title: [Lymph node slice][sectionD]

city: Marseille

first: chuang

last: dong

address: 163 Av. de Luminy

country: France

institute: CIML

description:
fresh frozen spatial transcriptome sequencing
Visium_merged.Rds

data_processing:
Raw FASTQ files were processed with SpaceRanger software (v1.3.1), which performs alignment on mm10 genome, filtering, barcode counting and UMI counting. Downstream analyses were performed using Seurat v4.2.1.
Assembly: mm10 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary files format and content: Processed data files contain aligned images on the capture areas of the slice (.json files), the images that allowed us to identify cells and structures (.tif files), object containing the datasets from the 4 slices after Seurat analysis is also added (.rds file)
Library strategy: Spatial transcriptomics

source_name: Lymph node

extract_protocol:
Briefly, we performed permeabilization (18 min), reverse transcription, second strand synthesis, denaturation, cDNA amplification (16 cycles of PCR) according to the manufacturer’s instructions.
library construction was performed according to the manufacturer’s instructions.
The resulting libraries were sequenced on an Illumina NextSeq2000, generating an average of 120 million reads per library (Read 1: 28 cycles, Read i7: 10 cycles, Read i5: 10 cycles, Read 2: 79 cycles).

value: Lymph node

tag: sampleID


title: Ipsilateral TG Tumor Burden Mouse 1

status: Public on Aug 30 2024

type: RNA

city: Sioux Falls

first: Paola

middle: Drapkin

last: Vermeer

state: SD

address: 2301 East 60th street north

department: Cancer Biology and Immunotherapies Group

country: USA

institute: Sanford Research

description: Test

data_processing: The normalization and data analysis was conducted according to manufacturers instructions. For the normalization, five housekeeping genes are included (actinb, B2M, Gusb, Gadph, and Hrpt). For normalization, actinb was not included in normalization due to significant expression differences between test and control samples. Normalization used the averages of B2M, Gusb, Gadph, and HRPT. Target gene signals were normalized to housekeeping genes: 2^-delta(Ct), where delta(Ct) = (CT_target - CT_HKG).

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: Ipsilateral trigeminal ganglia from Head and neck cancer injected mouse

label_protocol: cDNA was generated by RT reaction using High Capacity cDNA Reverse Transcription kit from Applied Biosciences. cDNA was used to run on ScienCell qPCR arrays per manufacturer  and analyzed on CFX-96 BioRad.

growth_protocol: All animal experiments were performed in the Sanford Research Animal Resource Center which is a specific pathogen free facility. All mice were maintained in IVC Tecniplast Green line Seal Safe Plus cages. Animal rooms were maintained at 75°F, 30-70% humidity, with a minimum of 15 air changes per hour, and a 14:10 light/dark cycle. MOC2-7 cells were maintained in DMEM + 10%FBS + 1% pencillin/streptomycin.

extract_protocol: At day 28 post injection, mice were euthanized with CO gas and desaguinated with PBS so to maintain CNS integrity. Trigeminal ganglia were dissected from the skull base and RNA was isolated via Qiazol extraction reagent and further isolated through phenol-chloroform purification.

treatment_protocol: Mice were injected with 5 x 104 in 50 uL of cell culture media. Mice were anesthetized with a ketamine (87.5 mg/kg)/xylazine (10 mg/kg) mixture for initial injection. Mice were injected orthotopically in oral cavity with a 25 gauge needle. Tumors were measured every 7 days with caliper measurements while mice were sedated with isofluorane.

tag: strain

tag: gender

value: Male

tag: tumor

tag: tumor location

value: Oral Cavity

tag: tumor growth time

value: 28 days


title: Hct116NCBP2_1

type: SRA

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

library_source: transcriptomic

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Homo sapiens

source_name: colorectal cancer

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: colorectal cancer

tag: cell line

tag: cell type

value: Hct116 colorectal cancer cells

tag: treatment

value: overexpressed NCBP2


title: SW-480 cells Vector#1

city: Nanjing

first: Zhihao

last: Chen

address: Jiangsu Province

institute: NANJING MEDICAL UNIVERSITY

data_processing:
CLC Genomics Workbench v.11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics benchwork(parameter-Quality limit:0.05).
Trimmed squence reads were mapped to GrCM38/mm10 suing CLC genomic benchwork(parameters-mismath cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample.

growth_protocol: SW-480 cells were mainteined in RPMI 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3 ug 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 manufacture's protocols.

value: Human colon adenocarcinoma cells

tag: genotype

value: WT


title: [Lymph node slice][sectionC]


title: SW-480 cells OE-PJA2#2

value: PJA2 OE


title: SW-480 cells OE-PJA2#1


title: C157

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA version (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.99 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Differentially expressed genes (DEGs) were determined if significance was reported by either DESeq2 (v1.22.1), or edgeR (v3.24.3) and a |log2(fold change)|≥ 0.25.
Assembly: GRCh38.99
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

source_name: Whole blood

extract_protocol:
Total RNA was extracted from whole blood pre-operative samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

value: Whole blood

tag: condition

value: SIRS-

tag: organ dysfunction

value: no

tag: Sex


title: [Lymph node slice][section-B]


title: C156


title: Xyn6h-mRNA_i with plasmid pCS58

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

description: Fragmented and rRNA depleted mRNA for ribosome profiling

data_processing:
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3) or customized  genome fasta (NC_000964.3+Plasmid)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3) or customized GFF3 file (NC_000964.3+Plasmid) and using "locus_tag" as the GFF gene identifier
For RNA-seq, DEseq2 was used to normalized the count reads and compare the differences in the transcriptome between AmyM overproducing (Amy) and non-producing (Emp) samples; For Ribo-seq we achieved Ribosome binding A site profiles from the RiboGalaxy platform.
Assembly: NC_000964.3
Supplementary files format and content: tabular file include normalized counts for each gene/RNA features for all samples
Library strategy: Ribo-Seq

organism: Bacillus subtilis

source_name: bacterial cell

growth_protocol: Cells were cultured at 37 °C in LB medium with 50 μg/ml kanamycin and sampled at 3 h (OD600~0.8) and 6 h growth (OD600 ~4).

extract_protocol:
P/C/I extraction
Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs), according to the manufacturer's protocol.

treatment_protocol: Cells overexpressing XynA,  AmyM or an empty plasmid

value: bacterial cell

value: with plasmid pCS58

tag: growth phase

value: 6h stationary growth


title: C149


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063FU]

description: scRNAseq with flow cytometry associated data

library_source: transcriptomic single cell

data_processing:
Base calls were processed to FASTQs by Dragen software onboard NextSeq2000; fastq files were processed as described in https://github.com/MilpiedLab/FB5P-seq. To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Assembly: mm10_2020A_eYFP
Supplementary files format and content: 3 files were uploaded : a file with the matrix count (matrix), a file with the barcodes (barcodes) and a file with the gene list (features).

molecule: polyA RNA

source_name: lymph node

extract_protocol: The protocol was performed as previously described by Attaf et al. (DOI : 10.3389/fimmu.2020.00216). Individual cells were sorted into a 96-well PCR plate, with each well containing 2 µL of lysis buffer. Index sort mode was activated to record the fluorescence intensities of all markers for each individual cell. Flow cytometry standard (FCS) files from the index sort were analyzed using FlowJo software, and compensation parameters were exported as CSV tables for subsequent bioinformatic analysis. Immediately after sorting, plates containing individual cells were stored at -80°C until further processing. Following thawing, reverse transcription was performed, and the resulting cDNA was preamplified for 22 cycles. Libraries were then prepared according to the FB5P-seq protocol. The FB5P-seq data were processed to generate both a single-cell gene count matrix and single-cell B cell receptor (BCR) repertoire sequences for B cell analysis. Two separate bioinformatic pipelines were employed for gene expression and repertoire analysis, as detailed in Attaf et al. (DOI : 10.3389/fimmu.2020.00216).

value: lymph node

value: B cells and PC


title: C179

value: Male


title: Hct116PCDH_1

value: PCDH control


title: TG Non-Tumor Burden Mouse 1

description: Control

source_name: Trigeminal ganglia from age-matched non-tumor burdened mouse


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063IB]


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063F5]


title: Ipsilateral TG Tumor Burden Mouse 4

description: Test

value: Oral Cavity

value: 28 days


title: C177


title: [Lymph node slice][sectionA]

value: Lymph node


title: SW-480 cells Vector#2


title: TG Non-Tumor Burden Mouse 4

description: Control


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063FT]


title: Ipsilateral TG Tumor Burden Mouse 2

description: Test


title: C168


title: S190

value: Sepsis+

value: yes


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063FW]


title: Xyn6h-mRNA_ii with plasmid pCS58


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063FX]


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063FV]


title: Xyn3h-RPF_ii with plasmid pCS58

description: Ribosome protected mRNA fragments for ribosome profiling

value: 3 h exponentail growth


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063I2]


title: C154


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063G2]


title: Amy6h_ii with plasmid pCS74

description: mRNA-enriched RNA-seq

data_processing:
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3) or customized  genome fasta (NC_000964.3+Plasmid)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3) or customized GFF3 file (NC_000964.3+Plasmid) and using "locus_tag" as the GFF gene identifier
For RNA-seq, DEseq2 was used to normalized the count reads and compare the differences in the transcriptome between AmyM overproducing (Amy) and non-producing (Emp) samples; For Ribo-seq we achieved Ribosome binding A site profiles from the RiboGalaxy platform.
Assembly: NC_000964.3
Supplementary files format and content: tabular file include normalized counts for each gene/RNA features for all samples

value: with plasmid pCS74


title: Xyn3h-mRNA_ii with plasmid pCS58


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063I3]


title: S157

value: Whole blood


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063I8]


title: Emp6h_ii with plasmid pBW17

description: mRNA-enriched RNA-seq

value: with plasmid pBW17


title: S191

value: UInf+

value: no


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063IA]


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063G0]


title: S177


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063I6]


title: Amy6h_i with plasmid pCS74

description: mRNA-enriched RNA-seq

value: bacterial cell


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063I5]


title: S168


title: [eYFP+ B cells and PC][C57BL/6M] [H9N063I4]


title: Emp6h_i with plasmid pBW17

description: mRNA-enriched RNA-seq

value: 6h stationary growth


title: S156


title: Xyn6h-RPF_ii with plasmid pCS58

value: with plasmid pCS58


title: Xyn3h-mRNA_i with plasmid pCS58


title: [GEX_PC_7_S3]

description: 10X Genomics GEX

data_processing:
Raw fastq files from gene expression libraries were processed using Cell Ranger and Cell Ranger VDJ (v6.1.2 for dataset #3), with alignment on the mm10 and vdj_GRCm38_alts_ensembl-7.0.0 reference genomes, respectively. Quality control was performed on each dataset independently to remove poor quality cells based on UMI counts, number of genes detected, percentage of transcripts from mitochondrial genes, and percentage of transcripts from ribosomal protein coding genes. For each cell, gene expression UMI count values were log-normalized with Seurat NormalizeData with a scale factor of 10,000 to generate normalized UMI count matrices. HTO barcodes for sample demultiplexing after hashing were counted using CITE-seq-count and were normalized for each cell using a centered log ratio (CLR) transformation across cells implemented in the Seurat function NormalizeData. Hashtags were demultiplexed 14  using MULTIseqDemux function and barcodes assigned as doublets or negative were excluded from further analysis.
Assembly: mm10_2020A_eYFP
Supplementary files format and content: 3 files were uploaded : a file with the matrix count (raw_mat), a file with the barcodes (barcode) and a file with the gene list (features).

extract_protocol:
cells from draining lymph nodes were washed and resuspended in FACS buffer (PBS containing 5% FCS and 2 mM EDTA) at a concentration of 108 cells/ml. Samples from different mice and different time points were processed separately using cell hashing as described54. Cells were individually stained with distinct barcoded anti-mouse CD45 antibodies (in-house conjugated) in FACS buffer for 30 minutes on ice. Subsequently, cells were washed and stained with a mix of primary antibodies, then Live/Dead Fixable Aqua Dead Cell Stain (Thermofisher). Live cells of interest (IgDneg eYFP+ PC and B cells) from each sample were bulk-sorted using a BD Influx cell sorter. PC and non-PC were captured in distinct wells for droplet-based scRNA-seq to maximize the recovery of BCR sequence information from non-PC. Within each fraction, cells from different samples were pooled and loaded for the 10x Genomics Single Cell 5' v2 workflow.
10x Genomics 5'-end library preparation for gene expression, BCR and hashtag oligonucleotides
Libraries were prepared according to the manufacturer's instructions with modifications for generating B cell receptor (BCR) sequencing libraries. Following cDNA amplification, SPRI select beads were used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from the hashtag oligonucleotide (HTO)-containing fraction (in supernatant). For the mRNA-derived cDNA fraction, 50 ng were used to generate the transcriptome library, and 10-20 ng were used for BCR library construction.

value: lymph node

value: PC


title: Amy3h_ii with plasmid pCS74

description: mRNA-enriched RNA-seq


title: Xyn3h-RPF_i with plasmid pCS58


title: [GEX_PC_8_S4]

description: 10X Genomics GEX


title: S174

value: Male


title: [GEX_PC_6_S2]

description: 10X Genomics GEX


title: Xyn6h-RPF_i with plasmid pCS58


title: Emp3h_ii with plasmid pBW17

description: mRNA-enriched RNA-seq


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063I9]

value: B cells and PC


title: S179


title: S154


title: [GEX_PC_4_S4]

description: 10X Genomics GEX


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063FZ]


title: [eYFP+ B cells and PC][C57BL/6F] [H9N063G1]


title: [eYFP+ B cells and PC] [C57BL/6F][H9N063I7]


title: S149


title: [HTO_PC_S9]

description: 10X Genomics HTO


title: [HTO_NonPC_S10]

description: 10X Genomics HTO

value: non-PC


title: [GEX_PC_3_S3]

description: 10X Genomics GEX


title: C144

value: SIRS-


title: S159

value: Sepsis+

value: Female


title: Emp3h_i with plasmid pBW17

description: mRNA-enriched RNA-seq

value: 3 h exponentail growth


title: [GEX_NonPC_7_S7]

description: 10X Genomics GEX


title: C129

value: yes


title: [GEX_NonPC_3_S7]

description: 10X Genomics GEX


title: C127

value: Whole blood


title: [GEX_NonPC_1_S6]

description: 10X Genomics GEX


title: C155


title: [GEX_PC_5_S1]

description: 10X Genomics GEX


title: [eYFP+ B cells][S12]

description: 10X Genomics BCR

data_processing:
Raw fastq files from gene expression libraries were processed using Cell Ranger and Cell Ranger VDJ (v3.0.1 for dataset #2), with alignment on the mm10 and vdj_GRCm38_alts_ensembl-7.0.0 reference genomes, respectively. Quality control was performed on each dataset independently to remove poor quality cells based on UMI counts, number of genes detected, percentage of transcripts from mitochondrial genes, and percentage of transcripts from ribosomal protein coding genes. For each cell, gene expression UMI count values were log-normalized with Seurat NormalizeData with a scale factor of 10,000 to generate normalized UMI count matrices. HTO barcodes for sample demultiplexing after hashing were counted using CITE-seq-count and were normalized for each cell using a centered log ratio (CLR) transformation across cells implemented in the Seurat function NormalizeData. Hashtags were demultiplexed 14  using MULTIseqDemux function and barcodes assigned as doublets or negative were excluded from further analysis.
Assembly: mm10_ERCC92_eYFP
Supplementary files format and content: 3 files were uploaded : a file with the matrix count (raw_mat), a file with the barcodes (barcode) and a file with the gene list (features).

extract_protocol:
cells from draining lymph nodes were washed and resuspended in FACS buffer (PBS containing 5% FCS and 2 mM EDTA) at a concentration of 10E8 cells/ml. Samples from different mice and different time points were processed separately using cell hashing as described. Cells were individually stained with distinct barcoded anti-mouse CD45 antibodies (in-house conjugated) in FACS buffer for 30 minutes on ice. Subsequently, cells were washed and stained with a mix of primary antibodies, then Live/Dead Fixable Aqua Dead Cell Stain (Thermofisher). Live cells of interest (IgDneg eYFP+ PC and B cells) from each sample were bulk-sorted using a BD Influx cell sorter. PC and non-PC were captured in distinct wells for droplet-based scRNA-seq to maximize the recovery of BCR sequence information from non-PC. Within each fraction, cells from different samples were pooled and loaded for the 10x Genomics Single Cell 5' v2 workflow.
10x Genomics 5'-end library preparation for gene expression, BCR and hashtag oligonucleotides
Libraries were prepared according to the manufacturer's instructions with modifications for generating B cell receptor (BCR) sequencing libraries. Following cDNA amplification, SPRI select beads were used to separate the large cDNA fraction derived from cellular mRNAs (retained on beads) from the hashtag oligonucleotide (HTO)-containing fraction (in supernatant). For the mRNA-derived cDNA fraction, 50 ng were used to generate the transcriptome library, and 10-20 ng were used for BCR library construction.


title: [GEX_NonPC_1_S5]

description: 10X Genomics GEX


title: C140


title: Amy3h_i with plasmid pCS74

description: mRNA-enriched RNA-seq

value: with plasmid pCS74


title: [eYFP+ B cells][S11]

description: 10X Genomics HTO


title: [GEX_PC_2_S2]

description: 10X Genomics GEX


title: [eYFP+ B cells][S10]

description: 10X Genomics mRNA


title: [BCR_NonPC_S12]

description: 10X Genomics BCR


title: [GEX_PC_1_S1]

description: 10X Genomics GEX


title: SIRS S131

value: SIRS+


title: [GEX_NonPC_8_S8]

description: 10X Genomics GEX


title: C139

value: no


title: C141


title: [BCR_PC_S11]

description: 10X Genomics BCR


title: [eYFP+ B cells][S6]

description: 10X Genomics BCR


title: [BCR_PC_S9]

description: 10X Genomics BCR


title: C146


title: [GEX_NonPC_5_S5]

description: 10X Genomics GEX


title: [GEX_NonPC_6_S6]

description: 10X Genomics GEX


title: [GEX_NonPC_4_S8]

description: 10X Genomics GEX


title: S127


title: Lavender oil (LO) + EPS

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description: Dye-swap (Cy3/Cy5) of EPS + Carrier oil vs EPS +Lavender oil (LO) treated C2C12 cells

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2600D SG17204584

data_processing: Software: Feature Extraction ver 12.0.3.1

source_name: Carrier oil and EPS 60 min treated C2C12 cells Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: C2C12 cells were seeded in 4-well plates at 1.25 × 105 cells/well and grown in Dulbecco's modified Eagle's medium (DMEM, 4.5%/L glucose) supplemented with 10% fetal bovine serum (FBS) and 30 g/mL penicillin-streptomycin at 37ºC, 5% CO2. After 3 days, at 80-90% confluent, the cells were allowed to differentiate in the Dulbecco's modified Eagle's medium (DMEM, 1.0%/L glucose) supplemented with 2.0% horse serum (HS) and 30 g/mL penicillin-streptomycin for 7-9 days at 37ºC, 5% CO2.

extract_protocol: QIAGEN, Rneasy Micro kit

treatment_protocol: After C2C12 cell differentiation, the medium was removed and 5 mL of serum-free Eagle's medium (MEM) was added. After 2 hours, the medium was removed, and 5 mL of a new batch of the serum-free Eagle's medium (MEM) was added. Simultaneously, C-Pace EM (IonOptix Corporation) C-Dish carbon electrodes were placed in the wells, and EPS treatment was performed for 120 min at 1Hz, 2ms, and 40 V. The adjusted test samples were added at 0.05%, and the C-Pace EM (IonOptix Corporation) C-Dish carbon electrode was placed in the wells for 60 min of EPS treatment at 1Hz, 2ms, and 40V.

value: Murine Muscle cell line

source_name: Lavender oil (LO) and EPS 60 min treated C2C12 cells Cy5


title: Lavender oil (LO) dye swap

description: Dye-swap (Cy5/Cy3) of Carrier oil vs Lavender oil (LO) treated C2C12 cells

source_name: Lavender oil (LO) treated C2C12 cells Cy3

source_name: Carrier oil treated C2C12 cells Cy5


title: Naive, scRNAseq

city: Riverside

first: Emma

middle: H

last: Wilson

state: CA

address: 900 University Avenue

institute: UC Riverside

description: 10x Genomics

data_processing:
We used the Cell Range software v5.0.1 to process raw sequencing data, and then Seurat v5.0 was applied for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Whole Brain

extract_protocol:
To isolate astrocytes, brains were intracardially perfused with sterile 1x PBS at respective time points and placed in RPMI media (Gibco, 11875101) containing 1% Fetal Bovine Serum (FBS) (Corning, MT35015CV) and 25 mM HEPES. Perfused brains were transferred to a chilled 60 mm petri dish, dissociated with a razor blade, and treated with 4 ml of 0.25% trypsin. Brain suspension was digested at 37C for 30 minutes in 50 ml conical tubes. During digestion, the mixture was inverted every 5 minutes. Trypsin digestion was stopped with the addition of 30 ml of RPMI containing 20% FBS and centrifuged at 1000 RCF (g) for 5 minutes at 4C. Supernatant was decanted, and the pellet resuspended in 1% FBS RPMI to a total volume of 7 ml. The suspension was transferred to a 15 ml conical tube with 3 ml of 100% Percoll (Sigma Aldrich, P1644), gently mixed and underlaid with 1 ml of 70% Percoll made in 1% FBS RPMI. Samples were centrifuged at 2500 RCF (g) for 20 minutes at 4C. Following density separation, glial cells were harvested from the interphase and washed in 1% FBS RPMI and resuspended in FACS buffer for flow cytometry staining. To identify transcriptional astrocyte subsets, single cell RNA sequencing (scRNAseq) was performed from murine cells. To obtain a pure astrocyte sample, extracellular staining with anti-astrocyte cell surface antigen-2 (ACSA-2) was performed (Miltenyi Biotec, 130-117-535). The viability stain 7-aminoactinomycin (ThermoFischer, A1310), was added to the FACS buffer to identify dead cells. ACSA-2+ astrocytes were sorted and collected in a flow tube containing 10% FBS complete astrocyte RPMI with the Beckman Coulter MoFlo Astrios EQ Cell Sorter. For reporter experiments, sorting was performed on live cells via DAPI and tdTomato expression to collect live Lcn2CreERT2+ RAs for sequencing. A maximum of 16,000 astrocytes from each time point following the astrocyte cell suspension protocol was collected and pre-loaded on a 10X Chromium chip and Chromium controller for barcoding. Single cell RNA sequencing steps from the 10X Genomics 3' kit (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 PN-1000128) were followed according to supplier instructions to extract RNA for sequencing
Cell purity throughout preparation was verified on the Agilent 2100 Bioanalyzer following cDNA amplification and library construction. When submitting samples to the 10X Genomics Core at UCSD, 1 billion reads per sample were requested to achieve a saturation level above 90%. After sequencing, the Cell Ranger program (v5.0.1) was utilized to align reads from the sequencing fastq data files to a mouse reference genome mm10 and generate gene-barcode expression matrices. Mean reads and median genes per cell were reviewed for statistical relevance and then aligned sequences were uploaded to R (v4.3.2) package to generate plots and obtain gene statistics per cell and cluster.

treatment_protocol: To induce chronic T. gondii infection, mice were infected interperitoneally (I.P.) with the cyst forming Me49 Type II T. gondii strain. Parasites were maintained in vivo by passaging alternatively in Swiss Webster (SW) and CBA mice (JAX). Following at least three weeks post infection, brains from CBA mice were harvested, homogenized in 3ml sterile 1X Phosphate Buffered Saline (PBS) through needle passing, and cysts were counted using a 30ul aliquot and a light microscope (average cyst burden/brain ~3000). Cyst homogenate was diluted in sterile 1X PBS and 10 Me49 cysts were injected in experimental mice via 200ul I.P. injections. To selectively activate reporter fluorescence of Lcn2CreERT2+ cells at chosen time points, mice were I.P. administered 150 ug/g of tamoxifen (Millipore Sigma, T5648) diluted in corn oil at the appropriate time points prior to the respective brain collections. Mice were then scarified via IACUC approved methods. For acute infection, I.P. TAM injections start on 5 days post infection (dpi) and are given every other day until collection at 14 dpi. This timeline was decided due to astrocyte activation starting around 5 days after initial T. gondii infection. For chronic infection, Lcn2CreERT2+ RA tdTomato red fluorescent protein expression was activated with TAM treatments starting on 14 dpi and given 3 times a week (MWF) until 42 dpi. To investigate how labeled Lcn2CreERT2+ RAs may change over time following long term infection, tamoxifen-rested RAs were labeled from day 14 dpi to 42 dpi, tamoxifen was then withdrawn, and the phenotype of the labeled Lcn2CreERT2+ RAs were analyzed after two additional weeks of infection.

value: Whole Brain

tag: age

value: 6-8 weeks old

value: Astrocytes/Infiltrating Immune Cells/ Brain Mononuclear Cells

value: Naïve


title: [eYFP+ B cells][S3]

description: 10X Genomics mRNA

value: lymph node


title: 42dpi, scRNAseq

description: 10x Genomics

value: Toxoplasma gondii chronic infection


title: S129

value: UInf+

value: Male


title: C122

value: SIRS-


title: [eYFP+ B cells][S9]

description: 10X Genomics mRNA

value: PC


title: [eYFP+ B cells][S8]

description: 10X Genomics mRNA


title: Lavender oil (LO) + EPS dye swap

description: Dye-swap (Cy5/Cy3) of EPS + Carrier oil vs EPS +Lavender oil (LO) treated C2C12 cells

source_name: Lavender oil (LO) and EPS 60 min treated C2C12 cells Cy3

source_name: Carrier oil and EPS 60 min treated C2C12 cells Cy5


title: [eYFP+ B cells][S7]

description: 10X Genomics mRNA


title: [eYFP+ B cells][S1]

description: 10X Genomics mRNA


title: [OVA-specific B cells][P14]

data_processing:
Base calls were processed to FASTQs by Dragen software onboard NextSeq2000; fastq files were processed as described in https://github.com/MilpiedLab/FB5P-seq. To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Assembly: GRCm38 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary files format and content: 3 files were uploaded : a file with the matrix count (raw_mat), a file with the barcodes (barcode) and a file with the gene list (features).
Library strategy: FB5P-seq

extract_protocol: Individual cells were sorted into a 96-well PCR plate, with each well containing 2 µL of lysis buffer. Index sort mode was activated to record the fluorescence intensities of all markers for each individual cell. Flow cytometry standard (FCS) files from the index sort were analyzed using FlowJo software, and compensation parameters were exported as CSV tables for subsequent bioinformatic analysis. Immediately after sorting, plates containing individual cells were stored at -80°C until further processing. Following thawing, reverse transcription was performed, and the resulting cDNA was preamplified for 22 cycles. Libraries were then prepared according to the FB5P-seq protocol. The FB5P-seq data were processed to generate both a single-cell gene count matrix and single-cell B cell receptor (BCR) repertoire sequences for B cell analysis. Two separate bioinformatic pipelines were employed for gene expression and repertoire analysis, as detailed in Attaf et al. (DOI : 10.3389/fimmu.2020.00216).

value: B cells

tag: immunization


title: [OVA-specific B cells][P13]

tag: sampleID


title: S140

value: Sepsis+

value: yes


title: 14dpi, scRNAseq

description: 10x Genomics

value: Toxoplasma gondii Acute infection


title: [OVA-specific B cells][P12]


title: S123

value: Whole blood


title: Sorted ACSA2 Astrocytes, Naive, scRNAseq

description: 10x Genomics

value: Astrocytes


title: S122

value: no

value: Female


title: [eYFP+ B cells][S5]

description: 10X Genomics HTO


title: [OVA-specific B cells][P10]


title: [eYFP+ B cells][S2]

description: 10X Genomics mRNA


title: S131


title: [OVA-specific B cells][P9]


title: 28dpi, scRNAseq

description: 10x Genomics

value: Whole Brain

value: 6-8 weeks old

value: Toxoplasma gondii early chronic infection


title: [OVA-specific B cells][P8]

value: lymph node


title: [OVA-specific B cells][P11]


title: [eYFP+ B cells][S4]

description: 10X Genomics mRNA


title: Sorted ACSA2 Astrocytes, 42dpi, scRNAseq

description: 10x Genomics

value: Toxoplasma gondii chronic infection


title: Sorted ACSA2 Astrocytes, 14dpi, scRNAseq

description: 10x Genomics

value: Toxoplasma gondii acute infection


title: Lavender oil (LO)

description: Dye-swap (Cy3/Cy5) of Carrier oil vs Lavender oil (LO) treated C2C12 cells

source_name: Carrier oil treated C2C12 cells Cy3

value: Murine Muscle cell line

source_name: Lavender oil (LO) treated C2C12 cells Cy5


title: [OVA-specific B cells][P1]


title: WT 6

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
Samples were processed using nf-core/smrnaseq (2.2.4) using default parameters.
Assembly: mm10
Supplementary files format and content: A comma-delimited text file containing raw counts for each sample.

source_name: thymus

growth_protocol: Thymi were isolated and dissociated to generate single cell suspensions.

extract_protocol:
FACS sorted iNKT cells were lysed in RLT plus lysis buffer from the miRNeasy plus kit (Qiagen, cat no: 217084). Total RNA was isolated following the instructions provided by the manufacturer and was quantified using Qubit RNA High Sensitivity assay (Invitrogen) in Qubit 4 Fluorometer (Invitrogen).
Total RNA was provided to the UNC High Throughput Sequencing Facility (HTSF). RNA integrity was evaluated with a Tapestation (Agilent) using High Sensitivity RNA ScreenTape (Agilent). RNA with RIN value>9 was used for library preparation. Small RNA libraries were generated using the Revvity NETFLEX small RNA sequencing kit V4.

value: thymus

value: primary thymocytes

value: iNKT cells

value: Wild type


title: C119

value: SIRS-

value: Male


title: dwaj1.3a_15

city: Cambridge

first: Elisa

last: Moutin

address: Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequence read quality was assessed using FastQC (v0.11.9). Adapter content was trimmed from the reads using Trimmomatic (v0.39). Trimmed reads were aligned to GRCm39 Ensembl release 103 for QC purposes using STAR version 2.7.7a and QC of the aligned reads was carried out using Picard tools (v2.27.3). Gene expression quantification was carried out using Salmon (v1.9.0) against indexes generated from Gencode Mouse release M30. Differential gene expression was performed using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: Table of normalised counts against gene IDs in tab separated value format

extract_protocol:
Freshly dissected tumours were immediately placed in RNAlater (Thermo Fisher, AM7021) and stored at 4 °C. RNA was extracted using an RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer’s instructions.
Library prep was performed using the Illumina Stranded mRNA Prep kit (Illumina, 20040532) according to the manufacturer’s instructions.

treatment_protocol: The animals involved were induced with 4mg tamoxifen IP when aged >8 weeks and had 200mg/kg ENU 10 days after.

value: male

value: microdissected tumour

value: Apchet

value: ENU


title: S146

value: Whole blood

value: UInf+

value: no


title: [OVA-specific B cells][P7]

value: lymph node

value: B cells


title: Sorted ACSA2 Astrocytes, 28dpi, scRNAseq

description: 10x Genomics

value: Whole Brain

value: 6-8 weeks old

value: Astrocytes

value: Toxoplasma gondii early chronic infection


title: WT 2

value: thymus

value: primary thymocytes

value: iNKT cells


title: [OVA-specific B cells][P5]


title: S145

value: Male


title: [OVA-specific B cells][P4]


title: [OVA-specific B cells][P3]


title: S141

value: Sepsis+

value: yes


title: SIRS S133

value: SIRS+

value: Female


title: dwaj1.3a_18

value: male

value: microdissected tumour

value: Apchet

value: ENU


title: DKO 4


title: [OVA-specific B cells][P2]

value: lymph node

value: B cells


title: dwba2.2d_28a

value: female


title: DKO 3


title: SIRS S125

value: Whole blood


title: dwaj1.3a_17


title: WT 5

value: Wild type


title: WT 4

value: thymus


title: C136

value: SIRS-


title: dwba2.2d_30b


title: C125

value: no


title: WT 3

value: primary thymocytes

value: iNKT cells


title: dwba2.2d_27a


title: WT 1


title: dwba2.2d_20b


title: DKO 7


title: C091


title: C132

value: yes

value: Male


title: sciMET-ATAC, human brain, BA46

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

description: Cell-level methylation calls, amethyst analysis object, and fragments file for sciMET-ATAC technology

library_source: genomic

data_processing:
Reads were processed using Premethyst and aligned to hg38
Methylation calls were analyzed using Amethyst
Assembly: hg38
Supplementary files format and content: Methylation calls in h5 format
Supplementary files format and content: Methylaiton metadata in amethyst object format
Supplementary files format and content: ATAC fragments in bed format
Library strategy: sciMET-ATAC

molecule: genomic DNA

source_name: Brain BA46

extract_protocol:
Nuclei were extracted using nuclei isolation buffer and gentle dounce homogenization
sciMET-ATAC libraries were prepared using 3-level single-cell combinatorial indexing workflow with an additional initial indexed tagmentation to capture chromatin accessibility prior to nucleosome disruption and genome-wide tagmentation

value: Brain BA46


title: DKO 6


title: DKO 5


title: Male, 4 months (T100_ADT)

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: CITE-seq

library_source: other

data_processing:
Base calling was performed by Real-Time Analysis software in the NextSeq2000
Fastq generation was performed by cellranger 6.0.1 mkfastq
Reads were not filtered before alignment
Alignment/counting/cell calling was performed by cellranger count
Assembly: The reference genome used is hg19
Supplementary files format and content: Processed data files are in H5, TSV and MTX formats. They contain the barcodes, features and matrix connecting both for each sample.
Library strategy: ADT-seq

molecule: other

source_name: Thymus

extract_protocol:
Briefly, fresh human thymus was minced into small pieces and digested in warm dissociation media (2mg/ml Stemxyme, 6.3 U/mL DNaseI, 1.5% BSA in RPMI) for two 30 min intervals. An additional 8 ml of dissociation cocktail was added for a final 30 min digestion. Cells from the third digestion were collected and depleted of CD45+ cells using the Miltenyi LD column prep kit. Cells were then sorted based on live cells and CD45 expression. For some samples fresh thymocytes were enriched for CD25+ cells and and CD8- cells using StemCell Technologies EasySep kits. Cells were recombined in a 3:2 ratio (CD45-:CD45+) or 2:2:1 ratio (CD45-:CD45+:CD25+) prior to library preparation.
Library was prepared using Chromium Single Cell 5ʹ v2 next gem kit and protocol (10x Genomics). All samples were prepared in accordance to the 10X user guidelines (cite user guide).

value: Thymus

value: male

value: 4 months

value: All, CD45- enriched, CD25+CD8- enriched

tag: antibodies/tags

value: list of tag IDs in feature_README.txt on series record and feature_reference file on each sample record.

tag: library type

value: ADT


title: dwaj1.3a_27b

value: microdissected tumour

value: Apchet

value: ENU


title: C121

value: Whole blood


title: DKO 1

value: thymus


title: SIRS S121

value: SIRS+


title: C115

value: SIRS-

value: no


title: sciMETv3, brain, 4 donors, capture and conversion experiments

description: Cell-level methylation calls and amethyst analysis object for sciMETv3 capture and enzymatic conversion experiments

data_processing:
Reads were processed using Premethyst and aligned to hg38
Methylation calls were analyzed using Amethyst
Assembly: hg38
Supplementary files format and content: Methylation calls in h5 format or a tar file with multiple h5 files included
Supplementary files format and content: Methylaiton metadata in amethyst object format, integrated with sciMETv3-only dataset

extract_protocol:
Nuclei were extracted using nuclei isolation buffer and gentle dounce homogenization
sciMETv3 libraries were prepared using 3-level single-cell combinatorial indexing workflows


title: dwaj1.3a_10


title: Male, 4 months (T098_ADT)

description: CITE-seq


title: dwaj1.3a_4


title: DKO 2

value: primary thymocytes

value: iNKT cells


title: Male, 4 months (T098_mRNA)

description: CITE-seq

data_processing:
Base calling was performed by Real-Time Analysis software in the NextSeq2000
Fastq generation was performed by cellranger 6.0.1 mkfastq
Reads were not filtered before alignment
Alignment/counting/cell calling was performed by cellranger count
Assembly: The reference genome used is hg19
Supplementary files format and content: Processed data files are in H5, TSV and MTX formats. They contain the barcodes, features and matrix connecting both for each sample.

value: mRNA


title: sciMETv3, brain, 4 donors, pilot experiment

description: Cell-level methylation calls and amethyst analysis object for sciMETv3 pilot experiment

value: Brain BA46


title: Female, 4 months (T097_ADT)

description: CITE-seq

value: Thymus

value: female

value: All, CD45- enriched


title: C133

value: Female


title: dwaj1.3a_19b

value: male


title: dwba2.2d_22a

value: microdissected tumour


title: C088


title: Female, 4 months (T099_mRNA)

description: CITE-seq

value: 4 months

value: All, CD45- enriched, CD25+CD8- enriched


title: S136

value: Whole blood

value: Sepsis+

value: yes

value: Male


title: Male, 4 months (T100_mRNA)

description: CITE-seq


title: dwba2.2d_23a

value: Apchet

value: ENU


title: Female, 4 months (T087_ADT)

description: CITE-seq

value: list of tag IDs in feature_README.txt on series record and feature_reference file on each sample record.

value: ADT


title: Female, 4 months (T087_mRNA)

description: CITE-seq

value: mRNA


title: dwaj1.3a_3


title: S119


title: S133

value: UInf+

value: no


title: Male, 5 months (T096_ADT)

description: CITE-seq

value: Thymus

value: All, CD45- enriched


title: dwaj1.3a_29a

value: male


title: Female, 4 months (T097_mRNA)

description: CITE-seq

value: female


title: C096

value: SIRS-


title: dwaj1.3a_6

value: microdissected tumour


title: Female, 4 months (T099_ADT)

description: CITE-seq

value: 4 months

value: All, CD45- enriched, CD25+CD8- enriched


title: Female, 4 months (T099)

description: ATAC-seq

library_source: genomic single cell

data_processing:
Base calling was performed by Real-Time Analysis software in the NextSeq2000
Fastq generation was performed by cellranger-atac 2.0.0 mkfastq
Reads were not filtered before alignment
Alignment/counting/cell calling was performed by cellranger-atac count
Assembly: The reference genome used is hg19
Supplementary files format and content: Processed data files are in H5, TSV, and CSV formats. They contain the filtered peak matrix, fragments and single cell information, respectively for each sample.

extract_protocol:
Briefly, fresh human thymus was minced into small pieces and digested in warm dissociation media (2mg/ml Stemxyme, 6.3 U/mL DNaseI, 1.5% BSA in RPMI) for two 30 min intervals. An additional 8 ml of dissociation cocktail was added for a final 30 min digestion. Cells from the third digestion were collected and depleted of CD45+ cells using the Miltenyi LD column prep kit. Cells were then sorted based on live cells and CD45 expression. For some samples fresh thymocytes were enriched for CD25+ cells and and CD8- cells using StemCell Technologies EasySep kits. Cells were recombined in a 3:2 ratio (CD45-:CD45+) or 2:2:1 ratio (CD45-:CD45+:CD25+) prior to library preparation. Nuclei were isolated following the 10X genomics cell line nuclei isolation kit using 0.1X lysis buffer and a 4 minute incubation.
All samples were prepared in accordance to the 10X user guidelines (cite user guide) using the ATAC v1 kit.


title: Female, 4 months (T097)

description: ATAC-seq


title: Male, 5 months (T096_mRNA)

description: CITE-seq


title: S125

value: Whole blood


title: Male, 5 months (T096)

description: ATAC-seq

value: 5 months


title: dwaj1.3a_28a

value: Apchet


title: Male, 33 months (T086_ADT)

description: CITE-seq

value: 33 months


title: dwba2.2d_2

value: ENU


title: S121

value: Male


title: Male, 4 months (T100)

description: ATAC-seq


title: NCI-N87_DMSO_24h_in_vitro_rep3

city: Vienna

first: Malgorzata

middle: Emilia

last: Kamuda

address: Dr.Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer-Ingelheim

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system or Illlumina NextSeq 2000. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Quality control was performed on samples using FASTQC (v.0.11.5), multiqc (v.1.12), picardmetrics(v0.2.4), and bioconductor-dupRadar (v1.0.0) at respective steps. Single-end reads were mapped against Homo sapiens genome (GRCh38) using the STAR (v2.5.2b) aligner. Samples were quantified with the transcript abundances using featureCount (v1.5.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

source_name: stomach

growth_protocol: Cell were seeded 24 h prior to treatment start at 500000 cells per 6-well plate in RPMI medium supplemented with 10 % FCS 0.5 µg/mL puromycin and 0.6 mg/mL G418. Cells were incubated in a humidified incubator at 5 % CO2 at 37 °C. Compounds were added for the indicated timepoints.

extract_protocol:
In vivo: Frozen tumours were cut into 5x5 mm pieces and ground using one steel bead (#69989 Qiagen) per 2 mL vial in 1 mL Trizol using a tissue lyser II (Quiagen) at 4 °C (1/s frequency, 30 sec, 30 cycles). Lysates were processed using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions. ; In vitro: After treatment, cells were washed with ice cold PBS and RNA extracted using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions using 1 mL Trizol per 6-well. RNA was eluted in 50 µL of ddH2O for further processing
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina from Lexogene according to manufacturer's instructions.

treatment_protocol: Engineered PC-9 cells cancer cells were tested in an in-vivo experiment involving 11 groups with 5 animals per group, totaling 55 animals. The treatments administered included Natrosol and BI01810631 (HER2-EXON20i). The sampling time points were set at 2h, 6h, and 24h. The samples were harvested either at day 1 or day 3 of the experiment. Also PC9 YVMA cl5 cells were tested in an in-vitro experiment where we treateded them with the HER2 inhibitor, BI01810631, as a mono-agent for 24 hours. The NCI-N87 cells were tested in an in-vitro experiment where they were treated with BI01810631 (HER2 inhibitor) at concentrations of 5nM and 250nM in monotherapy. The data was retrieved for the time points 2h and 24h.

value: stomach

value: cell culture

value: WT

value: DMSO

tag: time


title: Male, 33 months (T086_mRNA)

description: CITE-seq

value: Thymus

value: All, CD45- enriched

value: mRNA


title: Male, 4 months (T098)

description: ATAC-seq

value: male


title: NCI-N87_DMSO_24h_in_vitro_rep2


title: dwaj1.3a_20a

value: microdissected tumour


title: S115

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA version (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.99 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Differentially expressed genes (DEGs) were determined if significance was reported by either DESeq2 (v1.22.1), or edgeR (v3.24.3) and a |log2(fold change)|≥ 0.25.
Assembly: GRCh38.99
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

source_name: Whole blood

value: Sepsis+

value: yes


title: NCI-N87_BI01810631_5nM_2h_in_vitro_rep3


title: Male, 5 months (T096-2)

description: ATAC-seq

value: All


title: dwba2.2d_23b

value: female


title: NCI-N87_BI01810631_5nM_2h_in_vitro_rep2


title: NCI-N87_BI01810631_5nM_2h_in_vitro_rep1


title: NCI-N87_DMSO_2h_in_vitro_rep3


title: S096

value: Whole blood


title: NCI-N87_DMSO_2h_in_vitro_rep2


title: dwaj1.3a_29b

value: Apchet


title: dwaj1.3a_7

value: ENU


title: NCI-N87_BI01810631_5nM_24h_in_vitro_rep2


title: NCI-N87_BI01810631_250nM_2h_in_vitro_rep3


title: dwaj1.3a_1


title: S088

value: UInf+

value: no

value: Female


title: SIRS S003

value: SIRS+


title: NCI-N87_DMSO_24h_in_vitro_rep1

value: stomach

value: cell culture

value: WT

value: DMSO


title: SIRS S042


title: NCI-N87_BI01810631_250nM_2h_in_vitro_rep2


title: NCI-N87_BI01810631_5nM_24h_in_vitro_rep3


title: SIRS S041 & SIRS S087

value: Male


title: NCI-N87_BI01810631_250nM_24h_in_vitro_rep3


title: dwba2.2d_24b

value: microdissected tumour


title: dwba2.2d_22b


title: SIRS S032


title: PC-9_YVMA-5_DMSO_2h_in_vitro_rep1

source_name: lung

value: lung

value: mutant


title: PC-9_YVMA-5_DMSO_2h_in_vitro_rep2


title: NCI-N87_BI01810631_5nM_24h_in_vitro_rep1


title: dwaj1.3a_31a

value: male


title: PC-9_YVMA-5_DMSO_24h_in_vitro_rep3


title: NCI-N87_BI01810631_250nM_2h_in_vitro_rep1


title: SIRS S061

value: yes


title: dwba2.2d_5

value: female


title: PC-9_YVMA-5_BI01810631_5nM_2h_in_vitro_rep3


title: dwaj1.3a_8

value: Apchet


title: SIRS S021

value: Whole blood


title: NCI-N87_BI01810631_250nM_24h_in_vitro_rep2


title: SIRS S067


title: NCI-N87_BI01810631_250nM_24h_in_vitro_rep1


title: dwba2.2d_20a

value: ENU


title: PC-9_YVMA-5_BI01810631_5nM_24h_in_vitro_rep3


title: PC-9_YVMA-5_DMSO_2h_in_vitro_rep3


title: dwaj1.3a_31b


title: PC-9_YVMA-5_BI01810631_5nM_24h_in_vitro_rep1


title: dwaj1.3a_22b


title: dwba2.2d_30a


title: SIRS S044


title: PC-9_YVMA-5_DMSO_24h_in_vitro_rep1


title: PC-9_YVMA-5_BI01810631_5nM_2h_in_vitro_rep2


title: dwaj1.3a_2


title: PC-9_YVMA-5_BI01810631_250nM_2h_in_vitro_rep1


title: SIRS S083


title: PC-9_YVMA-5_DMSO_24h_in_vitro_rep2


title: SIRS S086


title: PC-9_YVMA-5_BI01810631_250nM_2h_in_vitro_rep3


title: dwba2.2d_6


title: C101

value: SIRS-

value: no


title: C093


title: PC-9_YVMA-5_BI01810631_5nM_2h_in_vitro_rep1


title: PC-9_YVMA-5_BI01810631_5nM_24h_in_vitro_rep2


title: C100


title: C097

value: Female


title: PC-9_YVMA-5_BI01810631_250nM_2h_in_vitro_rep2


title: dwba2.2d_8


title: Tumor, Iron_Pos, scRNAseq

city: Philadelphia

first: William

last: Molina Arocho

address: 421 Curie Blvd BRB II/III Rm 436

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10-3.0.0
Supplementary files format and content: Tab separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissue was minced and digested with collagenase b and dnase I for at 37C for 45 min. Samples were filtered, RBC lysed and resuspended in FACS buffer. Samples were then iron enriched using magnetic columns to obtain an iron enriched eluate and a non-iron enriched flowthrough.
Library was performed according to the manufacturers instructions (single cell 3' v3 protocol, 10x Genomics).

value: Tumor

value: WT C57BL/6

value: Magnetic Column Enriched


title: C090


title: dwaj1.3a_23b


title: dwba2.2d_24a


title: Tumor, Blood, scRNAseq

description: 10x Genomics

extract_protocol:
Tumor tissue was minced and digested with collagenase b and dnase I for at 37C for 45 min. Samples were filtered, RBC lysed and resuspended in FACS buffer.
Library was performed according to the manufacturers instructions (single cell 3' v3 protocol, 10x Genomics).

value: PBS injected


title: S101

extract_protocol:
Total RNA was extracted from whole blood pre-operative samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

value: Sepsis+


title: C094

value: Male


title: PC-9_YVMA-5_BI01810631_250nM_24h_in_vitro_rep2

value: lung

value: cell culture


title: dwba2.2d_27b

value: microdissected tumour


title: PC-9_YVMA-5_BI01810631_250nM_24h_in_vitro_rep3

value: mutant


title: dwaj1.3a_28b

value: male


title: PC-9_YVMA-5_BI01810631_250nM_24h_in_vitro_rep1


title: S100

value: yes


title: dwaj1.3a_19a

value: Apchet


title: S097

value: Whole blood


title: S093


title: Tumor, Iron_Neg, scRNAseq

description: 10x Genomics

value: Magnetic Column Flowthrough


title: Tumor, Control, scRNAseq

description: 10x Genomics

value: Erythrocyte injected


title: S091

value: UInf+

value: no

value: Female


title: Pool of 3 B16/F10-BrM brains

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

data_processing:
STARSolo
Assembly: GRCm38
Supplementary files format and content: Data matrices form STARSolo output

source_name: Brain microenvironment enriched in astrocytes

extract_protocol:
Mouse brains were processed with the Adult Brain Dissociation Kit (Miltenyi, ref. 130-107-677) using gentleMACS C Tubes (Miltenyi, ref. 130-093-237) and the gentleMACS™ Octo Dissociator (Miltenyi, ref.  130-096-427). For myelin removal, a 30% percoll gradient was used. To isolate the highest possible amount of astrocytes, Anti-ACSA-2 (Miltenyi, ref. 130-097-678) microbeads were used and for dead cell removal, Debris Removal solution (Miltenyi, ref. 130-109-398) was added prior to analysis.
~10,000 cells per condition were loaded onto a 10x Chromium Single Cell Controller chip B (10x Genomics) as described by the manufacturer (Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3, PN-1000075). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended in the manufacturer's protocol.

value: Brain

value: 10 weeks old


title: dwaj1.3a_5

value: ENU


title: Pool of 3 naive brains

value: Brain microenvironment enriched in astrocytes


title: S090


title: dwba2.2d_29b

value: female


title: S094

value: Sepsis+

value: Male


title: 20210122_5B_mGGCTsh3

city: Kyoto

first: Kozue

last: Nose

address: Misasagi-Nakauchicho 5, Yamashina-ku

institute: Kyoto Pharmaceutical University

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) 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 Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: murine gliolbastoma stem cell line

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The glioblastoma stem cell line was established with the neurosphere method from SB transposon-mediated de novo murine glioblastomas. The tumor tissues were minced with scalpels and digested with accutase (Innovative Cell Technologies, San Diego, CA, USA) at 37˚C for 20–30 min, and then washed and incubated with serum-free neural stem cell culture medium consisting of Neurobasal Medium supplemented with B27, N2 (Gibco/Thermo Fisher Scientific, Waltham, MA, USA), and 10 ng/ml EGF and bFGF (R&D Systems, Minneapolis, MN, USA). The neurospheres were dissociated by accutase (Innovative Cell Technologies) and maintained in the neural stem cell culture medium at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells lysed with Trizol (Thermo Fisher Scientific, Waltham, MA) and purified with the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Stably GGCT-knockdown glioblastoma stem cells were established via lentiviral-mediated shRNA. The cells were transducted with lentiviral non-target (control) or GGCT shRNA.

value: murine gliolbastoma stem cell line

value: GGCT shRNA


title: 20210205_5B_NT

value: control


title: SPIB-Positive_ICAM2-Positive_GP2-Negative-2

city: Utrecht

first: Daisong

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Sequencing reads from illumina sequencing were aligned to the human transcriptome with BWA (Li and Durbin, 2009).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

source_name: Intestine

extract_protocol:
Cells were lysed by 5 min at 65 ℃, after which RT and second strand mixes were dispersed with the Nanodrop II liquid handling platform (GC biotech). Aqueous phase was separated from the oil phase after pooling all cells in one library, followed by IVT transcription.
The CEL-Seq2 protocol was used for library prep. Primers consisted of a 24 bp polyT stretch, a 6bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 50 Illumina TruSeq small RNA kit adaptor and a T7 promoter. mRNA of each cell was then reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed for linear following the CEL-Seq 2 protocol (Hashimshony et al., 2016). Illumina sequencing libraries were then prepared with the TruSeq small RNA primers (Illumina) and sequenced at Illumina NextSeq

value: Intestine

value: orgnaoid

value: Enterocytes and M cells

value: wild-type

value: NO


title: dwaj1.3a_25b

value: male

value: microdissected tumour

value: Apchet


title: 20210205_5B_mGGCTsh3


title: dwba2.2d_4


title: SPIB-Negative-2


title: 20210128_5B_mGGCTsh3


title: SPIB-Positive_ICAM2-Positive_GP2-Positive-2


title: Differentiated M cells and enterocytes plate1

data_processing:
Paired-end reads from illumina sequencing were aligned to the human transcriptome with BWA (Li and Durbin, 2009). Read 1 was used for assigning reads to correct cells and libraries, while read 2 was mapped to gene models. Reads that mapped equally well to multiple locations were discarded. Read counts were first corrected for UMI barcode by removing duplicate reads that had identical combinations of library, cellular, and molecular barcodes and were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts, 256 possible UMI’s and poissonian counting statistics.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files

extract_protocol:
Cells were lysed by 5 min at 65 ℃, after which RT and second strand mixes were dispersed with the Nanodrop II liquid handling platform (GC biotech). Aqueous phase was separated from the oil phase after pooling all cells in one library, followed by IVT transcription.
The CEL-Seq2 protocol was used for library prep. Primers consisted of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific 8bp barcode, the 50 Illumina TruSeq small RNA kit adaptor and a T7 promoter. mRNA of each cell was then reverse transcribed, converted to double-stranded cDNA, pooled and in vitro transcribed for linear following the CEL-Seq 2 protocol (Hashimshony et al., 2016). Illumina sequencing libraries were then prepared with the TruSeq small RNA primers (Illumina) and sequenced paired-end at 75 bp read length the Illumina NextSeq


title: Differentiated M cells and enterocytes plate2


title: dwba2.2d_19a


title: 20210128_5B_NT


title: C086

value: Whole blood

value: SIRS-

value: no

value: Female


title: dwaj1.3a_26b

value: ENU


title: dwba2.2d_1

value: female


title: SPIB-Positive_ICAM2-Positive_GP2-Negative-1


title: dwba2.2d_9


title: SPIB-Positive_ICAM2-Positive_GP2-Positive-1


title: 20210122_5B_NT

value: murine gliolbastoma stem cell line


title: dwaj1.3a_27a


title: C087

value: Male


title: SPIB-Positive_ICAM2-Negative_GP2-Negative-1


title: SPIB-Positive_ICAM2-Negative_GP2-Negative-2


title: Venetoclax-resistant OSU-CLL CLL cell line treated with Venetoclax, EXP3

city: Omaha

first: Dalia

last: ElGamal

state: Nebraska

department: Eppley Institute for Research in Cancer and Allied Diseases

institute: University of Nebraska Medical Center

data_processing:
For each sample, quality control was assessed by the Fragment Analyzer Automated CE System.
Sequenced reads were mapped using HISAT2 version 2.1.0 to genome build hg38, guided by ENSEMBL GRCh38.99 transcript annotations.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: B-cell

growth_protocol: Wild-type HG-3, wild-type OSU-CLL, ibrutinib-resistant HG-3, and venetoclax-resistant OSU-CLL cells were cultured in RPMI-1640 with 2 mM L-glutamine, supplemented with 100 U/mL penicillin/100 μg/mL streptomycin, and 10% heat-inactivated fetal bovine serum

extract_protocol:
All cells (1.5e6 cells/mL) were collected for RNA extraction using the miRNeasy Mini Kit (Qiagen) according to manufacturer instructions
Samples were prepared using the Universal Plus mRNA-Seq with NuQuant kit

treatment_protocol: Wild-type and ibrutinib-resistant HG-3 CLL cells were treated with SpiD3 (2 μM), ibrutinib (1 μM), or DMSO for 4 h. Wild-type and venetoclax-resistant OSU-CLL cells were treated with SpiD3 (2 μM), venetoclax (1 μM), or DMSO for 4 h

value: B-cell

value: OSU-CLL

value: CLL B-cell

value: Cell line

value: Venetoclax 1 uM


title: Venetoclax-resistant OSU-CLL CLL cell line treated with Venetoclax, EXP1


title: Venetoclax-resistant OSU-CLL CLL cell line treated with Venetoclax, EXP2


title: Venetoclax-resistant OSU-CLL CLL cell line treated with SpiD3, EXP2

value: SpiD3 2 uM


title: S086

value: UInf+


title: dwaj1.3a_23a

value: male

value: microdissected tumour


title: Multiplex experiment 1 - AML1010.5 and AML1012.1 - Total-seq D

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
surface marker expression
Raw data available: dbGap phs003015.v3

data_processing:
Demultiplexing of llumina sequencer's base call files (BCLs).
Alignment of raw reads to hg38, extraction of cell barcodes, DNA amplicons and oligotags using Tapestri pipeline.
Extraction of called variants and surface marker expression using Tapestri Insights v3.0.2.
Demultiplexing of samples based on clustering of single nucleotide variants in Tapestri Insights v3.0.2
Assembly: GRCh38
Supplementary files format and content: Allele frequencies and surface marker expression in tsv file format.
Library strategy: Single cell DNA sequencing and CITE-seq using Total-seq D oligotags.

molecule: protein

source_name: bone marrow

extract_protocol:
Single cell suspensions were multiplexed and stained with Total-seq D surface marker oligotags followed loading onto Tapestri cartridge.
Single cell DNA and oligotag sequencing according to manufacturer's instructions (Mission Bio) using custom panels for mitochondrial and somatic nuclear DNA mutations.

value: bone marrow

tag: pool

value: ADT

value: C10 (AML1010), screening (AML1012)


title: SPIB-Negative-1

value: Intestine

value: orgnaoid

value: Enterocytes and M cells

value: wild-type

value: NO


title: C085

value: Whole blood

value: SIRS-

value: no

value: Male


title: dwaj1.3a_9

value: Apchet

value: ENU


title: Venetoclax-resistant OSU-CLL CLL cell line treated with DMSO (vehicle), EXP2

value: B-cell

value: OSU-CLL

value: CLL B-cell

value: Cell line

value: Vehicle (DMSO)


title: dwaj1.3a_25a

value: male

value: microdissected tumour


title: C070

value: Female


title: dwba2.2d_26a

value: female


title: Wild-type OSU-CLL cell line treated with ibrutinib, EXP2

value: Venetoclax 1 uM


title: S085

value: Sepsis+

value: yes


title: dwaj1.3a_20b


title: C082

value: Whole blood

value: SIRS-


title: Wild-type OSU-CLL cell line treated with ibrutinib, EXP1


title: Wild-type OSU-CLL cell line treated with SpiD3, EXP3

value: SpiD3 2 uM


title: dwba2.2d_29a

value: Apchet


title: Venetoclax-resistant OSU-CLL CLL cell line treated with SpiD3, EXP3


title: dwba2.2d_19b

value: ENU


title: Venetoclax-resistant OSU-CLL CLL cell line treated with SpiD3, EXP1

value: B-cell


title: S074

value: UInf+

value: no

value: Male


title: dwaj1.3a_26a


title: S082


title: Multiplex experiment 1 - AML1010.5 and AML1012.1 - scDNA-seq

description:
Allele frequencies
Raw data available: dbGap phs003015.v3

value: bone marrow

value: amplicon

value: C10 (AML1010), screening (AML1012)


title: Venetoclax-resistant OSU-CLL CLL cell line treated with DMSO (vehicle), EXP3

value: OSU-CLL

value: CLL B-cell

value: Cell line

value: Vehicle (DMSO)


title: C072


title: Venetoclax-resistant OSU-CLL cell line treated with DMSO (vehicle), EXP1


title: S087

value: Sepsis+

value: yes


title: dwba2.2d_7

value: female

value: microdissected tumour


title: Wild-type OSU-CLL cell line treated with SpiD3, EXP2

value: SpiD3 2 uM


title: C083

value: Whole blood

value: SIRS-

value: Female


title: dwaj1.3a_22a

value: male

value: Apchet

value: ENU


title: Wild-type OSU-CLL cell line treated with DMSO (vehicle), EXP3

value: B-cell


title: S083


title: Wild-type OSU-CLL cell line treated with SpiD3, EXP1


title: Wild-type OSU-CLL cell line treated with DMSO (vehicle), EXP1


title: S070

value: UInf+

value: no


title: Wild-type OSU-CLL cell line treated with ibrutinib, EXP3

value: OSU-CLL

value: CLL B-cell

value: Venetoclax 1 uM


title: Ibrutinib-resistant HG-3 CLL cell line treated with ibrutinib, EXP3

value: Cell line

value: Ibrutinib 1 uM


title: dwba2.2d_28b

value: female


title: S077

value: Sepsis+

value: yes

value: Male


title: S072

value: Whole blood


title: C074

value: SIRS-


title: Ibrutinib-resistant HG-3 CLL cell line treated with ibrutinib, EXP2


title: Wild-type HG-3 CLL cell line treated with ibrutinib, EXP3


title: Ibrutinib-resistant HG-3 CLL cell line treated with DMSO (vehicle), EXP1

value: Vehicle (DMSO)


title: Ibrutinib-resistant HG-3 CLL cell line treated with DMSO (vehicle), EXP3


title: dwba2.2d_3

value: microdissected tumour

value: Apchet


title: C055


title: Wild-type HG-3 CLL cell line treated with ibrutinib, EXP1

value: B-cell


title: Ibrutinib-resistant HG-3 CLL cell line treated with SpiD3, EXP2

value: SpiD3 2 uM


title: Ibrutinib-resistant HG-3 CLL cell line treated with SpiD3, EXP1


title: Ibrutinib-resistant HG-3 CLL cell line treated with SpiD3, EXP3


title: Ibrutinib-resistant HG-3 CLL cell line treated with ibrutinib, EXP1


title: Wild-type OSU-CLL cell line treated with DMSO (vehicle), EXP2


title: C062

value: no

value: Female


title: tumor, iron positive, POS4R

data_processing:
Kallisto v 0.46.2
Assembly: mm10-3.0.0
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample

extract_protocol:
Tumor tissue was minced and digested with collagenase b and dnase I for at 37C for 45 min. Samples were filtered, RBC lysed and resuspended in FACS buffer. Samples were then iron enriched using magnetic columns to obtain an iron enriched eluate and a non-iron enriched flowthrough. Total RNA was isolated using GenElute Mammalian Total RNA Miniprep Kit with DNAse I digestion (Sigma).
RNA libraries for RNA-seq were prepared by Novogene.

value: Tumor

value: WT C57BL/6


title: C046


title: Wild-type HG-3 CLL cell line treated with SpiD3, EXP1

value: CLL B-cell

value: Cell line


title: S055


title: dwba2.2d_10

value: female

value: ENU


title: Wild-type HG-3 CLL cell line treated with DMSO (vehicle), EXP1


title: Wild-type HG-3 CLL cell line treated with ibrutinib, EXP2

value: Ibrutinib 1 uM


title: tumor, iron positive, POS3L


title: dwba2.2d_26b


title: Human brain metastasis from lung cancer

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

institute: Spanish National Cancer Research Centre (CNIO)

description: 10x Genomics

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina).
Assembly: GRCh38
Supplementary files format and content: Data matrices from cellranger-7.0.0

source_name: Brain metastasis

extract_protocol:
25-50 mg of fresh biopsies were fixed and after 22 hours at 4 ºC, fixed tissue was digested and preserved for long term storage. Finally, single cell suspension was processed with the Chromium Chip/Single Cell Fixed RNA kit for Human Transcriptome
Fixed cell suspensions obtained with the "Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit" (10xGenomics PN-1000414) were processed with the "Chromium Fixed RNA Profiling Reagent Kit" according to the manufacturer's instructions (10xGenomics, user guide CG000527). Briefly, samples were hybridised to a *human* transcriptome probe set (Chromium Fixed RNA Kit, 10xGenomics *PN1000474*) and encapsulated in gel beads in emulsion (GEMs) in a Chromium iX instrument (10xGenomics). GEM recovery and gene expression library construction were all performed as recommended by the manufacturer. Libraries were sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
Libraries were sequenced with an Illumina NextSeq 550 (using v2.5 reagent kits) in paired-end fashion (28bp + 56bp bases). Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with bcl2fastq2 (Illumina)

value: Brain metastasis

value: Fixed tissue


title: tumor, iron positive, POS5L


title: Wild-type HG-3 CLL cell line treated with SpiD3, EXP2


title: PC-9_YVMA-5_Vehicle_QDx1_6h_in_vivo_rep5

value: lung

value: epithelial cell

value: xenograft


title: PC-9_YVMA-5_Vehicle_QDx1_6h_in_vivo_rep4


title: C038

value: Whole blood

value: SIRS-

value: Male


title: Wild-type HG-3 CLL cell line treated with SpiD3, EXP3

value: B-cell

value: SpiD3 2 uM


title: PC-9_YVMA-5_Vehicle_QDx1_6h_in_vivo_rep3


title: Wild-type HG-3 CLL cell line treated with DMSO (vehicle), EXP3

value: Vehicle (DMSO)


title: tumor, iron negative, NEG3R

value: Tumor

value: WT C57BL/6


title: C064

value: no


title: Ibrutinib-resistant HG-3 CLL cell line treated with DMSO (vehicle), EXP2

value: CLL B-cell

value: Cell line


title: Wild-type HG-3 CLL cell line treated with DMSO (vehicle), EXP2


title: tumor, iron positive, POS3R


title: S062

value: UInf+

value: Female


title: Human brain metastasis from breast cancer

description: 10x Genomics

value: Brain metastasis

value: Fixed tissue


title: tumor, iron negative, NEG5L


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_6h_in_vivo_rep2

value: lung

value: epithelial cell


title: tumor, SS_CD45 , scRNAseq

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made by using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: tumor

extract_protocol:
Single cell suspensions were generated by digesting the minced tumors with 2 mg/mL collagenase B and 30 U/ml DNase I for 45 minutes at 37°C. RBCs were lysed using ACK lysis buffer. Samples were filtered through 70-µM cell strainers and CD45+ cells were sorted before sequencing.
Library was constructed using the manufacturer's instructions (Single Cell 3' v3)

value: tumor

value: TAT-Cre protein injection


title: C065

value: Whole blood

value: SIRS-

value: Male


title: PC-9_YVMA-5_Vehicle_QDx1_6h_in_vivo_rep2

value: xenograft


title: tumor, KP 877, scRNAseq

description: 10x Genomics

extract_protocol:
Single cell suspensions were generated by digesting the minced tumors with 2 mg/mL collagenase B and 30 U/ml DNase I for 45 minutes at 37°C. RBCs were lysed using ACK lysis buffer. Samples were filtered through 70-µM cell strainers and Ficoll columns.
Library was constructed using the manufacturer's instructions (Single Cell 3' v3)

value: Tumor

value: KP (LSL-KrasG12D+; Trp53fl/fl)


title: PC-9_YVMA-5_Vehicle_QDx1_6h_in_vivo_rep1


title: C042

value: no


title: C067


title: tumor, iron negative, NEG3L

value: WT C57BL/6


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_6h_in_vivo_rep3


title: C066


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_6h_in_vivo_rep1


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_2h_in_vivo_rep3


title: C061


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_2h_in_vivo_rep4


title: tumor, iron negative, NEG4R


title: C069


title: C058

value: yes


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_2h_in_vivo_rep2


title: CD8+ T cells STAT3+ CM  replicate #3

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (GRCm39) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Assembly: GRCm39/vM26
Supplementary files format and content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values

source_name: CD8 + T cells

growth_protocol: CD8+ sorted  T cells were activated with anti-mouse CD3e clone 145-2C11 (BD Biosciences, ref. 553066, 1 µg/ml) coated plates, soluble anti-mouse CD28 (37.51) (Tonbo Biosciences, ref. 70-0281-U500, 1 µg/ml) and mouse IL-2 (Miltenyi Biotec, ref. 130-094-054, 0.1 µg/ml) in RPMI medium supplemented with 10% FBS and Penicillin-Streptomycin for one day before conditioned medium (CM) from pSTAT3+ and pSTAT3- astrospheres was added. Two days after addition of CM, total RNA was extracted.

extract_protocol:
RNA was harvested using PicoPure RNA isolation Kit (ThermoFisher).
Total RNA samples (500ng), with RNA Quality score of 9.4 on average (range 9.0-9.8 on a PerkinElmer LabChip analyzer), were converted into sequencing libraries with the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760). Briefly, polyA+ fraction is purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated library is completed by PCR with Illumina PE primers. The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: CD8 + T cells

tag: agent

value: INCUBATION CM STAT3+

value: WT

tag: time point

value: Day 3


title: CD8+ T cells STAT3+ CM  replicate #1


title: tumor, Bach1 KO, scRNAseq

description: 10x Genomics

extract_protocol:
Single cell suspensions were generated by digesting the minced tumors with collagenase B and DNase I for 45 minutes at 37°C. RBCs were lysed and samples were filtered through 70-µM cell strainers. CD45+ cells were then sorted for scRNAseq.
Library was constructed using the manufacturer's instructions (Single Cell 3' v3)

tag: tissue

value: T cell depletion with anti-CD3 antibody,


title: tumor, KP 849, scRNAseq

description: 10x Genomics


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_6h_in_vivo_rep4

value: lung

tag: cell line

tag: cell type

value: epithelial cell


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_6h_in_vivo_rep5

tag: genotype

tag: treatment


title: C041

tag: condition

tag: organ dysfunction


title: Spinal Cord, no shRNA3

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description:
10x Genomics Chromium 3' v.2
SCmerge_counts.tsv.gz
SCmerge_metadata.tsv.gz
barcode-1_3

data_processing:
CellRanger (version 7.07.1) pipeline and mouse transcriptome version mm10 were used to align reads and generate gene expression data.
Assembly: mm10
Supplementary files format and content: .tsv.gz files containing raw expression counts and corresponding metadata in separate .tsv.gz (meta) files

source_name: Spinal Cord, no shRNA

extract_protocol:
Single nucleus suspensions were prepared from isolated RVM and spinal cord samples via dounce homogenization in Tris buffer containing 0.1% Triton X-100, as well as protease/RNAse inhibitors, and where appropriate, Actinomycin D at a concentration of 15µM. Debris was removed via gradient centrifugation. To obtain enriched neuronal samples, nuclei suspensions were subjected to Fluorescence-activated cell sorting (FACS) for either NeuN (Figure 2a, Figure 5a), or tdTomato (Figure 2f). FACS was performed using a BD FACSAria III Sorter (BD Biosciences, Franklin Lakes, NJ USA). Single cell suspensions were prepared from WT mice previously injected intraspinally with AAVretro-EGFP to label descending projections from the RVM. The RVM was then sectioned via Vibratome and gently dissociated with Papain and DNase. Neurons were enriched and debris was removed via gradient centrifugation. Single EGFP-positive cells were selected via FACS.
Sorted nuclei or cells were loaded onto a 10X Genomics Chromium Chip and single nuclei/cell droplets were obtained. Reverse transcription, cDNA amplication and Library preparation were all performed according to the manufacturer's instructions.

value: Spinal cord

value: Neuron


title: tumor, KP 847, scRNAseq

description: 10x Genomics


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_6h_in_vivo_rep5

extract_protocol:
In vivo: Frozen tumours were cut into 5x5 mm pieces and ground using one steel bead (#69989 Qiagen) per 2 mL vial in 1 mL Trizol using a tissue lyser II (Quiagen) at 4 °C (1/s frequency, 30 sec, 30 cycles). Lysates were processed using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions. ; In vitro: After treatment, cells were washed with ice cold PBS and RNA extracted using the RNeasy Plus Universal Mini Kit (Qiagen Cat No 73404) following the manufacturer’s instructions using 1 mL Trizol per 6-well. RNA was eluted in 50 µL of ddH2O for further processing
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina from Lexogene according to manufacturer's instructions.


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_2h_in_vivo_rep1


title: C063

first: Alberto

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

value: Whole blood

value: SIRS-

tag: Sex


title: PC-9_YVMA-5_BI01810631_QDx1_3mpg_2h_in_vivo_rep5

value: xenograft


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_6h_in_vivo_rep4


title: CD8+ T cells STAT3- CM  replicate #3

value: INCUBATION CM STAT3-


title: Spinal Cord, no shRNA2

description:
10x Genomics Chromium 3' v.2
SCmerge_counts.tsv.gz
SCmerge_metadata.tsv.gz
barcode-1_2


title: CD8+ T cells STAT3- CM  replicate #2


title: CD8+ T cells STAT3- CM  replicate #1


title: Spinal Cord, no shRNA1

description:
10x Genomics Chromium 3' v.2
SCmerge_counts.tsv.gz
SCmerge_metadata.tsv.gz
barcode-1_1


title: CD8+ T cells STAT3+ CM  replicate #2


title: NC HSFBs rep 2 input

city: Shanghai

first: Qirui

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

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

description: MeRIP-seq for HSFBs

data_processing:
MACS2 and HOMER software were used to analyze the distributions of peaks and motifs.
Assembly: GRCh19
Supplementary files format and content: List of m6A modified sites on pri-mRNAs
Library strategy: MeRIP-seq

source_name: Hypertrophic scar-derived fibroblasts

extract_protocol:
MeRIP is based on the previous m6A-seq protocol. Briefly, we purify the RNA of the sample and then fragmented them into 100nt. Anti-m6A antibodies were then used to capture RNA fragments with m6A methylation modification.
After elution of the free m6A, a library was constructed and massively parallel sequencing was performed.

value: Hypertrophic scar-derived fibroblasts

value: Negative control


title: Spinal Cord, shBDNF3

description:
10x Genomics Chromium 3' v.2
ShBmerge_counts.tsv.gz
ShBmerge_metadata.tsv.gz
barcode-1_3

source_name: Spinal Cord, shBDNF


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_6h_in_vivo_rep3


title: C060

city: Jena

address: Adolf-Reichwein-Straße 23

value: no

value: Male


title: C056


title: NC HSFBs rep 2 IP

description: MeRIP-seq for HSFBs


title: Spinal Cord, shBDNF2

description:
10x Genomics Chromium 3' v.2
ShBmerge_counts.tsv.gz
ShBmerge_metadata.tsv.gz
barcode-1_2


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_6h_in_vivo_rep2


title: Spinal Cord, shBDNF1

description:
10x Genomics Chromium 3' v.2
ShBmerge_counts.tsv.gz
ShBmerge_metadata.tsv.gz
barcode-1_1


title: C044


title: C050

value: yes


title: NC HSFBs rep 1 input

description: MeRIP-seq for HSFBs


title: C040


title: NC HSFBs rep 1 IP

description: MeRIP-seq for HSFBs


title: Spinal Cord, shScrambled2

description:
10x Genomics Chromium 3' v.2
Scrmerge_counts.tsv.gz
Scrmerge_metadata.tsv.gz
barcode-1_2

source_name: Spinal Cord, shScrambled


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_6h_in_vivo_rep1


title: Mettl3_sh HSFBs rep 1

description:
RNA-seq sample for Mettl3-knockdown HSFBs
103-3sh

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double- stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA- tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor- ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).
Then libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. The sequences were processed and analyzed by GENEWIZ.

value: Mettl3 knockdown


title: Spinal Cord, shScrambled3

description:
10x Genomics Chromium 3' v.2
Scrmerge_counts.tsv.gz
Scrmerge_metadata.tsv.gz
barcode-1_3


title: S058

extract_protocol:
Total RNA was extracted from whole blood pre-operative samples and preserved with RNAlater (ThermoFisher). 1.8 mL of RNAlater-preserved blood was used for manual RNA extraction using the RiboPure-Blood Kit (Thermofisher) and following the manufacturer’s instructions.
mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs(dUTP, dATP, dGTP and dCTP), RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Purification followed by AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. The strand-specific cDNA library was generated after the final PCR enrichment. QC of the constructed library included testing library concentration preliminary with Qubit 2.0 Fluorometer (ThermoFisher), insert size with BioAnalyzer 2100 (Agilent) and qPCR to quantify effective library concentration. Qualified QC checked libraries were loaded on a NovaSeq 6000 S4 (Illumina) for sequencing using paired end mode with 150 bp read length (2x150 cycles)

value: UInf+


title: S040

value: Sepsis+


title: Spinal Cord, shScrambled1

description:
10x Genomics Chromium 3' v.2
Scrmerge_counts.tsv.gz
Scrmerge_metadata.tsv.gz
barcode-1_1


title: NC HSFBs rep 2

description:
RNA-seq sample for NC
824-con


title: Mettl3_sh HSFBs rep 2

description:
RNA-seq sample for Mettl3-knockdown HSFBs
824-3sh


title: RNA_IDH2_KDM3B_rep3

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: Idh2 R140Q  HSPCs with Kdm3b sgRNA, biol rep 3

data_processing:
FASTQ files were demultiplexed using a java script from Takara.
FASTQ files were mapped, and transcript counts were enumerated using STAR.
Counts were input into R and RNA-sequencing analysis was completed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited-text file includes raw counts for each sample

source_name: Primary hematopoetic stem and progenitor cell (lineage negative, ckit positive)

growth_protocol: Hematopoetic stem and progenitor cells were co-cultured with bone marrow endothelial cells in stemspan media at 37 C 5% CO2.

extract_protocol:
RNA was harvested using zymo direct-zol RNA microprep kit. 500 ng was used for construction of sequencing libraries.
cDNA was generated with the SMART-Seq HT Kit (Takara) and RNA-sequencing libraries were prepared with the Nextera XT (Illumina) Kit following manufacturers’ protocols.

treatment_protocol: Hematopoetic stem and progenitor cells were infected with lentivirus encoding sgRNAs, incubated overnight, and then co-cultured with bone marrow endothelial cells for 7 days.

value: Idh2 R140Q

value: Kdm3b sgRNA


title: S064

last: Garcia Lopez


title: S066


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_2h_in_vivo_rep5

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system or Illlumina NextSeq 2000. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Quality control was performed on samples using FASTQC (v.0.11.5), multiqc (v.1.12), picardmetrics(v0.2.4), and bioconductor-dupRadar (v1.0.0) at respective steps. Single-end reads were mapped against Homo sapiens genome (GRCh38) using the STAR (v2.5.2b) aligner. Samples were quantified with the transcript abundances using featureCount (v1.5.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

value: lung

value: epithelial cell


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_2h_in_vivo_rep3


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_2h_in_vivo_rep1


title: RNA_IDH2_KDM3B_rep2

description: Idh2 R140Q  HSPCs with Kdm3b sgRNA, biol rep 2

value: Primary hematopoetic stem and progenitor cell (lineage negative, ckit positive)


title: S057

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA version (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.99 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Differentially expressed genes (DEGs) were determined if significance was reported by either DESeq2 (v1.22.1), or edgeR (v3.24.3) and a |log2(fold change)|≥ 0.25.
Assembly: GRCh38.99
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

value: Whole blood


title: S056


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_24h_in_vivo_rep5


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_2h_in_vivo_rep4


title: 5637_70 μM

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

country: Taiwan

institute: China Medical University

data_processing:
1. trim adapter: trimmomatic
2. Alignment: Hisat2
3. Expression profiling: stringtie
Assembly: Homo_sapiens.GRCh38
hisat2_index: V97

source_name: Bladder cancer cells (5637)

growth_protocol: 5637 and T24 cells were both cultured in RPMI medium. All media were supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin.

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy mini kit. The quality of total RNA was analyzed by the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit.
RNA-seq libraries were prepared using Illumina® TruSeq RNA Library Prep Kit v2 and were sequenced using Illumina® Hiseq2500 to obtain 150-bp paired-end reads.

treatment_protocol: 5637 and T24 cells were treated with or without 70 and 60 mM protodioscin respectively for 6 hr.

value: protodioscin


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_2h_in_vivo_rep2

value: xenograft


title: RNA_IDH2_ROSA_rep3

description: Idh2 R140Q  HSPCs with Rosa sgRNA, biol rep 3

value: Rosa sgRNA


title: RNA_IDH2_KDM3B_rep1

description: Idh2 R140Q  HSPCs with Kdm3b sgRNA, biol rep 1


title: 5637_0 μM

value: untreated


title: S044

source_name: Whole blood


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_24h_in_vivo_rep3

source_name: lung


title: NC HSFBs rep 1

last: Wang

description:
RNA-seq sample for NC
103-con

value: Hypertrophic scar-derived fibroblasts

value: Negative control


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_24h_in_vivo_rep4


title: T24_60 μM

source_name: Bladder cancer cells (T24)


title: RNA_IDH2_ROSA_rep1

description: Idh2 R140Q HSPCs with Rosa sgRNA, biol rep 1


title: S046

value: Male


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_24h_in_vivo_rep2


title: RNA_IDH2_ROSA_rep2

description: Idh2 R140Q  HSPCs with Rosa sgRNA, biol rep 2


title: PC-9_YVMA-5_BI01810631_QDx1_10mpg_24h_in_vivo_rep1


title: S039

value: no


title: T24_0 μM


title: S042

value: yes

value: Female


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_6h_in_vivo_rep5


title: RNA_WT_KDM3B_rep2

description: WT HSPCs with Kdm3b sgRNA, biol rep 2

value: wild-type


title: C008

value: SIRS-


title: RNA_WT_KDM3B_rep1

description: WT HSPCs with Kdm3b sgRNA, biol rep 1

value: Kdm3b sgRNA


title: C024


title: RNA_WT_ROSA_rep3

description: WT HSPCs with Rosa sgRNA, biol rep 3


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_6h_in_vivo_rep4

value: lung


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_6h_in_vivo_rep3

value: epithelial cell


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_6h_in_vivo_rep2


title: C018


title: RNA_WT_KDM3B_rep3

description: WT HSPCs with Kdm3b sgRNA, biol rep 3

value: Primary hematopoetic stem and progenitor cell (lineage negative, ckit positive)


title: RNA_WT_ROSA_rep1

description: WT HSPCs with Rosa sgRNA, biol rep 1


title: C016 & C037

value: Whole blood


title: PC-9_YVMA-5_BI01810631_BIDx3_10mpg_6h_in_vivo_rep1


title: RNA_WT_ROSA_rep2

description: WT HSPCs with Rosa sgRNA, biol rep 2