title: FA5_1

description: Fermentation with 1mg/mL folic acid


title: FA2_1

status: Public on Mar 01 2024

type: SRA

city: Hangzhou

first: xiaogu

last: zheng

state: Zhejiang

address: Xiasha University Town

country: China

institute: Zhejiang Gongshang university

description: Fermentation with 1mg/mL folic acid

library_source: genomic

data_processing:
Briefly, raw data FASTQ files were imported into the format which could be operated by QIIME2 system using qiime tools import program. Demultiplexed sequences from each sample were quality filtered and trimmed , de-noised, merged, and then the chimeric sequences were identified and removed using the QIIME2 dada2 plugin to obtain the feature table of amplicon sequence variant (ASV) (Callahan et al. 2016).
The QIIME2 feature-classifier plugin was then used to align ASV sequences to a pre-trained GREENGENES 13_8 99% database (trimmed to the V3V4 region bound by the 338F/806R primer pair) to generate the taxonomy table (Bokulich et al. 2018)
Any contaminating mitochondrial and chloroplast sequences were filtered using the QIIME2 feature-table plugin. Appropriate methods include ANCOM, ANOVA, Kruskal Wallis, LEfSe and DEseq2 were employed to identify the bacteria with different abundance among samples and groups (Love, Huber, and Anders 2014; Mandal et al. 2015; Segata et al. 2011).
Diversity metrics were calculated using the core-diversity plugin within QIIME2. Feature level alpha diversity indices, such as observed OTUs, Chao1 richness estimator, Shannon diversity index, and Faith’s phylogenetics diversity index were calculated to estimate the microbial diversity within an individual sample.
Supplementary files format and content: allsample.txt: ASVs IDs of sample groups  (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)
Supplementary files format and content: table.tsv: ASVs IDs of sample groups  (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)
Supplementary files format and content: AllSample_GC_Q.stat.xls: Sample group (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF) processing process files
Supplementary files format and content: alpha_diversity.xls: Sample groups (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)alpha diversity index
Supplementary files format and content: alpha-summary.txt: Sample group (Ori, Ctrl2, FA, MTHF) alpha diversity index
Supplementary files format and content: assemble_stat.xls.txt: Sample group (Ori, Ctrl2, FA, MTHF) processing process files
Supplementary files format and content: feature-table.tsv: ASVs IDs of sample groups (Ori, Ctrl2, FA, MTHF)

molecule: genomic DNA

organism: human feces metagenome

source_name: fecal matter (not tissue)

extract_protocol:
Total genome DNA from samples was extracted using CTAB method. DNA concentration and purity was monitored on 1% agarose gels. According to the concentration, DNA was diluted to 1ng/µL using sterile water.
16S rRNA  genes of distinct regions(16S V3-V4 ) were amplified used specific primer( 341F(5’-CCTAYGGGRBGCASCAG-3’)和806R (5’-GGACTACNNGGGTATCTAAT-3’) )with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 2 µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10 s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30 s. Finally 72℃ for 5 min
The analysis was conducted by following the "Atacama soil microbiome tutorial" of Qiime2docs along with customized program scripts (https://docs.qiime2.org/2019.1/).

tag: tissue

value: fecal matter (not tissue)

tag: genotype

value: 16S rRNA

tag: treatment

value: Fermentation with 1mg/mL folic acid


title: Ctrl28_1

description: Fermentation of faeces

value: Fermentation of faeces


title: Ctrl26_1

description: Fermentation of faeces


title: Ctrl1_1

description: Fermentation of faeces


title: Ctrl27_1

description: Fermentation of faeces


title: Ctrl25_1

description: Fermentation of faeces


title: Ctrl23_1

description: Fermentation of faeces


title: Ctrl22_1

description: Fermentation of faeces


title: Ctrl24_1

description: Fermentation of faeces


title: MTHF5_1

description: Fermentation with 1mg/mL 5-methyltetrahydrofolate


title: K2_raw_1

description: Raw feces

value: Raw feces


title: Ctrl21_1

description: Fermentation of faeces


title: FA4_1

description: Fermentation with 1mg/mL folic acid


title: Ori6_1

description: Raw feces


title: Ori8_1

description: Raw feces


title: Ori7_1

description: Raw feces


title: FA3_1

description: Fermentation with 1mg/mL folic acid


title: Ori4_1

description: Raw feces


title: Ori5_1

description: Raw feces


title: Ori3_1

description: Raw feces


title: FA1_1

description: Fermentation with 1mg/mL folic acid


title: Reads obtained from sequencing of sample Blood10

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of human Saliva

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 --verbose
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 268 --p-trunc-len-r 175 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_GRCh38_analysis_set_BOWTIE2/GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV_1.fasta -S eucar_contaminants_ASV/bowtie2_HUMAN_SAM_output.txt -f -p 4
bowtie2 -x $BOWTIE2_DATABASE/INDEXED_mouse_GRCm39_BOWTIE2/GRCm39 -U dna-sequences.fasta --al eucar_contaminant_ASV_2.fasta -S eucar_contaminants_ASV/bowtie2_MICE_SAM_output.txt -f -p 4
qiime feature-classifier classify-consensus-vsearch --i-query clean_rep-seqs.qza --i-reference-reads ~/Scrivania/Tools/Database/silva-138-99-seqs.qza --i-reference-taxonomy ~/Scrivania/Tools/Database/silva-138-99-tax.qza --p-perc-identity 0.99 --p-threads 8 --o-classification taxonomy_vsearch.qza --o-search-results vsearch_hits.qza --verbose
R software (see the relative script publicly available at github.com/LeandroD94)
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundances of ASVs in each sample and the related taxonomic assignments
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

organism: human blood metagenome

source_name: Blood

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

value: Blood

tag: sample id

tag: sample gender

value: F

tag: kit dna_extraction

tag: sample type


title: Root total RNA isolate from six Months old Dendrobium Sonia under white light root total RNA

city: Khurda

first: Kishore

middle: Cs

last: Panigrahi

state: Odisha

address: NISER, P.O Jatni

department: School of Biological Sciences

country: India

institute: National Institute of Science Education and Research

library_source: transcriptomic

data_processing:
Fastq quality check: checking of quality parameters for the sequences obtained from sequencer.  The following checks are performed for an input fastq file • base quality score distributions • average base content per read • GC distribution in the reads
Preprocessing step : From the raw reads, the adaptor sequences and low quality bases are trimmed using AdapterRemoval-v2 (version 2.2.0). From the preprocessed reads, ribosomal rna sequences are removed by aligning the reads with silva database using bowtie2 (version 2.2.9) and subsequent workflow using sam-tools (version 0.1.19), sambamba (version 0.6.5), BamUtil (version 1.0.13) tools and in-house scripts. T
De novo transcriptome assembly :The high quality reads were then assembled using Trinity with default options
The trimmed reads were aligned to the assembled transcriptome (length >= 200bp) using Bowtie2 program. We allowed up to 1-mismatches in the seed region (length = 31bp) and all multiple mapped position were reported. Of all filtered reads about ~ 93.29% of reads from  sample were properly aligned back to the assembled transcriptome.
Annotation: The assembled transcript is annotated using our in-house pipeline for de novo transcriptome assembly. Briefly, we perform the following steps for annotation of assembled transcripts.  Comparison with  TAIR Araport protein database using BLASTX program  Gene and protein annotation to the matched transcript  Gene ontology annotation  Pathway annotation
Assembly: Araport11
Supplementary files format and content: Fasta file containing the sequence of respective assembeled transcripts
Supplementary files format and content: Tab delimited text file containing annotation for all the Transcripts along with their ReadCounts and FPKM

molecule: total RNA

organism: Dendrobium hybrid cultivar

source_name: Root

growth_protocol: Plants of Dendrobium Sonia in juvenile stage (6 months) with ~4’ in height were grown in plant growth chambers (Percival Scientific, USA). All plants growtt was maintained at 25 °C temperature and with 70 % relative humidity.The plants were sprayed with water regularly and with standard N, P, K nutrient solution once every week.

extract_protocol:
Plant root was cut out and immediately frozen in liquid nitrogen. The frozen roots were ground into powder form using RNAase treated mortar and pestle. The powder was then used for RNA extraction using Qiagen Plant RNeasy mini kit (Cat #74104). 1.26 μg RNA was used for preparation of Library.
SMARTer RNA-seq kit was used for preparation of the library using manufacturer's protocol

treatment_protocol: Plants were grown in gowth chambers with 16-hour light and 8-hour dark cycle in fluorescence cool white light (WL). The white light was obtained from Philips 17-watt F17T8/TL741 USA Alto II technology tubes with 100% light intensity, which is equivalent to ~100 μmols/min chambers under white light.

value: Root

value: WT

value: White light


title: Reads obtained from sequencing of sample Blood11


title: Reads obtained from sequencing of sample Blood7

value: M


title: Ori1_1

description: Raw feces


title: Reads obtained from sequencing of sample Blood9


title: Reads obtained from sequencing of sample Blood8


title: Reads obtained from sequencing of sample Blood4


title: Reads obtained from sequencing of sample Blood5


title: Reads obtained from sequencing of sample Blood1


title: Reads obtained from sequencing of sample Blood3


title: ∆mftG ethanol 3

city: Kulmbach

first: Gerald

last: Lackner

address: Fritz-Hornschuch-Str. 9

department: Chair of Biochemistry of Microorganisms

country: Germany

institute: University of Bayreuth

data_processing:
Raw reads were checked for quality using fastP and polyX tails (-x10)
low quality ends (-3, -5, -M 25) were removed, resulting sequences shorter than 25 were discarded (-l 25)
remaining reads were mapped to the reference genome (RefSeq accession GCF_000015005.1) using bwa-mem2 with default parameters for the affine gap scoring model
For each sample and every gene annotation, all overlapping reads were counted and a counts table was generated for every experiment condition using custom scripts
The counts' tables were used as an input to the R package DESeq2 to compute fold changes and false discovery rates of differentially expressed genes between the control condition and each experiment condition
Assembly: GCF_000015005.1
Supplementary files format and content: The counts' tables were used as an input to the R package DESeq2 to compute fold changes and false discovery rates of differentially expressed genes between the control condition and each experiment condition

organism: Mycolicibacterium smegmatis MC2 155

source_name: bacteria

growth_protocol: Biological triplicates of M. smegmatis WT and ∆mftG strains were incubated in two different conditions, Hartmans de Bont medium and 0.5 g L-1 tyloxapol (HdB-Tyl) with either 10 g L-1 absolute ethanol (TH.Geyer), 10 g L-1 glucose (Carl Roth) as the sole carbon sources. Pre-cultures were incubated in HdB-Tyl with 10 gL-1 of glucose for 24h, then were collected, centrifuged and supernatant removed. The pellet was re-suspended in plain HdB-Tyl. Cultures of each strain in each condition starting at OD600 0.1, were incubated at 37C in 250ml with total liquid volume 40ml. One sample of each culture was taken at 36 hours for WT and  ∆mftG grown on glucose, at 45h of WT grown on ethanol and 60h of ∆mftG grown on ethanol (conditions considered as exponential phase)

extract_protocol:
extraction protocol 3 (InnuPREP RNA Mini kit 2.0 – Analytik Jena) the following changes: lysozyme was incubated with the samples for 1h at 37 °C, when binding the total RNA onto spin filter R fresh 80% EtOH in RNAse free water was used and an additional step was added in before RNA elution with incubation of 7 µL DNAse with 50µL buffer for each sample at room temperature for 15min. In the final step, the samples were resuspended on 50µL RNAse free water.
illumina stranded total RNA prep Ligation with Ribo-Zero plus (illumina)

treatment_protocol: growth on minimal media with 10 g L-1 absolute ethanol (TH.Geyer)

tag: cell type

value: bacteria

value: {delta}mftG

value: ethanol


title: Reads obtained from sequencing of sample Blood2


title: ∆mftG ethanol 2


title: wt ethanol 3

value: wt


title: ∆mftG ethanol 1


title: ∆mftG glucose 2

value: glucose


title: Ori2_1

description: Raw feces


title: Reads obtained from sequencing of sample Blood6


title: siCrtl_STV_1

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

data_processing:
sequenced data were aligned to the UCSC hg38 genome
Assembly: UCSC hg38
Supplementary files format and content: Data was analyzed by Dr. Tom and .xlsx file with TPM values of all genes was extracted
Supplementary files format and content: DEseq2 was used for differential expression detection

organism: Homo sapiens

source_name: SGBS

growth_protocol: SGBS cells were maintained and differentiated to mature adipocytes as described in Wabitsch et al., Int J Obes, 2001

extract_protocol:
RNA was isolated with SV Total RNA Isolation System (Promega, Z3105) according to manufactureres protocol.
BGI Strand-Specific mRNA Library Preparation (DNBSEQ)
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Fully differentiated SGBS cells were transfected with 100 nM of siCtrl or sip53 (Thermo Fisher Scientific, Waltham, MA, United States) by using Lipofectamine RNAiMax (Thermo Fisher Scientific, Waltham, MA, United States) following the provider`s instructions. After transfection, ells were cultivated 24 h in normal and 24 h in starvation medium (HBSS and HEPES) before harvest.

tag: cell line

value: SGBS

value: fibroblast

value: siCrtl

value: adipogenic differentiation and starvation


title: wt glucose 2


title: ∆mftG glucose 3


title: ∆mftG glucose 1


title: wt ethanol 1


title: wt glucose 3


title: wt glucose 1


title: Group3-7, NGFP

city: Irvine

first: Samuel

last: Morabito

state: CA

address: Biological Sciences III

department: Neurobiology and Behavior

country: USA

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
Cellranger count (v 6.0.0) was used to map snRNA-seq reads to the reference transcriptome (mm10 2020-A, downloaded from the 10X Genomics website) to quantify gene expression in single nuclei from each sample. The “include-introns” option was used in cellranger count to account for pre-mRNA molecules present in the snRNA-seq data. Downstream data processing (e.g. normalization, dimensionality reduction, clustering) was performed using the SCANPY software ecosystem.
Assembly: mm10
Supplementary files format and content: Processed SeuratObject containing UMI counts matrix, normalized gene expression, cluster assignments, and UMAP representation.

molecule: nuclear RNA

organism: Mus musculus

source_name: habenula

extract_protocol:
Using a 0.5 mm biopsy punch and a dissecting microscope, habenula samples were collected from two 400 um slabs made on a Leica 1850 CM cryostat.
From habnenula biopsy punches, single nuclei were extracted into droplets containing barcoded GEMs (Gel Bead-In Emulsions) using the 10X v3.1 3’ snRNA-seq kit.  After a cleanup step, cDNA were amplified, and libraries were constructed for sequencing.

value: habenula

value: NGFP


title: Group3-2, NN

value: NN


title: Group3-8, NGFP


title: Group3-6, NGFP


title: Group3-5, NGFP


title: Group3-4, NN


title: Group3-1, NN


title: Group3-3, NN


title: batch4_mm_VEGFA-6

city: Melbourne

first: Guei-Sheung

last: Liu

address: 32 Gisborne Street

country: Australia

institute: Centre for Eye Research Australia

data_processing:
Raw data processing was performed using FASTQC to check the reads quality and Trimmomatic tool to further remove the bases and reads with low quality, adaptors and barcodes.  The clean reads were aligned to the reference human genome (version GRCh38), utilizing STAR v2.7 as the aligner. For RNA quantification, RSEM was employed to normalize raw read counts, transforming them into TPM (transcripts per million) values, providing a relative expression level that is theoretically comparable across samples. The magnitude (log2-transformed fold change) and significance (P-value) of differential expression between groups were then calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes FPKM and TPM values for each sample

source_name: Retina

extract_protocol:
RNA was extracted using Monarch Total RNA miniprep kit (New England Biolabs) and dried in RNA stabliistion tubes for sequencing.
Library was prepared using standard and optimised Genewiz's protocols

value: Retina

value: VEGFA


title: batch4_mm_VEGFA-4


title: batch4_mm_VEGFA-2


title: batch4_mm_VEGFA-5


title: batch4_mm_VEGFA-3


title: batch4_mm_XNT-4

value: XNT


title: batch4_mm_XNT-2


title: wt ethanol 2


title: batch4_mm_XNT-1


title: batch4_mm_XNT-6


title: batch4_mm_mCherry-4

value: mCherry


title: batch4_mm_mCherry-3


title: batch4_mm_mCherry-2


title: batch4_mm_VEGFA-1


title: batch4_mm_mCherry-1


title: batch4_mm_XNT-3


title: Liver, wild, M37959, RNA-Seq

city: Canberra

first: Erin

middle: Elizabeth

last: Hahn

state: ACT

address: Clunies Ross

department: National Research Collections Australia

institute: CSIRO

data_processing:
Genome preparation : We performed repeat masking with RepeatMasker v.4.1.0 (http://www.repeatmasker.org) through two rounds of masking, first with default settings and with standard Illumina adapters using -e rmblast enabled.
Alignment: We aligned RNA-Seq reads with kalign (ngskit4b tool suite version 200218) with options -c25 -l25 -d50 -U4. We removed PCR and optical duplicates using MarkDuplicates (PICARD) enabling REMOVE_DUPLICATES=TRUE.
FPKM: We calculated FPKM using the Tuxedo pipeline. We then z-transformed the FPKM values using the R package zFPKM.
Assembly: GRCm38.p6 RefSeq assembly
Supplementary files format and content: tab-delimited text file including FPKM and zFPKM for all samples

molecule: polyA RNA

source_name: liver

extract_protocol:
We extracted RNA from fresh mouse using an AllPrep DNA/RNA kit (Qiagen). We placed 5-10 mg tissue into 350 μL RLT Plus Buffer in a 2 mL tube with a 5 mm stainless steel bead and homogenised with a TissueLyzer (two 2 min rounds, 30 Hz). We then followed manufacturer’s instructions to isolate RNA, eluting in 30 μL RNase-free water.
Illumina stranded mRNA library prep

tag: specimen id

value: liver

tag: Sex

value: M


title: Liver, C57BL6, M37816, RNA-Seq


title: Liver, C57BL6, M37811, RNA-Seq


title: Liver, C57BL6, M37810, RNA-Seq


title: organoids grown from Cdx2-induced cells only

city: Santa Cruz

first: Ali

middle: S

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

data_processing:
Initial processing and mapping of Fastq files: kallisto-bustools, kb_python-0.28.2
Output count matrix processing and filtering: The following packages were installed and loaded in Rstudio v2023.12.1 Build 402, R v4.3.2: DropletUtils v1.22.0. Matrix v1.6-5. tidyverse v2.0.0. Seurat v5.0.1. ggpointdensity v0.1.0. scico v1.5.0. scales v1.3.0.
For preparing CellChat object and data:  The following packages were installed and loaded in Rstudio v2023.12.1 Build 402, R v4.3.2: circlize v0.4.16. ComplexHeatmap v2.18.0. NMF v0.26. CellChat v2.1.1. BiocManager v1.30.22. presto 1.0.0. Same parameters were used for each sample except for the following: FindClusters(), for resolution = 0.6 for Mix_4 sample, and resolution = 0.3 for Ctrl_only_1, Cdx2_only_2 and Gata6_only_3 samples
Assembly: mm10
Supplementary files format and content: kallisto-bustools output: .barcodes.txt, .genes and .mtx files. Filtered and annotated data: seu.rds objects. Cellchat annotated data: cellchat.rds object

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in 2i+Lif conditions in either ESGRO-2i medium +1x Pen/Strep  or N2B27 medium supplemented with 1x Pen/Strep , 1uM PD0325901, 3uM CHIR99021 and 1000 U/ml Lif. mESCs were grown on tissue culture treated plates coated with 0.1% gelatin. For routine passaging, cells were seeded at 5,000-10,000 cells per cm2 and passaged every 2-3 days using Accutase.

extract_protocol:
3D organoids were grown as described before for 72 hours. 1.5 ml of medium was removed and 1.5 ml of 1x PBS was added per well. 1.5 ml of this solution was removed and 0.5 ml of 1x PBS was added per well and organoids were transferred to microcentrifuge tubes using cut-off pipette tips. Tubes were centrifuged for 5 minutes at 300 rcf. Supernatant was removed and organoids were gently resuspended in 1ml of DMEM/F12, followed by centrifugation for 5 minutes at 300 rcf again. Supernatant was removed and organoids were resuspended in 1 ml of Trypsin-EDTA. Organoids were pipetted up and down 3 times before incubating for 5 minutes at 37°C. Organoids were pipetted up and down 6 times and 200 ul of ESC qualified FBS was added to each tube, followed by centrifugation for 5 minutes at 300 rcf. Supernatant was removed and cells were resuspended in 0.5 ml standard differentiation medium and transferred to a cryovial. 0.5 ml of 2x Freezing medium, consisting of 85% ESC qualified FBS / 15% DMSO, was added to each cryovial and gently mixed. Cryovials were placed into a cell freezing container and incubated at -80°C overnight, followed by storage in liquid nitrogen (vapor phase) cell storage before shipment for single-cell RNAseq preparation.
10X single cell 3' RNA library preparation v3

treatment_protocol: To grow and differentiate mESCs in 3D structures, cells were grown in 24 well AggreWell 400 plates. Each well was washed once with 1x PBS, followed by adding 0.5 ml of anti-adherence solution. Plates were centrifuged 5 minutes at 1,000 rcf and incubated 20 minutes at room temperature. Anti-adherence solution was removed and 1 ml 1x PBS was added to each well. Plates were kept at room temperature until seeding cells. Just before seeding, 1x PBS was removed and 1 ml of standard differentiation medium + 20 uM ROCK inhibitor was added. To treatment wells, 1 ug/ml doxycycline was added. sgCtrl-mESCs, sgGata6-mESCs and sgCdx2-mESCs were individually collected, counted, and mixed together in a 1:1:3 ratio. Then, 32,000 cells were added per well (6,000 sgCtrl, 6,000 sgGata6 and 20,000 sgCdx2) in a volume of 1 ml, so that the total volume per well was 2 ml, and the final concentration of ROCKi was 10 uM and doxycycline was 0.5 ug/ml. After 24 hours, 1.4 ml of medium per well was replaced using standard differentiation medium without ROCKi, and repeated once. After another 24 hours 1.4 ml of medium was replaced per well. For conditions with altered cell ratios, the amount of cells was adjusted accordingly.

value: mouse embryonic stem cell

value: PB-TRE3G-dCas9-VPR, sgCdx2

value: doxycycline


title: organoids grown from Gata6-induced cells only

value: PB-TRE3G-dCas9-VPR, sgGata6


title: organoids grown from a mixture of control-, Cdx2- and Gata6-induced cells

value: PB-TRE3G-dCas9-VPR, sgCtrl or sgCdx2 or sgGata6


title: organoids grown from control-induced cells only

value: PB-TRE3G-dCas9-VPR, sgCtrl


title: 24abNOD female, 18 weeks old, total kidney RNA, sample 2

city: Umeå

first: Dan

last: Holmberg

address: Building 6M

department: Medical Biosciences

country: Sweden

institute: Umeå university

data_processing:
The analysis was started from raw sequencing data in FASTQ format.
Quality and adapter trimming was carried out using TrimGalore version 0.6.4 [Krueger, 2016] in paired-end mode using Cutadapt version 2.4 [Martin, 2011].We utilised a PHRED score cut-off of 20, with any reads falling outside of this threshold being discarded.
Assembly: Only sequence reads over 20 base pairs in length that had an error rate of less than 10% were retained for further analysis.The quality of raw RNASeq and trimmed reads was inspected using FastQC, version 0.11.8 [Andrews at al., 2015].
Supplementary files format and content: RNA-Seq reads were aligned to the mouse reference library GRCm38.96.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Total kidney RNA

extract_protocol:
Total RNA was prepared from liver and kidney samples using  Rneasy mini plus kit (Qiagen).
Libraries for RNA-seq. Were prepared using the TruSeq library prep kit (Illumina) following manufacturer’s protocol.

value: Total kidney RNA

value: Female

tag: age

value: 18 weeks


title: NIF female, 18 weeks old, total kidney RNA, sample 2

value: NIF


title: batch4_mm_XNT-5


title: NIF female, 18 weeks old, total kidney RNA, sample 1


title: 24abNOD female, 8 weeks old, total kidney RNA, sample 2

value: 8 weeks


title: 24abNOD female, 8 weeks old,  total kidney RNA, sample 1


title: Liver, wild, M37971, RNA-Seq

value: F


title: NIF female, 8 weeks old, total kidney RNA, sample 1


title: NIF female, 8 weeks old, total kidney RNA, sample 2


title: Liver, wild, M37976, RNA-Seq


title: 24abNOD female, 4 weeks old, total kidney RNA, sample 2

value: 4 weeks


title: NIF female, 4 weeks old, total kidney RNA, sample 1


title: NIF female, 4 weeks old, total kidney RNA, sample 2


title: 24abNOD female, 18 weeks old, total kidney RNA, sample 3


title: NIF female, 4 weeks old, total kidney RNA, sample 3


title: NIF female, 18 weeks old, total liver RNA, sample 2

source_name: Total liver RNA

value: Total liver RNA


title: 24abNOD female, 18 weeks old, total liver RNA, sample 2


title: 24abNOD female, 6 weeks old, total liver RNA, sample 3

value: 6 weeks


title: 24abNOD female, 6 weeks old, total liver RNA, sample 2


title: NIF female, 18 weeks old, total liver RNA, sample 1


title: 24abNOD female, 18 weeks old, total kidney RNA, sample 1


title: 24abNOD female, 6 weeks old, total liver RNA, sample 1


title: NIF female, 6 weeks old, total liver RNA, sample 1


title: NIF female, 6 weeks old, total liver RNA, sample 2


title: 24abNOD female, 8 weeks old, total kidney RNA, sample 3


title: 24abNOD female, 3 weeks old, total liver RNA, sample 2

value: 3 weeks


title: 24abNOD female, 3 weeks old, total liver RNA, sample 3


title: 24abNOD female, 3 weeks old, total liver RNA, sample 1


title: NIF female, 3 weeks old, total liver RNA, sample 3


title: 24abNOD female, 4 weeks old, total kidney RNA, sample 1


title: 24abNOD female, 18 weeks old, total liver RNA, sample 1


title: lMTH2_raw_1

value: fecal matter (not tissue)

value: 16S rRNA

value: Fermentation with 1mg/mL 5-methyltetrahydrofolate


title: Proximal colon,B6D:WT,10 weeks,Sample BW7

city: Farmington

first: Masako

last: Nakanishi

state: CT

address: 263 Farmington Ave

department: Center for Molecular Oncology

institute: UConn Health Center

data_processing:
Raw reads were trimmed using Trimmomatic/0.36. NexteraPE-PE adapters were removed and trimming parameters were TRAILING:10 -phred33.
Trimmed reads were aligned to the Mus musculus GRCm38.102.gtf reference genome using star/2.5.3a.
Reads were quantified using featureCounts (subread/2.0.3). These quantifications were used to generate a counts matrix.
Assembly: mm10
Supplementary files format and content: .csv file. A counts matrix where rows are genes and columns are samples

source_name: Colon

growth_protocol: A/D and B6D mice were housed separately, and had access to maintenance diet (Teklad Global 19% Protein Extruded Rodent Diet) and drinking water ad libitum.

extract_protocol:
Tissues were homogenized by Polytron Homogenizer and total RNA was extracted from the tissues using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions.  Quality of RNA was assessed by 2100 Bioanalyzer system (Agilent Technologies).
mRNA-seq libraries were prepared using the TruSeq Standard mRNA Library Prep kit (Illumina)

treatment_protocol: No treatment

value: Colon

tag: strain

value: Male

value: 10 Weeks

value: WT


title: Proximal colon,B6D:WT,10 weeks,Sample BW9


title: NIF female, 3 weeks old, total liver RNA, sample 1


title: Proximal colon,B6D:WT,10 weeks,Sample BW6


title: Proximal colon,B6D:WT,10 weeks,Sample BW8


title: Proximal colon,B6D:WT,10 weeks,Sample BW5


title: Proximal colon,B6D:WT,10 weeks,Sample BW4


title: Proximal colon,B6D:WT,10 weeks,Sample BW2


title: Proximal colon,B6D:WT,10 weeks,Sample BW1


title: Proximal colon,B6D:WT,10 weeks,Sample BW3


title: Proximal colon,B6D:KO,10 weeks,Sample BK8

value: PTGES1 KO


title: Proximal colon,B6D:WT,10 weeks,Sample BW12


title: Proximal colon,B6D:KO,10 weeks,Sample BK6


title: Proximal colon,B6D:KO,10 weeks,Sample BK7


title: Proximal colon,B6D:WT,10 weeks,Sample BW10


title: NIF female, 3 weeks old, total liver RNA, sample 2

value: Female


title: Proximal colon,B6D:KO,10 weeks,Sample BK1


title: Proximal colon,B6D:KO,10 weeks,Sample BK3


title: Proximal colon,B6D:KO,10 weeks,Sample BK2


title: Proximal colon,B6D:KO,10 weeks,Sample BK4


title: Proximal colon,B6D:KO,10 weeks,Sample BK5


title: Proximal colon,B6D:KO,10 weeks,Sample BK10


title: Proximal colon,AD:WT,10 weeks,Sample AW8

value: AD


title: Proximal colon,AD:WT,10 weeks,Sample AW9


title: Proximal colon,B6D:KO,10 weeks,Sample BK13


title: Proximal colon,AD:WT,10 weeks,Sample AW7


title: Proximal colon,AD:WT,10 weeks,Sample AW6


title: Proximal colon,AD:WT,10 weeks,Sample AW4


title: Proximal colon,B6D:WT,10 weeks,Sample BW13


title: Proximal colon,AD:WT,10 weeks,Sample AW11


title: Proximal colon,AD:WT,10 weeks,Sample AW12


title: Proximal colon,AD:WT,10 weeks,Sample AW5


title: Proximal colon,AD:WT,10 weeks,Sample AW10


title: Proximal colon,B6D:KO,10 weeks,Sample BK9


title: Proximal colon,AD:WT,10 weeks,Sample AW3


title: Proximal colon,AD:WT,10 weeks,Sample AW1


title: Proximal colon,AD:KO,10 weeks,Sample AK9


title: NIF female, 6 weeks old, total liver RNA, sample 3

value: NIF


title: Proximal colon,AD:KO,10 weeks,Sample AK4


title: Proximal colon,AD:KO,10 weeks,Sample AK6


title: Proximal colon,AD:KO,10 weeks,Sample AK2


title: Proximal colon,AD:KO,10 weeks,Sample AK5


title: Proximal colon,AD:KO,10 weeks,Sample AK3


title: Proximal colon,AD:KO,10 weeks,Sample AK7


title: Proximal colon,AD:KO,10 weeks,Sample AK13


title: Proximal colon,AD:KO,10 weeks,Sample AK12


title: Proximal colon,AD:KO,10 weeks,Sample AK11


title: Proximal colon,AD:KO,10 weeks,Sample AK1


title: RNAseq of p-aKO2

city: Stony Brook

first: Richard

last: Lin

address: 1 Circle Road

institute: Stony Brook University

data_processing:
Fastqc --> trim_galore --> hisat2 --> samtools --> htseq
Assembly: mm38
Supplementary files format and content: txt file with counts

source_name: Pancreatic tumor

growth_protocol: αKO, and p-αKO were all cultured in complete DMEM media (Gibco, Thermo Fisher Scientific) with 10% FBS (Corning 35-015-CV) and 1% P/S (penicillin/streptomycin: Gibco 15140-122), incubated at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted by RNeasy Kit (Qiagen) according to the manufacturer's protocol. RNA quality and quantity were determined by NanoDrop ND-1000 spectrophotometer (Thermo Scientific).
Poly-AselectionwasusedtoenrichmRNA,followedbylibraryprepandsequencingwithPE150
RNA libraries were prepared by polyA enrichemt

value: Pancreatic tumor

value: p-aKO

value: pancreatic cancer cells


title: RNAseq of p-aKO3


title: RNAseq of p-aKO1


title: RNAseq of aKO2

value: aKO


title: RNAseq of aKO3


title: RNAseq of aKO1


title: CD8andCD4Tcellreceptorsfromp-KO1implantedB6mice [p-aKO1-TCR]

data_processing:
The Cell Ranger v7.0.0 pipeline was used to demultiplex and align sequencing data to the “ENSEMBL GRCm39” mouse transcriptome to generate gene expression matrices. The Cell Ranger VDJ pipeline was used to assemble sequences and identify paired clonotypes on the V(D)J libraries. The gene expression matrices were further analyzed by the Seurat R package. Three quality control criteria were employed to filter the matrices to exclude unwanted sources of variations: number of detected transcripts, genes, and percent of reads mapping to mitochondrial genes. Cells with UMIs over the interquartile range of 95% (potential doublets) and under 1000 (potential fragments) or a mitochondrial proportion higher than 20% (potential apoptotic) were removed. Moreover, we used the Doublet Finder R algorithm to further eliminate doublet contamination. After the quality control, we annotated cellular identity using the R package SingleR, which assigns each cell to a reference type that has the most similar expression profile with. In further analysis, sctransform package in Seurat was used to normalize UMI count data. The principal component analysis (PCA) of high-dimensional data was performed to identify highly variable genes in each sample, and the top principal components were selected for unsupervised clustering of cells with a graph-based clustering and visualized with Uniform Manifold Approximation and Projection (UMAP).
Assembly: ENSEMBL GRCm39
Supplementary files format and content: The GEX files are in the format of Serut object; the TCR files are in excel files with different cdr3 sequences

growth_protocol: Tumor cells were implanted to the pancreas of mice for 12 days

extract_protocol:
After 12 days post implantation, pancreaetic tumors were harvested and tumor infiltrating CD4 and CD8 were selected by beads.
Libraries for both 5' gene expression and T cell receptors were prepared by 10x genomics' protocol. Briefly,
scRNA seq of gene expression and correponding TCR sequencing

value: pancreatic cells

value: KrasG12D; Trp53R172H; Pdx1-Cre; Pik3ca-/-; Pccb-/-


title: CD8andCD4TcellreceptorsfromKO2implantedB6mice [aKO2-TCR]

value: KrasG12D; Trp53R172H; Pdx1-Cre; Pik3ca-/-


title: CD8andCD4Tcellsfromp-KO1implantedPD1-nullmice [PD1KO1-GEX]


title: CD8andCD4Tcellreceptorfromp-KO2implantedPD1-nullmice [PD1KO2-TCR]


title: CD8andCD4Tcellreceptorsfromp-KO2implantedB6mice [p-aKO2-TCR]


title: CD8andCD4Tcellreceptorfromp-KO1implantedPD1-nullmice [PD1KO1-TCR]


title: CD8andCD4Tcellsfromp-KO2implantedB6mice [p-aKO2-GEX]


title: CD8andCD4TcellreceptorsfromKO1implantedB6mice [aKO1-TCR]


title: CD8andCD4Tcellsfromp-KO1implantedB6mice [p-aKO1-GEX]


title: CD8andCD4TcellsfromKO1implantedB6mice [aKO1-GEX]


title: hippocampus, Sublibrary 1

city: Columbus

first: Ethan

last: Goodman

state: Ohio

address: 460 Medical Center Drive

institute: Ohio State University

description:
DGE_xcond_1-8.mtx
cell_metadata_xcond_1-8
all_genes.csv

data_processing:
Each fastq.gz file was downloaded and aligned to the Genome Reference Consortium Mouse Reference 39 (mm39) using the Parse Biosciences pipeline. Matrices were downloaded and filtered in RStudio using Seurat (v4.1.1)12. Nuclei showing greater than 20% mitochondrial DNA were filtered out prior to clustering.
Assembly: mm39
Supplementary files format and content: mtx and metadata; filtered or unfiltered

source_name: hippocampus

extract_protocol:
Hippocampi (n=3) were extracted and pooled. Pooled samples were homogenized using dounce homogenizers and a homogenization buffer (1.5 M NIM1 Buffer with 250mM sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris Buffer pH 8, 1uM DTT, 0.4U/uL Enzymatics RNAase-Inhibitor (#Y9240L), 0.2U/uL Superase-Inhibitor (Thermo Fisher Scientific, #AM2694), and .1% Triton X-100). Hippocampi homogenates were filtered (40uM strainer) and clarified. Resulting homogenates were resuspended in a PBS buffer with RNase Inhibitors (0.05U/ul of Enzymatics RNAase-Inhibitor and Superase-Inhibitor) and re-pelleted. To remove myelin debris, homogenates were incubated with Myelin Removal Beads II (Miltenyi Biotec, #130-096-731) for 15 minutes at 4°C. Homogenates were washed (50% PBS and 50% PBS + 1% BSA) and re-pelleted. Supernatant was removed and samples were resuspended in wash buffer. One LS column (Miltenyi Biotec, # 130-042-401) per sample was used to filter the samples followed by pelleting and resuspending in wash buffer. Nuclei were counted with AO/PI (Logos Biosystems, #F23001) on a Luna-FL Cell Counter and fixed with a Nuclei Fixation Kit (Parse Biosciences, #SB1003) per the manufacturer’s instructions followed by freezing at -80°C in a Mr. Frosty (Thermo Fisher Scientific, #5100-001).
Parse Biosciences Whole Transcription Kit was used to barcode and generate sub-libraries with 12,500 nuclei/sub-library comprised of all samples.
snRNAseq

treatment_protocol:
xcond_1 - Control Vehicle
xcond_2 - Control PLX5622
xcond_3 - RSD Vehicle
xcond_4 - RSD PLX5622
xcond_5 - Control WT
xcond_6 - Control KO
xcond_7 - RSD WT
xcond_8 - RSD KO

value: hippocampus

value: nuclei

tag: condition

value: Control or RSD

value: WT or nIL1R1

value: VEH or PLX5622


title: Hi-TrAC_IL4reporter_GFP+_rep3

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: Hi-TrAC

data_processing:
Raw reads of Hi-TrAC data were process by tracPre2.py in cLoops2 package (Cao et al., 2022).
Assembly: mm10
Supplementary files format and content: BEDPE files for Hi-TrAC with high quality uniquely mapped paired-end tags (PETs) were provided.
Library strategy: Hi-TrAC

source_name: Th2 cells

growth_protocol: Naive CD4+ T cells were purified from lympho nodes of IL-4/GFP (G4) mice according to manufacturer's manual (Stem Cell, EasySep Mouse Naive CD4+ T cell Isolation Kit). Naive CD4+ T cells were activated with plate-bound anti-CD3ℇ (1 µg/mL, eBioscience, clone: 145-2C11) and anti-CD28 antibodies (1 µg/mL, eBioscience, clone: 37.51), and cultured in complete RPMI1640 media under Th2 condition with anti-IFNˠ (10 µg/mL), anti-IL-12 (10 µg/mL), IL-2 (5 ng/mL), IL-4 (10 ng/mL). After 72 hours of differentiation, cells were collected and sorted into GFP postive and negative cells.

extract_protocol:
Genomic DNA was purified by Phenol-Chloroform extraction.
Gaps in purified genomic DNA were repaired with T4 DNA polymerase. Remove free bridging linker with AMPure XP beads. Digest purified DNA with restriction enzymes MluCI/NlaIII, and then enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers.

treatment_protocol: Cells for were fixed with 1% Formaldehyde in culture medium at room temperature for 10 minutes. Wash cells with ice-cold PBS twice, then resuspend cells  with 100 µL reaction buffer (50mM Tris-acetate, pH 7.5, 150mM potassium acetate, 10mM magnesium acetate, 4mM spermidine, 0.5% NP-40). Incubate at 37℃ for 4 hours.

value: IL-4/GFP (G4), mixed C57BL/6 and 129

value: CD4+ T cells stimulated under Th2 condition

value: cell culture

value: IL-4/GFP, GFP positive


title: hippocampus, Sublibrary 3


title: hippocampus, Sublibrary 4


title: CD8andCD4TcellsfromKO2implantedB6mice [aKO2-GEX]


title: Proximal colon,AD:KO,10 weeks,Sample AK10

value: Colon

value: AD

value: Male

value: 10 Weeks

value: PTGES1 KO


title: Hi-TrAC_IL4reporter_GFP-_rep2

description: Hi-TrAC

value: IL-4/GFP, GFP negative


title: Hi-TrAC_IL4reporter_GFP-_rep3

description: Hi-TrAC


title: Hi-TrAC_IL4reporter_GFP+_rep2

description: Hi-TrAC


title: Hi-TrAC_IL4reporter_GFP-_rep1

description: Hi-TrAC


title: MEF_3 Cut & Tag

city: Harbin

first: Xinglin

last: Hu

state: Heilongjiang

address: Harbin Medical University, 194 Xuefu Rd, Nangang District, Harbin, Heilongjiang Province, P.R. China 150081

department: Histology and Embryology

institute: Harbin Medical University

data_processing:
Sequenceweretrimmedby Trimmomatic-0.39
Trimmedsequencereadsweremappedtomm10bybowtie2.
Removing PCR duplication by sambamba
bw files were generated by bamCoverage
Assembly: mm10
Supplementary files format and content: bw files
Library strategy: CUT&Tag

source_name: 4F2A cell

extract_protocol:
To perform CUT & Tag analysis, we utilized the Hyperactive InSitu ChIP Library Prep Kit for Illumina (Vazyme Biotech). A total of 10,000 cells were collected as samples for the experimental group, with two replicates conducted.
The prepared libraries underwent PCR amplification after extraction using phenol-chloroform and ethanol precipitation. The PCR cycling conditions consisted of an initial step at 72°C for 5 minutes, followed by denaturation at 98°C for 30 seconds. This was succeeded by 14 cycles of denaturation at 98°C for 10 seconds and annealing at 60°C for 30 seconds. The amplification process was completed by performing a final extension step at a temperature of 72°C for a duration of 1 minute, followed by holding the samples at a temperature of 4°C. For the purpose of post-PCR cleanup, a volume of DNA Clean Beads (Vazyme Biotech) equal to 1.5 times the volume of the DNA was utilized. In order to guarantee a thorough and precise sequencing analysis, all libraries that were prepared underwent sequencing on the Illumina Nova Seq 6000 platform, while strictly adhering to the manufacturer's guidelines.

treatment_protocol: DUX was overexpression for 48h during iPSC reprogramming.

tag: time

value: 4F2A cell

value: MEF


title: MEF_1 Cut & Tag


title: ipsc_3 Cut & Tag

source_name: iPSC cell

value: iPSC cell

value: IPSC


title: D4_oeDUX_3 Cut & Tag

value: OE-DUX


title: ipsc_1 Cut & Tag


title: CD8andCD4Tcellsfromp-KO2implantedPD1-nullmice [PD1KO2-GEX]

value: Pancreatic tumor

value: pancreatic cells

value: KrasG12D; Trp53R172H; Pdx1-Cre; Pik3ca-/-; Pccb-/-


title: D4_oeDUX_1 Cut & Tag


title: hippocampus, Sublibrary 2

value: hippocampus

value: nuclei

value: Control or RSD

value: WT or nIL1R1

value: VEH or PLX5622


title: D4_3

data_processing:
SequenceweretrimmedbyTrimmomatic-0.39.
Trimmedsequencereadsweremappedtomm10byhista2.
ReadcountextractionwereperformedusingfeatureCounts.
AnalysisbyR.
Assembly: mm10
Supplementary files format and content: fpkm

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop)
RNA purification,  reverse  transcription,  library  construction  and  sequencing  were performed  at  Shanghai Majorbio  Bio-pharm  Biotechnology  Co.,  Ltd.  (Shanghai,  China)  according  to  the  manufacturer’s  instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded  mRNA Prep, Ligation from Illumina (San Diego, CA) using  1μg of total RNA.  Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and  ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion  DNA  polymerase  (NEB)  for  15  PCR  cycles.  After  quantified  by  Qubit  4.0,  paired-end  RNA-seq sequencing library was sequenced with the NovaSeq 6000 sequencer (2 × 150bp read length).

value: OE-NC


title: D4_DUX_3


title: iPSC_1


title: D4_DUX_2


title: iPSC_2


title: D4_DUX_1


title: D4_NC_1 Cut & Tag


title: D4_NC_3 Cut & Tag


title: MEF_2


title: iPSC_3


title: MEF_3


title: Hi-TrAC_IL4reporter_GFP+_rep1

description: Hi-TrAC

value: IL-4/GFP (G4), mixed C57BL/6 and 129

value: CD4+ T cells stimulated under Th2 condition

value: cell culture

value: IL-4/GFP, GFP positive


title: D4_1

value: 4F2A cell

value: MEF


title: MEF_1


title: Raw264.7 cells, THCaP3,1day

city: Chengdu

first: Chengdong

last: Zhang

address: Second Ring Road

institute: Southwest Jiaotong University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Raw 264.7 cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Raw 264.7 Cells were inoculated on samples, incubated for 12h, stimulated with 1 μg/mL LPS for 2h, then re-incubated for 1d and collected

value: macrophages

value: WT

value: LPS stimulation


title: Raw264.7 cells, THCaP1,1day


title: Raw264.7 cells, THCaP2,1day


title: Raw264.7 cells, TH1,1day


title: Proximal colon,AD:WT,10 weeks,Sample AW2

value: Colon

value: AD

value: Male

value: 10 Weeks


title: ABS9623

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
26_wt N_B16_ctrl
MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q.txt

growth_protocol: 8 to 10 weeks-old mice housed at the Weizmann Institute animal facility.

extract_protocol:
Mice were sacrificed at various time points by cervical dislocation. Tumor, spleen, and tdLN were collected and put through a process of mechanical and enzymatic digestion. For single-cell suspensions, tumors were chopped into small pieces and suspended in RPMI supplemented with DNase (2mg/ml, Sigma-Aldrich) and collagenase IV (100mg/ml, Worthington). Tumors were homogenized by GentleMacs tissue homogenizer (Miltenyi Biotec) and incubated at 37oC for 30min, with frequent agitation. Following dissociation procedures, cells were washed with cold PBS, filtered through a 70-μm cell strainer, and centrifuged at 300g for 5 min at 4 °C. Spleen and tdLN were mashed through a 100uM cell strainer and washed with ice-cold MACS buffer (PBS supplemented with 0.2mM EDTA, pH 8, and 0.5% BSA). Cells were centrifuged at 300g, 5 min, and 4°C. Spleen was suspended in red blood lysis buffer (Sigma-Aldrich) and DNase (0.33U/ml, Sigma-Aldrich), incubated for 5min at room temperature, washed with cold PBS, passed through a 70μm mesh strainer, centrifuged at 300g, 5 min, 4°C and then resuspended in ice-cold MACS buffer.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were anesthetized and the indicated inactivated pathogens were administered by intradermal injection into the ear pinna. PBS was injected into the ear pinna of control animals.
mice were treated with 250ug of aPD1 or/and 200ug of a41BB.

value: endogenous CD8+

tag: experiment id

tag: days post_adoptive_transfer

tag: mouse number

value: in-vitro


title: ABS9625

description:
28_OT1 N_B16_ctrl
MARSseq

tag: tissue

value: OT1 CD8+


title: D4_2

tag: treatment

value: OE-NC


title: ABS9629

description:
32_OT1 N_B16_aPD1_5ug
MARSseq


title: ABS9627

description:
30_wt N_B16_aPD1_5ug
MARSseq


title: ABS9626

description:
29_wt N_B16_aPD1_5ug
MARSseq


title: ABS9624

description:
27_OT1 N_B16_ctrl
MARSseq


title: ABS9628

description:
31_OT1 N_B16_aPD1_5ug
MARSseq


title: ABS9622

description:
25_wt N_B16_ctrl
MARSseq


title: ABS9619

description:
22_wt N_only_ctrl
MARSseq

value: InVitro


title: ABS9617

description:
20_OT1 A_B16_aPD1_a41bb
MARSseq


title: Raw264.7 cells, TH2,1day

tag: genotype


title: ABS9615

description:
18_wt A_B16_aPD1_a41bb
MARSseq


title: ABS9621

description:
24_OT1 N_only_ctrl
MARSseq


title: ABS9620

description:
23_OT1 N_only_ctrl
MARSseq


title: ABS9616

description:
19_OT1 A_B16_aPD1_a41bb
MARSseq


title: ABS9612

description:
15_OT1 A+B16+a41bb_5ug
MARSseq


title: ABS9611

description:
14_wt A+B16+a41bb_5ug
MARSseq


title: ABS9614

description:
17_wt A+B16+aPD1_a41bb
MARSseq


title: ABS9609

description:
12_OT1 A+B16+aPD1_5ug
MARSseq


title: ABS9606

description:
9_wt A+B16+aPD1_5ug
MARSseq


title: Raw264.7 cells, TH3,1day


title: ABS9608

description:
11_OT1 A+B16+aPD1_5ug
MARSseq


title: ABS9610

description:
13_wt A+B16+a41bb_5ug
MARSseq


title: ABS9605

description:
8_OT1 A+B16_ctrl
MARSseq


title: ABS9607

description:
10_wt A+B16+aPD1_5ug
MARSseq


title: ABS9604

description:
7_OT1 A+B16_ctrl
MARSseq


title: ABS9603

description:
6_wt A+B16_ctrl
MARSseq


title: ABS9602

description:
5_wt A+B16_ctrl
MARSseq


title: ABS9599

description:
2_wt A_only_ctrl
MARSseq


title: ABS9598

description:
1_wt A_only_ctrl
MARSseq


title: ABS9465

description:
Plate33_DTR+PD1_M20_endo_dLN
MARSseq

source_name: LN

value: LN


title: ABS9464

description:
Plate32_DTR+PD1_M19_endo_dLN
MARSseq


title: ABS9462

description:
Plate30_DTR_M14_endo_dLN
MARSseq

value: DTX


title: ABS9463

description:
Plate31_DTR+PD1_M19_endo_dLN
MARSseq


title: ABS9600

description:
3_OT1 A_only_ctrl
MARSseq


title: ABS9601

description:
4_OT1 A_only_ctrl
MARSseq


title: ABS9460

description:
Plate28_DTR+PD1_M18_endo_dLN
MARSseq


title: ABS9459

description:
Plate27_DTR+PD1_M18_endo_dLN
MARSseq


title: ABS9458

description:
Plate26_DTR+PD1_M17_OT1_dLN
MARSseq


title: ABS9618

description:
21_wt N_only_ctrl
MARSseq


title: ABS9461

description:
Plate29_DTR_M14_endo_dLN
MARSseq


title: ABS9454

description:
Plate22_DTR+PD1_M16_endo_dLN
MARSseq


title: ABS9455

description:
Plate23_DTR+PD1_M16_endo_dLN
MARSseq


title: ABS9457

description:
Plate25_DTR+PD1_M17_endo_dLN
MARSseq


title: ABS9456

description:
Plate24_DTR+PD1_M17_endo_dLN
MARSseq


title: ABS9450

description:
Plate18_PD1_M10_endo_dLN
MARSseq


title: ABS9448

description:
Plate16_PD1_M9_endo_dLN
MARSseq


title: ABS9453

description:
Plate21_DTR_M11_endo_dLN
MARSseq


title: ABS9451

description:
Plate19_PD1_M10_OT1_dLN
MARSseq


title: ABS9452

description:
Plate20_DTR_M11_endo_dLN
MARSseq


title: ABS9449

description:
Plate17_PD1_M10_endo_dLN
MARSseq


title: ABS9447

description:
Plate15_PD1_M9_endo_dLN
MARSseq


title: ABS9446

description:
Plate14_PD1_M8_OT1_dLN
MARSseq


title: ABS9444

description:
Plate12_PD1_M8_endo_dLN
MARSseq


title: ABS9443

description:
Plate11_PD1_M7_OT1_dLN
MARSseq


title: ABS9441

description:
Plate9_PD1_M7_endo_dLN
MARSseq


title: ABS9442

description:
Plate10_PD1_M7_endo_dLN
MARSseq


title: ABS9440

description:
Plate8_PD1_M6_endo_dLN
MARSseq


title: ABS9439

description:
Plate7_PD1_M6_endo_dLN
MARSseq


title: ABS9438

description:
Plate6_PBS_M5_endo_dLN
MARSseq


title: ABS9433

description:
Plate1_PBS_M3_endo_dLN
MARSseq


title: ABS8822

description:
24_OT1+B16+aPD1_10ug
MARSseq


title: ABS9435

description:
Plate3_PBS_M4_endo_dLN
MARSseq


title: ABS8816

description:
18_wt+B16+aPD1_5ug
MARSseq


title: ABS8819

description:
21_wt+B16+aPD1_10ug
MARSseq


title: ABS8817

description:
19_OT1+B16+aPD1_5ug
MARSseq


title: ABS8821

description:
23_OT1+B16+aPD1_10ug
MARSseq


title: ABS8818

description:
20_OT1+B16+aPD1_5ug
MARSseq


title: ABS8815

description:
17_wt+B16+aPD1_5ug
MARSseq


title: ABS8813

description:
15_OT1+B16+aPD1_2ug
MARSseq


title: ABS8814

description:
16_OT1+B16+aPD1_2ug
MARSseq


title: ABS9437

description:
Plate5_PBS_M5_endo_dLN
MARSseq


title: ABS8810

description:
12_OT1+B16+aPD1_1ug
MARSseq


title: ABS8820

description:
22_wt+B16+aPD1_10ug
MARSseq


title: ABS8811

description:
13_wt+B16+aPD1_2ug
MARSseq


title: ABS8808

description:
10_wt+B16+aPD1_1ug
MARSseq


title: ABS8807

description:
9_wt+B16+aPD1_1ug
MARSseq


title: ABS8812

description:
14_wt+B16+aPD1_2ug
MARSseq


title: ABS8806

description:
8_OT1+B16_ctrl
MARSseq


title: ABS8809

description:
11_OT1+B16+aPD1_1ug
MARSseq


title: ABS8803

description:
5_wt+B16_ctrl
MARSseq


title: ABS9434

description:
Plate2_PBS_M3_endo_dLN
MARSseq


title: ABS9436

description:
Plate4_PBS_M4_endo_dLN
MARSseq


title: ABS8801

description:
3_OT1_only_ctrl
MARSseq

value: mActb


title: ABS8802

description:
4_OT1_only_ctrl
MARSseq


title: ABS8800

description:
2_wt_only_ctrl
MARSseq


title: ABS8799

description:
1_wt_only_ctrl
MARSseq


title: ABS8797

description:
7__CD8In-vitro_wt_18cycles_halfSS2
MARSseq


title: ABS8798

description:
8__CD8In-vitro_wt_18cycles_halfSS2
MARSseq


title: ABS8792

description:
2__CD8In-vitro_wt_12cycles_normalSS2
MARSseq


title: ABS8790

description:
76_D6_B16_OVA_11_Tet-_Tumor
MARSseq

source_name: tumor

value: tumor

value: Tet-&Tet+


title: ABS8789

description:
75_D6_B16_OVA_11_Tet-_Tumor
MARSseq


title: ABS8795

description:
5__CD8In-vitro_wt_12cycles_halfSS2
MARSseq


title: ABS8786

description:
72_D6_Ctrl_5_Tet+_Tumor
MARSseq

value: Tet+


title: ABS8794

description:
4__CD8In-vitro_wt_18cycles_normalSS2
MARSseq


title: ABS8787

description:
73_D6_B16_OVA_10_Tet-_Tumor
MARSseq


title: ABS8793

description:
3__CD8In-vitro_wt_18cycles_normalSS2
MARSseq


title: ABS8796

description:
6__CD8In-vitro_wt_12cycles_halfSS2
MARSseq


title: ABS8805

description:
7_OT1+B16_ctrl
MARSseq


title: ABS8788

description:
74_D6_B16_OVA_10_Tet-_Tumor
MARSseq


title: ABS8781

description:
67_D6_Ctrl_3_Tet+_Tumor
MARSseq


title: ABS8784

description:
70_D6_Ctrl_4_Tet+_Tumor
MARSseq


title: ABS8783

description:
69_D6_Ctrl_4_Tet-_Tumor
MARSseq

value: Tet-


title: ABS8780

description:
66_D6_Ctrl_3_Tet-_Tumor
MARSseq


title: ABS8779

description:
65_D6_Ctrl_2_Tet+_Tumor
MARSseq


title: ABS8776

description:
62_D6_aPD1_9_Tet+_Tumor
MARSseq


title: ABS8778

description:
64_D6_Ctrl_2_Tet-_Tumor
MARSseq


title: ABS8777

description:
63_D6_aPD1_9_Tet+_Tumor
MARSseq


title: ABS8774

description:
60_D6_aPD1_9_Tet-_Tumor
MARSseq


title: ABS9613

description:
16_OT1 A+B16+a41bb_5ug
MARSseq


title: ABS8785

description:
71_D6_Ctrl_5_Tet-_Tumor
MARSseq


title: ABS8772

description:
58_D6_aPD1_8_Tet+_Tumor
MARSseq


title: ABS8782

description:
68_D6_Ctrl_4_Tet-_Tumor
MARSseq


title: ABS8791

description:
1__CD8In-vitro_wt_12cycles_normalSS2
MARSseq


title: ABS8771

description:
57_D6_aPD1_8_Tet-_Tumor
MARSseq


title: ABS8769

description:
55_D6_aPD1_7_Tet+_Tumor
MARSseq


title: ABS8767

description:
53_D6_aPD1_6_Tet+_Tumor
MARSseq


title: ABS8760

description:
46_D3_Ctrl_2_Tet+_Tumor
MARSseq


title: ABS8762

description:
48_D3_aPD1_5_Tet+_Tumor
MARSseq


title: ABS8770

description:
56_D6_aPD1_7_Tet+_Tumor
MARSseq


title: ABS8765

description:
51_D6_Ctrl_1_Tet+_Tumor
MARSseq


title: ABS8763

description:
49_D3_aPD1_6_Tet+_Tumor
MARSseq


title: ABS8759

description:
45_D3_Ctrl_1_Tet+_Tumor
MARSseq


title: ABS9445

description:
Plate13_PD1_M8_endo_dLN
MARSseq


title: ABS8473

description:
12_PBS_2_OT1_Tumor
MARSseq

value: OT1 CD8+_naive


title: ABS8766

description:
52_D6_aPD1_6_Tet-_Tumor
MARSseq


title: ABS8761

description:
47_D3_Ctrl_3_Tet+_Tumor
MARSseq


title: ABS8768

description:
54_D6_aPD1_7_Tet-_Tumor
MARSseq


title: ABS8471

description:
10_PD1_7_OT1_Tumor
MARSseq


title: ABS8472

description:
11_PBS_2_OT1_Tumor
MARSseq


title: ABS8470

description:
9_PD1_7_OT1_Tumor
MARSseq


title: ABS8469

description:
8_PD1_7_OT1_Tumor
MARSseq


title: ABS8468

description:
7_PD1_6+10_OT1_Tumor
MARSseq


title: ABS8466

description:
5_PD1_9_OT1_Tumor
MARSseq


title: ABS8465

description:
4_PD1_9_OT1_Tumor
MARSseq


title: ABS8467

description:
6_PD1_9_OT1_Tumor
MARSseq


title: ABS8773

description:
59_D6_aPD1_8_Tet+_Tumor
MARSseq


title: ABS8464

description:
3_PD1_8_OT1_Tumor
MARSseq


title: ABS8463

description:
2_PD1_8_OT1_Tumor
MARSseq


title: ABS8461

description:
17_PBS_1_OT1_Tumor
MARSseq


title: ABS8764

description:
50_D6_Ctrl_1_Tet-_Tumor
MARSseq


title: ABS8462

description:
1_PD1_8_OT1_Tumor
MARSseq


title: ABS8459

description:
15_PBS_3_OT1_Tumor
MARSseq


title: ABS8460

description:
16_PBS_3_OT1_Tumor
MARSseq


title: ABS8458

description:
14_PBS_3_OT1_Tumor
MARSseq


title: ABS8455

description:
Plate69_PBS_M5_endo_Tumor
MARSseq


title: ABS8452

description:
Plate66_PBS_M4_endo_Tumor
MARSseq


title: ABS8449

description:
Plate63_Dtx_M14_endo_Tumor
MARSseq


title: ABS8450

description:
Plate64_Dtx_M14_OT1_Tumor
MARSseq


title: ABS8457

description:
13_PBS_2_OT1_Tumor
MARSseq


title: ABS8456

description:
Plate70_PBS_M5_endo_Tumor
MARSseq


title: ABS8448

description:
Plate62_Dtx_M14_endo_Tumor
MARSseq


title: ABS8453

description:
Plate67_PBS_M4_OT1_Tumor
MARSseq


title: ABS8804

description:
6_wt+B16_ctrl
MARSseq


title: ABS8445

description:
Plate56_Dtx+PD1_M16_endo_Tumor
MARSseq


title: ABS8447

description:
Plate58_Dtx+PD1_M16_OT1_Tumor
MARSseq


title: ABS8444

description:
Plate55_Dtx+PD1_M17_OT1_Tumor
MARSseq


title: ABS8446

description:
Plate57_Dtx+PD1_M16_endo_Tumor
MARSseq


title: ABS8441

description:
Plate52_Dtx_M11_OT1_Tumor
MARSseq


title: ABS8442

description:
Plate53_Dtx+PD1_M17_endo_Tumor
MARSseq


title: ABS8436

description:
Plate47_PD1_M8_endo_Tumor
MARSseq


title: ABS8437

description:
Plate48_PD1_M8_OT1_Tumor
MARSseq


title: ABS8440

description:
Plate51_Dtx_M11_endo_Tumor
MARSseq


title: ABS8439

description:
Plate50_Dtx_M11_endo_Tumor
MARSseq


title: ABS8438

description:
Plate49_PD1_M8_OT1_Tumor
MARSseq


title: ABS8435

description:
Plate46_PD1_M8_endo_Tumor
MARSseq


title: ABS8433

description:
Plate44_PD1_M7_OT1_Tumor
MARSseq


title: ABS8434

description:
Plate45_PD1_M7_OT1_Tumor
MARSseq


title: ABS8454

description:
Plate68_PBS_M4_OT1_Tumor
MARSseq


title: ABS8451

description:
Plate65_PBS_M4_endo_Tumor
MARSseq


title: ABS8430

description:
Plate41_PBS_M2_OT1_Tumor
MARSseq


title: ABS8428

description:
Plate39_PBS_M2_endo_Tumor
MARSseq


title: ABS8431

description:
Plate42_PD1_M7_endo_Tumor
MARSseq


title: ABS8429

description:
Plate40_PBS_M2_OT1_Tumor
MARSseq


title: ABS8426

description:
Plate37_PBS_M1_OT1_Tumor
MARSseq


title: ABS8427

description:
Plate38_PBS_M2_endo_Tumor
MARSseq


title: ABS8443

description:
Plate54_Dtx+PD1_M17_endo_Tumor
MARSseq


title: ABS8425

description:
Plate36_PBS_M1_endo_Tumor
MARSseq


title: ABS8420

description:
Plate31_PBS_M3_endo_Tumor
MARSseq


title: ABS8421

description:
Plate32_PBS_M3_endo_Tumor
MARSseq


title: ABS8775

description:
61_D6_aPD1_9_Tet-_Tumor
MARSseq


title: ABS8423

description:
Plate34_PBS_M3_OT1_Tumor
MARSseq


title: ABS8415

description:
Plate26_PD1_M9_OT1_Tumor
MARSseq


title: ABS8417

description:
Plate28_PD1_M10_endo_Tumor
MARSseq


title: ABS8416

description:
Plate27_PD1_M10_endo_Tumor
MARSseq


title: ABS8410

description:
Plate21_Dtx_M13_endo_Tumor
MARSseq


title: ABS8432

description:
Plate43_PD1_M7_endo_Tumor
MARSseq


title: ABS8411

description:
Plate22_Dtx_M13_OT1_Tumor
MARSseq


title: ABS8413

description:
Plate24_PD1_M9_endo_Tumor
MARSseq


title: ABS8409

description:
Plate19_Dtx+PD1_M20_OT1_Tumor
MARSseq


title: ABS8408

description:
Plate17_Dtx+PD1_M20_endo_Tumor
MARSseq


title: ABS8407

description:
Plate16_Dtx+PD1_M20_endo_Tumor
MARSseq


title: ABS8414

description:
Plate25_PD1_M9_endo_Tumor
MARSseq


title: ABS8404

description:
Plate13_Dtx+PD1_M19_endo_Tumor
MARSseq


title: ABS8406

description:
Plate15_Dtx+PD1_M19_OT1_Tumor
MARSseq


title: ABS8405

description:
Plate14_Dtx+PD1_M19_endo_Tumor
MARSseq


title: ABS8422

description:
Plate33_PBS_M3_OT1_Tumor
MARSseq


title: ABS8419

description:
Plate30_PD1_M10_OT1_Tumor
MARSseq


title: ABS8418

description:
Plate29_PD1_M10_OT1_Tumor
MARSseq


title: ABS8401

description:
Plate10_Dtx+PD1_M18_endo_Tumor
MARSseq


title: ABS8400

description:
Plate9_Dtx+PD1_M18_endo_Tumor
MARSseq


title: ABS8399

description:
Plate8_Dtx_M12_OT1_Tumor
MARSseq


title: ABS8395

description:
Plate4_PD1_M6_OT1_Tumor
MARSseq


title: ABS8396

description:
Plate5_Dtx_M12_endo_Tumor
MARSseq


title: ABS8402

description:
Plate11_Dtx+PD1_M18_OT1_Tumor
MARSseq


title: ABS8397

description:
Plate6_Dtx_M12_endo_Tumor
MARSseq


title: ABS8398

description:
Plate7_Dtx_M12_OT1_Tumor
MARSseq


title: ABS8394

description:
Plate3_PD1_M6_OT1_Tumor
MARSseq


title: ABS8393

description:
Plate2_PD1_M6_endo_Tumor
MARSseq


title: ABS8254

description:
52_OT1_non_Active_In-vitro_12cycles
MARSseq

value: OT1 CD8+_active


title: ABS8412

description:
Plate23_Dtx_M13_OT1_Tumor
MARSseq


title: ABS8392

description:
Plate1_PD1_M6_endo_Tumor
MARSseq


title: ABS8253

description:
51_OT1_non_Active_In-vitro_9cycles
MARSseq


title: ABS8250

description:
48_OT1_non_naïve_In-vitro_12cycles
MARSseq


title: ABS8251


title: ABS8249

description:
47_OT1_non_naïve_In-vitro_9cycles
MARSseq


title: ABS8248

description:
46_OT1_non_naïve_In-vitro_12cycles
MARSseq


title: ABS8247

description:
45_OT1_non_naïve_In-vitro_9cycles
MARSseq


title: ABS8252

description:
50_OT1_non_Active_In-vitro_12cycles
MARSseq


title: ABS8186

description:
43_OT1_Active_B16+PD1_In-vitro
MARSseq


title: ABS8403

description:
Plate12_Dtx+PD1_M18_OT1_Tumor
MARSseq


title: ABS8182

description:
39_Bystander_Active_B16+PD1_In-vitro
MARSseq


title: ABS8178

description:
35_OT1_Active_B16_In-vitro
MARSseq


title: ABS8179

description:
36_OT1_Active_B16_In-vitro
MARSseq


title: ABS8187

description:
44_OT1_Active_B16+PD1_In-vitro
MARSseq


title: ABS8175

description:
32_Bystander_Active_B16_In-vitro
MARSseq


title: ABS8174

description:
31_Bystander_Active_B16_In-vitro
MARSseq


title: ABS8170

description:
27_OT1_Active_only_In-vitro
MARSseq


title: ABS8167

description:
24_Bystander_Active_only_In-vitro
MARSseq


title: ABS8162

description:
19_Activated_OT1_In-vitro
MARSseq


title: ABS8166

description:
23_Bystander_Active_only_In-vitro
MARSseq


title: ABS8163

description:
20_Activated_OT1_In-vitro
MARSseq


title: ABS8160

description:
17_Activated_OT1_In-vitro
MARSseq


title: ABS8159

description:
16_Activated_wt_In-vitro
MARSseq


title: ABS8161

description:
18_Activated_OT1_In-vitro
MARSseq


title: ABS8158

description:
15_Activated_wt_In-vitro
MARSseq


title: ABS8424

description:
Plate35_PBS_M1_endo_Tumor
MARSseq


title: ABS8157

description:
14_Activated_wt_In-vitro
MARSseq


title: ABS8144

description:
44_D6_B16_OVA_8_Tet- & Tet+_Tumor
MARSseq


title: ABS8143

description:
43_D6_B16_OVA_8_Tet- & Tet+_Tumor
MARSseq


title: ABS8156

description:
13_Activated_wt_In-vitro
MARSseq


title: ABS8141

description:
41_D6_B16_OVA_7_Tet- & Tet+_Tumor
MARSseq


title: ABS8140

description:
40_D6_Ctrl_3_Tet+_Tumor
MARSseq


title: ABS8142

description:
42_D6_B16_OVA_7_Tet- & Tet+_Tumor
MARSseq


title: ABS8183

description:
40_Bystander_Active_B16+PD1_In-vitro
MARSseq


title: ABS8137

description:
37_D6_aPD1_5_Tet+_Tumor
MARSseq


title: ABS8139

description:
39_D6_Ctrl_3_Tet+_Tumor
MARSseq


title: ABS8136

description:
36_D6_aPD1_5_Tet+_Tumor
MARSseq


title: ABS8135

description:
35_D6_aPD1_5_Tet-_Tumor
MARSseq


title: ABS8131

description:
31_D6_Ctrl_2_Tet-_Tumor
MARSseq


title: ABS8133

description:
33_D6_aPD1_6_Tet- & Tet+_Tumor
MARSseq


title: ABS8171

description:
28_OT1_Active_only_In-vitro
MARSseq


title: ABS8138

description:
38_D6_Ctrl_3_Tet-_Tumor
MARSseq


title: ABS8130

description:
30_D6_aPD1_4_Tet+_Tumor
MARSseq


title: ABS8134

description:
34_D6_aPD1_5_Tet-_Tumor
MARSseq


title: ABS8132

description:
32_D6_Ctrl_2_Tet+_Tumor
MARSseq


title: ABS8129

description:
29_D6_aPD1_4_Tet-_Tumor
MARSseq


title: ABS8128

description:
28_D6_Ctrl_1_Tet+_Tumor
MARSseq


title: ABS8126

description:
25_D6_Ctrl_1_Tet-_Tumor
MARSseq


title: ABS8125

description:
23_D3_B16_OVA_8_Tet- & Tet+_dLN
MARSseq


title: ABS8123

description:
21_D3_B16_OVA_7_Tet- & Tet+_dLN
MARSseq


title: ABS8120

description:
18_D3_aPD1_4_Tet+_dLN
MARSseq


title: ABS8121

description:
19_D3_aPD1_5_Tet- & Tet+_dLN
MARSseq


title: ABS8119

description:
17_D3_aPD1_4_Tet-_dLN
MARSseq


title: ABS8118

description:
16_D3_Ctrl_2_Tet- & Tet+_dLN
MARSseq


title: ABS8127

description:
27_D6_Ctrl_1_Tet+_Tumor
MARSseq


title: ABS8114

description:
12_D3_B16_OVA_8_Tet- & Tet+_Tumor
MARSseq


title: ABS8112

description:
10_D3_B16_OVA_7_Tet- & Tet+_Tumor
MARSseq


title: ABS8117

description:
15_D3_Ctrl_2_Tet- & Tet+_dLN
MARSseq


title: ABS8115

description:
13_D3_Ctrl_1_Tet- & Tet+_dLN
MARSseq


title: ABS8111

description:
9_D3_aPD1_6_Tet- & Tet+_Tumor
MARSseq


title: ABS8113

description:
11_D3_B16_OVA_8_Tet-_Tumor
MARSseq


title: ABS8110

description:
8_D3_aPD1_5_Tet+_Tumor
MARSseq


title: ABS8109

description:
7_D3_aPD1_5_Tet- & Tet+_Tumor
MARSseq


title: ABS8107

description:
3_D3_Ctrl_2_Tet-_Tumor
MARSseq


title: ABS8106

description:
2_D3_Ctrl_1_Tet+_Tumor
MARSseq


title: ABS8108

description:
5_D3_aPD1_4_Tet- & Tet+_Tumor
MARSseq


title: ABS8124

description:
22_D3_B16_OVA_7_Tet- & Tet+_dLN
MARSseq


title: ABS7912

description:
13_Naïve_7_OT1_dLN
MARSseq


title: ABS7908

description:
9_Active_1_OT1_Tumor
MARSseq


title: ABS7910

description:
11_Active_4_OT1_Tumor
MARSseq


title: ABS7911

description:
12_Naïve_5_OT1_dLN
MARSseq


title: ABS8122

description:
20_D3_aPD1_5_Tet- & Tet+_dLN
MARSseq


title: ABS7909

description:
10_Active_3_OT1_Tumor
MARSseq


title: ABS7913

description:
16_Active_4_OT1_dLN
MARSseq


title: ABS7905

description:
6_Naïve_7_OT1_Tumor
MARSseq


title: ABS7904

description:
5_Naïve_7_OT1_Tumor
MARSseq


title: ABS7903

description:
4_Naïve_6_OT1_Tumor
MARSseq


title: ABS7901

description:
2_Naïve_5_OT1_Tumor
MARSseq


title: ABS7777

description:
16_pd1_4_CD8
MARSseq

value: CRTAM test


title: ABS8116

description:
14_D3_Ctrl_1_Tet- & Tet+_dLN
MARSseq


title: ABS8105

description:
1_D3_Ctrl_1_Tet-_Tumor
MARSseq


title: ABS7906

description:
7_Naïve_8_OT1_Tumor
MARSseq


title: ABS7900

description:
1_Naïve_5_OT1_Tumor
MARSseq


title: ABS7772

description:
11_41bb+pd1_9_CD8
MARSseq


title: ABS7773

description:
12_41bb+pd1_9_CD8
MARSseq


title: ABS7776

description:
15_pd1_4_CD8
MARSseq


title: ABS7771

description:
10_41bb+pd1_8_CD8
MARSseq


title: ABS7769

description:
7_41bb+pd1_7_CD8
MARSseq


title: ABS7907

description:
8_Naïve_8_OT1_Tumor
MARSseq


title: ABS7774

description:
13_41bb_6_CD8
MARSseq


title: ABS7767

description:
5_41bb_5_CD8
MARSseq


title: ABS7770

description:
9_41bb+pd1_8_CD8
MARSseq


title: ABS7775

description:
14_41bb_6_CD8
MARSseq


title: ABS7768

description:
6_41bb_5_CD8
MARSseq


title: ABS7765

description:
3_pd1_3_CD8
MARSseq


title: ABS7370

description:
Plate58_DTx+PD1_M20_OT1_Tumor
MARSseq


title: ABS7374

description:
Plate62_PBS_M3_endo_Tumor
MARSseq


title: ABS7761

description:
17_Ctrl_2_CD8
MARSseq


title: ABS7762

description:
18_Ctrl_2_CD8
MARSseq


title: ABS7372

description:
Plate60_DTx_M15_endo_Tumor
MARSseq


title: ABS7376

description:
Plate64_PBS_M5_endo_Tumor
MARSseq


title: ABS7378

description:
Plate66_PBS_M5_OT1_Tumor
MARSseq


title: ABS7377

description:
Plate65_PBS_M5_endo_Tumor
MARSseq


title: ABS7379

description:
Plate67_DTx_M15_OT1_Tumor
MARSseq


title: ABS7371

description:
Plate59_DTx_M15_endo_Tumor
MARSseq


title: ABS7373

description:
Plate61_PBS_M3_endo_Tumor
MARSseq


title: ABS7367

description:
Plate39_DTx+PD1_M18_OT1_Tumor
MARSseq


title: ABS7764

description:
2_Ctrl_1_CD8
MARSseq


title: ABS7902

description:
3_Naïve_6_OT1_Tumor
MARSseq


title: ABS7375

description:
Plate63_PBS_M3_OT1_Tumor
MARSseq


title: ABS7763

description:
1_Ctrl_1_CD8
MARSseq


title: ABS7363

description:
Plate26_PBS_M2_OT1_Tumor
MARSseq


title: ABS7366

description:
Plate38_DTx+PD1_M18_endo_Tumor
MARSseq


title: ABS7364

description:
Plate36_DTx_M12_OT1_Tumor
MARSseq


title: ABS7359

description:
Plate20_PBS+PD1_M7_endo_Tumor
MARSseq


title: ABS7766

description:
4_pd1_3_CD8
MARSseq


title: ABS7361

description:
Plate22_PBS+PD1_M7_OT1_Tumor
MARSseq


title: ABS7365

description:
Plate37_DTx+PD1_M18_endo_Tumor
MARSseq


title: ABS7362

description:
Plate25_PBS_M2_endo_Tumor
MARSseq


title: ABS7360

description:
Plate21_PBS+PD1_M7_endo_Tumor
MARSseq


title: ABS7358

description:
Plate16_DTx+PD1_M17_OT1_Tumor
MARSseq


title: ABS7357

description:
Plate15_DTx+PD1_M17_endo_Tumor
MARSseq


title: ABS7369

description:
Plate46_DTx_M14_OT1_Tumor
MARSseq


title: ABS7368

description:
Plate42_DTx+PD1_M19_OT1_Tumor
MARSseq


title: ABS7356

description:
Plate14_DTx+PD1_M17_endo_Tumor
MARSseq


title: ABS7354

description:
Plate12_DTx+PD1_M16_endo_Tumor
MARSseq


title: ABS7350

description:
Plate45_DTx_M14_endo_Tumor
MARSseq


title: ABS7355

description:
Plate13_DTx+PD1_M16_OT1_Tumor
MARSseq


title: ABS7353

description:
Plate11_DTx+PD1_M16_endo_Tumor
MARSseq


title: ABS7338

description:
Plate28_PBS_M4_endo_Tumor
MARSseq


title: ABS7347

description:
Plate41_DTx+PD1_M19_endo_Tumor
MARSseq


title: ABS7337

description:
Plate27_PBS_M4_endo_Tumor
MARSseq


title: ABS7343

description:
Plate33_PBS+PD1_M8_OT1_Tumor
MARSseq


title: ABS7349

description:
Plate44_DTx_M14_endo_Tumor
MARSseq


title: ABS7348

description:
Plate43_DTx+PD1_M19_OT1_Tumor
MARSseq


title: ABS7352

description:
Plate5_PBS+PD1_M6_endo_Tumor
MARSseq


title: ABS7333

description:
Plate18_DTx_M13_endo_Tumor
MARSseq


title: ABS7345

description:
Plate35_DTx_M12_endo_Tumor
MARSseq


title: ABS7332

description:
Plate17_DTx_M13_endo_Tumor
MARSseq


title: ABS7340

description:
Plate30_PBS+PD1_M8_endo_Tumor
MARSseq


title: ABS7346

description:
Plate40_DTx+PD1_M19_endo_Tumor
MARSseq


title: ABS7331

description:
Plate10_DTx_M11_OT1_Tumor
MARSseq


title: ABS7344

description:
Plate34_DTx_M12_endo_Tumor
MARSseq


title: ABS7339

description:
Plate29_PBS_M4_OT1_Tumor
MARSseq


title: ABS7342

description:
Plate32_PBS+PD1_M8_OT1_Tumor
MARSseq


title: ABS7330

description:
Plate9_DTx_M11_endo_Tumor
MARSseq


title: ABS7341

description:
Plate31_PBS+PD1_M8_endo_Tumor
MARSseq


title: ABS7334

description:
Plate19_DTx_M13_OT1_Tumor
MARSseq


title: ABS7336

description:
Plate24_PBS_M2_endo_Tumor
MARSseq


title: ABS7335

description:
Plate23_PBS+PD1_M7_OT1_Tumor
MARSseq


title: ABS7329

description:
Plate8_DTx_M11_endo_Tumor
MARSseq


title: ABS7328

description:
Plate4_PBS+PD1_M6_endo_Tumor
MARSseq


title: ABS7327

description:
Plate3_PBS_M1_OT1_Tumor
MARSseq


title: ABS7351

description:
Plate53_PBS+PD1_M10_endo_Tumor
MARSseq


title: ABS7325

description:
Plate1_PBS_M1_endo_Tumor
MARSseq


title: ABS7326

description:
Plate2_PBS_M1_endo_Tumor
MARSseq


title: ABS7324

description:
Plate57_DTx+PD1_M20_endo_Tumor
MARSseq


title: ABS7323

description:
Plate56_DTx+PD1_M20_endo_Tumor
MARSseq


title: ABS7322

description:
Plate55_PBS+PD1_M10_OT1_Tumor
MARSseq


title: ABS7321

description:
Plate54_PBS+PD1_M10_OT1_Tumor
MARSseq


title: ABS7320

description:
Plate52_PBS+PD1_M10_endo_Tumor
MARSseq


title: ABS7316

description:
Plate48_DTx_M14_OT1_Tumor
MARSseq


title: ABS6529

description:
Plate9_Day4_T cntrl 1_CD45.1
MARSseq


title: ABS6523

description:
Plate3_Day4_T cntrl 4_CD45.1
MARSseq


title: ABS6524

description:
Plate4_Day4_T CD19 5_CD45.1
MARSseq


title: ABS7315

description:
Plate47_DTx+PD1_M18_OT1_Tumor
MARSseq


title: ABS6525

description:
Plate5_Day4_T CD19 2_CD45.1
MARSseq


title: ABS7317

description:
Plate49_PBS+PD1_M9_endo_Tumor
MARSseq


title: ABS6522

description:
Plate2_Day4_T CD19 4_CD45.1
MARSseq


title: ABS6528

description:
Plate8_Day4_T CD19 3_CD45.1
MARSseq


title: ABS7319

description:
Plate51_PBS+PD1_M9_OT1_Tumor
MARSseq


title: ABS6152

description:
Plate13_Day5_cntrl tumor 2_CD45.1
MARSseq


title: ABS6521

description:
Plate1_Day4_T cntrl 3_CD45.1
MARSseq


title: ABS7318

description:
Plate50_PBS+PD1_M9_endo_Tumor
MARSseq


title: ABS6150

description:
Plate11_Day5_CD19 tumor 3_CD45.1
MARSseq


title: ABS6526

description:
Plate6_Day4_T CD19 1_CD45.1
MARSseq


title: ABS6149

description:
Plate10_Day5_CD19 tumor1_CD45.1
MARSseq


title: ABS6527

description:
Plate7_Day4_T cntrl 5_CD45.1
MARSseq


title: ABS6148

description:
Plate9_Day5_CD19 tumor 1_CD45.1
MARSseq


title: ABS6147

description:
Plate6_Day3_Tumor cntrl 1_CD45.1
MARSseq


title: ABS6146

description:
Plate5_Day3_Tumor CD19 3_SNIPR+
MARSseq


title: ABS6145

description:
Plate4_Day3_Tumor CD19 3_CD45.1
MARSseq


title: ABS6143

description:
Plate2_Day3_Tumor CD19 1_CD45.1
MARSseq


title: AB9949

description:
20200315_D5_Tumor10_endo_2
MARSseq


title: AB9947

description:
20200315_D5_Tumor7_endo_2
MARSseq


title: ABS6142

description:
Plate1_Day3_Tumor CD19 1_SNIPR+
MARSseq


title: AB9948

description:
20200315_D5_Tumor7_endo_3
MARSseq


title: ABS6153

description:
Plate14_Day5_cntrl tumor 2_CD45.1
MARSseq


title: ABS6151

description:
Plate12_Day5_cntrl tumor 2_CD45.1
MARSseq


title: AB9946

description:
20200315_D5_Tumor7_endo_1
MARSseq


title: AB9945

description:
20200315_D5_Tumor6_endo_2
MARSseq


title: AB9941

description:
20200315_D5_Tumor3_endo_1
MARSseq


title: AB9940

description:
20200315_D5_Tumor2_endo_3
MARSseq


title: AB9939

description:
20200315_D5_Tumor2_endo_2
MARSseq


title: AB9937

description:
20200315_D5_Tumor1_endo_3
MARSseq


title: AB9935

description:
20200315_D5_Tumor1_endo_1
MARSseq


title: AB9944

description:
20200315_D5_Tumor6_endo_1
MARSseq


title: AB9760

description:
25_05_2020_PD1ko_OT1_T5_1_Index
MARSseq


title: AB9758

description:
25_05_2020_PD1ko_OT1_T4_2_Index
MARSseq


title: AB9943

description:
20200315_D5_Tumor3_endo_3
MARSseq


title: AB9942

description:
20200315_D5_Tumor3_endo_2
MARSseq


title: AB9755

description:
25_05_2020_PD1ko_OT1_T2_2_Index
MARSseq


title: AB9762

description:
25_05_2020_PD1ko_OT1_T5_3_Index
MARSseq


title: AB9757

description:
25_05_2020_PD1ko_OT1_T4_1_Index
MARSseq


title: AB9761

description:
25_05_2020_PD1ko_OT1_T5_2_Index
MARSseq


title: AB9759

description:
25_05_2020_PD1ko_OT1_T4_3_Index
MARSseq


title: AB9756

description:
25_05_2020_PD1ko_OT1_T2_3_Index
MARSseq


title: AB9753

description:
25_05_2020_PD1ko_OT1_T1_3_Index
MARSseq


title: AB9754

description:
25_05_2020_PD1ko_OT1_T2_1_Index
MARSseq


title: ABS6144

description:
Plate3_Day3_Tumor CD19 3_CD45.1
MARSseq


title: AB9752

description:
25_05_2020_PD1ko_OT1_T1_2_Index
MARSseq


title: AB9751

description:
25_05_2020_PD1ko_OT1_T1_1_Index
MARSseq


title: AB9750

description:
23_05_2020_onlyOT1_T7_1_Index
MARSseq


title: AB9747

description:
23_05_2020_onlyOT1_T1_1
MARSseq


title: AB9746

description:
23_05_2020_OT1_T8_1_Index
MARSseq


title: AB9748

description:
23_05_2020_onlyOT1_T4_1
MARSseq


title: AB9936

description:
20200315_D5_Tumor1_endo_2
MARSseq


title: AB9749

description:
23_05_2020_onlyOT1_T5_1
MARSseq


title: AB9743

description:
23_05_2020_OT1_T2_2_Index
MARSseq


title: AB9744

description:
23_05_2020_OT1_T4_1_Index
MARSseq


title: AB9745

description:
23_05_2020_OT1_T7_1_Index
MARSseq


title: AB9738

description:
20200312_D2_Tumor1_endo_1
MARSseq


title: AB9739

description:
20200312_D2_Tumor3_endo_1
MARSseq


title: AB9741

description:
20200312_D2_Tumor6_endo_1
MARSseq


title: AB9740

description:
20200312_D2_Tumor4_endo_1
MARSseq


title: AB9742

description:
23_05_2020_OT1_T2_1_Index
MARSseq


title: AB9735

description:
20200311_D1_Tumor3_endo_1
MARSseq


title: AB9736

description:
20200311_D1_Tumor4_endo_1
MARSseq


title: AB9733

description:
20200310_D0_Tumor3_endo_2
MARSseq


title: AB9729

description:
20200310_D0_Tumor1_endo_1
MARSseq


title: AB9559

description:
20200315_D5_LN7_OT1_2
MARSseq


title: AB9732

description:
20200310_D0_Tumor3_endo_1
MARSseq


title: AB9731

description:
20200310_D0_Tumor2_endo_2
MARSseq


title: AB9558

description:
20200315_D5_LN7_OT1_1
MARSseq


title: AB9938

description:
20200315_D5_Tumor2_endo_1
MARSseq


title: AB9737

description:
20200311_D1_Tumor5_endo_1
MARSseq


title: AB9549

description:
20200315_D5_Spleen7_OT1_2
MARSseq

source_name: Spleen

value: Spleen


title: AB9557

description:
20200315_D5_LN6_OT1_1
MARSseq


title: AB9550

description:
20200315_D5_Spleen10_OT1_1
MARSseq


title: AB9555

description:
20200315_D5_LN3_OT1_1
MARSseq


title: AB9551

description:
20200315_D5_LN1_OT1_1
MARSseq


title: AB9546

description:
20200315_D5_Spleen6_OT1_1
MARSseq


title: AB9556

description:
20200315_D5_LN3_OT1_2
MARSseq


title: AB9552

description:
20200315_D5_LN1_OT1_2
MARSseq


title: AB9553

description:
20200315_D5_LN2_OT1_1
MARSseq


title: AB9734

description:
20200311_D1_Tumor1_endo_1
MARSseq


title: AB9554

description:
20200315_D5_LN2_OT1_2
MARSseq


title: AB9544

description:
20200315_D5_Spleen2_OT1_2
MARSseq


title: AB9543

description:
20200315_D5_Spleen2_OT1_1
MARSseq


title: AB9730

description:
20200310_D0_Tumor2_endo_1
MARSseq


title: AB9545

description:
20200315_D5_Spleen3_OT1_2
MARSseq


title: AB9547

description:
20200315_D5_Spleen6_OT1_2
MARSseq


title: AB9541

description:
20200315_D5_Spleen1_OT1_1
MARSseq


title: AB9540

description:
20200314_D4_LN6_OT1_1
MARSseq


title: AB9542

description:
20200315_D5_Spleen1_OT1_2
MARSseq


title: AB9539

description:
20200314_D4_LN5_OT1_2
MARSseq


title: AB9538

description:
20200314_D4_LN5_OT1_1
MARSseq


title: AB9537

description:
20200314_D4_LN4_OT1_1
MARSseq


title: AB9536

description:
20200314_D4_LN2_OT1_2
MARSseq


title: AB9534

description:
20200314_D4_LN1_OT1_2
MARSseq


title: AB9532

description:
20200314_D4_Spleen6_OT1_2
MARSseq


title: AB9533

description:
20200314_D4_LN1_OT1_1
MARSseq


title: AB9535

description:
20200314_D4_LN2_OT1_1
MARSseq


title: AB9531

description:
20200314_D4_Spleen6_OT1_1
MARSseq


title: AB9548

description:
20200315_D5_Spleen7_OT1_1
MARSseq


title: AB9529

description:
20200314_D4_Spleen4_OT1_1
MARSseq


title: AB9524

description:
20200313_D3_LN6_OT1_1
MARSseq


title: AB9526

description:
20200314_D4_Spleen1_OT1_2
MARSseq


title: AB9523

description:
20200313_D3_LN5_OT1_1
MARSseq


title: AB9525

description:
20200314_D4_Spleen1_OT1_1
MARSseq


title: AB9522

description:
20200313_D3_LN4_OT1_2
MARSseq


title: AB9527

description:
20200314_D4_Spleen2_OT1_1
MARSseq


title: AB9519

description:
20200313_D3_LN2_OT1_1
MARSseq


title: AB9528

description:
20200314_D4_Spleen2_OT1_2
MARSseq


title: AB9516

description:
20200313_D3_Spleen5_OT1_2
MARSseq


title: AB9530

description:
20200314_D4_Spleen4_OT1_2
MARSseq


title: AB9521

description:
20200313_D3_LN4_OT1_1
MARSseq


title: AB9515

description:
20200313_D3_Spleen5_OT1_1
MARSseq


title: AB9520

description:
20200313_D3_LN2_OT1_2
MARSseq


title: AB9512

description:
20200313_D3_Spleen2_OT1_2
MARSseq


title: AB9513

description:
20200313_D3_Spleen4_OT1_1
MARSseq


title: AB9509

description:
20200313_D3_Spleen1_OT1_1
MARSseq


title: AB9510

description:
20200313_D3_Spleen1_OT1_2
MARSseq


title: AB9504

description:
20200312_D2_LN3_OT1_2
MARSseq


title: AB9505

description:
20200312_D2_LN4_OT1_1
MARSseq


title: AB9501

description:
20200312_D2_LN1_OT1_1
MARSseq


title: AB9508

description:
20200312_D2_LN6_OT1_2
MARSseq


title: AB9503

description:
20200312_D2_LN3_OT1_1
MARSseq


title: AB9507

description:
20200312_D2_LN6_OT1_1
MARSseq


title: AB9506

description:
20200312_D2_LN4_OT1_2
MARSseq


title: AB9517

description:
20200313_D3_LN1_OT1_1
MARSseq


title: AB9502

description:
20200312_D2_LN1_OT1_2
MARSseq


title: AB9514

description:
20200313_D3_Spleen4_OT1_2
MARSseq


title: AB9518

description:
20200313_D3_LN1_OT1_2
MARSseq


title: AB9511

description:
20200313_D3_Spleen2_OT1_1
MARSseq


title: AB9500

description:
20200312_D2_Spleen6_OT1_2
MARSseq


title: AB9499

description:
20200312_D2_Spleen6_OT1_1
MARSseq


title: AB9496

description:
20200312_D2_Spleen3_OT1_2
MARSseq


title: AB9497

description:
20200312_D2_Spleen4_OT1_1
MARSseq


title: AB9491

description:
20200311_D1_LN5_OT1_1
MARSseq


title: AB9490

description:
20200311_D1_LN4_OT1_2
MARSseq


title: AB9495

description:
20200312_D2_Spleen3_OT1_1
MARSseq


title: AB9492

description:
20200311_D1_LN5_OT1_2
MARSseq


title: AB9487

description:
20200311_D1_LN3_OT1_1
MARSseq


title: AB9486

description:
20200311_D1_LN1_OT1_2
MARSseq


title: AB9485

description:
20200311_D1_LN1_OT1_1
MARSseq


title: AB9484

description:
20200311_D1_Spleen5_OT1_2
MARSseq


title: AB9483

description:
20200311_D1_Spleen5_OT1_1
MARSseq


title: AB9481

description:
20200311_D1_Spleen4_OT1_1
MARSseq


title: AB9482

description:
20200311_D1_Spleen4_OT1_2
MARSseq


title: AB9480

description:
20200311_D1_Spleen3_OT1_2
MARSseq


title: AB9474

description:
20200310_D0_LN1_OT1_1
MARSseq


title: AB9494

description:
20200312_D2_Spleen1_OT1_2
MARSseq


title: AB9476

description:
20200310_D0_LN3_OT1_1
MARSseq


title: AB9473

description:
20200310_D0_Spleen3_OT1_2
MARSseq


title: AB9479

description:
20200311_D1_Spleen3_OT1_1
MARSseq


title: AB9493

description:
20200312_D2_Spleen1_OT1_1
MARSseq


title: AB9471

description:
20200310_D0_Spleen2_OT1_2
MARSseq


title: AB9472

description:
20200310_D0_Spleen3_OT1_1
MARSseq


title: AB9475

description:
20200310_D0_LN2_OT1_1
MARSseq


title: AB9489

description:
20200311_D1_LN4_OT1_1
MARSseq


title: AB9468

description:
20200310_D0_Spleen1_OT1_1
MARSseq


title: AB9469

description:
20200310_D0_Spleen1_OT1_2
MARSseq


title: AB9470

description:
20200310_D0_Spleen2_OT1_1
MARSseq


title: AB9276

description:
20200315_D5_Tumor10_OT1_2
MARSseq


title: AB9273

description:
20200315_D5_Tumor7_OT1_2
MARSseq


title: AB9272

description:
20200315_D5_Tumor7_OT1_1
MARSseq


title: AB9274

description:
20200315_D5_Tumor9_OT1_1
MARSseq


title: AB9271

description:
20200315_D5_Tumor6_OT1_1
MARSseq


title: AB9478

description:
20200311_D1_Spleen1_OT1_2
MARSseq


title: AB9477

description:
20200311_D1_Spleen1_OT1_1
MARSseq


title: AB9275

description:
20200315_D5_Tumor10_OT1_1
MARSseq


title: AB9270

description:
20200315_D5_Tumor3_OT1_2
MARSseq


title: AB9268

description:
20200315_D5_Tumor2_OT1_2
MARSseq


title: AB9264

description:
20200314_D4_Tumor6_OT1_2
MARSseq


title: AB9265

description:
20200315_D5_Tumor1_OT1_1
MARSseq


title: AB9266

description:
20200315_D5_Tumor1_OT1_2
MARSseq


title: AB9263

description:
20200314_D4_Tumor6_OT1_1
MARSseq


title: AB9261

description:
20200314_D4_Tumor4_OT1_1
MARSseq


title: AB9498

description:
20200312_D2_Spleen4_OT1_2
MARSseq


title: AB9262

description:
20200314_D4_Tumor4_OT1_2
MARSseq


title: AB9260

description:
20200314_D4_Tumor3_OT1_2
MARSseq


title: AB9256

description:
20200314_D4_Tumor1_OT1_2
MARSseq


title: AB9259

description:
20200314_D4_Tumor3_OT1_1
MARSseq


title: AB9257

description:
20200314_D4_Tumor2_OT1_1
MARSseq


title: AB9255

description:
20200314_D4_Tumor1_OT1_1
MARSseq


title: AB9258

description:
20200314_D4_Tumor2_OT1_2
MARSseq


title: AB9254

description:
20200313_D3_Tumor6_OT1_2
MARSseq


title: AB9251

description:
20200313_D3_Tumor5_OT1_1
MARSseq


title: AB9253

description:
20200313_D3_Tumor6_OT1_1
MARSseq


title: AB9250

description:
20200313_D3_Tumor4_OT1_2
MARSseq


title: AB9247

description:
20200313_D3_Tumor3_OT1_1
MARSseq


title: AB9248

description:
20200313_D3_Tumor3_OT1_2
MARSseq


title: AB9249

description:
20200313_D3_Tumor4_OT1_1
MARSseq


title: AB9246

description:
20200313_D3_Tumor2_OT1_2
MARSseq


title: AB9245

description:
20200313_D3_Tumor2_OT1_1
MARSseq


title: AB9244

description:
20200313_D3_Tumor1_OT1_2
MARSseq


title: AB9243

description:
20200313_D3_Tumor1_OT1_1
MARSseq


title: AB9269

description:
20200315_D5_Tumor3_OT1_1
MARSseq


title: AB9267

description:
20200315_D5_Tumor2_OT1_1
MARSseq


title: AB9242

description:
20200312_D2_Tumor6_OT1_2
MARSseq


title: AB9241

description:
20200312_D2_Tumor6_OT1_1
MARSseq


title: AB9240

description:
20200312_D2_Tumor4_OT1_2
MARSseq


title: AB9239

description:
20200312_D2_Tumor4_OT1_1
MARSseq


title: AB9236

description:
20200312_D2_Tumor1_OT1_2
MARSseq


title: AB9235

description:
20200312_D2_Tumor1_OT1_1
MARSseq


title: AB9231

description:
20200311_D1_Tumor4_OT1_1
MARSseq


title: AB9238

description:
20200312_D2_Tumor3_OT1_2
MARSseq


title: AB9229

description:
20200311_D1_Tumor3_OT1_1
MARSseq


title: AB9237

description:
20200312_D2_Tumor3_OT1_1
MARSseq


title: AB9233

description:
20200311_D1_Tumor5_OT1_1
MARSseq


title: AB9252

description:
20200313_D3_Tumor5_OT1_2
MARSseq


title: AB9232

description:
20200311_D1_Tumor4_OT1_2
MARSseq


title: AB9234

description:
20200311_D1_Tumor5_OT1_2
MARSseq


title: AB9230

description:
20200311_D1_Tumor3_OT1_2
MARSseq


title: AB9227

description:
20200311_D1_Tumor1_OT1_1
MARSseq


title: AB9228

description:
20200311_D1_Tumor1_OT1_2
MARSseq


title: AB9226

description:
20200310_D0_Tumor3_OT1_2
MARSseq


title: AB9225

description:
20200310_D0_Tumor3_OT1_1
MARSseq


title: AB9223

description:
20200310_D0_Tumor2_OT1_1
MARSseq


title: AB9224

description:
20200310_D0_Tumor2_OT1_2
MARSseq


title: AB8993

description:
20191217_D5_Ctrl_LN10_2
MARSseq

value: OT1 CD8+_or_bystander CD8+


title: AB8990

description:
20191217_D5_Ctrl_LN8_1
MARSseq


title: AB9222

description:
20200310_D0_Tumor1_OT1_1
MARSseq


title: AB8991

description:
20191217_D5_Ctrl_LN9_1
MARSseq


title: AB8992

description:
20191217_D5_Ctrl_LN10_1
MARSseq


title: AB8989

description:
20191217_D5_PD1_LN5_2
MARSseq


title: AB8988

description:
20191217_D5_PD1_LN5_1
MARSseq


title: AB8987

description:
20191217_D5_PD1_LN4_1
MARSseq


title: AB8985

description:
20191217_D5_PD1_LN2_1
MARSseq


title: AB8982

description:
20191214_D2_Ctrl_LN9_2
MARSseq


title: AB8981

description:
20191214_D2_Ctrl_LN9_1
MARSseq


title: AB8980

description:
20191214_D2_Ctrl_LN6_1
MARSseq


title: AB8979

description:
20191214_D2_PD1_LN5_2
MARSseq


title: AB8984

description:
20191214_D2_Ctrl_LN10_2
MARSseq


title: AB8977

description:
20191214_D2_PD1_LN4_1
MARSseq


title: AB8975

description:
20191214_D2_PD1_LN2_1
MARSseq


title: AB8978

description:
20191214_D2_PD1_LN5_1
MARSseq


title: AB8974

description:
cd8_in_vitro
MARSseq


title: AB8973

description:
20191214_D2_Ctrl_spleen10_2
MARSseq

source_name: spleen

value: spleen


title: AB8969

description:
20191214_D2_Ctrl_spleen6_1
MARSseq


title: AB8971

description:
20191214_D2_Ctrl_spleen9_1
MARSseq


title: AB8976

description:
20191214_D2_PD1_LN2_2
MARSseq


title: AB8968

description:
20191214_D2_PD1_spleen5_2
MARSseq


title: AB8972

description:
20191214_D2_Ctrl_spleen10_1
MARSseq


title: AB8966

description:
20191214_D2_PD1_spleen4_2
MARSseq


title: AB8970

description:
20191214_D2_Ctrl_spleen6_2
MARSseq


title: AB8967

description:
20191214_D2_PD1_spleen5_1
MARSseq


title: AB8986

description:
20191217_D5_PD1_LN2_2
MARSseq


title: AB8963

description:
20191214_D2_PD1_spleen2_1
MARSseq


title: AB8983

description:
20191214_D2_Ctrl_LN10_1
MARSseq


title: AB8965

description:
20191214_D2_PD1_spleen4_1
MARSseq


title: AB8961

description:
20191217_D5_Ctrl_spleen10_1
MARSseq


title: AB8960

description:
20191217_D5_Ctrl_spleen9_2
MARSseq


title: AB8958

description:
20191217_D5_Ctrl_spleen8_2
MARSseq


title: AB8962

description:
cd8_in_vitro
MARSseq


title: AB8964

description:
20191214_D2_PD1_spleen2_2
MARSseq


title: AB8959

description:
20191217_D5_Ctrl_spleen9_1
MARSseq


title: AB9488

description:
20200311_D1_LN3_OT1_3
MARSseq


title: AB8953

description:
20191217_D5_PD1_spleen4_1
MARSseq


title: AB8951

description:
20191217_D5_PD1_spleen2_1
MARSseq


title: AB8952

description:
20191217_D5_PD1_spleen2_2
MARSseq


title: AB14014

description:
11.8.21_262_Ctrl_5_CD45_FSCW,
MARSseq

value: endogenous CD45+


title: AB14007

description:
11.8.21_255_pd1_10_CD45_FSCW,
MARSseq


title: AB14010

description:
11.8.21_258_pd1_10_CD45_FSCW,
MARSseq


title: AB14011

description:
11.8.21_259_41bb_15_CD45_FSCW,
MARSseq


title: AB14006

description:
11.8.21_254_pd1_9_CD45_FSCW,
MARSseq


title: AB14013

description:
11.8.21_261_41bb_15_CD45_FSCW,
MARSseq


title: AB14008

description:
11.8.21_256_pd1_10_CD45_FSCW,
MARSseq


title: AB14012

description:
11.8.21_260_41bb_15_CD45_FSCW,
MARSseq


title: AB14009

description:
11.8.21_257_pd1_10_CD45_FSCW,
MARSseq


title: AB14005

description:
11.8.21_253_pd1_9_CD45_FSCW,
MARSseq


title: AB14004

description:
11.8.21_252_pd1_9_CD45_FSCW,
MARSseq


title: AB14002

description:
11.8.21_249_41bb+pd1_19_CD45_FSCW,
MARSseq


title: AB14003

description:
11.8.21_251_pd1_9_CD45_FSCW,
MARSseq


title: AB8957

description:
20191217_D5_Ctrl_spleen8_1
MARSseq


title: AB14000

description:
11.8.21_247_41bb_14_CD45_FSCW,
MARSseq


title: AB13998

description:
11.8.21_245_41bb_14_CD45_FSCW,
MARSseq


title: AB8955

description:
20191217_D5_PD1_spleen5_1
MARSseq


title: AB13995

description:
11.8.21_241_Ctrl_4_CD45_FSCW,
MARSseq


title: AB13997

description:
11.8.21_243_pd1_8_CD45_FSCW,
MARSseq


title: AB8954

description:
20191217_D5_PD1_spleen4_2
MARSseq


title: AB13994

description:
11.8.21_240_Ctrl_4_CD45_FSCW,
MARSseq


title: AB13996

description:
11.8.21_242_Ctrl_4_CD45_FSCW,
MARSseq


title: AB13993

description:
11.8.21_239_Ctrl_4_CD45_FSCW,
MARSseq


title: AB13999

description:
11.8.21_246_41bb_14_CD45_FSCW,
MARSseq


title: AB8956

description:
20191217_D5_PD1_spleen5_2
MARSseq


title: AB13992

description:
11.8.21_238_Ctrl_3_CD45_FSCW,
MARSseq


title: AB13988

description:
11.8.21_236_41bb_13_CD45_FSCW,
MARSseq


title: AB13987

description:
11.8.21_235_41bb_13_CD45_FSCW,
MARSseq


title: AB13984

description:
11.8.21_232_41bb+pd1_18_CD45_FSCW,
MARSseq


title: AB13983

description:
11.8.21_231_41bb+pd1_17_CD45_FSCW,
MARSseq


title: AB13982

description:
11.8.21_230_41bb+pd1_17_CD45_FSCW,
MARSseq


title: AB13986

description:
11.8.21_234_41bb+pd1_18_CD45_FSCW,
MARSseq


title: AB13980

description:
11.8.21_224_41bb_11_CD45_FSCW,
MARSseq


title: AB13985

description:
11.8.21_233_41bb+pd1_18_CD45_FSCW,
MARSseq


title: AB13979

description:
11.8.21_223_41bb_11_CD45_FSCW,
MARSseq


title: AB13981

description:
11.8.21_229_41bb+pd1_16_CD45_FSCW,
MARSseq


title: AB13976

description:
11.8.21_220_pd1_7_CD45_FSCW,
MARSseq


title: AB13978

description:
11.8.21_222_41bb_11_CD45_FSCW,
MARSseq


title: AB14001

description:
11.8.21_248_41bb_14_CD45_FSCW,
MARSseq


title: AB13975

description:
11.8.21_219_pd1_6_CD45_FSCW,
MARSseq


title: AB13977

description:
11.8.21_221_pd1_7_CD45_FSCW,
MARSseq


title: AB13971

description:
11.8.21_211_ctrl_1_CD45_FSCW,
MARSseq


title: AB13973

description:
11.8.21_217_pd1_6_CD45_FSCW,
MARSseq


title: AB13970

description:
11.8.21_210_ctrl_1_CD45_FSCW,
MARSseq


title: AB13969

description:
11.8.21_209_ctrl_1_CD45_FSCW,
MARSseq


title: AB13991

description:
11.8.21_237_Ctrl_3_CD45_FSCW,
MARSseq


title: AB13499

description:
18.7.21_MC38_150_4-1BB_CD45_FSCW
MARSseq


title: AB13497

description:
18.7.21_MC38_148_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13972

description:
11.8.21_216_pd1_6_CD45_FSCW,
MARSseq


title: AB13501

description:
18.7.21_MC38_152_PD-1_CD45_FSCW
MARSseq


title: AB13498

description:
18.7.21_MC38_149_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13974

description:
11.8.21_218_pd1_6_CD45_FSCW,
MARSseq


title: AB13502

description:
18.7.21_MC38_153_PD-1_CD45_FSCW
MARSseq


title: AB13496

description:
18.7.21_MC38_147_PD1/4-1BB_CD45_FSCW
MARSseq


title: AB13495

description:
18.7.21_MC38_146_PD1/4-1BB_CD45_FSCW
MARSseq


title: AB13500

description:
18.7.21_MC38_151_4-1BB_CD45_FSCW
MARSseq


title: AB13494

description:
18.7.21_MC38_145_4-1BB_CD45_FSCW,
MARSseq


title: AB13493

description:
18.7.21_MC38_142_ctl_CD45_FSCW,
MARSseq


title: AB13491

description:
18.7.21_MC38_140_ctl_CD45_FSCW
MARSseq


title: AB13490

description:
18.7.21_MC38_139_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13488

description:
18.7.21_MC38_135_4-1BB_CD45_FSCW
MARSseq


title: AB13489

description:
18.7.21_MC38_136_4-1BB_CD45_FSCW
MARSseq


title: AB13486

description:
18.7.21_MC38_133_4-1BB_CD45_FSCW
MARSseq


title: AB13492

description:
18.7.21_MC38_141_ctl_CD45_FSCW
MARSseq


title: AB13485

description:
18.7.21_MC38_132_PD-1_CD45_FSCW
MARSseq


title: AB13481

description:
18.7.21_MC38_128_ctl_CD45_FSCW
MARSseq


title: AB13483

description:
18.7.21_MC38_130_PD-1_CD45_FSCW
MARSseq


title: AB13484

description:
18.7.21_MC38_131_PD-1_CD45_FSCW
MARSseq


title: AB13480

description:
18.7.21_MC38_127_ctl_CD45_FSCW
MARSseq


title: AB13482

description:
18.7.21_MC38_129_PD-1_CD45_FSCW
MARSseq


title: AB13479

description:
18.7.21_MC38_124_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13478

description:
18.7.21_MC38_123_PD1/4-1BB_CD45_FSCW
MARSseq


title: AB13476

description:
18.7.21_MC38_121_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13475

description:
18.7.21_MC38_120_4-1BB_CD45_FSCW,
MARSseq


title: AB13474

description:
18.7.21_MC38_119_4-1BB_CD45_FSCW
MARSseq


title: AB13477

description:
18.7.21_MC38_122_PD1/4-1BB_CD45_FSCW
MARSseq


title: AB13472

description:
18.7.21_MC38_115_Ctl_CD45_FSCW
MARSseq


title: AB13471

description:
18.7.21_MC38_114_Ctl_CD45_FSCW
MARSseq


title: AB13469

description:
18.7.21_MC38_112_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13470

description:
18.7.21_MC38_113_PD1/4-1BB_CD45_FSCW,
MARSseq


title: AB13467

description:
18.7.21_MC38_110_4-1BB_CD45_FSCW
MARSseq


title: AB13465

description:
18.7.21_MC38_108_PD-1_CD45_FSCW
MARSseq


title: AB13464

description:
18.7.21_MC38_107_PD-1_CD45_FSCW
MARSseq


title: AB13468

description:
18.7.21_MC38_111_4-1BB_CD45_FSCW,
MARSseq


title: AB13487

description:
18.7.21_MC38_134_4-1BB_CD45_FSCW
MARSseq


title: AB13113

description:
30.6.21_MC38_100_Ctl_TCRb+
MARSseq


title: AB13112

description:
30.6.21_MC38_97_Ctl_CD45_FSCW
MARSseq


title: AB13110

description:
30.6.21_MC38_93_PD-1_CD45_FSCW
MARSseq


title: AB13109

description:
30.6.21_MC38_92_PD-1_CD45_FSCW
MARSseq


title: AB13111

description:
30.6.21_MC38_96_Ctl_CD45_FSCW
MARSseq


title: AB13105

description:
30.6.21_MC38_3_Ctl_CD45_FSCW
MARSseq


title: AB13473

description:
18.7.21_MC38_118_4-1BB_CD45_FSCW
MARSseq


title: AB12218

description:
50_Tumor_11_PD1-XCR1_CD11c
MARSseq

value: endogenous CD8+


title: AB12216

description:
48_Tumor_4_PBS_CD3
MARSseq


title: AB12219

description:
52_Tumor_8_PD1-Syn_Pic
MARSseq


title: AB12215

description:
47_Tumor_4_PBS_CD11c
MARSseq


title: AB12184

description:
20.2.21_D3_8_PD1+41BB_Endo
MARSseq


title: AB12183

description:
28.2.21_D6_8_aPD1+41BB_Endo
MARSseq


title: AB12185

description:
20.2.21_D3_8_PD1+41BB_Endo
MARSseq


title: AB12214

description:
46_Tumor_4_PBS_Pic
MARSseq


title: AB12182

description:
28.2.21_D6_8_aPD1+41BB_Endo
MARSseq


title: AB12180

description:
28.2.21_D6_7_aPD1+41BB_Endo
MARSseq


title: AB12181

description:
28.2.21_D6_7_aPD1+41BB_Endo
MARSseq


title: AB12179

description:
28.2.21_D6_7_aPD1+41BB_Endo
MARSseq


title: AB13108

description:
30.6.21_MC38_91_PD-1_CD45_FSCW
MARSseq


title: AB13466

description:
18.7.21_MC38_109_4-1BB_CD45_FSCW
MARSseq


title: AB12178

description:
28.2.21_D6_7_aPD1+41BB_Endo
MARSseq


title: AB12176

description:
28.2.21_D6_6_aPD1+41BB_Endo
MARSseq


title: AB12177

description:
28.2.21_D6_5_aPD1+41BB_Endo
MARSseq


title: AB12173

description:
28.2.21_D6_5_aPD1+41BB_Endo
MARSseq


title: AB12174

description:
28.2.21_D6_5_aPD1+41BB_Endo
MARSseq


title: AB13107

description:
30.6.21_MC38_59_PD-1_CD45_FSCW
MARSseq


title: AB12172

description:
28.2.21_D6_5_aPD1+41BB_Endo
MARSseq


title: AB12171

description:
28.2.21_D6_12_aPD1 _Endo
MARSseq


title: AB12170

description:
28.2.21_D6_12_aPD1 _Endo
MARSseq


title: AB12169

description:
28.2.21_D6_10_Ctrl_Endo
MARSseq


title: AB12168

description:
28.2.21_D6_10_Ctrl_Endo
MARSseq


title: AB12217

description:
49_Tumor_11_PD1-XCR1_Pic
MARSseq


title: AB12167

description:
28.2.21_D6_4_41BB_Endo
MARSseq


title: AB12166

description:
28.2.21_D6_4_41BB_Endo
MARSseq


title: AB12165

description:
28.2.21_D6_4_41BB_Endo
MARSseq


title: AB12164

description:
28.2.21_D6_3_41BB_Endo
MARSseq


title: AB12163

description:
28.2.21_D6_3_41BB_Endo
MARSseq


title: AB12161

description:
28.2.21_D6_2_41BB_OT1
MARSseq

value: OT1 CD8+


title: AB12159

description:
28.2.21_D6_2_41BB_Endo
MARSseq