpeak -t ../align/$sample.bam -c ../align/Input_norm_sorted.bam -n $sample -f BAM -g mm --keep-dup all --nomodel -p 1e-2 --broad --nomodel --extsize 160 -B --SPMR --tempdir $sample_tmp
Generate p-value signals versus input with MACS2 2.1.1.20160309 macs2 bdgcmp -t $sample_treat_pileup.bdg -c $sample_control_lambda.bdg -o $sample_ppois.bdg -m ppois -S $sval
Convert to bedGraph to bigWig for display on UCSC genome browser bedGraphToBigWig $sample.pval.signal.bedGraph ~/GENOME/mm10/mm10.chrom.sizes  $sample.pval.signal.bigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for p-value ChIP-Seq Signals

source_name: E13.5 Mandibular Incisor

growth_protocol: Samples flash frozen immediately after collection.

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
Rubicon Genomics Thruplex 48S

treatment_protocol: Cotney and Noonan, CSHL Protocols 2015.

tag: antibody catalog/lot#

tag: antibody


title: CML423-IM0

value: IM


title: Incisor H3K4me1


title: WT_20_2

source_name: liver

growth_protocol: Mice were grown in 24h light-dark cycles. Time points represent Zeitgeber time when the light is switched on.

extract_protocol:
Snap-frozen liver tissues were homogenized in 5ml stench solution (guanidinium thiocyanate, Na-citrate, Na-acetate, beta-mercaptoethanol) followed by a standard phenol-chloroform RNA extraction protocol.
RNA-seq libraries were prepared from triplicates/condition according to standard protocols (TruSeq® Stranded Total RNA Library Prep Gold, Illumina) using 1 µg starting material.

value: liver

value: WT

tag: zeitgeber time

tag: replicate


title: WT_20_3

tag: tissue

tag: genotype


title: WT_20_1


title: MUT_20_3

value: smg6 flox/flox


title: CML423-CsA-3

tag: patient


title: Incisor H3K36me3


title: Incisor H3K27me3


title: MUT_20_1


title: MUT_20_2


title: GM19314

city: Copenhagen

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were trimmed to remove linker sequences, filtered for minimum sequence quality of Q30 in 50%, and rRNA reads matching U13369.1 were removed using rRNAdust (version 1.06 (FANTOM Consortium and the RIKEN PMI and CLST (DGT) et al. 2014))
Mapping to the human reference genome (hg38) was performed using BWA (version 0.7.15-r1140) allowing for max two mismatches per read. To limit mapping biases, reads were re-mapped using the WASP pipeline (van de Geijn et al. 2015) and BWA using the same parameters, taking into account biallelic SNVs (Lowy-Gallego et al. 2019). Reads with a mapping quality of at least 20 were retained for further analyses.
CAGE-defined transcription start sites (CTSSs) were identified from 5’ ends of CAGE read using CAGEfightR (version 1.10 (Thodberg et al. 2019))
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files of CAGE transcriptions start sites (CTSSs) with the score column containing the raw counts

source_name: B-Lymphocyte

growth_protocol: Epstein-Barr virus immortalized LCLs were obtained from the NIGMS Human Genetic Cell Repository at Coriell Institute for Medical Research. Cells were incubated at 37°C at 5% carbon dioxide in the Roswell Park Memorial Institute (RPMI) Medium 1640 supplemented with 2mM L-glutamine and 20% of non-inactivated fetal bovine serum and antibiotics. Cell cultures were split every few days for maintenance. As these cell lines were freshly purchased, mycoplasma contamination screening was not undertaken.

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol, and gDNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen).
CAGE libraries were prepared as described in (Takahashi et al, 2012, PMID: 22362160) with an input of 1.5mg of total RNA.

treatment_protocol: Samples were untreated.

value: untreated

tag: ethnicity

value: LWK

value: wildtype

tag: e-gel

value: No