title: NB4_sh-Control

city: Shanghai

first: Xuefei

last: Ma

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with fastp-v0.20.0, then mapped to GRCh38 whole genome using HISAT2 2.0.4, stringtie 1.2.3, ballgown_1.0.1 with default parameter.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Salzberg SL et al. (Nat Protoc. 2016;11(9):1650-67). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of paired reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: NB4 cells infected with the non-targeting control shRNA (sh-Control)

growth_protocol: NB4 cells were cultured in RPMI 1640 (Gibco, Carlsbad, CA, USA) containing 10 % (vol/vol) fetal bovine serum (Moregate Biotech, Bulimba, QLD, Australia), and maintained in a humidified atmosphere with 5% CO2 at 37 ºC.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer’s protocol. Illumina TruSeq RNA Sample Prep Kit-v2 (San Diego, CA, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the standard Illumina protocols

treatment_protocol: NB4 cells were infected with the CRNDE shRNA (sh-CRNDE) or the non-targeting control shRNA (sh-Control) lentivirus for three days.

value: Infected with the non-targeting control shRNA (sh-Control)


title: Donor 1, Time 6

status: Public on Apr 03 2023

type: SRA

city: Oxford

first: Philippa

last: Hulley

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: mini organotypic culture

library_source: transcriptomic

data_processing:
Reads were trimmed using trimmomatic
Reads were pseaudoaligned using kallisto with an index built from the hg38 cDNA fasta reference sequence
Differential gene expression was performed using the sleuth package in R
Assembly: hg38
Supplementary files format and content: Tab separated values files containing transcript lengths, estimated counts and tpm as calculated by kallisto

molecule: polyA RNA

organism: Homo sapiens

source_name: Trabecullar Bone

growth_protocol: Osteoblasts from 4 donors were seeded onto 20 constructs. Constructs were constructed as described: Calcium phosphate (brushite / β-TCP) posts were pinned into a Sylgard 184 silicone elastomer (base and curing agent, Dow Corning Corporation) base layer in 6-well dishes. Cells were seeded in fibrinogen onto a thrombin gel and subsequently cultured in 3ml of proliferation media (osteoblast media, 50 μg/ml ascorbate-2-phosphate, 40 μg/ml proline) per well until cells had fully contracted the gel between the support posts.

extract_protocol:
Snap frozen constructs were pulverised in a Cryo-Cup grinder on dry ice and RNA extracted using Trizol and cleaned up with a Direct-Zol RNA miniprep kit and RNA clean and concentrator (Zymo Research, Cambridge, UK) according to the manufacturer’s instructions.
RNA libraries were constructed using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biosystems, Ipswich, UK) and then the NEBNext ultra-directional RNA library prep kit was used to create the final library.
The sample was sequenced using 41bp paired end configuration with an Illumina NextSeq 500 sequencing device.

treatment_protocol: Week 0 constructs were harvested and snap-frozen at this point with the remainder transferred to osteogenic media (proliferation media, 10 mM β-glycerophosphate, 10 nM dexamethasone) and harvested at 2, 4, 6 and 8 weeks.

tag: Sex

value: Male

tag: age

tag: passage

tag: tissue

value: Trabecullar Bone

tag: cell line

value: primary

tag: cell type

value: osteoblast

tag: time

value: 6 weeks

tag: treatment

value: osteogenic - differentiation


title: Donor 4, Time 0

description: mini organotypic culture

value: 0 weeks


title: Donor 3, Time 8

description: mini organotypic culture

value: Female

value: 8 weeks


title: VUILD69-MF

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

country: USA

institute: TGen - Translational Genomics Research Institute

library_source: transcriptomic single cell

data_processing:
Reads with a read quality <3 were filtered and CellRanger Count v3.02 (10x Genomics) was used to align reads to the GRCh38 reference genome.
Assembly: GRCh38
Supplementary files format and content: Matrix file containing counts
Supplementary files format and content: Tab-separated values file containing features
Supplementary files format and content: Tab-separated values file containing cell barcodes

molecule: total RNA

source_name: Lung

extract_protocol:
Tissue samples were digested in either collagenase I/dispase II (1 μg/ml) or Miltenyi Multi-Tissue Dissociation Kit using a gentleMACS Octo Dissociator (Miltenyi Inc.). Tissue lysates were serially filtered through sterile gauze, 100- and 40-μm sterile filters (Fischer). The resulting suspensions then underwent cell sorting using serial columns (Miltenyi Microbeads, CD235a and CD45) or fluorescence-activated cell-sorting (FACS) at VUMC or FACSat the Translational Genomics Research Institute (TGen). CD45− and C45+ populations were mixed 2:1 in samples processed at VUMC and used to generate the scRNA-seq libraries. At TGen, calcein acetoxymethyl was used to stain live cells, and 10,000 to 15,000 live cells were sorted directly into the 10x reaction buffer and transferred to the 10x 5′ chip A (10x Genomics).
scRNA-seq libraries were generated using the 10x Chromium platform 3′ v2 or 5′ library preparation kits (10x Genomics) according to the manufacturer’s recommendations and targeting 5000 to 10,000 cells per sample.

value: Lung

tag: disease state

value: IPF

tag: diagnosis

value: M

tag: tobacco status_(ever-smoker)

value: Y

tag: self-reported ethnicity

value: European

tag: tissue type


title: VUILD67-MF

value: N


title: Progenitor Smooth Muscle Cells, 30 hours, Replicate 1

type: RNA

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the Robust Multichip Average (RMA) method.

label: biotin

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: Progenitor SMCs were grown to confluence in M231 medium supplemented with smooth muscle growth supplement (SMGS; Cascade Biologics Inc.), 1x antibiotic/antimycotic (AA) mix and 20% FCS. Progenitor ECs were cultured in phenol red free endothelial basal medium (EBM-2; Lonza) supplemented with 1x AA, endothelial growth supplement (EGM-2 bullet kit; Lonza) and 20% FCS.

extract_protocol: Total RNA was extracted from vehicle-treated and estradiol-treated samples using QIA shredder and RNAeasy Mini kit (Qiagen) according to manufacturer’s instruction. The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only the samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2.0 were further processed.

treatment_protocol: When P-SMC and P-EC reached 80% confluence, the cells washed thrice with phenol red free DMEM/F12 medium and subsequently fed medium (DMEM/F12 supplemented with 2.5% steroid free serum and 1x AA) containing either vehicle (DMSO 1ul/ml) or 17β-estradiol (10nM). Following  treatment with estradiol for the prescribed times (0, 4 and 30 hours) the cells were washed with PBS and processed for total RNA isolation.

value: Progenitor Smooth Muscle Cells

tag: estradiol treatment


title: Progenitor Endothelial Cells, 30 hours, Replicate 2

value: Progenitor Endothelial Cells


title: VUILD68-LF


title: VUILD68-MF


title: Progenitor Smooth Muscle Cells, 0 hours, Replicate 1


title: Donor 3, Time 6

description: mini organotypic culture


title: Donor 3, Time 2

description: mini organotypic culture

value: 2 weeks


title: Donor 4, Time 4

description: mini organotypic culture

value: Male

value: Trabecullar Bone

value: 4 weeks


title: Donor 4, Time 2

description: mini organotypic culture

value: primary

value: osteoblast


title: VUHD080

value: Control

value: Former smoker

value: Caucasian


title: Donor 3, Time 0

description: mini organotypic culture

value: Female

value: 0 weeks

value: osteogenic - differentiation


title: NB4_sh-CRNDE

country: China

source_name: NB4 cells infected with the CRNDE shRNA (sh-CRNDE)

value: Infected with the CRNDE shRNA (sh-CRNDE)


title: Donor 2, Time 8

description: mini organotypic culture

value: 8 weeks


title: Donor 2, Time 6

description: mini organotypic culture

value: 6 weeks


title: Donor 3, Time 4

description: mini organotypic culture


title: VUHD073-Control (F01494)

value: Lung

value: F

value: Y

value: European


title: VUHD073-Control (F01495)


title: TUH84 GILT_D7

city: paris

first: Jerome

last: Tamburini

address: 22 rue mechain

country: France

institute: Cochin Institute

data_processing:
Single cell RNA sequencing output bcl2 files were converted to FASTQ format by using Cell Ranger v.6.1.1.1(99). Count matrices from Cell Ranger were imported with the Seurat package v4.1.0(100) into the R programming environment v4.1.2. Cells that were deemed of lower quality were removed, based on their number of unique genes (<200 or >7500 unique genes) and the proportion of mitochondrial RNA (>20%). Gene counts were normalized with a regularized negative binomial regression, using the SCT normalization workflow from the Seurat package(101). In order to compare gene expression and signatures values after GILT treatment with those before treatment, the datasets from pre and post GILT treatment from each of the PDX sample were integrated following the Seurat dataset integration protocol(102). For dataset integration we used 30 principal components and 3000 genes. We then applied dimensional reduction where the 30 principal components were further summarized using UMAP dimensionality reduction. Cell clusters were identified using Louvain clustering within the Seurat workflow, the resolution parameter was set to 0.25. We identified clustering of co-expressing genes by hierarchical cluster with the package nclust (https://gitlab.com/pwirapati/nclust). We computed the values of the signatures on SCT transformed data with the AddModuleScore method from Seurat(103). The signature values were compared with UMAP and violin plots.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hematopoietic

extract_protocol:
Purification of hCD45+CD33+ from PDX : After red blood cells lysis with EL buffer (Qiagen, 79217), 10x106 cells from mice bone marrow of PDXs treated with vehicle or GILT were stained with Fixable Viability Stain 510 (BD Biosciences Cat# 564406, RRID:AB_2869572) and the fluorescent conjugated antibodies hCD45-APC (BD Biosciences Cat# 555485, RRID:AB_398600) and hCD33-PE (BD Biosciences Cat# 555450, RRID:AB_395843) in cell staining buffer (Biolegend, BLE420201) following to the manufacturer’s instructions. Viable hCD45+CD33+ were sorted using BD FACSAria Fusion flow cytometer (Becton Dickinson) and gently re-suspended at 1500cells/µL in PBS1X supplemented with 0.04% Ultrapure BSA (Invitrogen, Cat# AM2616).
Up to 10,000 cells per sample were encapsulated using the 10X Chromium controller (10X Genomics) following the Chromium Next GEM Single Cell 3ʹ User Guide v3.1 (10X Genomics). Briefly, cells were encapsulated into oil droplets with barcoded Gel Beads and reagents to convert mRNA into complementary DNA (cDNA). cDNAs were then amplified, fragmented and Illumina adapters were added during ligation. After performing a last index PCR, libraries quality was assessed using Tapestation 2200 (Agilent) and frozen before quantitation and sequencing. Barcoding was done on three levels: cell barcodes allow attribution of each sequence read to its cell of origin; unique molecular identifiers (UMIs) upstream to poly(d)T primers allow tagging of each original molecule to avoid amplification bias; and index allows pooling of different samples. scRNA-seq libraries were quantified with HSD1000 reagents on TapeStation 2200 system (Agilent) and pooled at equimolar concentrations within 200 to 700bp. Pool libraries were sequenced at 1.8pM 1% phiX using a NextSeq 500 sequencer (Illumina), at a sequencing depth of 40,000-50,000 reads per cell. Sequencing were configured Paired-End at 28 cycles for the first read, 91 cycles for the second one and 8 cycles for a single index.

treatment_protocol: PDX models: After engraftment (defined as >20/μL human leukemic cells in peripheral blood), mice were randomly assigned to the different treatment arms. PDXs were treated with vehicle or GILT after engraftment of human leukemic cells (8–18 weeks after AML cells transplantation). GILT was solubilized in water containing 0.5% methylcellulose 400cp (Sigma-Aldrich, Cat# M0262), mice were treated daily for 7 days by oral gavage with 30 mg per kg (mpk) GILT.

value: acute myeloid leukemia

value: hematopoietic

value: GILT


title: VUHD078

value: M


title: Progenitor Smooth Muscle Cells, 0 hours, Replicate 2

value: Progenitor Smooth Muscle Cells


title: VUHD077

value: Control


title: TUH84 CTL

value: vehicle


title: TILD041-MF

value: ILD

value: Former Smoker


title: TUH110 CTRL


title: TUH93 GILT_D7


title: VUILD67-LF

value: IPF

value: N


title: TILD039-MF


title: TUH93 CTL


title: TILD039-LF


title: X_9

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#16_2

data_processing:
We mapped the reads to the human genome reference “hg38_chr_only_and_herpes.fa” using STAR aligner (STAR v2.6.1a). Base-calling accuracy scores (Phred quality score, Q30) were obtained from demultiplexer bcl2fastq v2.20.. Paired-end reads were aligned to the human reference transcriptome “Homo_sapiens.GRCh38.cdna.all.fa.gz” using Salmon 1.3.0. For mapping, we used salmon quant command with parameters like –gcBias, --useVBOpt, --seqBias, and –validateMappings, correcting specific biases in the sequenced reads and increasing the sensitivity and specificity of the mapping. After mapping, R (R version R version 4.0.2) packages tximport (version 1.14.0) and DESeq2 (version 1.26.0) were used to summarize transcript-level estimate to the gene-level estimates. Further, we used the raw gene-level abundance estimates from salmon to perform to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files, salmon.merged.transcript_counts_Batch_1 (samples L1982b to L2240I), _Batch_2 (samples X152_Bef to X207_post) and _Batch_3 (samples X10 to X_9)
Supplementary files format and content: tab-delimited text files, salmon.merged.transcript_tpm_Batch_Batch_1 (samples L1982b to L2240I), _Batch_2 (samples X152_Bef to X207_post) and _Batch_3 (samples X10 to X_9)

extract_protocol:
Total RNA was prepared with GenElute Mammalian Total RNA miniprep (Sigma-Aldrich). RNA quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit, Santa Clara, USA).
RNA sequencing library preparation was performed using Illumina TruSeq stranded mRNA protocol.

treatment_protocol: Samples identities in the column title refers to the Table describing patients characteristics in the publication. Three samples were sequenced but not analyzed in our study (due to redundancy with other samples), and therefore do not have a study number.

value: gilteritinib


title: TILD037-MF


title: TILD037-LF


title: VUHD072


title: X_8

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#16_1

value: no treatment


title: X_6

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#15_1


title: VUILD77-MF

value: Lung

value: Hispanic


title: X_7

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#15_2


title: X_5

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#14_2


title: VUILD73-LF

value: Other


title: VUILD73-MF


title: VUILD79-MF

value: F

value: Y

value: European


title: X_4

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#14_1

value: hematopoietic

value: acute myeloid leukemia


title: X_3

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#13


title: X_2

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#12_2


title: X_1

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#12_1


title: TILD062-MF

value: Sarcoidosis

value: M

value: Former smoker


title: VUHD84

value: Control

value: Caucasian


title: TILD062-LF


title: X20

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#10_2


title: TILD041-LF

value: ILD

value: Former Smoker


title: TILD059-MF

value: IPF


title: X18

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#9_1

value: no treatment


title: TILD059-LF

value: Lung


title: X17

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#19_2

value: gilteritinib


title: TILD055-MF


title: X16

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#19_1


title: TILD055-LF


title: X15

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#18_2


title: VUHD85

value: N


title: TILD051-LF


title: X14

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#18_1


title: TILD049-MF


title: TILD049-LF


title: X13

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#17_2


title: X11

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#17_1


title: X10

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#21_1


title: THD0012


title: THD0009

value: F


title: X21

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#11_1


title: X207_post

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#5_2


title: X206_post

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#4_2


title: THD0008

value: Y


title: X19

description:
salmon.merged.transcript_counts_Batch_3
salmon.merged.transcript_tpm_Batch_3
AML#10_1


title: THD0006


title: X206_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#4_1


title: THD0007


title: TILD030-LF

value: European


title: X205_post

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#3_2

value: hematopoietic


title: TILD051-MF


title: X204_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
sequenced, not analyzed

value: acute myeloid leukemia


title: X203_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#2_1


title: X207_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#5_1


title: X203_post

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#2_2


title: X205_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#3_1


title: MGC_803

city: wuhan

first: Meimei

last: Yang

address: Bayi Road

department: China Center for Type Culture Collection

institute: Wuhan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: MGC 803

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: MGC 803

value: mixed origins of the MGC 803 cell line

tag: genotype


title: Control1

city: Guangzhou

first: Yang

last: Guang

state: Guangdong

address: No. 601 West Huangpu Avenue, Tianhe District

institute: Jinan University

data_processing:
llumina Casava software used for basecalling.
(1) Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted ).(2)Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both readswill be filtered if either end is low-quality).(3)Remove reads which contain N higher than 5% (For paired-endsequencing, both reads will be filtered if either end has N beyond the offset 5%) .
The reference genomes and the annotation file were downloaded from ENSEMBL database(http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched. The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Cervix

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

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent(Invitrogen). Illumina TruSeq RNA Sample  Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Group Gala Cells treated with galaxamide for 48h

value: Cervix

value: HeLa(Human Cervical Cancer Cells)

value: Epithelial

value: WT

value: control


title: X152_post

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#1_2


title: Gala1

value: Cells treated with galaxamide for 48h


title: Gala2


title: Control2


title: X152_Bef

description:
salmon.merged.transcript_counts_Batch_2
salmon.merged.transcript_tpm_Batch_2
AML#1_1

value: no treatment


title: L2240l

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
sequenced, not analyzed


title: L2240j

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#8_1


title: L2196e


title: Patient_tofacitinib_16_wks

city: Tainan

first: Yu-Chen

last: Lin

address: 138 Sheng-Li Rd

country: Taiwan

institute: National Cheng Kung University

data_processing:
Quality control and data filtering were done using fastp.
Alignment of the reads to the human genome was done using HISAT2.
The raw reads generated was counted using featureCounts.
Differential analysis of the gene counts was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts for each Sample.

source_name: Skin

extract_protocol:
RNA was extracted by the RNeasy Mini Kit (QIAGEN, Hilden, Germany).
Library was prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

value: Skin

value: Autosomal recessive congenital ichthyosis

value: Tofacitinib

tag: time point

value: 16 weeks post-treatment


title: L2240k

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#8_2

value: gilteritinib


title: L2196d

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#7_2


title: L2196c

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#7_1


title: Patient_before_treatment

value: pre-treatment


title: PPIA_2

city: Urumqi

middle: wen

last: wen

address: Liyushan South Road

department: The Second Department of General Internal Medicine

institute: the First Affiliated Hospital of Xinjiang Medical University

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
clean reads were aligned to the GRch38 genome by tophat2 allowing 4 mismatches.   Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million Fragments mapped)
The R Bioconductor package edgeR (Robinson, McCarthy et al. 2010) was utilized to screen out  the differentially expressed genes (DEGs). A P-value <0.01 and fold change>1.5 or < 2/3 were set  as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) betweenRNA biNdiNg pRoteiN coNNects the futuRe the samples were defined and quantified by using the ABLas pipeline as described previously. In brief, ABLas detection of ten types of ASEs was based on the splice junction reads, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), intron retention (IR), mutually exclusive exons (MXE), mutually exclusive 5'UTRs (5pMXE), mutually exclusive 3'UTRs (3pMXE), cassette exon, A3SS&ES and A5SS&ES
Assembly: GRch38 genome
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: PPIA overexpression in HUVECs

extract_protocol:
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using Nanodrop One (Thermo). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For high-throughput sequencing, the libraries were applied to Illumina Novaseq 6000 system for  150 nt paired-end sequencing.

value: HUVECs

value: PPIA overexpression


title: L1982c

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#6_2

value: hematopoietic

value: acute myeloid leukemia


title: NC_3

source_name: HUVECs(Empty virus)

value: Empty virus


title: PPIA_3


title: L1982b

description:
salmon.merged.transcript_counts_Batch_1
salmon.merged.transcript_tpm_Batch_1
AML#6_1


title: NC_2


title: Visceral WT Adipose stem and progenitor cells [Visce_3]

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: 1The Centre for Physical Activity Research

country: Denmark

institute: Rigshospitalet

description:
Visce_3
Progenitors_4_depots.tar.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V 2.0.1
Assembly: hg19
Supplementary files format and content: TSV and matrix files

source_name: Visceral white adipose tissue

growth_protocol: human ASPCs were maintained in proliferation media (DMEM/F-12 supplemented with 10% FBS, 1% PenStrep and 1 nM FGF-1)

extract_protocol:
Cells were disassociated from culture plates and single-cell RNA-seq libraries prepared according to Chromium 3' V2 kit
10X Genomics Chromium 3' V2

treatment_protocol:
Adipogenic differentiation was induced in 48 hours post-confluent ASPCs wtih a differentiation cocktail containing DMEM/F12, 1% PenStrep, 100 nM Insulin, 100 nM Dexamethasone, 200 nM Rosiglitazone, 540 uM isobutylmethylxanthine.
After 3 days, media was replaced by the same differentiation cocktail without IBMX. From day 6 until day 12 of differentiation, cells were maintained in differentiation media 2 (DMEM/F12, 1% PenStrep, 100 nM Insulin, 100 nM Dexamethasone)

value: Visceral white adipose tissue

value: Primary

value: Adipose stem and progenitor cells

value: Proliferation media


title: NC_1


title: Visceral WT Adipose stem and progenitor cells [Visce_2]

description:
Visce_2
Progenitors_4_depots.tar.gz


title: BaF3-T315I treated with I13_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: FPKM value

source_name: BaF3-T315I cell line treated with  I13 3

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.


title: Visceral WT Adipose stem and progenitor cells [Visce_1]

description:
Visce_1
Progenitors_4_depots.tar.gz


title: BaF3-T315I treated with I13_2

source_name: BaF3-T315I cell line treated with  I13 2


title: BaF3-T315I treated with I13_1

source_name: BaF3-T315I cell line treated with  I13 1


title: Supraclavicular BAT Adipose stem and progenitor cells [Supra_3]

description:
Supra_3
Progenitors_4_depots.tar.gz

source_name: Supraclavicular brown adipose tissue

value: Supraclavicular brown adipose tissue


title: Supraclavicular BAT Adipose stem and progenitor cells [Supra_2]

description:
Supra_2
Progenitors_4_depots.tar.gz


title: Patient_tofacitinib_26_wks

value: 26 weeks post-treatment


title: Supraclavicular BAT Adipose stem and progenitor cells [Supra_1]

description:
Supra_1
Progenitors_4_depots.tar.gz


title: BaF3-T315I treated with control_3

source_name: BaF3-T315I cell line treated with control 3

value: Control


title: BaF3-T315I treated with control_2

source_name: BaF3-T315I cell line treated with control 2


title: Subcutaneous WAT Adipose stem and progenitor cells [Subq_3]

description:
Subq_3
Progenitors_4_depots.tar.gz

source_name: Subcutaneous white adipose tissue

value: Subcutaneous white adipose tissue


title: BaF3-T315I treated with control_1

source_name: BaF3-T315Icell line treated with control 1


title: Subcutaneous WAT Adipose stem and progenitor cells [Subq_2]

description:
Subq_2
Progenitors_4_depots.tar.gz


title: Subcutaneous WAT Adipose stem and progenitor cells [Subq_1]

description:
Subq_1
Progenitors_4_depots.tar.gz


title: PPIA_1


title: EOC733_iOme_scRNA_ORG

city: Helsinki

first: Matías

last: M. Falco

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

data_processing:
de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification were performed using the Cell Ranger Software Suite (Version 6.0.1)
cell quality control was performed using Seurat v4
Assembly: GRCh38.d1.vd1
Supplementary files format and content: Matrix table with raw UMI counts

source_name: Omentum-derived

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and hyaluronidase to obtain single-cell suspensions. Resulting cell suspensions were used without any selection/enrichment to create single-cell RNA sequencing libraries
Chromium Single Cell 3′ Reagent Kit v. 3.1 (10x Genomics)

value: high-grade serous ovarian cancer (HGSOC)

tag: individual

tag: treatment phase

value: Post-NACT

value: Omentum-derived


title: EOC883_p2Ome_scRNA

source_name: Omentum

value: Treatment-naive

value: Omentum


title: EOC883_p2Ome_scRNA_ORG


title: Perirenal BAT Adipose stem and progenitor cells [Peri_3]

description:
Peri_3
Progenitors_4_depots.tar.gz

source_name: Perirenal brown adipose tissue

value: Perirenal brown adipose tissue


title: EOC677_rAsc_scRNA

source_name: Ascites

value: Relapse

value: Ascites


title: Perirenal BAT Adipose stem and progenitor cells [Peri_2]

description:
Peri_2
Progenitors_4_depots.tar.gz


title: EOC677_r2Asc_scRNA_ORG

source_name: Ascites-derived

value: Ascites-derived


title: Perirenal BAT Adipose stem and progenitor cells [Peri_1]

description:
Peri_1
Progenitors_4_depots.tar.gz


title: Supraclavicular BAT Adipose stem and progenitor cells [BAT8]

description:
BAT8
44BSAT_BAT8.tar.gz


title: EOC677_pAsc_scRNA_ORG


title: EOC677_pAsc_scRNA


title: Pool of differentiating cells - T5 (day 6)

description:
180831_10x_s6
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz

source_name: Pool of subcutaneous, visceral, supraclavicular, perirenal adipose differentiating cells

value: Differentiating adipocytes

value: Differentiation media


title: EOC883_pAsc_scRNA_ORGre-analyzed


title: Pool of differentiating cells - T4 (day 3)

description:
180831_10x_s5
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz

value: Pool of subcutaneous, visceral, supraclavicular, perirenal adipose differentiating cells

value: Primary


title: EOC883_pAsc_scRNAre-analyzed


title: Pool of differentiating cells - T3 (day1)

description:
180831_10x_s4
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz


title: Pool of differentiating cells - T2 (day 0)

description:
180831_10x_s3
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz


title: Pool of differentiating cells - T0 (proliferating)

description:
180831_10x_s1
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz


title: EOC382_pOme_scRNA_ORGre-analyzed


title: Pool of differentiating cells - T1 (confluent)

description:
180831_10x_s2
180831_DifferentiatingCells_T1toT5_4Depots.tar.gz


title: EOC382_pOme_scRNAre-analyzed


title: EOC733_pPer_scRNA_ORGre-analyzed

source_name: Peritoneum-derived

value: Peritoneum-derived


title: FAP_Adenoma

city: BOSTON

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INSTITUTE

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Pre-processing, alignment and gene counts: De-multiplexing, alignment to the transcriptome, and unique molecular identifier (UMI) collapsing were performed using the Cellranger toolkit provided by 10X Genomics.
General Clustering: Standard procedures for QC filtering, data scaling and normalization, detection of highly variable genes, and hashtag oligo (HTO) demultiplexing were followed using the Seurat v3 in RStudio. Cells with unique feature counts lower than 100 and greater than 25,000 as well as cells with greater than 25% mitochondrial DNA were excluded. Counts were log-normalized and scaled by a factor of 10,000 according to the default parameters when using the Seurat LogNormalize function. Variable features were identified, and the data were scaled using the default parameters (Ngenes = 2000) of the FindVariableFeatures FIG. caleData Seurat functions, respectively. HTOs were demultiplexed using the HTODemux function, and cells were identified as containing HTO-1 or HTO-2 based on their maximal HTO-ID signal. The cell population was filtered to contain only HTO-positive, singlet cells for further analysis.
HASHING CONDITIONS:72 day induced samples:  - HTO-1 = ApcKO, Sox9WT (mouse 2792)  - HTO-2 = ApcKO, Sox9 F/+ (mouse 3012)  30 day induced sample:  - HTO-3 = ApcKO, Sox9 F/+ (mouse 3047)
Note: The Day 28: WT and Sox9KO and Day 10 data were done using 5' kit with single index, while the rest of the samples were done with 5' v2 kit with dual index.
Assembly: mm10,hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Isolated intestines from euthanized mice were washed with ice-cold PBS; villi were scraped using glass slides and dissociated in 5mM EDTA in PBS at 4ºC for 20 minutes, shaking every 5-7 minutes for about 30 seconds. The epithelial fraction was collected by centrifugation and incubated at 37ºC for 30 minutes in pre-warmed 4x TrypLE. Single cells filtered through 70um filter post trypsinization, washed with complete media, and collected in FACS buffer.
About 17,000 viable cells were loaded onto a 10X Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s recommendations.  The scRNAseq libraries were processed using ChromiumTM single cell 5’ or 3' library & gel bead kit (10× Genomics). Matched cell hashing libraries were prepared using single cell 5’ feature barcode library kit. Quality controls for amplified cDNA libraries, cell hashing libraries, and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq and scTCRseq were normalized to 4nM concentration and pooled using a volume ratio of 4:1. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform. The sequencing parameters were: Read 1 of 150bp, Read 2 of 150bp and Index 1 of 8bp. The sequencing data were demultiplexed and aligned to mm10 or hg19-3.0.0 using cell ranger version 3.1.0 pipeline (10× Genomics).

value: Microdissected Lesion

value: Colon

tag: strain

tag: age


title: 0218_17_S17_SWAT cells_ProliferationMedia_R4

data_processing:
Salmon transcript classification
tximeta import
DESeq2 counts normalization
Assembly: GENCODE 39
Supplementary files format and content: Normalized counts from DESeq2 as csv

extract_protocol:
RNA was harvested in TRIzol from proliferating ASPCs grown in proliferation media for 96 hours.
RNA was harvested in TRIzol 24 hours after seeding of enriched SWAT cells.
RNA was isolated with the Qiagen RNeasy Micro kit using the "RNA Cleanup after lysis and homogenization with QIAzol lysis reagent".
250 ng total RNA were used for the construction of sequencing libraries.
Tecan Universal Plus Total RNA-seq library preparation kit

treatment_protocol:
Adipogenic differentiation was induced in 48 hours post-confluent ASPCs wtih a differentiation cocktail containing DMEM/F12, 1% PenStrep, 100 nM Insulin, 100 nM Dexamethasone, 200 nM Rosiglitazone, 540 uM isobutylmethylxanthine.
After 3 days, media was replaced by the same differentiation cocktail without IBMX. From day 6 until day 12 of differentiation, cells were maintained in differentiation media 2 (DMEM/F12, 1% PenStrep, 100 nM Insulin, 100 nM Dexamethasone)
At day 12 of differentiation, the cells were detached and enriched for adipogenic cells and SWAT cells using percoll density gradient centrifugation (densities: 1.01, 1.02 and 1.03 g/mL). SWAT cells were enriched in the pellet after centrifugation (30 min, 1000 g at room temperature).
Enriched SWAT cells were cultured in proliferation media or differentiation media for 24 hours.

tag: tissue

value: Supraclavicular brown adipose tissue

value: SWAT cells

value: Proliferation media


title: FAP_Normal

description: 10x Genomics


title: 0218_12_S12_SWAT cells_ProliferationMedia_R3

tag: cell line


title: 0218_7_S7_SWAT cells_ProliferationMedia_R2

tag: cell type


title: 0218_2_S2_SWAT cells_ProliferationMedia_R1


title: MFX285

city: Birmingham

first: Susanne

middle: N

last: Wijesinghe

address: Mindelsohn Way

department: Institute of Inflammation and Ageing

institute: University of Birmingham

data_processing: DESeq2 normalised counts

source_name: knee, obese, load bearing

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy Mini Kit and DNase treated on column with Qiagen's DNase kit.  4.5 ng of total RNA was used for the construction of sequencing libraries.
Library construction using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina following manufacturer's protocol for low input (<10ng), including adjustments to incubation times.

value: synovium

value: synovial fibroblast

tag: patient diagnosis

value: osteoartheritis

tag: bmi

value: obese

tag: loading

value: load bearing

tag: Sex

value: male


title: 0218_18_S18_SWAT cells_DifferentiationMedia_R4

tag: treatment


title: MFX242


title: RHH022

source_name: knee, normal weight, load bearing

value: normal weight

value: female


title: RHH012


title: 0218_13_S13_SWAT cells_DifferentiationMedia_R3

value: Differentiation media


title: 0218_8_S8_SWAT cells_DifferentiationMedia_R2


title: MFX314


title: RHH011


title: 0218_3_S3_SWAT cells_DifferentiationMedia_R1


title: 0218_16_S16_Progenitors_ProliferationMedia_R4

value: Progenitors


title: Subcutaneous WAT Adipose stem and progenitor cells [44BSAT]

description:
44BSAT
44BSAT_BAT8.tar.gz

value: Subcutaneous white adipose tissue

value: Primary

value: Adipose stem and progenitor cells


title: MFX231

source_name: hip, obese, load bearing


title: 0218_11_S11_Progenitors_ProliferationMedia_R3


title: MFX044


title: 0218_6_S6_Progenitors_ProliferationMedia_R2


title: MFX243


title: 0218_1_S1_Progenitors_ProliferationMedia_R1


title: MFX349

source_name: hip, normal weight, load bearing


title: MFX037


title: Normal, SOX9

library_source: genomic

data_processing:
CUT&RUN sequencing data was analyzed as described previously(71), following the standard pipeline (https://yezhengstat.github.io/CUTTag_tutorial/index.html). In brief, paired-end 150-bp reads were aligned to GRCh38 human genome using Bowtie2 version 2.2.5(72) with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Technical replicates (n = 4 per condition) were merged before reads alignment to increase the power of peak calling. macs2(73) was used to call peaks from bam files. For SOX9 CUT&RUN peak calling, parameters ùt input_file ûp 1e-5 ûf BAM ûkeep-dup all ûn out_name was used to call narrow peaks. To check the SOX9 binding profile and enhancer activity of specific gene sets, proximal peaks (-2kb to 2kb relative to TSS) called by macs2 were linked/annotated to genes by ChIPseeker version 1.34.1(74). Then, computeMatrix and plotHeatmap functions from deepTools(75) were used to visualize peaks.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Normal organoids derived from a patient with Familial Adenomatous Polyposis syndrome

extract_protocol: CUT&RUN for SOX9 and IgG control in Adenoma and Normal organoids was done using CUTANA ChIC/CUT&RUN kit (Epicypher #14-1048) following manufacturerÆs protocol. Briefly, 5???105 cells were captured with Concanavalin A, permeabilized using 0.01% digitonin and incubated with 0.5?g antibody (anti-Sox9 (CST, #82630) and IgG (# 13-0042; Epicypher) in 50?L antibody buffer (20mM HEPES at pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x protease inhibitor cocktails (EDTA-free tablet; Roche), 2 mM EDTA, 0.01% digitonin) overnight. After removing unbound antibody, pAG-MNase (20X) in 50?L cell permeabilization buffer was added to the cells and incubated for 10 min at RT. Then CaCl2 (2mM) was added to activate MNase and incubated at 4??C for 2 hr. The reaction was stopped using 33?L of 2X STOP buffer and E. coli spike-in DNA (0.5ng) was added as a control. The DNA from the released chromatin in the supernatant was purified and then quantified using Qubit dsDNA HS assay kit (Agilent Technologies). CUT&RUN libraries were constructed using NEBNext Ultra II DNA library preparation kit as described previously (Skene et al., 2018) with a few modifications. Briefly, end repair and dA-tailing were conducted on 6?ng of CUT&RUN eluted DNA for 30 min at 20?C followed by 1hr at 50?C. After adaptor ligation for 30 min at 20?C, the DNA fragments were purified by 1.75X vol of AMPure XP beads (Beckman Coulter) followed by 10-12 cycles of PCR amplification with Next Ultra II Q5 master mix. The PCR products were purified with 1X vol of AMPure XP beads. After quantitative and qualitative analysis, libraries with different indexes were pooled and sequenced on Illumina Novaseq platform with paired-end 150-bp reads.

treatment_protocol: Colonic glands were isolated, treated with EDTA, and then resuspended in 30-50 ul of Matrigel (BD Bioscience) and plated in 24-well plates. WNT/R-spondin/Noggin (WRN) containing DMEM/F12 with HEPES (Sigma-Aldrich) containing 20% FBS, 1% penicillin/streptomycin and 50ng/ml recombinant mouse EGF (Life Technologies) was used for culturing ApcKO colon organoids. For the first 2-3 days after seeding, the media was also supplemented with 10 mM ROCK inhibitor Y-27632 (Sigma Aldrich) and 10 mM SB431542 (Sigma Aldrich), an inhibitor for the transforming growth factor (TGF)-? type I receptor to avoid anoikis. For passage, colon organoids were dispersed by trypsin-EDTA and transferred to fresh Matrigel. Passage was performed every 3-4 days with a 1:3û1:5 split ratio. For human colon organoid culture, the previous media was supplemented with antibiotics 100 ug/ml Primocin (Invivogen), 100 ug/ml Normocin (Invivogen); serum-free supplements 1X B27 (Thermo Fisher (Gibco)), 1X N2 (Thermo Fisher (Gibco)); chemical supplements 10mM Nicotinamide (Sigma), 500mM N-acetylcysteine (Sigma), hormone 50mM [Leu15]-Gastrin (Sigma), growth factor 100ug/ml FGF10 (recombinant human) ( Thermo Fisher) and 500nM A-83-01 (Sigma), which is an inhibitor of the TGF-B Receptors ALK4, 5, and 7.

value: Colon epithelium, Normal mucosa

tag: chip antibody

value: SOX9, EMD/Millipore, AB5535


title: Adenoma, SOX9

source_name: Adenoma organoids derived from a patient with Familial Adenomatous Polyposis syndrome

value: Colon epithelium, Adenoma


title: Normal, IgG

value: Normal organoids derived from a patient with Familial Adenomatous Polyposis syndrome

value: IgG, Epicypher


title: MFX340

source_name: hand, obese, non-load bearing

value: synovium

value: synovial fibroblast

value: non-load bearing


title: Adenoma, IgG

value: Adenoma organoids derived from a patient with Familial Adenomatous Polyposis syndrome


title: LAM32 snRNA-Seq

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: 10X Multiome (snRNA-seq)

data_processing:
Further processing was done with Seurat v4.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: 10X output: filtered_feature_bc_matrix.h5 files

source_name: Lung

extract_protocol:
Frozen tissue from LAM32 was minced and lysed in buffer, then filtered. Nuclei were sorted using Sony SH800 and 150,000 nuclei were collected. Nuclei were spun and resuspended and concentrations adjusted for 10X multiome: 11,000 nuclei were loaded to target recovery of 7,000 nuclei. Fresh tissue from LAM44 was minced lysed in buffer yielding 300,000 nuclei. Nuclei were washed and resuspended. Final nuclei (11,000) were loaded for 10X.
Library was constructed by following 10X protocol: Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression User Guide (CG000338).

value: Lung


title: MFX291

source_name: hand, normal weight, non-load bearing

value: osteoartheritis

value: normal weight


title: MFX260

value: female


title: LAM32 snATAC-Seq

description: 10X Multiome (snATAC-seq)

library_source: genomic single cell

data_processing:
Further processing was done with Seurat v4.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz


title: LAM44 snATAC-Seq

description: 10X Multiome (snATAC-seq)


title: MFX230

value: obese

value: male


title: RHH002


title: MFX337

source_name: foot, obese, load bearing

value: load bearing


title: MFX368


title: MFX223


title: Tumor M2372

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

description: 10x Genomics

data_processing:
CellRanger (10x Genomics) analysis pipeline was used for library demultiplexing, read alignment to human genome GRCh38 and UMI quantification per gene per cell. Nuclei with greater than 1500 unique genes detected and fewer than 15% reads attributed to mitochondrial transcripts were retained. Genes dected in less than three cells were removed. The raw gene expression matrix was normalized, and variance stabilized by SCTransform in Suerat version 3.0 using UMI count and percent reads aligned to mitochondrial transcripts as covariates
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MPNST

growth_protocol: Samples were collected fresh from the patients at the time of surgical resection and stored at -80ºC.

extract_protocol:
Flash frozen archived tumor specimens were minced with sterile scalpel and mechanically dissociated with a dounce tissue grinder (size A and B, Sigma Aldrich) in ice cold lysis buffer (0.32 M sucrose, 5mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 20 mM Tris-HCl, 40U/ml RNase inhibitor and 0.1% Triton X-100 in DEPC-treated water). After centrifuged at 800g for 10 mins and resuspended in 1m of wash buffer (1x PBS, 1% BSA and 0.2 U/l RNase Inhibitor). Nuclei were filtered twice in 40m strainers (Flowmi cell strainer, Sigma Aldrich). Isolated nuclei were stained with DAPI at concentrations suggested by the manufacturer and sorted by FACS (BD Influx BRV, Becton Dickinson Biosciences). Nuclei were collected, washed and resuspended in wash buffer.
Nuclei were counted and appropriate volume for each sample was calculated for a target capture of 6000 nuclei. Samples were loaded onto a 10x Chromium controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics). After droplet generation, Libraries were sequenced on an Illumina NovaSeq (10x specific protocol) with > 50, 000 reads per cell.

value: tumor cells

value: MPNST

value: F


title: Tumor NF110

description: 10x Genomics

source_name: Neurofibroma

value: Neurofibroma

value: NF


title: Tumor M803

description: 10x Genomics

value: M


title: Tumor M3048

description: 10x Genomics


title: MFX292

source_name: foot, normal weight, load bearing

value: synovium


title: MFX218

value: synovial fibroblast


title: Tumor M1933

description: 10x Genomics


title: Tumor M1677

description: 10x Genomics


title: MFX282


title: EOC883_pAsc_scRNA_ORG

source_name: Ascites-derived

tag: disease state

value: high-grade serous ovarian cancer (HGSOC)

value: Treatment-naive

value: Ascites-derived


title: MFX224

value: osteoartheritis

value: non-load bearing


title: MFX328

value: normal weight

value: female


title: LAM44 snRNA-Seq

description: 10X Multiome (snRNA-seq)

value: Lung


title: CT44-3 [bulk ATAC-seq]

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10, hg38
Supplementary files format and content: Comma-delimited normalized mouse Bulk ATAC-Seq counts file and P-values: Mm_norm_counts_ATAC.csv
Supplementary files format and content: Tab-delimited eJTK_cycle output from synchronized human Bulk ATAC-Seq: Hs_eJTK_cycle_ATAC.txt

source_name: pancreatic islet

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq

treatment_protocol: Cells synchronized using 1 hour 10 micromolar forskolin pulse

value: pancreatic islet

value: Donor 6

value: 44 hours post-synchronization


title: EOC382_pOme_scRNA_ORG

source_name: Omentum-derived

value: Omentum-derived


title: EOC883_pAsc_scRNA

source_name: Ascites

value: Ascites


title: EOC733_pPer_scRNA_ORG

source_name: Peritoneum-derived

value: Peritoneum-derived


title: CT40-4 [bulk ATAC-seq]

value: Donor 7

value: 40 hours post-synchronization


title: CT44-1 [bulk ATAC-seq]

value: Donor 4


title: CT40-3 [bulk ATAC-seq]


title: TUH110 GILT_D7

data_processing:
Single cell RNA sequencing output bcl2 files were converted to FASTQ format by using Cell Ranger v.6.1.1.1(99). Count matrices from Cell Ranger were imported with the Seurat package v4.1.0(100) into the R programming environment v4.1.2. Cells that were deemed of lower quality were removed, based on their number of unique genes (<200 or >7500 unique genes) and the proportion of mitochondrial RNA (>20%). Gene counts were normalized with a regularized negative binomial regression, using the SCT normalization workflow from the Seurat package(101). In order to compare gene expression and signatures values after GILT treatment with those before treatment, the datasets from pre and post GILT treatment from each of the PDX sample were integrated following the Seurat dataset integration protocol(102). For dataset integration we used 30 principal components and 3000 genes. We then applied dimensional reduction where the 30 principal components were further summarized using UMAP dimensionality reduction. Cell clusters were identified using Louvain clustering within the Seurat workflow, the resolution parameter was set to 0.25. We identified clustering of co-expressing genes by hierarchical cluster with the package nclust (https://gitlab.com/pwirapati/nclust). We computed the values of the signatures on SCT transformed data with the AddModuleScore method from Seurat(103). The signature values were compared with UMAP and violin plots.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hematopoietic

value: acute myeloid leukemia

value: hematopoietic

value: GILT


title: CT40-2 [bulk ATAC-seq]

value: Donor 5


title: VLDL4

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC, location AMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: hg38
Supplementary files format and content: matrix of raw reads

source_name: blood

growth_protocol: Peripheral blood mononuclear cells were isolated from buffy coats using Lymphoprep (Axis-Shield) followed by isolation of the complete CD4+ cell population using CD4+ beads (Miltenyi Biotec). Purity of the CD4+ was assessed by flow cytometry by to be a minimum of 95%. Cells were cultured in in RPMI 1640 Medium with HEPES (Thermo Fisher Scientific) supplemented with 10% FCS (Gibco), Pen/Strep (Gibco), 50 μM 2-Mercaptoethanol (Sigma) and 20 ng/ml IL-2 (R&D systems)

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were activated by adding anti-CD3/CD28 beads (Thermo Fisher Scientific) in a 1:1 cell to bead ratio and exposed to either 5 μg/ml LDL (STEMCELL Technologies) or 5 μg/ml VLDL (Sigma) and left to divide for 72 hours before medium and beads were removed.

value: blood

value: CD4+ T cells

value: VLDL


title: VLDL3


title: VLDL1


title: LDL3

value: LDL


title: CT36-3 [bulk ATAC-seq]

value: pancreatic islet

value: 36 hours post-synchronization


title: CT40-1 [bulk ATAC-seq]


title: LDL4


title: CT36-1 [bulk ATAC-seq]


title: CT36-2 [bulk ATAC-seq]


title: CT32-4 [bulk ATAC-seq]

value: 32 hours post-synchronization


title: LDL1


title: hHEP_day 12_TCBPA-2

city: 北京市

first: Renjun

state: 北京

address: 双清路18号林业大学北门

institute: RCEES

data_processing:
Base calling were conducted with BGISEQ-500
Data were filtered with SOAPnuke and trimmomatic software for removing the reads of adapter sequences; the reads containing more than 5% unknown nucleotides; the reads contain more than 20% low quality nucleotides, whose quality is lower than 10. The clean data generated by filtration were saved as fastq format and subjected to further analysis
The clean data were alignment to the reference sequence and the expected counts were calculated by using Bowtie2 (ver. 2.3.4.1-1) and RSEM (ver. 1.2.28)
Genome_build: GCA_000001405.28_hg38.p13
Supplementary_files_format_and_content: .xls file with table showing expected counts of genes in different samples

source_name: hESCs hepatic differentiation

extract_protocol:
The samples were extracted with trizol reagent according to the manufactures guidance
Library was constructed by Beijin Genomic Institude (BGI) with the standard operating procedure

tag: differentiation stage

value: hepatoblast

tag: original strain


title: EOC382_pOme_scRNA

source_name: Omentum

value: high-grade serous ovarian cancer (HGSOC)

value: Treatment-naive

value: Omentum


title: Ctrl4

value: untreated


title: CT32-3 [bulk ATAC-seq]

tag: genotype

value: Donor 6


title: hHEP_day 12_TCBPA-1

address: 双清路18号林业大学北门


title: CT32-1 [bulk ATAC-seq]

value: Donor 4


title: Ctrl3


title: CT28-4 [bulk ATAC-seq]

value: Donor 7

value: 28 hours post-synchronization


title: CT28-3 [bulk ATAC-seq]


title: CT44-4 [bulk ATAC-seq]

value: 44 hours post-synchronization


title: CT28-1 [bulk ATAC-seq]


title: CT28-2 [bulk ATAC-seq]

value: Donor 5


title: CT36-4 [bulk ATAC-seq]


title: Ctrl1

value: blood

value: CD4+ T cells


title: CT24-2 [bulk ATAC-seq]

value: 24 hours post-synchronization


title: CT24-3 [bulk ATAC-seq]

value: pancreatic islet


title: CT24-1 [bulk ATAC-seq]


title: hHEP_day 12_TBBPS-1

address: 双清路18号林业大学北门


title: hHEP_day 12_Ctrl-2

address: 双清路18号林业大学北门


title: hHEP_day 12_TBBPA-2

address: 双清路18号林业大学北门


title: hHEP_day 12_TBBPA-1

address: 双清路18号林业大学北门


title: hHEP_day 4_TCBPA-2

address: 双清路18号林业大学北门

value: endoderm


title: Adipose visceral_81a996df-7bc9-4ffc-bb37-57397e10014b at day D8

city: Cambridge

first: Melina

last: Claussnitzer

state: MA

address: 75 Ames Street

institute: Broad Institute of MIT and Harvard

data_processing:
Generating count tables using featureCounts function (Liao, Smyth, and Shi 2013) in the Rsubread package
Normalization using DESeq2
Analysis of variance (ANOVA) in R
Genome_build: hg19
Supplementary_files_format_and_content: normalized count

source_name: Adipose visceral

growth_protocol: For RNAseq, cells were seeded at 40K cells/well in 12-well dishes (Corning). Before Induction cells were cultured in proliferation medium (Basic medium consisting of DMEM-F12 1% Penicillin - Streptomycin, 33µM Biotin and 17µM Pantothenate supplemented with 0.13µM Insulin, 0.01ug/ml EGF, 0.001ug/ml FGF, 2.5%FCS). Adipogenic differentiation was induced by changing culture medium to induction medium. (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin, 1μM Rosiglitazone, 25nM Dexamethasone, 2.5nM IBMX). On day 3 of adipogenic differentiation culture medium was changed to differentiation medium (Basic medium supplemented with 0.861μM Insulin, 1nM T3, 0.1μM Cortisol, 0.01mg/ml Transferrin). Medium was changed every 3 days. Visceral-derived AMSCs were differentiated by further adding 2% FBS as well as 0.1mM oleic and linoleic acid to the induction and differentiation media.

extract_protocol: Library preparation, sequencing and reference genome alignment was carried out by the Genomics Platform at the Broad Institute. After final quality control samples were sequenced generating 50 million paired end reads per sample

treatment_protocol: We used the same differentiation media to investigate different days of differentiation under the same conditions.

value: adipose

tag: depot

value: visceral

tag: differentation day


title: Adipose visceral_81a996df-7bc9-4ffc-bb37-57397e10014b at day D14


title: Adipose visceral_81a996df-7bc9-4ffc-bb37-57397e10014b at day D3


title: scATAC_Hs_set3-2

description:
Hs_scATAC.rds
Hs_peak_matrix.h5
Hs_fragments.tsv.gz

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10, hg38
Supplementary files format and content: scATAC 10X Cellranger h5 compressed peak matrix: Hs_peak_matrix.h5, Mm_peak_matrix.h5
Supplementary files format and content: scATAC 10X Cellranger single-cell metadata (*metadata*.csv)
Supplementary files format and content: scATAC 10X Cellranger tab-delimited fragments file (*fragments*.tsv)
Supplementary files format and content: Seurat R data structure files: Hs_scATAC.rds, Mm_scATAC.rds

value: Donor 3


title: Adipose visceral_81a996df-7bc9-4ffc-bb37-57397e10014b at day D0


title: scATAC_Hs_set3


title: scATAC_Hs_set2

value: Donor 2


title: Adipose subcutaneous_81a996df-7bc9-4ffc-bb37-57397e10014b at day D3

source_name: Adipose subcutaneous

value: subcutaneous


title: hHEP_day 12_Ctrl-1

address: 双清路18号林业大学北门

value: hepatoblast


title: zmp-2-br3

city: Riverside

first: Brandon

last: Le

state: CA

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

data_processing:
Raw paired-end reads were trimmed using TrimGalore and mapped to the Arabidopsis genome (TAIR10) with the Araport11 gff annotations using the STAR aligner v2.5.3a
Genome_build: Arabidopsis thaliana (TAIR10 genome), Araport11 annotations
Supplementary_files_format_and_content: Tab-delimited text file containing the mapped reads count for each gene from the STAR aligner. The column headers for each file are as follows: Gene_ID, number of mapped reads

organism: Arabidopsis thaliana

source_name: 12-day-old seedlings

growth_protocol: Plants (Col-0 ecotype) were grown in a growth room under long-day conditions (16 hr light/8 hr dark) at 23oC.

extract_protocol:
Total RNA was extracted using TRI reagent (MRC) according to the manufacturer's protocol.
5 ug of total RNA from each genotype was used to generate mRNA-seq libraries using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs). All size selection and clean-up steps were performed using AMPure XP beads (Beckman Coulter)

value: 12-day-old seedlings

tag: replicate

tag: t-dna line

tag: ecotype


title: hHEP_day 4_TBBPS-1

address: 双清路18号林业大学北门


title: Adipose subcutaneous_81a996df-7bc9-4ffc-bb37-57397e10014b at day D14

tag: tissue


title: scATAC_Hs_set1

value: Donor 1


title: hHEP_day 4_TBBPA-2

address: 双清路18号林业大学北门


title: hHEP_day 4_TCBPA-1

address: 双清路18号林业大学北门


title: zmp-2-br2


title: hHEP_day 4_TBBPA-1

address: 双清路18号林业大学北门


title: hHEP_day 4_Ctrl-2

address: 双清路18号林业大学北门


title: Adipose subcutaneous_81a996df-7bc9-4ffc-bb37-57397e10014b at day D0


title: Adipose subcutaneous_81a996df-7bc9-4ffc-bb37-57397e10014b at day D8


title: hHEP_day 4_TBBPS-2

address: 双清路18号林业大学北门


title: Adipose subcutaneous_a90289a4-771b-4c31-b1e2-c53dd9c96fcd at day D8


title: Adipose subcutaneous_a90289a4-771b-4c31-b1e2-c53dd9c96fcd at day D3


title: zmp-1-br3


title: Tumor Sample NF453

data_processing:
Sequence data was processed and aligned to human reference genome (hg38) using STAR aligner. The gene expression in raw counts for each sample was calculated by the algorithm “featureCounts” from the SUBREAD-1.5.0 package.
The data was normalized by counts-per-million (CPM) and then subjected to trimmed means of M (TMM). Differentially expressed genes (DEG) was determined using Quasi-likelihood F-test in EdgeR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2CPM values for each Sample

source_name: tumor cells

extract_protocol:
The isolated RNA was processed using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold Prep kit according to manufacturer’s protocol.
Libraries were sequenced on the Illumina NextSeq500 platform with 75-cycle paired-end protocol to obtain minimum 40 million reads.

tag: cell line

value: tumor cells

tag: cell type

value: Sporadic

value: M


title: SLE3 Tregs

first: Mingfang

last: Li

address: 2 Lujing Road

institute: Dermatology Hospital, Southern Medical University

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression(4*44K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software  (version 11.0.1.1) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring GX v11.5.1 (Agilent). Probe that at least 2 out of 4 samples flagged as Detected were maintained.

source_name: SLE3 Tregs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Freshly isolated peripheral blood Treg cells from healthy subjects and SLE patients.

extract_protocol: RNA was extracted according to the isopropanol/chloroform protocols with Trizol reagent (Invitrogen Life Technologies, USA).

treatment_protocol: The cells were not treated in vitro.

tag: subject status

value: Systemic Lupus Erythematosus (SLE) patient

tag: gender

value: female

tag: age

tag: duration

tag: sledai

tag: proteinuria (mg/24h)

tag: ana

tag: anti-ds-dna

value: positive

tag: medication

value: no

value: Tregs from Peripheral Blood


title: hHEP_day 4_Ctrl-1

address: 双清路18号林业大学北门

tag: differentiation stage

value: endoderm

tag: original strain


title: zmp-1-br2

tag: genotype

tag: replicate


title: SLE2 Tregs

source_name: SLE2 Tregs


title: Tumor Sample NF3175

tag: Sex

tag: disease state

value: Sporadic Spinal NF_G5


title: Adipose subcutaneous_a90289a4-771b-4c31-b1e2-c53dd9c96fcd at day D14

tag: tissue

value: adipose

tag: depot

tag: differentation day


title: SLE1 Tregs

source_name: SLE1 Tregs

tag: subject status

tag: gender

tag: cell type


title: NC Tregs

source_name: NC Tregs

value: healthy control

tag: age


title: H9-2

address: 双清路18号林业大学北门

source_name: hESCs

value: embryonic stem cell


title: Adipose subcutaneous_a90289a4-771b-4c31-b1e2-c53dd9c96fcd at day D0

value: subcutaneous


title: zmp-2-br1

tag: t-dna line

tag: ecotype


title: Tumor Sample NF990

tag: cell line

value: F


title: Tumor Sample NF882

value: Neurofibroma


title: Tumor Sample NF3011


title: H9-1

address: 双清路18号林业大学北门


title: Tumor Sample NF2797


title: zmp-1-br1

value: 12-day-old seedlings


title: RFCW3

city: Qingdao

first: zhongjiao

last: liu

state: Shandong

address: Aoshanwei

institute: Shandong University

description: RFCW3 FPKM

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Penicillium oxalicum

source_name: strain

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: strain

value: Fbx23 recover strain

tag: treatment

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: WT-br2

value: WT


title: Tumor Sample NF2525

value: tumor cells

value: Sporadic


title: RFCW2

description: RFCW2 FPKM


title: WT-br3


title: Adipose visceral_865b4bdb-e1b5-4636-8a0b-5e63023932e3 at day D14

value: visceral


title: WT-br1


title: Adipose visceral_f560827f-32b2-4650-b4cf-a2de26e0f01d at day D3


title: Tumor Sample NF2414

value: M


title: Adipose visceral_f560827f-32b2-4650-b4cf-a2de26e0f01d at day D14


title: Tumor Sample NF2401


title: DFCW3

description: DFCW3 FPKM

value: Fbx23 deletion strain


title: RFCW1

description: RFCW1 FPKM


title: DFCW2

description: DFCW2 FPKM


title: Adipose visceral_f560827f-32b2-4650-b4cf-a2de26e0f01d at day D0


title: Adipose visceral_865b4bdb-e1b5-4636-8a0b-5e63023932e3 at day D3


title: Tumor Sample NF2314

value: Sporadic Spinal NF_G5


title: Tumor Sample NF2300


title: WTCW3

description: WTCW3 FPKM

value: 114-2(wild type)


title: Adipose visceral_865b4bdb-e1b5-4636-8a0b-5e63023932e3 at day D0

value: adipose


title: Adipose visceral_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D14


title: Tumor Sample NF2474


title: Adipose visceral_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D0


title: Tumor Sample NF2179


title: hHEP_day 12_TBBPS-2

last: Yang

address: 双清路18号林业大学北门

tag: differentiation stage

value: hepatoblast


title: WTCW1

description: WTCW1 FPKM


title: Adipose subcutaneous_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D8

value: subcutaneous


title: pd-JAO-dc_Normoxia [pt#14]

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

hyb_protocol: 6.6 ug were fragmented; following fragmentation,20 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: primary pd-JAO derived cells under normoxia condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 5 to 50ng of Total RNA using the Affymetrix 3’IVT Pico Kit and 12 PCR cycles

growth_protocol: JMML cells were cultured in  RPMI 1640 Colture Medium supplemented with 10% BIT9500 Serum Substitute, 2mM L-Glutamine and 0.5% Penicillin/Streptomycin antibiotics and SCF (50ng/mL), TPO (50ng/mL), FLT-3L (50ng/mL), IL-3 (20ng/mL) and IL-6 (20ng/mL) cytokines.

extract_protocol: RNA was extracted using MiRNeasy Micro Kit (QIAGEN, Hilden, DE)

treatment_protocol: Normoxia (20% of oxygen level); Hypoxia (<2% of oxygen level)

tag: subject source id

value: Patient JMML#14

value: primary JMML pd-JAO derived cells

value: normoxia treatment


title: RFG3

description: RFG3 FPKM

value: strain

tag: genotype

value: Modified Mendal’s medium with 2percent glucose as carbon resource


title: pd-JAO-dc_Hypoxia [pt#14]

source_name: primary pd-JAO derived cells under hypoxia condition

value: hypoxia treatment


title: DFCW1

description: DFCW1 FPKM

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: Adipose visceral_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D3


title: Tumor Sample NF2130

value: tumor cells


title: Adipose subcutaneous_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D3


title: pd-JAO-dc_Normoxia [pt#15]

value: Patient JMML#15


title: Tumor Sample NF1901

value: F


title: RFG2

description: RFG2 FPKM

value: Fbx23 recover strain


title: WTCW2

description: WTCW2 FPKM


title: pd-JAO-dc_Normoxia [pt#3]

value: Patient JMML#3


title: pd-JAO-dc_Hypoxia [pt#3]


title: Tumor Sample NF1890

value: Neurofibroma

value: Sporadic

value: Sporadic Spinal NF_G5


title: pd-JAO-dc_Hypoxia [pt#15]


title: Adipose subcutaneous_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D14

value: adipose


title: RFG1

description: RFG1 FPKM


title: Tumor Sample NF2166

value: M


title: Tumor Sample NF1886


title: Adipose subcutaneous_43f4ce7d-263d-41c2-977b-5257c4642f09 at day D0

value: subcutaneous


title: DFG3

description: DFG3 FPKM

value: Fbx23 deletion strain


title: pd-JAO-dc_Normoxia [pt#12]

value: Patient JMML#12

value: primary JMML pd-JAO derived cells

value: normoxia treatment


title: Tumor Sample NF1856


title: Tumor Sample NF1847


title: Cvs_GA_C57_4209_(MTA-1_0)

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

description: RNA expression value derived from Expression Console software

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse MTA arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for comnined RNA analyses dabg .CHP files.

organism: Mus musculus

source_name: gastrocmnemius

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: C57/Bl6 male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.

extract_protocol: Total RNA extraction from muscle tissue was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief,  the  Cvs protocoll consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days.

tag: strain

value: Cvs

value: m. gastrocnemius


title: Adipose visceral_ac52c7cc-e913-4513-a117-1dfecabe42d2 at day D3

value: visceral


title: Cvs_GA_C57_4208_(MTA-1_0)


title: DFG1

description: DFG1 FPKM

value: strain

value: Modified Mendal’s medium with 2percent glucose as carbon resource


title: Adipose visceral_ac52c7cc-e913-4513-a117-1dfecabe42d2 at day D0


title: Adipose visceral_ac52c7cc-e913-4513-a117-1dfecabe42d2 at day D14


title: Cvs_GA_C57_4206_(MTA-1_0)


title: Tumor Sample NF1799

value: tumor cells

tag: Sex

value: F


title: pd-JAO-dc_Normoxia [pt#10]

value: Patient JMML#10


title: pd-JAO-dc_Hypoxia [pt#10]

value: hypoxia treatment


title: pd-JAO-dc_Hypoxia [pt#12]


title: Ctrl_GA_C57_4220_(MTA-1_0)

value: Ctrl


title: Tumor Sample NF1783

tag: disease state


title: WTG2

description: WTG2 FPKM

tag: tissue

value: 114-2(wild type)


title: Ctrl_GA_C57_4219_(MTA-1_0)


title: WTG3

description: WTG3 FPKM


title: Adipose visceral_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D8

value: adipose

tag: depot


title: Cvs_GA_C57_4210_(MTA-1_0)


title: DFG2

description: DFG2 FPKM


title: Adipose visceral_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D14

tag: differentation day


title: Ctrl_GA_C57_4218_(MTA-1_0)


title: Tumor Sample NF1682

value: Neurofibroma

value: Sporadic


title: Severe-February-rep 4

city: Lake Alfred

first: Faisal

last: Shahzad

state: FL

address: 700 Experiment Station Road, CREC

department: Horticultural Sciences

institute: University of Florida

description:
75_S34
Mild-02_severe-02_RNAseq_results

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 Csinensis_154_v1.1 using STAR 2.5.1b
Gene expression was calculated using RSEM 1.2.28
Differential expressed genes were called using edgeR
Assembly: Citrus. sinensis genome v1.1;  https://phytozome.jgi.doe.gov/pz/portal.html
Supplementary files format and content: The Final*RNAseq_results.xlsx files represent mapped reads

organism: Citrus sinensis

source_name: citrus buds

growth_protocol: Fifteen-year-old early-maturing ‘Hamlin’ sweet orange trees grafted on ‘Swingle’ citrumelo rootstock grown in an experimental citrus grove located at the University of Florida Citrus Research and Education Center, Lake Alfred, USA.

extract_protocol:
Total RNA was extracted from 100 mg of the ground bud tissues using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). RNA quality and quantity were determined using a spectrophotometer and denaturing formaldehyde 1.2% agarose gels, respectively.
RNA libraries were prepared for sequencing using the Illumina TruSeq 3000 mRNA protocol.

treatment_protocol: Citrus trees (n = 4) exhibiting severe and mild visual symptoms of HLB, i.e., blotchy mottling on leaves and branch dieback were selected for comparison.

value: citrus buds

value: Severe (treatment; high disease index)

tag: time after treatment

value: February (when buds show active growth)

tag: biological replicate

value: Biological replicate 4


title: WTG1

description: WTG1 FPKM


title: Adipose visceral_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D0


title: EOC733_iOme_scRNA

data_processing:
de-multiplexing, alignment, barcode processing and unique molecular identifier (UM)I quantification were performed using the Cell Ranger Software Suite (Version 6.0.1)
cell quality control was performed using Seurat v4
Assembly: GRCh38.d1.vd1
Supplementary files format and content: Matrix table with raw UMI counts

extract_protocol:
Tumor samples were dissected and enzymatically digested in a mixture of collagenase and hyaluronidase to obtain single-cell suspensions. Resulting cell suspensions were used without any selection/enrichment to create single-cell RNA sequencing libraries
Chromium Single Cell 3′ Reagent Kit v. 3.1 (10x Genomics)

value: high-grade serous ovarian cancer (HGSOC)

tag: individual

tag: treatment phase

value: Post-NACT

value: Omentum


title: Severe-February-rep 3

description:
74_S33
Mild-02_severe-02_RNAseq_results

value: Biological replicate 3


title: Tumor Sample NF1547

value: tumor cells

tag: cell type

value: M

value: Sporadic Spinal NF_G5


title: Severe-February-rep 2

description:
72_S32
Mild-02_severe-02_RNAseq_results

value: Biological replicate 2


title: Adipose subcutaneous_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D8

value: subcutaneous


title: Tumor Sample NF1537


title: Tumor Sample NF1693


title: Tumor Sample NF1467

value: F


title: Adipose visceral_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D3

value: adipose

value: visceral


title: Severe-February-rep 1

description:
71_S31
Mild-02_severe-02_RNAseq_results

value: Biological replicate 1


title: Adipose subcutaneous_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D14


title: Adipose subcutaneous_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D3


title: STEAP1-mBBz CAR T Cells + CBD-IL12 -3

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Adaptive Biotechnologies’ ImmunoSEQ platform

data_processing:
library strategy: TCR-seq
Processed data file from Immunoseq data analyzer for each sample is submitted as tab separated value (tsv) files
Supplementary files format and content: Processed data file from Immunoseq data analyzer for each sample is submitted as tab separated value (tsv) files

source_name: Tumor inflitrating T cells

growth_protocol: RM9-hSTEAP1 tumors were injected into C57BL/6J (hSTEAP1-KI) mice. Untransduced T cells and STEAP1-mBBz CAR T cells along with or without CBD-IL-12 were treated. Relapse tumors (n=4) were collected from individual treatment groups. Tumors cells were dissociated and infiltrating T cells were isolated, followed by extraction of genomic DNA and were subjected to TCRβ DNA sequencing

extract_protocol:
Genomic DNA from metastatic lung tumors were isolated using the GeneJET Genomic DNA Purification Kit (Thermo Fisher). Subsequent TCRV-β sequencing was performed on the immunoSEQ platform (Adaptive Biotechnologies)
Library prepration was performed according to the immunoSEQ platform (Adaptive Biotechnologies)

value: Tumor inflitrating T cells

value: CD3+ T cells

value: STEAP1-mBBz CAR T cells and CBD-IL-12 treatmemt

value: Tumor infiltrating T cells collected from lung metastases of mice treated with STEAP1-mBBζ CAR T and CBD-IL-12


title: STEAP1-mBBz CAR T Cells + CBD-IL12 -4


title: STEAP1-mBBz CAR T Cells + CBD-IL12 -2


title: Mild-February-rep 4

description:
65_S30
Mild-02_severe-02_RNAseq_results

value: citrus buds

value: Mild (control)

value: February (when buds show active growth)

value: Biological replicate 4


title: Adipose subcutaneous_c4cbcd9f-b183-4782-9564-b87a706c3ac3 at day D0


title: Tumor Sample NF1397

value: tumor cells

value: Neurofibroma

value: Sporadic


title: Tumor Sample NF1377


title: Mild-February-rep 3

description:
64_S29
Mild-02_severe-02_RNAseq_results

value: Biological replicate 3


title: STEAP1-mBBz CAR T Cells + CBD-IL12 -1


title: CT24-4 [bulk ATAC-seq]

source_name: pancreatic islet

value: pancreatic islet

value: Donor 7

value: 24 hours post-synchronization


title: CT44-2 [bulk ATAC-seq]

value: Donor 5

value: 44 hours post-synchronization


title: Adipose visceral_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D8

value: adipose

value: visceral


title: Tumor Sample NF1349

value: F


title: Mild-February-rep 2

description:
63_S28
Mild-02_severe-02_RNAseq_results

value: Biological replicate 2


title: STEAP1-mBBz CAR T Cells -3

value: Tumor inflitrating T cells

value: CD3+ T cells

value: STEAP1-mBBz CAR T cells treatmemt

value: Tumor infiltrating T cells collected from lung metastases of mice treated with STEAP1-mBBζ CAR T


title: Adipose visceral_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D3


title: STEAP1-mBBz CAR T Cells -4


title: Tumor Sample NF1301

value: tumor cells

value: M


title: Mild-February-rep 1

description:
62_S27
Mild-02_severe-02_RNAseq_results

value: citrus buds

value: Mild (control)

value: February (when buds show active growth)

value: Biological replicate 1


title: Severe-November-rep 4

description:
30_S26
Mild-11_severe-11_RNAseq_results

value: Severe (treatment; high disease index)

value: November (when buds were dormant)

value: Biological replicate 4


title: Adipose visceral_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D14

value: adipose


title: STEAP1-mBBz CAR T Cells -2


title: Tumor Sample NF1117


title: Adipose visceral_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D0

value: visceral


title: Tumor Sample NF1083

value: Sporadic

value: F


title: Severe-November-rep 3

description:
29_S25
Mild-11_severe-11_RNAseq_results

value: Biological replicate 3


title: STEAP1-mBBz CAR T Cells -1

value: Tumor inflitrating T cells

value: CD3+ T cells


title: Untransduced T Cells + CBD-IL12 -4

value: Untransduced T cells and CBD-IL-12 treatmemt

value: Tumor infiltrating T cells collected from lung metastases of mice treated with Untransduced CAR T cells and CBD-IL-12


title: Tumor Sample NF1059

value: tumor cells

value: Neurofibroma


title: Adipose subcutaneous_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D8

value: subcutaneous


title: Severe-November-rep 2

description:
28_S24
Mild-11_severe-11_RNAseq_results

value: citrus buds

value: Biological replicate 2


title: Tumor Sample M9413

value: MPNST

value: M


title: Adipose subcutaneous_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D3


title: Untransduced T Cells + CBD-IL12 -3


title: Severe-November-rep 1

description:
26_S23
Mild-11_severe-11_RNAseq_results

value: Severe (treatment; high disease index)

value: November (when buds were dormant)

value: Biological replicate 1


title: Untransduced T Cells + CBD-IL12 -2


title: Tumor Sample M803

value: Sporadic


title: Mild-November-rep 4

description:
20_S22
Mild-11_severe-11_RNAseq_results

value: Mild (control)

value: Biological replicate 4


title: Adipose subcutaneous_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D14

value: adipose


title: Adipose subcutaneous_ceaefb96-80ca-4c82-a667-6ef8a7d874f4 at day D0


title: Tumor Sample M4719


title: Untransduced T Cells + CBD-IL12 -1

value: Tumor inflitrating T cells

value: CD3+ T cells


title: Mild-November-rep 3

description:
19_S21
Mild-11_severe-11_RNAseq_results

value: Biological replicate 3


title: Tumor Sample M3048

value: tumor cells


title: Mild-November-rep 2

description:
17_S20
Mild-11_severe-11_RNAseq_results


title: Adipose visceral_773424b4-483e-4618-b51c-8f7643097fbd at day D14

value: visceral


title: Tumor Sample M2491


title: Untransduced T Cells -4

value: Untransduced T cells

value: Tumor infiltrating T cells collected from lung metastases of mice treated with Untransduced CAR T cells


title: Untransduced T Cells -3


title: Tumor Sample M2377


title: Adipose subcutaneous_773424b4-483e-4618-b51c-8f7643097fbd at day D3

value: subcutaneous


title: Adipose visceral_773424b4-483e-4618-b51c-8f7643097fbd at day D0


title: Tumor Sample M2372

value: MPNST

value: F


title: Untransduced T Cells -1


title: 90min_9min

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
Single end reads were first stripped of 3' ligated adapter using a custom python script.
Adapter stripped reads were then aligned to rRNA using bowtie 0.12.8 to remove remaining rRNA reads.  Reads that did not align to rRNA were then aligned to the full C. crescentus NA1000 genome using bowtie 0.12.8.
mRNA levels were then calcualted by normalizing using the reads per kilobase per million mapped reads (RPKM).  The relative mRNA levels over time were then calculated using the rifcorrect software [Aretakis et al. BioRxiv 2022].
Assembly: NA1000 operon annotation (Bharmal et al. MRA 2020)
Supplementary files format and content: tab delimited text

organism: Caulobacter vibrioides

growth_protocol: WT(Caulobacter crescentus NA1000) cells, were grown in M2G media overnight at 28 C. The next day, the cells were diluted and grown until midlog-phase  (0.3 to 0.5 OD600) which were used for mRNA half-life profiling.

extract_protocol:
The cells were pelleted at 20,000 x g for 1 min in 1.5 mL eppendorf tubes to prepare for RNA extraction.Pelleted cells were resuspended in 1mL of pre-warmed (to 65 0C) TRizol Reagent (Ambion) and incubated for 10 min at 65 0C in a heat block. 200 mL of chloroform were added to the samples and tubes were gently inverted a few times. Then samples were incubated at room temperature for 5 min and spun at 20,000 x g for 10 min. The supernatant was moved to siliconized tubes and 500 mL of chloroform was added, vortexed, and spun at 20,000 x g for 10 minutes. RNA samples were precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at – 80 0C. The RNA samples were spun at 20,000 x g at 4 0C for 1 hour. Pellets were washed with cold 80% ethanol and spun for 10 min at 20,000 x g, air-dried, and resuspended in 10 mM Tris-HCl (pH 7.0). The RNA-Seq libraries were made using 5µg of total RNA of each sample. Ribosomal RNAs were removed by ribozero gram negative kit and library construction was performed according to the protocol in (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].  Updated adapter oligos that are compatible with the novaseq were used from [Aretakis et al. Methods in Enzymology (2019)].

treatment_protocol: The cells were treated with 100µg/mL rifampicin and placed immediately in RNAprotect bacterial reagent (QIAGEN) at the indicated timepoint (0,1,2,4,8,and 15 min).  0 minute time-points were collected just prior to rifampicin addition.

value: C. crescentus cells

value: WT


title: Tumor Sample M2346

value: M


title: 90min_3min


title: 90min_1min


title: Untransduced T Cells -2


title: 90min_0min


title: Replicate 4, GFP low

city: London

first: Gordon

last: Beattie

address: Gower Street

institute: UCL

data_processing:
A FASTA and GTF file of mm10 was modified to contain eGFP, Tdtomato and EDGFR  sequences (complete with associated UTRs), raw reads were then mapped to this reference using cellranger count (v5.0.1)
Assembly: mm10
Supplementary files format and content: filtered (for cells) h5 matrix files of raw counts

source_name: Brain (GBM tumour)

extract_protocol:
Tumours were dissociated using papain and cells sorted based on tdTomato and GFP fluorescence into 0.04% BSA in PBS.
Cells were processed according to 10X Genomics User Guide (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)). Cells were resuspended with RT Master Mix and loaded onto Chip G along with the barcoded gel beads and partitioning oil in order to generate the gel bead-in-emulsion (GEM) on the Chromium Controller. Once complete, the GEMS are loaded onto a thermocycler to complete the RT inside each GEM to produce cDNA, which contain Illumina R1 primer sequence primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. Silane Dynabeads are used to clean up the pooled barcoded cDNA. The cDNA is then amplified and a quick QC is conducted to look at the fragment sizes. 10ul of the amplified cDNA is taken forward for the library construction which involves 3 steps of fragmentation (to obtain fragments around 450bp), ligation (to add the Illumina p5 and p7 primers) and Indexing (to add unique sample index to each sample). These steps are always followed by a SPRI Select bead purification. Once Indexing is complete the libraries were pooled and submitted for sequencing.

value: Brain (GBM tumour)

value: Female

tag: cell fraction

value: GFP low


title: Adipose subcutaneous_773424b4-483e-4618-b51c-8f7643097fbd at day D0

value: adipose


title: Replicate 4, GFP high

value: GFP high


title: Adipose visceral_536e8e82-761b-453a-ad72-1c925afb6d04 at day D3

source_name: Adipose visceral


title: 45min_9min

tag: cell line


title: Adipose visceral_536e8e82-761b-453a-ad72-1c925afb6d04 at day D14


title: Replicate 3, GFP low


title: Mild-November-rep 1

description:
16_S19
Mild-11_severe-11_RNAseq_results

value: citrus buds

tag: treatment

value: Mild (control)

value: November (when buds were dormant)

value: Biological replicate 1


title: Adipose subcutaneous_773424b4-483e-4618-b51c-8f7643097fbd at day D14

source_name: Adipose subcutaneous


title: Tumor Sample M2297

value: tumor cells

value: Low-Grade MPNST


title: Replicate 3, GFP high


title: 45min_3min


title: Tumor Sample M2252

value: Sporadic


title: 45min_1min


title: Adipose visceral_536e8e82-761b-453a-ad72-1c925afb6d04 at day D0

description: Low quality sample removed from the analysis

value: visceral


title: Tumor Sample M1677

value: MPNST


title: Replicate 2, GFP low

value: Male


title: Adipose subcutaneous_536e8e82-761b-453a-ad72-1c925afb6d04 at day D3

value: subcutaneous


title: Tumor Sample M1508

value: M


title: 45min_0min

value: C. crescentus cells

value: WT


title: Tumor Sample M2325

value: F


title: Replicate 2, GFP high

value: Brain (GBM tumour)


title: Tumor Sample M1014


title: SW_9min


title: Adipose subcutaneous_536e8e82-761b-453a-ad72-1c925afb6d04 at day D0

value: adipose