title: Batch 2 bulk RNAseq HGR0000124_T1


title: Batch 2 bulk RNAseq HGR0000391_T0

status: Public on Feb 10 2021

type: SRA

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

country: USA

institute: Yale School of Medicine

description:
For each sample, a sample of 100,000 cells was processed in Trizol using the miRNAeasy micro kit (Qiagen, Germantown, MD; catalogue number 217084) and standard RNA sequencing libraries were generated using Illumina Truseq library (Illuimna, San Diego, CA; 20020595) preparation kits. Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The sequencing reads were adapter and quality trimmed and then aligned to the human genome using the splice-aware STAR aligner and SNP calls were generated using the previously published protocol: Nucleic Acids Research, Volume 47, Issue 21, 02 December 2019, Page e136. These SNP calls were then used along with the demuxlet software (https://github.com/statgen/demuxlet) to demultiplex the single cell multimodal RNAseq data (see supplemental demux.best files). Counts per gene were generated using htseq count (version 0.9.1) and the UCSC hg19 genome annotation.
B2_B3_bulkRNAseq_countmtx.csv

library_source: transcriptomic

data_processing:
fastq generation: Illumina bcl2fastq 2.20
mapping, CellRanger 3.1.0 (10x Genomics)
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
secondary analysis: Seurat 3.1.0 (R package)
T cell receptor VDJ analysis: CellRanger 3.1.0
One anonymized donor (SDH8) was excluded from further analysis, as we discovered an extremely expanded B phenotype consistent lymphoma in this sample. An additional leukopack-derived PBMC sample (CHI014, anonymized and without demographic information)  was used in each experimental batch as a technical control, but not used in later comparisons. Samples HDVO_bc and HDML_bc in Batch 2 were used as a test of cyropreserving buffy coat samples, and were not used in the furtehr analysis.
Genome_build: hg19 (cellranger version 1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_1.2.0)
Supplementary_files_format_and_content: CellRanger count matrices in h5 data format; T cell clonal analysis, comma seperated values

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Frozen PBMC samples were thawed, recovered and washed using RPMI media with 10% FBS and 10mg/mL DNase I (STEMCELL 07470). Samples from different donors were pooled evenly before staining; single cells can be demultiplexed in silico using individual specific single nucleotide polymorphism (SNP) information during data analysis (see below; demultiplexing for each lane is provided in the *demux.best supplemental files). Multiple cell pools were prepared, such that cells from the same individual but different timepoints would be in different pools. PBMC pools were Fc blocked (Human TruStain FcX, BioLegend 422302) and stained with Totalseq-C human ‘hashtag’ antibodies (BioLegend), washed with staining buffer (2% BSA in PBS). This round of hashtag staining allows the different pools to be identified in the analysis, which when combined with the SNP-based demultiplexing, allows full identification of each sample. A fraction of the combined cells was used for sorting total B, T, CD14+ monocyte and CD14- innate cell populations (batch 1) or non-naïve T and B cells (batches 2 and 3). Separately for the unsorted and sorted cell fractions, hashtagged PBMC pools were combined and cells were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 192 surface proteins. Then, cells were washed three times, resuspended in PBS, and counted before proceeding immediately to the single cell partition step. Flow cytometry sorting to enrich certain cell populations was performed as follows: Pooled PBMC samples from different donors were washed with PBS and incubated with Zombie Red Fixable viability dye (1:1000 in PBS, BioLgend) for 20 minutes at 4°C protected from light. Then cells were washed with flow staining buffer (10% FBS in PBS) and Fc blocked (Human TruStain FcX, BioLegend) for 15 minutes on ice. For experimental batches 2 and 3, the non-naïve B- and T- cell populations were sorted. The fluorescence-labeled antibody cocktail against human CD45(APC/Cyanine7, BioLegend 368516), CD3(AF488, BioLegend 344810), CD19(APC, BioLegend 363006), CCR7(BV786, BioLegend 353230), CD95(BV650, BioLgend 305642), IgD(PerCP-Cy5.5, BioLegend 348208) and CD27(PE/Cyanine7, BioLegend 356412) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). Non-naïve B cell population was gated by CD45+CD19+IgD- or CD27+ and non-naïve T cell population was gated by CD45+CD3+CCR7low or CD95+. Sorted cells were CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step. For experimental batch 1, total B, T, CD14+ monocyte and CD14- innate cell populations were sorted and pooled with unsorted PBMCs by ratio 1:1:1:1:1 to balance the number of each population captured in the final pool for CITE-seq assay. The fluorescence-labeled antibody cocktail against human CD14(BV421, BioLegend 325628), CD3(AF488, BioLegend 344810), CD45(PE/Cyanine7, BioLegend 393408), CD19(APC, BioLegend 363006) and Totalseq-C human hashtag antibodies(BioLegend) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). B cell population was gated by CD45+CD19+CD3-; T cell population was gated by CD45+CD3+CD19-; monocyte population was gated by CD45+CD3-CD19-CD14+; other myeloid cells were gated by CD45+CD3-CD19-CD14-. Sorted 4 populations and unsorted PBMCs were pooled evenly. Then the final pool was CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step.
PBMC samples were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry (10x Genomics, Pleasanton, CA). The RT step was conducted in the Veriti Thermo Cycler (ThermoFisher Scientific, Waltham, MA). Single cell gene expression, cell surface protein, and T cell receptor (TCR) libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA) and quantified using Qubit Fluorometric (ThermoFisher). 10x Genomics 5’ Single cell gene expression, cell surface protein tag, TCR and BCR libraries were pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics 5’ v1.1 user guide. Sequencing saturation of the libraries ranged from approximately 60-80% for the cDNA and 20-40% for the surface protein tag libraries.

tag: unsorted or sorted t/b cells

value: Unsorted

tag: timepoint

value: Timepoint 0

tag: molecule

value: mRNA


title: Batch 2 bulk RNAseq SHD2

value: Healthy Control


title: Batch 2 bulk RNAseq HGR0000124_T0


title: Batch 2 bulk RNAseq HGR0000395_T0


title: Batch 2 bulk RNAseq HGR0000144_T0


title: Batch 2 bulk RNAseq HGR0000094_T1

value: Timepoint 1


title: PF-SE2

status: Public on Mar 22 2021

type: genomic

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

country: Germany

institute: Charite

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip and Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
using R (version 4.0.2)  minfi_1.36.0 package
arrays from different plattforms were combined using combineArrays function; beta values were normalized using minfi PreprocessFunnorm function; detection p-values was calculated using detectionP function; for methylated and unmethylated signals preprocess, Illumina function was used for normalization

label: cy3, cy5

molecule: genomic DNA

source_name: infratentorial

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tumor samples using Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol

tag: gender

value: m

tag: age

tag: subtype

value: pure SE


title: Batch 3 bulk RNAseq HGR0000051_T2

value: Timepoint 2


title: Batch 2 bulk RNAseq HGR0000094_T0


title: Batch 2 bulk RNAseq HGR0000092_T1


title: Batch 2 bulk RNAseq HGR0000418_T1


title: Batch 2 bulk RNAseq HGR0000115_T1


title: Batch 2 bulk RNAseq HGR0000042_T1


title: Batch 2 bulk RNAseq HGR0000069_T2


title: Batch 2 bulk RNAseq HGR0000144_T2


title: Batch 2 bulk RNAseq HGR0000069_T0


title: PF-SE44

value: f


title: Batch 2 bulk RNAseq HGR0000069_T1


title: Batch 2 bulk RNAseq HGR0000042_T0


title: Batch 2 bulk RNAseq HD_VO_PBMC


title: Batch 1 bulk RNAseq IM000040

description:
For each sample, a sample of 100,000 cells was processed in Trizol using the miRNAeasy micro kit (Qiagen, Germantown, MD; catalogue number 217084) and standard RNA sequencing libraries were generated using Illumina Truseq library (Illuimna, San Diego, CA; 20020595) preparation kits. Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The sequencing reads were adapter and quality trimmed and then aligned to the human genome using the splice-aware STAR aligner and SNP calls were generated using the previously published protocol: Nucleic Acids Research, Volume 47, Issue 21, 02 December 2019, Page e136. These SNP calls were then used along with the demuxlet software (https://github.com/statgen/demuxlet) to demultiplex the single cell multimodal RNAseq data (see supplemental demux.best files). Counts per gene were generated using htseq count (version 0.9.1) and the UCSC hg19 genome annotation.
B1_bulkRNAseq_countmtx.csv


title: Batch 2 bulk RNAseq HD_ML_bc

value: Technical test sample


title: Batch 2 bulk RNAseq HD_ML_PBMC


title: Batch 2 bulk RNAseq HD_VO_bc


title: Batch 1 bulk RNAseq HGR0000143


title: Batch 1 bulk RNAseq HGR0000137


title: Batch 1 bulk RNAseq HGR0000141


title: Batch 1 bulk RNAseq HGR0000098


title: Batch 1 bulk RNAseq HGR0000110


title: Batch 1 bulk RNAseq HGR0000093_T1


title: Batch 1 bulk RNAseq HGR0000093_T0


title: Batch 1 bulk RNAseq HGR0000091


title: Batch 1 bulk RNAseq HGR0000083_T0


title: Batch 1 bulk RNAseq HGR0000083_T1


title: Batch 1 bulk RNAseq HGR0000089


title: Batch 1 bulk RNAseq HGR0000079_T1


title: Batch 2 bulk RNAseq CHI014_B2


title: Batch 1 bulk RNAseq HGR0000078_T1


title: Batch 1 bulk RNAseq HGR0000071


title: Batch 1 bulk RNAseq HGR0000079_T0


title: Batch 1 bulk RNAseq CHI-014

value: Technical Control


title: Batch 1 bulkRNAseq AA220014


title: Batch 1 bulk RNAseq AA220907


title: Batch 1 bulk RNAseq HGR0000078_T0


title: Batch 1 bulk RNAseq HGR0000074


title: Batch1 bulkRNAseq AA220534


title: Batch 1 bulk RNAseq HGR0000136


title: Batch 3 PBMC 10x Lane 24 RNA

description: Multple donor samples are combined within each lane; demultiplexing information is in the demuxletResults.tar.gz and allbatches.HTOandTimepointMetadata.csv supplemental files. A filtered dataset of all cells is provided as a Seurat object in R data format, as supplemental file AllBatches_SeuratObj.rds.

value: Sorted

value: mixed

value: mRNA (cDNA) reads from mulitmodal scRNAseq


title: Batch 3 PBMC 10x Lane 22 RNA


title: Batch 3 PBMC 10x Lane 23 RNA


title: Batch 3 PBMC 10x Lane 21 RNA


title: Batch 3 PBMC 10x Lane 18 RNA


title: Batch 3 PBMC 10x Lane 20 RNA


title: Batch 3 PBMC 10x Lane 17 RNA


title: Batch 3 PBMC 10x Lane 15 RNA


title: Batch 3 PBMC 10x Lane 13 RNA


title: Batch 3 PBMC 10x Lane 19 RNA


title: Batch 3 PBMC 10x Lane 16 RNA


title: Batch 3 PBMC 10x Lane 14 RNA


title: Batch 3 PBMC 10x Lane 12 RNA


title: Batch 3 PBMC 10x Lane 11 RNA


title: Batch 3 PBMC 10x Lane 8 RNA


title: Batch 3 PBMC 10x Lane 9 RNA


title: Batch 3 PBMC 10x Lane 10 RNA


title: Batch 3 PBMC 10x Lane 6 RNA


title: Batch 3 PBMC 10x Lane 5 RNA


title: Batch 3 PBMC 10x Lane 22 TCR

description:
Multple donor samples are combined within each lane; demultiplexing information is in the demuxletResults.tar.gz and allbatches.HTOandTimepointMetadata.csv supplemental files. A filtered dataset of all cells is provided as a Seurat object in R data format, as supplemental file AllBatches_SeuratObj.rds.
B3_TCR_filtered_contig_annotations.csv

value: T cell receptor VDJ region reads from mulitmodal scRNAseq


title: Batch 3 PBMC 10x Lane 7 RNA


title: Batch 3 PBMC 10x Lane 4 RNA


title: Batch 3 PBMC 10x Lane 24 TCR


title: Batch 3 PBMC 10x Lane 21 TCR


title: Batch 3 PBMC 10x Lane 1 RNA


title: Batch 3 PBMC 10x Lane 2 RNA


title: Batch 3 PBMC 10x Lane 23 TCR


title: Batch 3 PBMC 10x Lane 15 TCR


title: Batch 3 PBMC 10x Lane 16 TCR


title: Batch 3 PBMC 10x Lane 19 TCR


title: Batch 3 PBMC 10x Lane 11 TCR


title: Batch 3 PBMC 10x Lane 10 TCR


title: Batch 3 PBMC 10x Lane 20 TCR


title: Batch 3 PBMC 10x Lane 14 TCR


title: Batch 3 PBMC 10x Lane 12 TCR


title: Batch 3 PBMC 10x Lane 9 TCR


title: Batch 3 PBMC 10x Lane 8 TCR


title: Batch 3 PBMC 10x Lane 7 TCR


title: Batch 3 PBMC 10x Lane 6 TCR


title: Batch 3 PBMC 10x Lane 3 RNA


title: Batch 3 PBMC 10x Lane 5 TCR


title: Batch 3 PBMC 10x Lane 3 TCR


title: Batch 3 PBMC 10x Lane 4 TCR


title: Batch 3 PBMC 10x Lane 2 TCR


title: Batch 3 PBMC 10x Lane 1 TCR


title: Batch 3 PBMC 10x Lane 18 TCR


title: Batch 3 PBMC 10x Lane 17 TCR


title: Batch 3 PBMC 10x Lane 23 CSP

value: Cell Surface Protein Tag reads from mulitmodal scRNAseq


title: Batch 3 PBMC 10x Lane 13 TCR


title: Batch 3 PBMC 10x Lane 22 CSP


title: Batch 3 PBMC 10x Lane 21 CSP


title: Batch 3 PBMC 10x Lane 19 CSP


title: Batch 3 PBMC 10x Lane 20 CSP


title: Batch 3 PBMC 10x Lane 18 CSP


title: Batch 3 PBMC 10x Lane 15 CSP


title: Batch 3 PBMC 10x Lane 16 CSP


title: Batch 3 PBMC 10x Lane 14 CSP


title: Batch 3 PBMC 10x Lane 12 CSP


title: Batch 3 PBMC 10x Lane 17 CSP


title: Batch 3 PBMC 10x Lane 10 CSP


title: Batch 3 PBMC 10x Lane 11 CSP


title: Batch 3 PBMC 10x Lane 8 CSP


title: Batch 3 PBMC 10x Lane 7 CSP


title: Batch 3 PBMC 10x Lane 3 CSP


title: Batch 3 PBMC 10x Lane 4 CSP


title: Batch 3 PBMC 10x Lane 2 CSP


title: Batch 3 PBMC 10x Lane 5 CSP


title: Batch 3 PBMC 10x Lane 24 CSP


title: Batch 3 PBMC 10x Lane 6 CSP


title: Batch 3 PBMC 10x Lane 1 CSP


title: Batch 2 PBMC 10x Lane 24 RNA


title: Batch 2 PBMC 10x Lane 23 RNA


title: Batch 2 PBMC 10x Lane 22 RNA


title: Batch 2 PBMC 10x Lane 19 RNA


title: Batch 2 PBMC 10x Lane 20 RNA


title: Batch 2 PBMC 10x Lane 21 RNA


title: Batch 3 PBMC 10x Lane 13 CSP


title: Batch 2 PBMC 10x Lane 16 RNA


title: Batch 2 PBMC 10x Lane 18 RNA


title: Batch 2 PBMC 10x Lane 15 RNA


title: Batch 3 PBMC 10x Lane 9 CSP


title: Batch 2 PBMC 10x Lane 14 RNA


title: Batch 2 PBMC 10x Lane 12 RNA


title: Batch 2 PBMC 10x Lane 13 RNA


title: Batch 2 PBMC 10x Lane 11 RNA


title: Batch 2 PBMC 10x Lane 10 RNA


title: Batch 2 PBMC 10x Lane 9 RNA


title: Batch 2 PBMC 10x Lane 7 RNA


title: Batch 2 PBMC 10x Lane 5 RNA


title: Batch 2 PBMC 10x Lane 4 RNA


title: Batch 2 PBMC 10x Lane 3 RNA


title: Batch 2 PBMC 10x Lane 1 RNA


title: Batch 2 PBMC 10x Lane 2 RNA


title: Batch 2 PBMC 10x Lane 17 RNA


title: Batch 2 PBMC 10x Lane 24 TCR

description:
Multple donor samples are combined within each lane; demultiplexing information is in the demuxletResults.tar.gz and allbatches.HTOandTimepointMetadata.csv supplemental files. A filtered dataset of all cells is provided as a Seurat object in R data format, as supplemental file AllBatches_SeuratObj.rds.
B2_TCR_filtered_contig_annotations.csv


title: Batch 2 PBMC 10x Lane 22 TCR


title: Batch 2 PBMC 10x Lane 21 TCR


title: Batch 2 PBMC 10x Lane 11 TCR


title: Batch 2 PBMC 10x Lane 8 RNA


title: Batch 2 PBMC 10x Lane 10 TCR


title: Batch 2 PBMC 10x Lane 15 TCR


title: Batch 2 PBMC 10x Lane 18 TCR


title: Batch 2 PBMC 10x Lane 16 TCR


title: Batch 2 PBMC 10x Lane 20 TCR


title: Batch 2 PBMC 10x Lane 19 TCR


title: Batch 2 PBMC 10x Lane 8 TCR


title: Batch 2 PBMC 10x Lane 6 RNA


title: Batch 2 PBMC 10x Lane 14 TCR


title: Batch 2 PBMC 10x Lane 12 TCR


title: Batch 2 PBMC 10x Lane 6 TCR


title: Batch 2 PBMC 10x Lane 23 TCR


title: Batch 2 PBMC 10x Lane 4 TCR


title: Batch 2 PBMC 10x Lane 3 TCR


title: Batch 2 PBMC 10x Lane 2 TCR


title: Batch 2 bulk RNAseq HGR0000092_T0


title: Batch 2 PBMC 10x Lane 1 TCR


title: Batch 2 PBMC 10x Lane 23 CSP


title: Batch 2 PBMC 10x Lane 22 CSP


title: Batch 2 PBMC 10x Lane 17 TCR


title: Batch 2 PBMC 10x Lane 13 TCR


title: Batch 2 PBMC 10x Lane 21 CSP


title: Batch 2 PBMC 10x Lane 7 TCR


title: Batch 2 PBMC 10x Lane 9 TCR


title: Batch 2 PBMC 10x Lane 20 CSP


title: Batch 2 PBMC 10x Lane 19 CSP


title: Batch 2 PBMC 10x Lane 17 CSP


title: Batch 2 PBMC 10x Lane 18 CSP


title: Batch 2 PBMC 10x Lane 16 CSP


title: Batch 2 PBMC 10x Lane 13 CSP


title: Batch 2 PBMC 10x Lane 12 CSP


title: Batch 2 PBMC 10x Lane 10 CSP


title: Batch 2 PBMC 10x Lane 11 CSP


title: Batch 2 PBMC 10x Lane 9 CSP


title: Batch 2 PBMC 10x Lane 7 CSP


title: Batch 2 PBMC 10x Lane 15 CSP


title: Batch 2 PBMC 10x Lane 6 CSP


title: Batch 2 PBMC 10x Lane 5 CSP


title: Batch 2 PBMC 10x Lane 24 CSP


title: Batch 2 PBMC 10x Lane 4 CSP


title: Batch 2 PBMC 10x Lane 3 CSP


title: Batch 2 PBMC 10x Lane 2 CSP


title: Batch 1 PBMC 10x Lane 8 RNA

value: Sorted and Unsorted


title: Batch 2 PBMC 10x Lane 1 CSP

value: Unsorted


title: Batch 1 PBMC 10x Lane 7 RNA


title: Batch 1 PBMC 10x Lane 5 RNA


title: Batch 1 PBMC 10x Lane 4 RNA


title: Batch 2 PBMC 10x Lane 14 CSP


title: Batch 2 PBMC 10x Lane 8 CSP


title: Batch 1 PBMC 10x Lane 6 RNA


title: Batch 1 PBMC 10x Lane 3 RNA


title: Batch 1 PBMC 10x Lane 7 TCR

description:
Multple donor samples are combined within each lane; demultiplexing information is in the demuxletResults.tar.gz and allbatches.HTOandTimepointMetadata.csv supplemental files. A filtered dataset of all cells is provided as a Seurat object in R data format, as supplemental file AllBatches_SeuratObj.rds.
B1_TCR_filtered_contig_annotations.csv


title: Batch 1 PBMC 10x Lane 1 RNA


title: Batch 1 PBMC 10x Lane 2 RNA


title: Batch 1 PBMC 10x Lane 6 TCR


title: Batch 1 PBMC 10x Lane 5 TCR


title: Batch 1 PBMC 10x Lane 4 TCR


title: Batch 1 PBMC 10x Lane 2 TCR


title: Batch 1 PBMC 10x Lane 3 TCR


title: Batch 1 PBMC 10x Lane 6 CSP


title: Batch 1 PBMC 10x Lane 8 CSP


title: Batch 1 PBMC 10x Lane 5 CSP


title: Batch 1 PBMC 10x Lane 7 CSP


title: Batch 1 PBMC 10x Lane 3 CSP


title: Batch 1 PBMC 10x Lane 2 CSP


title: Batch 1 PBMC 10x Lane 1 CSP


title: WD39_iPast

status: Public on Dec 16 2020

city: Tokyo

first: Nicolas

last: Leventoux

state: Tokyo

address: 35, Shinanomachi

department: Physiology

country: Japan

institute: Keio University

data_processing:
Libraries were sequenced using a NovaSeq6000 (Illumina) to obtain 150-bp paired-end reads.
Raw FASTQ files were trimmed for adapters by Cutadapt and aligned to the GRCh37 genome build using HISAT2.
Counts were calculated using featureCounts, and normalized by vst transformation using the DESeq2.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: astrocytes

growth_protocol: iPSC grew in DMEM/F12 + KSR + NEAA + 2-mercaptoethanol and hFGF ; EB grew in DMEM/F12 + KSR + NEAA + 2-mercaptoethanol and L-Gluta + DM, SB and CHIR then with RA then with PM ; Spheres grew in KBM + NEAA + B27 + FGF + EGF and PM ; iPast grew in MHM + B27 + NEAA + BDNF and GDNF

extract_protocol:
We extracted RNA using the RNeasy kit (QIAGEN) according to manufacturer's protocol.
The indexed cDNA libraries were prepared using the Nextera XT library preparation kit (Illumina)

treatment_protocol: iPSC were dissociated by trypsin and collagenase ; spheres and iPast by TrypLE Select.

tag: cell type

value: iPSC-derived astrocytic cells


title: Batch 1 PBMC 10x Lane 8 TCR


title: 551PE041

status: Public on Dec 07 2020

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts derived with Subread:featureCount 1.46.p5.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 GRCh38.76
Supplementary_files_format_and_content: The counts per million (CPM) reads were log-transformed (attached processed data file) and used to select genes that were significantly (P<0.005) positively and negatively associated with AT pO2 by using Pearson’s correlation.

source_name: MUO_Subcutaneous adipose tissue

growth_protocol: RNA was isolated from frozen subcutaneous adipose tissue samples obtained from people who were metabolically-healthy lean (MHL), metabolically-healthy obese (MHO), and metabolically-unhealthy obese (MUO).

extract_protocol:
RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA)

tag: subject status

value: metabolically-unhealthy obese (MUO)

value: Baseline

tag: tissue

value: Subcutaneous adipose tissue


title: 981PSQ469


title: 276PE028


title: 976PSQ379


title: 273PE009


title: 980PSQ441


title: 977PSQ397


title: 973PSQ354


title: 550PE035


title: 272PE007


title: Batch 1 PBMC 10x Lane 1 TCR


title: 967PSQ294


title: 968PSQ297


title: 975PSQ366


title: 562PSQ286


title: Batch 1 PBMC 10x Lane 4 CSP


title: 560PSQ267


title: 556PSQ251


title: 554PSQ196


title: 265PSQ086


title: 264PSQ070


title: 960PSQ393

source_name: MHO_Subcutaneous adipose tissue

value: metabolically-healthy obese (MHO)


title: 962PSQ428


title: 201B7_iPast


title: 957PSQ291


title: 958PSQ332


title: 258PSQ168


title: 253PSQ127


title: 242PSQ027


title: 239PSQ019


title: 251PSQ115


title: 245PSQ042


title: 257PSQ162


title: 236PSQ005


title: 555PSQ250

source_name: MHL_Subcutaneous adipose tissue

value: metabolically-healthy lean (MHL)


title: 233PSQ150


title: 232PSQ147


title: 951PSQ211


title: 246PSQ052


title: 952PSQ252


title: 552PSQ064


title: 194PSQ116


title: 195PSQ044


title: 231PSQ141


title: 553PSQ185


title: 229PSQ073


title: 559PSQ256


title: Cdk6 knock out (KO3) [RNA-seq]

status: Public on Nov 24 2020

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

description:
6_KO3_S43886
processed data file: Count_table.txt

data_processing:
Fastq files were quality and adapter trimmed using Trim_Galore! Software.
Trimmed reads were aligned to GRCm38 using STAR.
DESeq2 pipeline/SeqMonk.
Bam files are unaligned.
Genome_build: GRCm38
Supplementary_files_format_and_content: Count_table.txt: Tab-delimited text file contains counts of 6 RNA-seq samples.

organism: Mus musculus

source_name: Cell line

growth_protocol: BCR-ABL+ cell lines were maintained in RPMI medium supplemented with 10% FCS, 50 μmol/L 2-mercaptoethanol, 100 U/mL penicillin, and 100 μg/mL streptomycin (PAA, Linz, Austria).

extract_protocol:
RNA was extracted using Qiagen RNeasy kit.
TruSeq RNA Sample Preparation Kit (Illumina Inc).

treatment_protocol: Cells were electroporated (one single pulse with a voltage of 1600 V and a pulse width of 20 ms; NeonTM Transfection System, Invitrogen, Carlsbad, CA, USA) with 1µg control plasmid pSpCas9(BB)-2A-GFP(px458) or the plasmid expressing sgRNAs against CDK6 pSpCas9(BB)-2A-GFP(px458)-hCDK6del. For each transfection, 2x10e5 cells were resuspended in Buffer R (NeonTM) in a reaction volume of 10µl. Transfected cells were cultured in RPMI (supplemented with 10% FCS and 50 μmol/L 2-mercaptoethanol) for 24h. GFP+ cells were sorted using a FACSAriaTM II cell sorter (BD Biosciences, San Jose, CA, USA) and plated as single cell suspension into 96-well plates. The outgrowth of clones was monitored by microscopic inspection and CDK6 knockout was verified by Western Blotting.

tag: ph chromosome

value: BCR-ABL positive

tag: cdk6 genotype

value: Cdk6 knock out


title: Cdk6 knock out (KO2) [RNA-seq]

description:
5_KO2_S43885
processed data file: Count_table.txt


title: Cdk6 knock out (KO1) [RNA-seq]

description:
4_KO1_S43883
processed data file: Count_table.txt


title: Cdk6 wild type (WT3) [RNA-seq]

description:
3_WT3_S43887
processed data file: Count_table.txt

value: Cdk6 wild type


title: Cdk6 wild type (WT1) [RNA-seq]

description:
1_WT1_S43888
processed data file: Count_table.txt


title: Cdk6 knock out + Cdk6 (HA_FL3) [RRBS]

library_source: genomic

data_processing:
Fastq files were quality and adapter trimmed using Trim_Galore! Software and the --rrbs option.
Trimmed reads were aligned to GRCm38 using Bismark.
Methylation calls were extracted using Bismark methylation extractor.
Genome_build: GRCm38
Supplementary_files_format_and_content: .cov from Bismark methylation extractor.

extract_protocol:
Genomic DNA was extracted using Qiagen DNeasy kit.
Genomic DNA was MspI (NEB) digested, end-repaired and A-tailed using Klenow Polymerase (NEB) followed by adapter ligation using Quick Ligase (NEB) and AMPure XP size selection (Beckman Coulter, Fullerton, CA, USA). RRBS libraries were sodium bisulfite treated using the EZ-DNA Methylation-Direct kit (Zymo Research Corp, Orange, CA, USA) and quantified by qPCR. Enrichment PCR was performed using the PfuTurboCx Hotstart Kit (Agilent Technologies, Santa Clara, CA, USA) followed by AMPure XP clean up. Quality of final RRBS libraries was determined by Experion analysis (Biorad). Sequencing was performed on a HiSeq2000 sequencer (Illumina Inc, San Diego, CA, USA).

treatment_protocol: Cells were electroporated (one single pulse with a voltage of 1600 V and a pulse width of 20 ms; NeonTM Transfection System, Invitrogen, Carlsbad, CA, USA) with 1µg control plasmid pSpCas9(BB)-2A-GFP(px458) or the plasmid expressing sgRNAs against CDK6 pSpCas9(BB)-2A-GFP(px458)-hCDK6del. For each transfection, 2x10e5 cells were resuspended in Buffer R (NeonTM) in a reaction volume of 10µl. Transfected cells were cultured in RPMI (supplemented with 10% FCS and 50 μmol/L 2-mercaptoethanol) for 24h. GFP+ cells were sorted using a FACSAriaTM II cell sorter (BD Biosciences, San Jose, CA, USA) and plated as single cell suspension into 96-well plates. For the re-expression of HA-CDK6, pMSCV-IRES-GFP plasmids were used. The outgrowth of clones was monitored by microscopic inspection and CDK6 knockout/re-expression was verified by Western Blotting.

value: Cdk6 knock out + Cdk6


title: Cdk6 wild type (WT2) [RNA-seq]

description:
2_WT2_S43889
processed data file: Count_table.txt


title: 561PSQ285


title: Cdk6 knock out + Cdk6 (HA_FL1) [RRBS]


title: Cdk6 knock out + Cdk6 (HA_FL2) [RRBS]


title: Cdk6 knock out (KO2) [RRBS]


title: Cdk6 knock out (KO1) [RRBS]


title: Cdk6 wild type (WT2) [RRBS]


title: Cdk6 wild type (WT3) [RRBS]


title: Cdk6 knock out (KO3) [RRBS]


title: JHK_12: Macrophage, LPS + ERG240 rep 3

status: Public on Nov 23 2020

city: London, United Kingdom

first: Norzawani

middle: Binti

last: Buang

state: London

address: 9N15 Commonwealth Buidling, Ducane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina CASAVA-1.8.4 software used for basecalling.
Sequencing adapters were removed using Trimmomatic (v.0.36) and the reads quality was checked using FastQC (v.0.11.2) before and after trimming. Reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf) using tophat2 package (v.2.1.0: -b2-sensitive,--library-type fr-firststrand). Mapping quality, read distribution, gene body coverage, GC content and rRNA contamination, were checked using picard (v.2.6.0) software.
Gene level read counts were computed using HT-Seq-count (v.0.6.1, annotation: gencode.v25.annotation.gtf)1 with strict "-m intersection-strict” mode. Genes with less than 10 aligned reads across all samples were filtered out as lowly expressed genes.
Differential gene expression analysis between groups was performed using DESeq2 (v.1.14.1)4 and significantly differentially expressed genes were reported using fold-change at 1.5 times and below 1 % Benjamini-Hochberg (BH) adjusted p-value.
In order to visualize the similarities between samples, unsupervised hierarchical clustering and principal component analysis (PCA) were performed using pcaExplorer (v.2.6.0, https://github.com/federicomarini/pcaExplorer) and pheatmap (v 1.0.10, https://CRAN.R-project.org/package=pheatmap) packages respectively. Volcano plots of differentially expressed genes were generated using ggplot2 (v.3.0.0, https://cran.r-project.org/web/packages/ggplot2/index.html) package.
Genome_build: GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf)

source_name: Macrophage

extract_protocol:
Total RNA was extracted using Trizol and Rneasy mini kit with an additional purification step by on-column DNAse treatment using Rnase-free Dnase Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep kit for Illumina

value: Macrophage

tag: treatment

value: LPS + ERG240

tag: treatment time


title: JHK_8: Macrophage, LPS + ERG240 rep 2


title: JHK_4: Macrophage, LPS + ERG240 rep 1


title: Cdk6 wild type (WT1) [RRBS]


title: JHK_7: Macrophage, LPS rep 2

value: LPS


title: JHK_11: Macrophage, LPS rep 3


title: JHK_3: Macrophage, LPS rep 1


title: Blood_PR8_rep3

status: Public on Oct 27 2020

data_processing:
Reads were mapped to the M. musculus UCSC mm9 genome assembly using Bowtie2 (Langmead and Salzberg, 2012). Counting of reads mapping to each gene was performed in R using featureCounts from the R package Subread.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts (reads per gene) for each sample

source_name: blood

extract_protocol:
Blood was collected post mortem via heart puncture on day two after infection (n = 3 mice/treatment) and kept at -20 °C in RNAlater (Thermo Fisher Scientific). RNA was extracted using the Mouse RiboPure Blood RNA Isolation Kit and globin RNA depleted using the GLOBINclear Kit, mouse/rat (Thermo Fisher Scientific). Quality and amount of RNA were determined using the Qubit RNA BR Assay Kit with Qubit 2.0 (Thermo Fisher Scientific) and Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer. Only samples with RIN score above 7 were further analyzed.
Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina, NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 and 2) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Library quantification was performed by real-time PCR using the KAPA Library Quantification Kit - Illumina Platforms - Complete kit (Universal) and KAPA Library Amplification Kit - Real-time PCR library amplification, with fluorescent standards (KAPA Biosystems). Libraries were sequenced twice on the Illumina Nextseq platform (Illumina) using V1 reagents to a total read depth of 60 million paired-end, 75 base-pair reads.

tag: strain

value: blood

value: Influenza PR8


title: Blood_PR8_rep2


title: Blood_PR8_rep1


title: Blood_PBS_rep3

value: PBS


title: Blood_PBS_rep1


title: Blood_PBS_rep2


title: HS 1_Myeloid

status: Public on Aug 27 2020

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

description:
HS17
scRNA-Seq

data_processing:
Fastq files were analyzed with Cell Ranger Version 3.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix. matrix.mtx, features.tsv, barcodes.tsv.

molecule: polyA RNA

source_name: sort-purified CD45+CD3-CD19- cells

extract_protocol:
Cells were sort-purified as live CD45+ CD3- CD19- cells from enzymatically digested skin.
scRNASeq was performed using the 10x Single Cell 3' v3 Chemistry.

value: Skin

tag: diagnosis

value: Hidradenitis suppurativa (HS)

value: CD45+CD3-CD19- cells


title: Healthy 2_Myeloid

description:
NL16
scRNA-Seq

value: Normal


title: Healthy 1_Myeloid

description:
NL15
scRNA-Seq


title: HS 2_Myeloid

description:
HS22
scRNA-Seq


title: wildtype_vein_graft_4wk

status: Public on Jul 06 2020

city: London

first: Zhichao

last: Ni

address: 125 Coldharbour Lane, James Black Centre, King's College London

institute: King's College London

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.0.2.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files for cells from vein graft of wildtype mice.

extract_protocol:
Vein grafts were harvested from the mice. Adventitial layer of the grafts was first dissected from the medial and neointimal layers. After three times washes of PBS, grafts were cut into fine pieces and digested in digestion solutions (which consist of 1 mg/ml papain, 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS) at 37 °C with reciprocal shaking for a total 40 min. Detached cells were then collected through a 40 μm cell strainer and suspended in DMEM with 10% FBS. Cells were further stained with DAPI and DRAQ5 for 20 mins. After PBS washing, cells were resuspended in PBS and single nucleated live cells (DAPI and DRAQ Cell Stain) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Cells were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v3 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a Hiseq 2500 System (Illumina)

tag: genotype

value: wild type

value: Vein graft


title: 17686X3 Matching Blood Normal

status: Public on May 28 2020

city: Durham

first: Trudy

last: Oliver

email: tgo@duke.edu, trudy.oliver@duke.edu

state: NC

address: Duke University, Box 3813, LSRC Room C138B, 308 Research Drive

department: Pharmacology & Cancer Biology

institute: Duke University

description: Whole genome seq

data_processing:
Library strategy: WGS
Sequencing reads were aligned to mouse genome mm10 by BWA 0.7.17-r1188 (Li and Durbin, 2009).
Rb1 and Trp53 deletions were examined in the Integrated Genome Viewer (IGV) software v2.5.0.
SNVs were jointly called by Freebayes 1.2.0 and somatic SNVs were filtered by the following criteria: DP >15, AO < 2 and AF <0.05 in the normal sample.
Variants were annotated by SnpEff 4.3 (Cingolani et al., 2012).
Somatic non-synonymous coding variants were manually reviewed in IGV.
Genome_build: mm10 mouse genome
Supplementary_files_format_and_content: VCF file

source_name: mouse whole blood

extract_protocol:
Genomic DNA was extracted from flash frozen cell pellets of Day 4 and -23 cells along with whole blood from the same RPM mouse using Qiagen’s DNeasy Blood and Tissue kit.
Libraries were prepared using the Nextera DNA Flex Library Prep Kit (Illumina cat#20018705).
Libraries were sequenced on a NovaSeq 6000 instrument targeting 300 million read-pairs on a 2 x 150 bp run (~30x coverage of whole genome).

tag: gnomex id

value: mouse whole blood


title: 17686X2 RPM Transition Cells Day 23

description: Whole genome seq

source_name: mouse RPM tumor cells transitioning in culture


title: 17686X1 RPM Transition Cells Day 4

description: Whole genome seq

value: mouse RPM tumor cells transitioning in culture


title: 17751X2 AI115F RPM4 (bulk tumor)

description:
Single-cell RNA seq
RPM4_barcodes.tsv.gz
RPM4_features.tsv.gz
RPM4_matrix.mtx.gz

data_processing:
Demulitplexed with 10x cellranger mkfastq version 3.1.0 to create fastq files with the I1 sample index, R1 cell barcode+UMI and R2 sequence
Reads were aligned to the mouse genome (refdata-cellranger-mm10-3.0.0 from 10X Genomics with  EGFP+Cas9 added) and count barcodes and UMIs were generated using cellranger count 3.1.0 with expected-cells set to 8000 per library
tumor cells were identified in the Loupe browser and with Seurat and combined into a single experiment containing all timepoints
Genome_build: mm10 with EGFP+Cas9
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.  The time course samples from day 4 to 21 are aggregated into one feature barcode matrix

source_name: RPM-CAS9 GEMM

extract_protocol:
Enzymatic/mechanical digestion into single cell suspension then immediate sequencing for bulk tumors, or growth in culture for transition timepoints
10X Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3
Targeted cell recovery of 8k cells, 10x gel beads and reverse transcription reagents were added to cell suspensions and loaded to chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D1000 ScreenTape on Agilent tech 2200 tapestation system and quantified KAPA Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq.

tag: ID

tag: mouse genotype

value: Rb1 fl/fl;Trp53 fl/fl;MycT58A LSL/LSL-Cas9-Ires-GFP


title: 17520X1 AI106F RPM2 (bulk tumor)

description:
Single-cell RNA seq
RPM2_barcodes.tsv.gz
RPM2_features.tsv.gz
RPM2_matrix.mtx.gz


title: 15844X2 AI122F RPM1 (bulk tumor)

description:
Single-cell RNA seq
RPM1_barcodes.tsv.gz
RPM1_features.tsv.gz
RPM1_matrix.mtx.gz


title: 15841X1 Day14 (time-series cells)

description:
Single-cell RNA seq
Filtered_TimeCourse_barcodes.tsv.gz
Filtered_TimeCourse_features.tsv.gz
Filtered_TimeCourse_matrix.mtx.gz


title: 17536X2 MC811 RPR2

description: Bulk RNA Sequencing

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Optical duplicates removed from NovaSeq runs via Clumpify v38.34
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix and log2 normalized counts from DESeq2

source_name: RPR2 GEMM

extract_protocol:
RNeasy Mini Kit (Qiagen) with the standard protocol
Illumina TruSeq Stranded mRNA Sample Preparation Kit (RPM, n=10)
Illumina TruSeq Stranded Total RNA Library Ribo-Zero Gold Prep kit (RPM, n=5)
HiSeq 50 Cycle Single-Read Sequencing v4 (RPM, n=2)


title: 17751X1 AI114F RPM3 (bulk tumor)

description:
Single-cell RNA seq
RPM3_barcodes.tsv.gz
RPM3_features.tsv.gz
RPM3_matrix.mtx.gz


title: 15806X2 Day4 (rep2, time-series cells)


title: 15817X1 Day7 (time-series cells)


title: 17536X3 MC794 RPR2

description: Bulk RNA Sequencing


title: 15821X1 Day11 (time-series cells)


title: 15844X1 Day17 (time-series cells)


title: 17536X1 MC803 RPR2

description: Bulk RNA Sequencing


title: 15806X1 Day4 (rep1, time-series cells)


title: 14797X7 RPM Day 19 Cells

description: Bulk RNA Sequencing

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes and transcripts in the GTF file using RSEM version 1.3.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: RSEM estimated gene counts and RPKMs

source_name: RPM GEMM transition cells in culture

extract_protocol:
RNeasy Mini Kit (Qiagen) with the standard protocol
Illumina TruSeq Stranded RNA kit with Ribo-Zero Gold
HiSeq 50 Cycle Single-Read Sequencing v4

value: Rb1 fl/fl;Trp53 fl/fl;MycT58A LSL/LSL


title: 16080X4 MC794 RPR2

description: Bulk RNA Sequencing


title: 14797X8 RPM Day 21 Cells

description: Bulk RNA Sequencing


title: 14797X6 RPM Day 14 Cells

description: Bulk RNA Sequencing


title: 14797X4 RPM Day 10 Cells

description: Bulk RNA Sequencing

source_name: RPM GEMM transition cell line in culture


title: 14797X3 RPM Day 7 Cells

description: Bulk RNA Sequencing


title: 14797X2 RPM Day 5 Cells

description: Bulk RNA Sequencing


title: 12135X11 PB281F RPM

description: Bulk RNA Sequencing

source_name: RPM GEMM


title: 12135X10 PB281E RPM

description: Bulk RNA Sequencing


title: 12135X9 PB280H RPM

description: Bulk RNA Sequencing


title: 14797X1 RPM Day 3 Cells

description: Bulk RNA Sequencing


title: 12135X8 PB191A RPM

description: Bulk RNA Sequencing


title: 15862X1 Day21 (time-series cells)


title: 12135X7 PB190C RPM

description: Bulk RNA Sequencing


title: 12135X5 PB189B RPM

description: Bulk RNA Sequencing


title: 16080X3 MC776 RPR2

description: Bulk RNA Sequencing


title: 12135X1 PB115 RPM

description: Bulk RNA Sequencing


title: 12135X4 PB124 RPM

description: Bulk RNA Sequencing


title: 14797X5 RPM Day 12 Cells

description: Bulk RNA Sequencing


title: SCLC biopsy from the liver (TWAD)

description: Single-cell RNA seq

data_processing:
Reads were aligned to the human genome from 10x genomics and count barcodes and UMIs were generated using cellranger count version 3.0.1
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx (enerated by Cellranger)

source_name: Human SCLC liver biopsy

extract_protocol:
The SCLC  biopsy specimen was collected from the liver of a patient with relapsed SCLC and was viably frozen before being made into a single cell suspension through gentle enzymatic digestion with type 1A collagenase (Sigma, cat#C9891) for 10-20 min with shaking at RT. The cell suspension was filtered through a 40 micron cell filter and the resulting single cell suspension was flow sorted to isolate viable cells using the Zombie Green viability fluorescent dye (Biolegend, cat#423111) on a Sony Synergy SY3200 cell sorter.
10X Chromium Single-cell 5' PE chemistry
Prepared according to manufacturer's instructions at the McDonnell Genome Institute, Washington University School of Medicine in St. Louis

tag: disease state

value: relapsed small cell lung cancer (SCLC)

value: initial treatment with carboplatin and etoposide; progressed on carboplatin-irinotecan

value: liver biopsy


title: 12135X3 PB120 RPM

description: Bulk RNA Sequencing


title: 12135X6 PB190A RPM

description: Bulk RNA Sequencing


title: Pre5

status: Public on Apr 14 2020

description:
PWL124Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx

data_processing:
Human. B38 was used for alignment reference.
Ensembl.R86 (57992 gene IDs) was used for anlysis of RNA-Seq data.
Upper quartile nomalized log2 transformed FPKM data were generated from raw read counts data.
Genome_build: Ensembl.R86 (57992 gene IDs
Supplementary_files_format_and_content: Upper quartile nomalized log2 transformed FPKM data were provided as processed data files.

source_name: Subcutaneous adipose tissue

growth_protocol: RNA was isolated from frozen subcutaneous adipose tissue samples obtained from 1) MHO vs MUO and 2) before and after weight loss.

extract_protocol:
RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
Truseq-total RNA (Ribozero depletion)

tag: condition

value: Pre


title: Pre6

description:
RB17Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post5

description:
PWL124Post
Subcutaneous adipose tissue
WL_FPKM.xlsx

value: Post


title: Post6

description:
RB17Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post7

description:
PWL140Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre7

description:
PWL140Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre8

description:
RB55Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post9

description:
RB16Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post3

description:
PWL158Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre10

description:
RB45Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre4

description:
RB53Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post8

description:
RB55Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre9

description:
RB16Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post4

description:
RB53Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre2

description:
RB48Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Post1

description:
PWL136Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: Pre3

description:
PWL158Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: MUO15

description:
PE40
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx

value: MUO


title: Pre1

description:
PWL136Pre
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: MUO14

description:
PE28
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: Post10

description:
RB45Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: MUO12

description:
PE7
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO13

description:
PE9
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO11

description:
PE6
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO10

description:
PE4
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO8

description:
PSQ251
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO9

description:
PSQ255
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO7

description:
PSQ191
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO4

description:
PSQ137
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO5

description:
PSQ164
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO6

description:
PSQ185
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO8

description:
PSQ120
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx

value: MHO


title: MUO3

description:
PSQ86
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO9

description:
PSQ127
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO2

description:
PSQ70
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO12

description:
PSQ162
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MUO1

description:
PSQ1
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO13

description:
PSQ168
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO15

description:
PSQ256
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO10

description:
PSQ146
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO14

description:
PSQ170
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO11

description:
PSQ161
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO4

description:
PSQ31
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO2

description:
PSQ23
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO5

description:
PSQ42
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO6

description:
PSQ89
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO3

description:
PSQ27
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: MHO7

description:
PSQ100
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: Post2

description:
RB48Post
Subcutaneous adipose tissue
WL_FPKM.xlsx


title: MHO1

description:
PSQ13
Subcutaneous adipose tissue
MHOvsMUO_FPKM.xlsx


title: L60_1

status: Public on Apr 07 2020

type: RNA

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

hyb_protocol: cRNA was hybridized to Clariom D Assay human array (Thermofisher), washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Transcriptome Analysis Console Software, and obtained normalized intensity values.

label: biotin

source_name: Peripheral blood, CD8+ sorted

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit (ThermoFisher) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

value: Non-small cell lung cancer

value: Blood

value: Pre-treatment

tag: individual


title: L57_1


title: L56_1


title: L42_1


title: L46_1


title: L52_1


title: L59_1


title: L41_1


title: L53_1


title: L55_1


title: L51_1


title: L37_1


title: L50_1


title: L39_1


title: L30_1


title: L48_1


title: L36_1


title: L45_1


title: L54_1


title: L47_1


title: L49_1


title: L31_1


title: L33_1


title: L32_1


title: L34_1


title: L27_1


title: L25_1


title: MYC_Twist1_HCC_4

status: Public on Jan 21 2020

city: Stanford

first: Renumathy

last: Dhanasekaran

address: 300 Pasteur Drive, Alway M211

institute: Stanford University

data_processing:
Trim adapters and low quality bases (Trimmomatic).
Align to the reference genome (STAR).
Determine the distribution of the bases within the transcripts and 5'/3' biases (Picard).
FPKM value was quantified by FeatureCounts tool
DESeq2 was used for differential expression analysis
Genome_build: mm10

source_name: Tumor tissue

extract_protocol:
Liver tumors were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard BGI protocols

tag: organ

value: Liver

value: hepatocellular carcinoma


title: MYC_Twist1_HCC_5


title: L44_1

tag: cell type


title: MYC_Twist1_HCC_2


title: L23_1


title: L35_1


title: MYC_Twist1_HCC_3


title: MYC_Twist1_HCC_1


title: L22_1


title: MYC_HCC_4


title: MYC_HCC_2


title: L14_1


title: MYC_HCC_1


title: H3K27Ac_ChIPSeq_RPM5  (PB490)

status: Public on Dec 22 2019

data_processing:
Reads were aligned to the mm10 build of the mouse genome with bowtie using the following parameters: -m 1 -t --best -q -S -l 32 -e 80 -n 2.
Peaks were called with MACS2 using a p value cutoff of 1e-10 and the mfold parameter bounded between 15 and 100.
For visualization, MACS2 produced bedgraphs with the –B and –SPMR options.
Genome_build: mm10

source_name: SCLC lung tumor cells

growth_protocol: Lung tumor growth initiated in Rb1fl/fl;p53fl/fl;MycT58ALSL/LSL mice following intratracheal administration of Ad-CGRP-Cre

extract_protocol:
Individual lung tumors from mice were micro-dissected, flash frozen and stored at -80°C until ChIP. Tumors were prepared for ChIP by pulverizing frozen tumors into a fine powder.
Samples were resuspended in PBS and DNA was crosslinked in 1% formaldehyde. Fixation was terminated by adding glycine.
Chromatin was sheared using a Diagenode Bioruptor and mouse tumor chromatin was immunoprecipitated with anti-MYC or anti-H3K27Ac (Active-Motif, 39133), followed by either anti-rabbit Dyna beads or Protein G Dyna beads.
The immunoprecipitated chromatin was purified with the Zymo ChIP DNA Clean and Concentrator kit.
Libraries were prerpared using a NEBBext ChIP-Seq Library kit and sequenced on an Illumina HiSeq 2500 (single-end 50 bp reads with a min of 35 million reads per sample).

treatment_protocol: Untreated tumors

value: Lung

tag: antibody

value: anti-H3K27Ac (Active-Motif, 39133)


title: L16_1

tag: tissue


title: H3K27Ac_ChIPSeq_RPM4  (PB499)


title: L13_1


title: L21_1


title: H3K27Ac ChIP RPM2 (PB503)


title: L12_1


title: MYC ChIP RPM4 (PB499)

value: anti-MYC (CST, 13987)


title: L15_1


title: H3K27Ac_ChIPSeq_RPM3  (PB502)


title: MYC ChIP RPM3 (PB502)


title: L10_1


title: L11_1


title: MYC ChIP RPM2 (PB503)


title: MYC_HCC_3


title: MYC ChIP RPM1 (PB500G)


title: ANKO1

status: Public on Nov 14 2019

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.  RPKM calculated from gene counts with standard RPKM transformation with custom R scripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

source_name: Brown adipose tissue

growth_protocol: ANKO mice were generated by using adiponectin-Cre transgenic mice and Nampt flox mice.

extract_protocol:
BAT samples were removed, flash frozen by liquid nitrogen, and RNA was harvested using Qiazol Reagent with Rneasy Mini Kit (Qiagen).
Ribo-Zero Gold kit

treatment_protocol: Mice were kept at room temperature under a normal regular-chow fed condition.

value: Brown adipose tissue

tag: genotype/variation

value: ANKO (adipocyte specific Nampt knockout)


title: WT3

value: Wild type (flox/flox)


title: WT1


title: ANKO4


title: WT4


title: ANKO2


title: ANKO3


title: WT2


title: Nephrectomy [REF6]

status: Public on Oct 28 2019

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

description:
REF6
processed data file: Eadon_processed_QN_101419.csv

data_processing:
For Illumina Sequencing data, FastQC for sequencing quality check.
Adapter sequences were removed with cutadapt (1.14+).
Reads were aligned to the human reference genome Hg38 using STAR-2.5.2b with parameters adjusted to short reads and Integrative Genomics Viewer (IGV) alignment.
Expression counts determined by edgeR / rbamtools.
Genes removed from analysis with 0 read counts in more than half of all specimens, total genes included 20,139.
Quantile normalization.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Eadon_processed_QN_101419.csv: Comma-separated text file

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
Nephrectomies were obtained and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input.
RNA seq, 10 millions input reads per sample.

tag: disease

value: Kidney

tag: age

tag: gender

value: Male

tag: storage

value: OCT at -80C

tag: sequencing id


title: Nephrectomy [REF7]

description:
REF7
processed data file: Eadon_processed_QN_101419.csv

value: Female


title: Nephrectomy [REF8]

description:
REF8
processed data file: Eadon_processed_QN_101419.csv


title: Nephrectomy [REF5]

description:
REF5
processed data file: Eadon_processed_QN_101419.csv


title: Nephrectomy [REF9]

description:
REF9
processed data file: Eadon_processed_QN_101419.csv


title: L19_1

tag: diagnosis

tag: treatment


title: Nephrectomy [REF3]

description:
REF3
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI9]

description:
AKI9
processed data file: Eadon_processed_QN_101419.csv

value: AKI


title: Nephrectomy [REF2]

description:
REF2
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI8]

description:
AKI8
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI4]

description:
AKI4
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI7]

description:
AKI7
processed data file: Eadon_processed_QN_101419.csv


title: Nephrectomy [REF1]

description:
REF1
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI6]

description:
AKI6
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI3]

description:
AKI3
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI5]

description:
AKI5
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI38]

description:
AKI38
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI31]

description:
AKI31
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI32]

description:
AKI32
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI36]

description:
AKI36
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI34]

description:
AKI34
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI39]

description:
AKI39
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI33]

description:
AKI33
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI2]

description:
AKI2
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI30]

description:
AKI30
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI27]

description:
AKI27
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI28]

description:
AKI28
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI25]

description:
AKI25
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI26]

description:
AKI26
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI29]

description:
AKI29
processed data file: Eadon_processed_QN_101419.csv


title: MYC_HCC_5


title: Renal Biopsy [AKI24]

description:
AKI24
processed data file: Eadon_processed_QN_101419.csv


title: Nephrectomy [REF4]

description:
REF4
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI35]

description:
AKI35
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI20]

description:
AKI20
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI37]

description:
AKI37
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI22]

description:
AKI22
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI1]

description:
AKI1
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI21]

description:
AKI21
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI19]

description:
AKI19
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI14]

description:
AKI14
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI13]

description:
AKI13
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI18]

description:
AKI18
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI11]

description:
AKI11
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI12]

description:
AKI12
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI15]

description:
AKI15
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI10]

description:
AKI10
processed data file: Eadon_processed_QN_101419.csv


title: WT LY6D-SCA1low population rep1

status: Public on Sep 02 2019

city: Manchester

first: Esther

last: Baena

address: The University of Manchester, Wilmslow Road

department: Prostate Oncobiology

institute: Cancer Research UK Manchester Institute

data_processing:
Base calling: Illumina NextSeq Control Program (ver 2.0.2.1) RTA (ver 2.4.11) bclTofastq (ver  2.17.1.14)
Read trimming: reads were trimmed to remove the initial 12 bases with BBDUK (ver 36.20) and trimmed to remove trailing polyG and polyA repeats with fqtrim (ver 0.9.4) and cutadapt (ver 1.9.1).
Alignment: trimmed read were aligned to mm38 (mm10) geneome using STAR (ver 2.5.1) and the individual lane alignments were merged with samtools (ver 1.3.1)
Filtering of duplicate: the merged bamfiles were filtered for duplicates using picard tools (ver 1.96).
Assignment: of aligned reads to annotated features using the featureCounts program from the Subread suit of software tools (ver 1.5.0)
Normalization: with edgeR CPM function using the trimmed mean of M values (TMM) method
Genome_build: mm38 (ENSEMBL v86)
Supplementary_files_format_and_content: Raw Counts, Normalized Counts

source_name: Prostate

extract_protocol:
Prostate were removed, FACS-sroted based on cell surface markers, and RNA was harvested using Trizol reagent.  Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit (FWD, Cat. No. 015) for Illumina was used with 10-20 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: prostate

value: 6-8 week-old

tag: genotype

value: wild type

tag: cell population

value: LY6D-SCA1low population


title: WT LY6D-SCA1low population rep2


title: WT LY6D-SCA1Int population rep2

value: LY6D-SCA1Int population


title: WT LY6D-SCA1Int population rep1


title: Renal Biopsy [AKI23]

description:
AKI23
processed data file: Eadon_processed_QN_101419.csv


title: WT LY6D-SCA1high population rep1

value: LY6D-SCA1high population


title: WT LY6D-SCA1high population rep2


title: WT LY6D+SCA1Int population rep2

value: LY6D+SCA1Int population


title: WT LY6D+SCA1Int population rep1


title: Renal Biopsy [AKI16]

description:
AKI16
processed data file: Eadon_processed_QN_101419.csv


title: Renal Biopsy [AKI17]

description:
AKI17
processed data file: Eadon_processed_QN_101419.csv


title: WT LY6D+SCA1high population rep1

value: LY6D+SCA1high population


title: WT LY6D+SCA1high population rep2


title: L95_EGFR

status: Public on Jul 23 2019

data_processing:
Standard Illumina base calling
Adapter/QC trimming using TrimGalore
Alignment to mm10 using HopHat2
Differential expression using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts for each feature per sample

source_name: hair follicle stem cells (HFSC)

extract_protocol:
PicoPure RNA Isolation Kit
SMARTer Ultra Kit (Clontech, #63482)

tag: phenotype

value: EGFR Knock out

value: hair follicle stem cells (HFSC)


title: E359_FC8

source_name: sorted outer root sheath (ORS) cells

value: sorted outer root sheath (ORS) cells


title: L97_EGFR


title: WT LY6D+SCA1low population rep1

value: LY6D+SCA1low population


title: E359_FC7

source_name: sorted inner root sheath (IFE) cells

value: sorted inner root sheath (IFE) cells


title: L136_EGFR

value: Control


title: L94_EGFR


title: E360_FC7


title: E358_FC8


title: E358_FC7


title: Batch 2 PBMC 10x Lane 5 TCR

status: Public on Feb 10 2021

description:
Multple donor samples are combined within each lane; demultiplexing information is in the demuxletResults.tar.gz and allbatches.HTOandTimepointMetadata.csv supplemental files. A filtered dataset of all cells is provided as a Seurat object in R data format, as supplemental file AllBatches_SeuratObj.rds.
B2_TCR_filtered_contig_annotations.csv

data_processing:
fastq generation: Illumina bcl2fastq 2.20
mapping, CellRanger 3.1.0 (10x Genomics)
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
secondary analysis: Seurat 3.1.0 (R package)
T cell receptor VDJ analysis: CellRanger 3.1.0
One anonymized donor (SDH8) was excluded from further analysis, as we discovered an extremely expanded B phenotype consistent lymphoma in this sample. An additional leukopack-derived PBMC sample (CHI014, anonymized and without demographic information)  was used in each experimental batch as a technical control, but not used in later comparisons. Samples HDVO_bc and HDML_bc in Batch 2 were used as a test of cyropreserving buffy coat samples, and were not used in the furtehr analysis.
Genome_build: hg19 (cellranger version 1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_1.2.0)
Supplementary_files_format_and_content: CellRanger count matrices in h5 data format; T cell clonal analysis, comma seperated values

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Frozen PBMC samples were thawed, recovered and washed using RPMI media with 10% FBS and 10mg/mL DNase I (STEMCELL 07470). Samples from different donors were pooled evenly before staining; single cells can be demultiplexed in silico using individual specific single nucleotide polymorphism (SNP) information during data analysis (see below; demultiplexing for each lane is provided in the *demux.best supplemental files). Multiple cell pools were prepared, such that cells from the same individual but different timepoints would be in different pools. PBMC pools were Fc blocked (Human TruStain FcX, BioLegend 422302) and stained with Totalseq-C human ‘hashtag’ antibodies (BioLegend), washed with staining buffer (2% BSA in PBS). This round of hashtag staining allows the different pools to be identified in the analysis, which when combined with the SNP-based demultiplexing, allows full identification of each sample. A fraction of the combined cells was used for sorting total B, T, CD14+ monocyte and CD14- innate cell populations (batch 1) or non-naïve T and B cells (batches 2 and 3). Separately for the unsorted and sorted cell fractions, hashtagged PBMC pools were combined and cells were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 192 surface proteins. Then, cells were washed three times, resuspended in PBS, and counted before proceeding immediately to the single cell partition step. Flow cytometry sorting to enrich certain cell populations was performed as follows: Pooled PBMC samples from different donors were washed with PBS and incubated with Zombie Red Fixable viability dye (1:1000 in PBS, BioLgend) for 20 minutes at 4°C protected from light. Then cells were washed with flow staining buffer (10% FBS in PBS) and Fc blocked (Human TruStain FcX, BioLegend) for 15 minutes on ice. For experimental batches 2 and 3, the non-naïve B- and T- cell populations were sorted. The fluorescence-labeled antibody cocktail against human CD45(APC/Cyanine7, BioLegend 368516), CD3(AF488, BioLegend 344810), CD19(APC, BioLegend 363006), CCR7(BV786, BioLegend 353230), CD95(BV650, BioLgend 305642), IgD(PerCP-Cy5.5, BioLegend 348208) and CD27(PE/Cyanine7, BioLegend 356412) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). Non-naïve B cell population was gated by CD45+CD19+IgD- or CD27+ and non-naïve T cell population was gated by CD45+CD3+CCR7low or CD95+. Sorted cells were CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step. For experimental batch 1, total B, T, CD14+ monocyte and CD14- innate cell populations were sorted and pooled with unsorted PBMCs by ratio 1:1:1:1:1 to balance the number of each population captured in the final pool for CITE-seq assay. The fluorescence-labeled antibody cocktail against human CD14(BV421, BioLegend 325628), CD3(AF488, BioLegend 344810), CD45(PE/Cyanine7, BioLegend 393408), CD19(APC, BioLegend 363006) and Totalseq-C human hashtag antibodies(BioLegend) were added at the end of blocking, and incubated for 20 minutes at 4°C in the dark. Cells were washed and sorted on a BD Aria sorter in Biosafety Level 3 (BSL3) lab (BD Biosciences). B cell population was gated by CD45+CD19+CD3-; T cell population was gated by CD45+CD3+CD19-; monocyte population was gated by CD45+CD3-CD19-CD14+; other myeloid cells were gated by CD45+CD3-CD19-CD14-. Sorted 4 populations and unsorted PBMCs were pooled evenly. Then the final pool was CITE-seq stained, washed three times, resuspended in PBS and counted before proceeding to the single cell partition step.
PBMC samples were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry (10x Genomics, Pleasanton, CA). The RT step was conducted in the Veriti Thermo Cycler (ThermoFisher Scientific, Waltham, MA). Single cell gene expression, cell surface protein, and T cell receptor (TCR) libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA) and quantified using Qubit Fluorometric (ThermoFisher). 10x Genomics 5’ Single cell gene expression, cell surface protein tag, TCR and BCR libraries were pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics 5’ v1.1 user guide. Sequencing saturation of the libraries ranged from approximately 60-80% for the cDNA and 20-40% for the surface protein tag libraries.

tag: unsorted or sorted t/b cells

value: Unsorted

tag: timepoint

value: mixed

tag: molecule

value: T cell receptor VDJ region reads from mulitmodal scRNAseq


title: E341_FC8

tag: cell type


title: LPS+DEF rep3

status: Public on Jul 09 2019

data_processing:
Illumina CASAVA-1.8.4 software used for basecalling.
Sequencing adapters were removed using Trimmomatic (v.0.36) and the reads quality was checked using FastQC (v.0.11.2) before and after trimming. Reads were aligned to the human genome (GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf) using tophat2 package (v.2.1.0: -b2-sensitive,--library-type fr-firststrand). Mapping quality, read distribution, gene body coverage, GC content and rRNA contamination, were checked using picard (v.2.6.0) software.
Gene level read counts were computed using HT-Seq-count (v.0.6.1, annotation: gencode.v25.annotation.gtf)1 with strict "-m intersection-strict” mode. Genes with less than 10 aligned reads across all samples were filtered out as lowly expressed genes.
Differential gene expression analysis between groups was performed using DESeq2 (v.1.14.1)4 and significantly differentially expressed genes were reported using fold-change at 1.5 times and below 1 % Benjamini-Hochberg (BH) adjusted p-value.
In order to visualize the similarities between samples, unsupervised hierarchical clustering and principal component analysis (PCA) were performed using pcaExplorer (v.2.6.0, https://github.com/federicomarini/pcaExplorer) and pheatmap (v 1.0.10, https://CRAN.R-project.org/package=pheatmap) packages respectively. Volcano plots of differentially expressed genes were generated using ggplot2 (v.3.0.0, https://cran.r-project.org/web/packages/ggplot2/index.html) package.
Genome_build: GRCh38.primary_assembly.genome.fa; annotation: gencode.v25.annotation.gtf)

source_name: Macrophage

extract_protocol:
Total RNA was extracted using Trizol and Rneasy mini kit with an additional purification step by on-column DNAse treatment using Rnase-free Dnase Kit (Qiagen)
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA Library Prep kit for Illumina

value: Macrophage

value: LPS+DEF

tag: treatment time

value: 16h (DEF); 3h (LPS)


title: E341_FC7


title: WT LY6D+SCA1low population rep2

tag: tissue

value: prostate

value: 6-8 week-old

value: wild type


title: DEF rep2

value: DEF


title: LPS rep3

value: LPS


title: LPS rep2


title: LPS+DEF rep2


title: LPS+DEF rep1


title: CONTROL rep3

value: No treatment


title: DEF rep1


title: CONTROL rep2


title: LPS rep1


title: DEF rep3


title: 53E96hSINACT: E9 Resting CD8+ T cells

status: Public on May 29 2019

city: Madrid

first: Santos

last: Mañes

state: Madrid

address: C/Darwin, 3

department: Immunology and Oncology

country: Spain

institute: National Center of Biotechnology (CNB/CSIC)

data_processing:
Image analysis, base calling, and quality scoring of the run were processed by Real Time Analysis (RTA 1.13.48) software, followed by generation of FASTQ sequence files by CASAVA 1.8.
RNA-seq reads were aligned with the human reference genome (gencode v19) using the GEMtools RNA-seq pipeline v1.7 (http://gemtools.github.io), which is based on the GEM mapper. Expression quantification at the gene level was calculated with Flux (http://sammeth.net/confluence/display/FLUX/Home)
RNA-seq data were analyzed using the DESeq2 R Bioconductor package. Raw counts of sequencing reads were normalized to the effective library size.
Genome_build: gencode v19
Supplementary_files_format_and_content: Tabulated txt

source_name: CD8+ T cells

extract_protocol:
Tri-Reagent (Sigma-Aldrich)
The RNA-seq libraries were prepared using an Illumina TruSeq Stranded Total RNA Sample Preparation kit (Illumina). Library size and quality was assessed in an Agilent DNA 7500 Bioanalyzer assay (Agilent). Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with read length 2x 76bp. On average, we generated 36 million paired-end reads for each sample in a fraction of a sequencing lane on HiSeq2000 (Illumina).

treatment_protocol: Negatively isolated CD8+ T cells from healthy donors were incubated for different times with tosyl-activated magnetic beads (Dynabeads M-450; Thermo Scientific) coated with 8% anti-CD3 (HIT3a, BD Biosciences), 10% anti-CD28 (CD28.2, BioLegend), and 82% control IgG1 (Activated), or with anti-CD3, anti-CD28, and 82% PD-L1-Fc chimeric protein (R&D Systems) (PD-L1); IgG1-coated beads were used as control (CTRL)

value: Human embryonic kidney (HEK)-293T cells


title: E344

value: sorted outer root sheath (ORS) cells


title: 49E948hACT: E9 Activated CD8+ T cells, time point 48h


title: 47E96hACT: E9 Activated CD8+ T cells, time point 6h


title: 50E96hPDL1: E9 Activated+PDL1 CD8+ T cells, time point 6h


title: 52E948hPDL1: E9 Activated+PDL1 CD8+ T cells, time point 48h


title: 51E924hPDL1: E9 Activated+PDL1 CD8+ T cells, time point 24h


title: 44E824hPDL1: E8 Activated+PDL1 CD8+ T cells, time point 24h


title: 42E848hACT: E8 Activated CD8+ T cells, time point 48h


title: CONTROL rep1


title: 46E86hSINACT: E8 Resting CD8+ T cells


title: 48E924hACT: E9 Activated CD8+ T cells, time point 24h


title: 45E848hPDL1: E8 Activated+PDL1 CD8+ T cells, time point 48h


title: 40E86hACT: E8 Activated CD8+ T cells, time point 6h


title: 37E724hPDL1: E7 Activated+PDL1 CD8+ T cells, time point 24h


title: 41E824hACT: E8 Activated CD8+ T cells, time point 24h


title: 36E76hPDL1: E7 Activated+PDL1 CD8+ T cells, time point 6h


title: 38E748hPDL1: E7 Activated+PDL1 CD8+ T cells, time point 48h


title: 35E748hACT: E7 Activated CD8+ T cells, time point 48h


title: 34E724hACT: E7 Activated CD8+ T cells, time point 24h


title: Sort2B:CX3CR1_GFP

status: Public on Apr 04 2019

data_processing:
Illumina bcl2fastq 2.18, demultplexing nextseq run data, with options: --use-bases-mask Y*,I8Y*,Y* --minimum-trimmed-read-length 0 --mask-short-adapter-reads 0
cutadapt/1.8.3, trimmed 1 base off 5' of read 1
salmon v0.11.3, transcript abundance quantification. Parameters: -l IU --useVBOpt --biasCorrect
tximport 1.4.0 (Bioconductor R package); import TPM calculated by Salmon in R, and summarize to gene symbol. Transcript-gene mapping from org.Mm.eg.db 3.4.1 (Bioconductor R package)
Genome_build: mm10, UCSC annotation
Supplementary_files_format_and_content: Comma-seperated values of transcripts per million summarized at the gene level.

source_name: peritoneal wall_CX3CR1_GFP

growth_protocol: All mice were maintained in specific-pathogen-free conditions at an American Association for Laboratory Animal Care–accredited animal facility at the NIAID (National Institute of Allergy and Infectious Diseases) and were used under a study protocol approved by NIAID Animal Care and Use Committee (National Institutes of Health).

extract_protocol:
Trizol LS; RNA further purified using the Zymo RNA Direct-zol spin column kit.
RNAseq libraries were prepared using the Nugen Ovation SoLo (NuGEN; Cat# 0501-32) with 1 ng total RNA input. Sequencing was performed using Illumina NextSeq V2 reagents (Illumina; Cat# FC-404-2005) using paired end 75 base pair reads. The custom Read 1 primer provided by Nugen in the Ovation SoLo kit was used.

treatment_protocol: One day prior to the experiments, Cx3cr1gfp/+Ccr2rfp/+ animals received an iv-injection of 50 μg Dextran-Cascade Blue (ThermoFisher; Cat# D1976) to label interstitial phagocytes. On the day of the experiment, animals were transcardially perfused with pre-warmed PBS to remove circulating leukocytes. The peritoneal wall was then carefully removed, spread out in a 6-well plate, and covered with 2.5 ml dissociation buffer: RPMI (Gibco; Cat# 11875093); 1% FCS (Gemini; Lot# A20G001; Cat# 100-106); 250 μg/ml Liberase TL (Sigma-Aldrich; Cat# 5401020001); 100 μg/ml DNAse II (Sigma-Aldrich; Cat# D8764); 25 μM Z-VAD-FMK (Tocris; Cat# 2163); 10 mM HEPES (Gibco; Cat# 15630080). After 20 minutes of incubation at 37 °C, dissociation was stopped with ice-cold FACS-buffer: PBS (Gibco; Cat# 10010-23; Lot# 1943335); 2% FCS, 2 mM EDTA (Quality Biological; Cat# 351-027-101). The most superficial tissue layers were gently scraped off the underlying abdominal wall using a plastic cell scraper and forced through a 70 μm cell strainer. Cells were resuspended in buffer containing 25 μM Z-VAD-FMK and stained with antibodies for CD11b (Biolegend; clone M1/70; Cat# 101220), I-A/I-E (Biolegend; clone M5/114.15.2; Cat# 107615) and Ly6G (Biolegend; clone 1A8; Cat# 127633). CD11b+Ly6G- cells were sorted into Dextran+MHCII-Ccr2-Cx3cr1- (majority of sessile RTM; 85-90 % of CD11b+Ly6G- cells), MHCII+Ccr2+Cx3cr1- (migratory tissue monocytes; 10-15 %) and MHCII+Ccr2-Cx3cr1+ (sessile RTM; 0.5 - 1.5 %) populations, directly into 0.5 ml TRIZOL (Invitrogen; #15596026) using a FACS-Aria cell sorter (BD Bioscience).

tag: mouse strain

value: Cx3cr1gfp/+ Ccr2rfp/+:Jackson Laboratories; F1 crossbreed:Jax 008455 x Jax 017586

value: peritoneal wall


title: Sort2B:CCR2_RFP

source_name: peritoneal wall_CCR2_RFP


title: Sort2A:CCR2_RFP


title: 33E76hACT: E7 Activated CD8+ T cells, time point 6h


title: 43E86hPDL1: E8 Activated+PDL1 CD8+ T cells, time point 6h


title: Sort2A:CX3CR1_GFP


title: Sort2A:CCR2negCX3CR1neg

source_name: peritoneal wall_CCR2negCX3CR1neg


title: 39E76hSINACT: E7 Resting CD8+ T cells


title: Sort1:CCR2_RFP


title: Sort1:CX3CR1_GFP


title: Sort1:CCR2negCX3CR1neg


title: Untransformed_murine_B_cells_Stat1_KO_2

status: Public on Feb 05 2019

data_processing:
Basecalls performed using RTA v2
Fastq files were adapter and quality trimmed using TrimGalore! Software
Alignment was performed using STAR aligner
SeqMonk software was used to calculate differential expression based on DESeq2 algorithm
Genome_build: GRCm38 and GRCh38
Supplementary_files_format_and_content: DESeq2 count table

extract_protocol:
Qiagen, Rneasy kit, according to protocol
Clontech, SMARTer Stranded Total RNA Sample Prep Kit, according to protocol

tag: status

value: Untransformed

value: Stat1 -/-

value: B cells


title: Untransformed_murine_B_cells_Stat1_WT_2

value: Stat1 wt


title: Patient_1_Ctrl

tag: disease state

value: lymphoma

tag: individual

value: Patient 1

value: Healthy B cells


title: Untransformed_murine_B_cells_Stat1_KO_3


title: Untransformed_murine_B_cells_Stat1_WT_3


title: Patient_2_TU

value: Patient 2

value: FFPE tumor, lymphoma


title: Patient_1_TU

value: B cells from lymphoma patient


title: Untransformed_murine_B_cells_Stat1_KO_1


title: Transformed_murine_B_cells_Stat1_KO_4

value: Transformed


title: Untransformed_murine_B_cells_Stat1_WT_1


title: Transformed_murine_B_cells_Stat1_KO_3


title: Untransformed_murine_B_cells_Stat1_KO_4


title: Patient_2_Ctrl

value: Healthy lymph node


title: Transformed_murine_B_cells_Stat1_KO_1


title: Transformed_murine_B_cells_Stat1_KO_2


title: Sort2B:CCR2negCX3CR1neg


title: I_Control-2: Primary islets, control, rep2

status: Public on Jan 01 2019

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The background-subtracted raw microarray data were also normalized by Z score transformation to obtain Z ratios.  All data were analyzed by the R statistical software package.

label: Biotin

source_name: Primary islets, control

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

growth_protocol: Primary hepatocyte or pancreatic islets were isolated from wild type B6 mice and cultured.

extract_protocol: Total RNA was isolated from primary hepatocytes and pacreatic islets treated with DMSO or FK866 using Rneasy Mini Kit (Qiagen).

treatment_protocol: Primary hepatocytes were treated with 0.1% DMSO (control) or 200 nM FK866 (NAMPT inhibitor) for 48 hours.  Primary islets were treated with 0.1% DMSO or 10 nM FK866 for 48 hours.

value: Primary islets


title: I_FK-4: Primary islets, FK866, rep4

description: replicate 4

source_name: Primary islets, FK866


title: I_Control-4: Primary islets, control, rep4

description: replicate 4


title: H_FK-4: Primary hepatocyte, FK866, rep4

description: replicate 4

source_name: Primary hepatocyte, FK866

value: Primary hepatocyte


title: I_FK-3: Primary islets, FK866, rep3

description: replicate 3


title: H_FK-3: Primary hepatocyte, FK866, rep3

description: replicate 3


title: H_FK-1: Primary hepatocyte, FK866, rep1

description: replicate 1


title: I_FK-2: Primary islets, FK866, rep2

description: replicate 2


title: I_Control-3: Primary islets, control, rep3

description: replicate 3


title: I_Control-1: Primary islets, control, rep1

description: replicate 1


title: H_FK-2: Primary hepatocyte, FK866, rep2

description: replicate 2


title: I_FK-1: Primary islets, FK866, rep1

description: replicate 1


title: JC163 RNA-seq

status: Public on Oct 16 2018

description: RNA isolated from FFPE

data_processing:
Trim  paired-end reads from FASTQ files prefixed with '11139_' to 50bp with software cutadapt using parameter -u -75 to trim off the first 75 bases.
Mouse read mapping with STAR (v2.5.2b) to genomic reference GRCm38.p4. The following command was executed (paths relative):  STAR/2.5.2b/STAR --readFilesCommand gunzip -c --runThreadN $NCPU --genomeDir Mouse/GRCm38.p4/star50 --readFilesIn *txt.gz --outFilterType BySJout --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigNorm RPM --outWigStrand Unstranded --outFilterMultimapNmax 1 --clip3pAdapterSeq AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
Mouse: Generate per gene read counts using SubRead's FeatureCounts software. The following command was executed (paths relative): Subread/bin/featureCounts -a Mouse/GRCm38.p4/Mus_musculus.GRCm38.85.chr.gtf -o Mouse_counts.txt -s 2 -T 20 --largestOverlap *bam
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Mouse raw read counts output by FeatureCounts, with minor column-reformatting for convenience of the user, is reported in the tab-delimited file  'Mouse_counts.txt'.

source_name: Lenti-Sox2-Cre Lkb1fl/fl

extract_protocol:
5 µm serial sections of FFPE tissue were stained with H&E and Aniline blue. H&E stained slides were used to confirm histology of tumors and guide bordering consecutive serial sections of Aniline blue stained tissue samples. Bordered tissue samples were microdissected using sterile disposable scalpels and razor blades with the assistance of a dissection scope. 10 – 14 pieces of each sample isolated from serial sections were pooled in a microcentrifuge tube containing 100% ethanol. RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Thermo Fisher Cat#AM1975) was used to isolate RNA from FFPE tissues according to the manufacturer’s protocol.
RNA samples were quantified using NanoDrop 8000 and Qubit RNA HS Assay. RNA integrity numbers were calculated on Agilent HS RNA ScreenTape. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Cat#RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (Cat#GD-401-4001). Following the transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50-cycle single-read or 125-cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (Cat#FC-401-4002).

tag: genotype/variation

value: Lenti-Sox2-Cre Lkb1fl/fl

value: Lung

value: Lung squamous cell carcinoma


title: JC231 RNA-seq

description: RNA isolated from FFPE


title: JC243A RNA-seq

description: RNA isolated from FFPE

source_name: KrasLSL-G12D/+;Trp53fl/fl (KP)

value: KrasLSL-G12D/+;Trp53fl/fl (KP)

value: Lung adenocarcinoma


title: JC242C RNA-seq

description: RNA isolated from FFPE


title: JC247C RNA-seq

description: RNA isolated from FFPE


title: JC193A RNA-seq

description: RNA isolated from FFPE

source_name: Normal lung from uninfected Lkb1fl/fl

value: Normal lung from uninfected Lkb1fl/fl

value: Normal (healthy) tissue


title: H_Control-3: Primary hepatocyte, control, rep3

description: replicate 3

source_name: Primary hepatocyte, control


title: JC248B RNA-seq

description: RNA isolated from FFPE


title: JC229 RNA-seq

description: RNA isolated from FFPE


title: JC194A RNA-seq

description: RNA isolated from FFPE


title: JC245A RNA-seq

description: RNA isolated from FFPE


title: JC243B RNA-seq

description: RNA isolated from FFPE


title: JC198 RNA-seq

description: RNA isolated from FFPE


title: H_Control-1: Primary hepatocyte, control, rep1

description: replicate 1


title: H_Control-4: Primary hepatocyte, control, rep4

description: replicate 4


title: JC243D RNA-seq

description: RNA isolated from FFPE


title: H_Control-2: Primary hepatocyte, control, rep2

description: replicate 2


title: JC192A RNA-seq

description: RNA isolated from FFPE


title: JC264A RNA-seq

description: RNA isolated from FFPE


title: JC262 RNA-seq

description: RNA isolated from FFPE


title: JC156 RNA-seq

description: RNA isolated from FFPE


title: JC191 RNA-seq

description: RNA isolated from FFPE


title: GM335_5 RNA-seq

description: RNA isolated from FFPE

source_name: Lkb1fl/fl;Ptenfl/fl (LP)

value: Lkb1fl/fl;Ptenfl/fl (LP)


title: JC233 RNA-seq

description: RNA isolated from FFPE


title: GM182_6 RNA-seq

description: RNA isolated from FFPE


title: JC230 RNA-seq

description: RNA isolated from FFPE


title: GM286_3 RNA-seq

description: RNA isolated from FFPE


title: GM184_2 RNA-seq

description: RNA isolated from FFPE


title: GM347_7 RNA-seq

description: RNA isolated from FFPE

source_name: Rosa26LSL-Sox2-IRES-GFP;Lkb1fl/fl (SL)

value: Rosa26LSL-Sox2-IRES-GFP;Lkb1fl/fl (SL)


title: GM356_3 RNA-seq

description: RNA isolated from FFPE


title: GM346_4 RNA-seq

description: RNA isolated from FFPE


title: GM254_6 RNA-seq

description: RNA isolated from FFPE


title: GM249_2 RNA-seq

description: RNA isolated from FFPE


title: KPS1 ChIP-seq

data_processing:
Reads were aligned to the mm10 build of the human genome using Bowtie V 1.1.2 with the following arguments: bowtie --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Cell line generated from Lenti-Sox2-Cre infected KrasLSL-G12D/+;Trp53fl/fl (KPS) tumors

growth_protocol: KPS cells were grown in DMEM with 10% FBS, 1% Pen/Strep, 1% L-Glutamine at 37°C and 5% CO2.

extract_protocol:
20 million cells per ChIP were cross-linked in 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with 125 mM glycine and nuclei were extracted. Alternatively, flash-frozen tumors were directly used. Chromatin was sonicated using an Epishear Probe Sonicator (Active Motif) for 4 min at 40% power. SOX2 antibody (R&D Systems Cat#AF2018) was used for IP.
Libraries were prepared using a standard Illumina library construction protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and purified using Ampure XP beads.

value: KPS1 cell line generated from Lenti-Sox2-Cre infected KrasLSL-G12D/+;Trp53fl/fl (KPS) tumors

tag: time

value: <10 passages

tag: chip antibody

value: SOX2 antibody (R&D Systems Cat#AF2018)


title: GM184 ChIP-seq

source_name: Lung squamous cell carcinoma from Lkb1fl/fl;Ptenfl/fl (LP) mouse model; infected with Ad5-CMV-Cre virus; harvested approximately 10 months post-infection.

value: Flash-frozen


title: TANs single-cell RNA-seq

data_processing:
For each sample, demultiplex raw base call files (BCL) from Illumina with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger (version 2.1.1), using the 'mkfastq' pipeline.
For each sample, perform alignment, filtering, barcode counting, and UMI (unique molecular identifier) counting with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger (version 2.1.1), using the 'count' pipeline. Default parameters were used with exception of the parameter 'expected-cells' was set to 3500,  in estimation of the expected number of recovered cells. We used the genomic reference, 'refdata-cellranger-mm10-2.1.0',  prepared by 10x Genomics; the mm10 mouse genomic reference had filtered Ensembl GTF files and UCSC FASTA files.
Aggregate multiple libraries' (i.e. samples') UMI counts with 10x Genomics' Single-Cell Gene Expression software, Cell Ranger (version 2.1.1), using the 'aggr' pipeline. Sample aggregation was evaluated with normalizing for sequencing depth differences in the libraries. Normalized UMI counts used the 'mapped' normalization mode, which according to 10x Genomics' documentation, "subsample[s] reads from higher-depth libraries until they all have an equal number of confidently mapped reads per cell." Analysis of the data was based on the normalized UMI counts.
Genome_build: mm10
Supplementary_files_format_and_content: There are three MEX-formatted UMI count matrices available. Sample-specific MEX-formatted matrices are prefixed by sample identifiers, '14931X1_', '14931X2_' with no normalization between samples;  samples were aggregated and between-sample normalized into a MEX-formatted matrix prefixed with "agg_14931R_". 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix...Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.

source_name: Lung tumors from Rosa26LSL-Sox2-IRES-GFP;Nkx2-1fl/fl;Lkb1fl/fl (SNL) mice; infected with Ad5-CMV-Cre.

extract_protocol:
CD45+CD11B+LY6G+ neutrophils were flow sorted and pooled to prepare TAN single cell population (n = 9 tumors from 2 SNL mice) and PBN population (n = blood from 2 SNL mice). Without any freezing or fixation steps, the single cell populations were immediately processed.
Cell suspensions were partitioned into an emulsion of nanoliter-sized droplets using a 10X Genomics Chromium Single Cell Controller and RNA sequencing libraries were constructed using the Chromium Single Cell 3’ Reagent Kit v2 (10X Genomics Cat#PN-120237). Briefly, droplets contained individual cells, reverse transcription reagents and a gel bead loaded with poly(dT) primers that include a 16 base cell barcode and a 10 base unique molecular index. Lysis of the cells and gel bead enables priming and reverse transcription of poly-A RNA to generate barcoded cDNA molecules. Libraries were constructed by End Repair, A-Tailing, Adapter Ligation and PCR amplification of the cDNA molecules. Purified cDNA libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (Agilent Cat#5067-5582 and Cat#5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (Kapa Biosystems Cat#KK4824). HiSeq 125 Cycle Paired-End Sequencing v4: Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003).

value: CD45+CD11B+LY6G+ cells purified by fluorescence activated cell sorting (FACS)


title: PBNs single-cell RNA-seq

source_name: Peripheral blood from Rosa26LSL-Sox2-IRES-GFP;Nkx2-1fl/fl;Lkb1fl/fl (SNL) tumor-bearing mice; infected with Ad5-CMV-Cre.


title: KPS3 ChIP-seq

value: KPS3 cell line generated from Lenti-Sox2-Cre infected KrasLSL-G12D/+;Trp53fl/fl (KPS) tumors


title: GM184_1 RNA-seq

description: RNA isolated from FFPE


title: Cell line input

value: Cell line generated from Lenti-Sox2-Cre infected KrasLSL-G12D/+;Trp53fl/fl (KPS) tumors


title: Tumor input

source_name: Lung squamous cell carcinoma from Lkb1fl/fl;Ptenfl/fl (LP) mouse model


title: GM347_1 RNA-seq

description: RNA isolated from FFPE


title: KPS2 ChIP-seq

value: KPS2 cell line generated from Lenti-Sox2-Cre infected KrasLSL-G12D/+;Trp53fl/fl (KPS) tumors


title: GM356_5 RNA-seq

description: RNA isolated from FFPE


title: GM183_4 RNA-seq

description: RNA isolated from FFPE


title: 201247460057_R08C01: ependymoma tissue 202

status: Public on Jul 17 2018

city: Toronto

first: Vijay

last: Ramaswamy

state: ON

address: 555 University Avenue

country: Canada

institute: Hospital for Sick Children

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 or MethylationEPIC Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

label: Cy3, Cy5

source_name: ependymoma tissue

extract_protocol: genomic DNA was extracted and purified from posterior fossa ependymoma using Qiagen DNeasy Kit according to standard instructions

value: primary posterior fossa ependymoma

tag: tissue type

value: FFPE Tumor

tag: gender

value: M

tag: age

tag: pfs

tag: os

tag: progression (1=progression event)

tag: status (1=dead)

tag: pfb subtype


title: GM356_8 RNA-seq

description: RNA isolated from FFPE

value: Lung

tag: cell type

value: Lung squamous cell carcinoma


title: 200397860005_R04C02: ependymoma tissue 201

tag: tissue


title: 201247460059_R01C01: ependymoma tissue 52


title: 201332340055_R01C01: ependymoma tissue 54


title: 201247490036_R07C01: ependymoma tissue 53


title: 201247460058_R03C01: ependymoma tissue 51


title: 201332340088_R02C01: ependymoma tissue 55


title: 201247460057_R02C01: ependymoma tissue 50

value: F


title: 201247460055_R07C01: ependymoma tissue 49


title: 201247460012_R01C01: ependymoma tissue 48


title: 201194010126_R06C01: ependymoma tissue 47


title: 201194000036_R05C01: ependymoma tissue 46


title: 200928190015_R05C01: ependymoma tissue 44

value: Frozen Tumor


title: 200788260036_R05C01: ependymoma tissue 41


title: 200848860124_R06C01: ependymoma tissue 42


title: 200970160058_R08C01: ependymoma tissue 45


title: 200397860043_R01C02: ependymoma tissue 37


title: 200925700197_R04C01: ependymoma tissue 43


title: 200397860043_R03C01: ependymoma tissue 38


title: 200397860042_R06C02: ependymoma tissue 36


title: 200394870007_R01C01: ependymoma tissue 32


title: 200325530167_R02C01: ependymoma tissue 31


title: 200397540073_R01C01: ependymoma tissue 33


title: 200397860047_R01C02: ependymoma tissue 39


title: 200397860007_R02C02: ependymoma tissue 34


title: 200325530166_R04C02: ependymoma tissue 30


title: 200325530067_R03C01: ependymoma tissue 29


title: 101231000138_R01C02: ependymoma tissue 1


title: 6752625133_R06C02: ependymoma tissue 210


title: 6026818094_R03C01: ependymoma tissue 209


title: 9533774102_R04C02: ependymoma tissue 212


title: 101231000134_R03C01: ependymoma tissue 27


title: 3999688058_R02C02: ependymoma tissue 206


title: 6026818091_R05C01: ependymoma tissue 208


title: 200091640007_R04C02: ependymoma tissue 28


title: 3999875132_R01C02: ependymoma tissue 207


title: 3999688006_R05C02: ependymoma tissue 205


title: 3999543105_R04C01: ependymoma tissue 204


title: 200397860107_R04C01: ependymoma tissue 40


title: 200397860007_R05C02: ependymoma tissue 35


title: 3999095046_R03C01: ependymoma tissue 203


title: 9996247142_R02C02: ependymoma tissue 200


title: 9992576055_R04C02: ependymoma tissue 199


title: 9969477063_R05C01: ependymoma tissue 197


title: 9969477057_R06C02: ependymoma tissue 196


title: 9969477057_R02C02: ependymoma tissue 195


title: 9968646156_R03C01: ependymoma tissue 192


title: 9426020061_R06C02: ependymoma tissue 211


title: 9968646155_R06C02: ependymoma tissue 190


title: 9968646156_R02C02: ependymoma tissue 191


title: 9968646156_R03C02: ependymoma tissue 193


title: 9968646155_R05C01: ependymoma tissue 189


title: 9968646139_R02C02: ependymoma tissue 188


title: 9968646103_R06C02: ependymoma tissue 186


title: 9968646108_R03C01: ependymoma tissue 187


title: 9968646103_R02C01: ependymoma tissue 183


title: 9968646103_R04C02: ependymoma tissue 184


title: 9968646099_R04C02: ependymoma tissue 181


title: 9968646103_R05C01: ependymoma tissue 185


title: 9968646096_R06C02: ependymoma tissue 177


title: 9968646098_R03C02: ependymoma tissue 179


title: 9968646098_R06C01: ependymoma tissue 180