title: Ctrl DCs PD1 biol rep 1 [CP 1]

value: brain tumor

tag: time

value: Day 21 post implantation

value: immune cells

value: WT

tag: treatment


title: RNAseq,TamPos,E15.5,EC,rep2

status: Public on Jan 25 2024

type: SRA

city: Jamaica Plain

first: Xiaoran

last: Zhang

state: MA

address: 14 Perkins Square, Apt 11

department: Cardiology

country: USA

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
RNA-seq mapping and quantitation was done using STAR v. 2.6.147 with a hg38 STAR index.
The mapped reads were further analyzed by HTSeq-count v.0.11.2 and annotated using a RefSeq database.
The reads count were normalized by DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized readscount values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: whole embryo

extract_protocol:
Cellular samples were treated with TRIzol reagent then total RNA was purified with RNA Clean & Concentrator-5 Kit (Zymo). Genomic DNA disgestion was performed with Dnase I on column treatment.
Completely followed the protocol of NEBNext Ultra II RNA Library Prep Kit for use with NEBNext rRNA Depletion Kit v2.

tag: tissue

value: whole embryo

tag: developmental stage

tag: cell type

value: Endothelial cell

tag: genotype

value: wild type

value: tamoxifen gavage


title: Tongue WT Candida-infected_rep4

city: Milwaukee

first: Anna

middle: R

last: Huppler

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: deseq/Differential_Expression__DESeq2__compare_2_groups__on_WT_Infected_on_WT_sham.diffexpr.w_symbols.txt

data_processing:
(1) Remove reads containing adapters.
(2) Remove reads containing N > 10% (N represents the base cannot be determined).
(3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality
Genome_build: mm10

source_name: tongue

extract_protocol:
tongues were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy mini kit. The concentration was measured with Nanodrop 2000c. RNA samples then were sent on dry ice to Novogene for library preparation and sequecing. Contract ID is H202SC20072776 . Batch ID is X202SC20072776-Z01-F001. Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After enrichment, mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization. In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.

tag: strain

tag: infection

value: Candida albicans, strain CAF2-1

tag: day after infection

value: whole tongue


title: RNAseq,TamPos,E15.5,EC,rep1


title: Fgf4 mutant mESCs, unstimulated, clone 1, rep2

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

country: Germany

institute: University Leiden

data_processing:
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: All Reads; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: All Reads; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
TPMs filtered for features with a raw count above 50 in one of the samples
Assembly: GRCm39, release 108
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: Probes_with_raw_count>50_TPMs.txt: Contains log2(TPMs) per sample (columns) for each gene with over 50 raw counts over all samples (rows) including gene information (e.g. genomic location, strand, ID, etc.)

molecule: polyA RNA

source_name: mESCs

growth_protocol: 55k cells/cm2 of Fgf4-mutant cells and Fgf4 Med12 double-mutant cells were seeded into N2B27 + Chiron + LIF and grown for 18h.

extract_protocol:
Trizol-based total RNA extraction
Poly-A-enriched

treatment_protocol: Stimulation with or without 40 ng/ml FGF4 in N2B27 + 1 μg/ml heparin for 6 h.

value: mESCs


title: RNAseq,Tam-,E15.5,EC,rep4


title: RNAseq,Tam-,E15.5,EC,rep3


title: Tongue WT Candida-infected_rep3

description:
deseq/Differential_Expression__DESeq2__compare_2_groups__on_WT_Infected_on_WT_sham.diffexpr.w_symbols.txt
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_WT_infected.diffexpr.w_symbols.txt


title: Tongue WT sham-infected_rep4

description:
deseq/Differential_Expression__DESeq2__compare_2_groups__on_WT_Infected_on_WT_sham.diffexpr.w_symbols.txt
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Sham_on_WT_Sham.diffexpr.w_symbols.txt

value: sham


title: RNAseq,Tam-,E15.5,EC,rep2


title: RNAseq,Tam-,E15.5,EC,rep1


title: Ctrl DCs IgG biol rep 3 [CI 3]

city: Gainesville

first: Duane

last: Mitchell

state: Florida

address: 1333 Center Drive, BSB B1-150

institute: University of Florida

description: CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection. Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.

data_processing:
Sequence reads were trimmed and for adaptor sequence and low quality reads by trimgalore 0.6.5 (--stringency 5)
Bulk RNA seq fastq data was aligned and quantifies using RSEM 1.3.3
Read count extraction and normalization were applied using RSEM 1.3.3
Assembly: gencode.vM24_GRCm38 (mm10)
Supplementary files format and content: Processed .tsv file contains TPM values for each sample

source_name: brain tumor

extract_protocol:
RNA was extracted using Zymo mini/midi RNA extraction kit.
Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.

value: unloaded DCs + IgG ab


title: Tongue WT Candida-infected_rep1


title: NC3

city: Qinhuangdao

first: Dongmei

last: Fan

address: 258 Wenhua Road, Haigang District

country: China

institute: The first hospital of QinHuangdao

data_processing:
Adapter sequence, 5’ segment, 3’ segment, bases with quality <20 and reads with N >10% were trimmed.
Small fragments with length less than 25 bp after quality trimming were discarded.
Hisat2 (version 2.1.0, https://ccb.jhu.edu/software/hisat2/index.shtml) was used to align the clean data after quality control to the human reference genome.
Stringtie (version 1.3.3b, http://ccb.jhu.edu/software/stringtie/) calculates the fragments per kilobase of exon model per million mapped reads (FPKM) value of each gene / transcript in the sample according to the results in Hisat2, and used this value as the expression level of mRNA in the sample.
Assembly: mm39
Supplementary files format and content: salmon_fpkm.csv

growth_protocol: The sequencing samples in this study included C2C12 cell control group (NC group), C2C12 cell high glucose (25 mmol/L) treated group (H group) and C2C12 cell high glucose (25 mmol/L) + liraglutide (200 nmol/L) treated group (H+L group). RNA sequencing was performed to obtain the differentially expressed mRNAs (DEmRNAs).The treatment time of each group was 48h.

extract_protocol:
Total RNA was extracted from cell samples using Trizol kit. Firstly, the mRNA was enriched and fragmented. Then, cDNA synthesis, terminal repair and connector linking were performed.
Polymerase chain reaction (PCR) reaction and product recovery were performed to complete the preparation of the library. Agilent 2100 BioAnalyzer was used to detect library quality. The Illumina HiSeq high-throughput sequencing platform was used to sequence cDNA library.

tag: cell line

value: myoblasts

value: C2C12 cell control group (NC group)


title: Tox3_OPC_3

city: Cleveland

first: Erin

last: Cohn

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University School of Medicine

data_processing:
Salmon was used to align, normalize, and tabulate reads
Assembly: RefSeq mm10
Supplementary files format and content: .txt file represents GENEs and TPMs

source_name: mPSC-derived oligodendrocyte progenitor cells (OPCs)

growth_protocol: OPCs were cultured in DMEM F12 supplemented with N2max, B27, rhNoggin, rhNT3,cAMP, and rhIGF-1

extract_protocol:
Phenol-chloroform with TRIzol
Total RNA submitted to Novogene for library preparation and sequencing
150 paired-end

treatment_protocol: OPCs were plated in differentiation permissive media and allowed to attach for one hour. OPCs were incubated with vehicle (DMSO), cetylpyridinium chloride (Tox1), C12-C14-Alkyl(ethylbenzyl)dimethylammonium chloride (Tox2), or methyltrioctylammonium chloride (Tox3), at their IC75 for 4 hours and collected.

value: methyltrioctylammonium chloride


title: Tox3_OPC_2

value: mPSC-derived oligodendrocyte progenitor cells (OPCs)


title: Tongue WT sham-infected_rep3


title: Tongue WT sham-infected_rep2


title: Tongue WT sham-infected_rep1


title: Tox3_OPC_1


title: NC1


title: Tox2_OPC_3


title: HL3

value: C2C12 cell high glucose (25 mmol/L) + liraglutide (200 nmol/L) treated group (H+L group)


title: HL2


title: Tox2_OPC_1


title: Tox1_OPC_2

value: cetylpyridinium chloride


title: Tox2_OPC_2


title: Tongue WT Candida-infected_rep2


title: Control_OPC_3

value: vehicle (DMSO)


title: Tox1_OPC_1


title: Control_OPC_2


title: spo11-Y135F Mre11-HA6 t5 WCE

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

library_source: genomic

data_processing:
Unaligned bam files were converted to fastq files with the help of SamToFastq (picard v2.20.5). After removal of adapter sequences with cutadapt (-O 1 -e 0.15 -m 15 –max-n 3), read pairs were aligned to both the ASMv1 and the calibration genome CBS138 with NextGenMap (“global”, allowing up to 4% error), in order to get specific alignments from either species.
Aligned read pairs were "filled up" to cover the whole insert length before calculation of the depths per position ("filled dpp") with a custom Java script. Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.cbs138 / IP.cbs138 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M).
For calibration the depth counts were multiplied by the sample-specific calibration factors (see also supplemental file) and rounded to three digits.
Assembly: Reference genome version ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer. SK1; genome version s02-m07-r01 for C. gla. CBS138
Supplementary files format and content: For each ChIP-seq sample, calibrated filled dpp files (chrom, position, depth) are provided.

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: meiotic yeast cells

growth_protocol: S. cer. SK1 cells (experimental strain) were induced to sporulate in 2% potassium acetate supplemented with 0.1% (w/v) polypropylene glycol (PPG) to undergo synchronous meiosis at 30°C by the SPS pre-growth method described in Mendoza et al., Methods Mol Biol. 2009;557:267-83. C. gla. CBS138 cells (calibrating strain) were grown in YPD to reach a density of 0.6 at OD660 (Hu et al., Nucleic Acids Res. 2015).

extract_protocol:
Cells were opened by FastPrep-24™ 5G Instrument (MP Biomedicals) followed by sonication with Bioruptor® Pico instrument. After removing the cell debris, the supernatant was used for the ChIP with anti-HA antibody. To reverse crosslink, all the samples were incubated in 65°C overnight. DNA purification was conducted by regular phenol/chloroform/isoamyl alcohol extraction.
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit according to the manufacturer´s protocol. Amplified library DNA was purified and subjected to 300 bp - 500 bp size selection using Agencourt AMPure XP beads (Beckman Coulter) and quantified by NanoDrop 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.

treatment_protocol: All cells were crosslinked for 15 min in 1 % formaldehyde at room temperature. The formaldehyde was stopped by addition of glycine to 131 mM. For each ChIP, 2x109 S. cer. cells were mixed with 2x108 C. gla. cells which where crosslinked separately. ChIP from meiotic cultures was performed as described in Mendoza et al., Methods Mol Biol. 2009;557:267-83.

value: meiotic yeast cells

value: spo11-Y135F Mre11-HA6


title: Control_OPC_1


title: H2

value: C2C12 cell high glucose (25 mmol/L) treated group (H group)


title: H1


title: HL1


title: H3


title: NC2


title: Dp1Tyb, L21, 3

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
nf-core Nextflow RNAseq pipeline, revision 3.10.1 (https://github.com/nf-core/rnaseq), with STAR aligner and RSEM quantification - all other parameers as default
Assembly: GRCm38, release 95
Supplementary files format and content: tab-delimited text file containing expected counts, TPM, FPKM per gene detected

source_name: heart

extract_protocol:
E13.5 frozen embryonic hearts were placed in lysis buffer and homogenized using a cordless Pellet pestle (Sigma-Aldrich) followed by RNA extraction using RNAeasy micro kit (Qiagen)
polyA enriched libraries usingNEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. An average 25 million pair end reads per library (PE100) were generated on a NovaSeq6000 (Illumina).

treatment_protocol: Pregnant mice were treated daily by oral gavage with 30mg/kg of L21 or Iso-L21 from embryonic day 5.5 to E13.5.

value: heart


title: Dp1Tyb, L21, 4


title: Dp1Tyb, L21, 5


title: Dp1Tyb, L21, 2


title: Dp1Tyb, L21, 1


title: mESCs, stimulated, 6h 0.625 ng/ml FGF4

data_processing:
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: Opposite Strand to Probe; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: Opposite Strand to Probe; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Assembly: GRCm39, release 97
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: All_Probes_TPMs.txt: Contains TPMs per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)

growth_protocol: E14 Fgf4-mutant mESCs were seeded at 45k cells/cm2 were grown in N2B27 + Chiron + LIF for 18 h

extract_protocol:
Trizol-based total RNA extraction
Strand-specific, Poly-A-enriched

treatment_protocol: Stimulation with 0, 0.625, 1.25, 2.5, 5, 10, 20 or 40 ng/ml FGF4 in N2B27 + 1 μg/ml heparin for 6 h

value: 0.625 ng/ml FGF


title: Dp1Tyb, IsoL21, 5


title: Tox1_OPC_3


title: wild type mre11-d663-HA6 t5 WCE

value: wild type mre11-d663-HA6


title: wild type mre11-d676-HA6 t5 WCE

value: wild type mre11-d676-HA6


title: spo11-delta Mre11-HA6 t5 WCE

value: spo11-delta Mre11-HA6


title: wild type untagged t5 WCE

value: wild type untagged


title: wild type Mre11-HA6 t5 WCE

value: wild type Mre11-HA6


title: Dp1Tyb, IsoL21, 4


title: spo11-Y135F Mre11-HA6 t5 HA-ChIP


title: Dp1Tyb, IsoL21, 3


title: wild type mre11-d663-HA6 t5 HA-ChIP


title: wild type  Mre11-HA6 t5 HA-ChIP


title: Dp1Tyb, IsoL21, 2


title: wild type mre11-d676-HA6 t5 HA-ChIP


title: spo11-delta Mre11-HA6 t5 HA-ChIP


title: WT, L21, 5

value: WT


title: wild type untagged t5 HA-ChIP


title: WT, L21, 4


title: WT, L21, 3


title: WT, IsoL21, 5


title: WT, L21, 2


title: 293T-13a-mRuby-NT

city: Guangzhou

first: Lizhen

last: Huang

state: Guangdong

address: xaioguwei street

department: School of Biology and Biological Engineering

institute: South China University of technology

data_processing:
Sequencing data quality assessment was performed using software FastQC (v0.10.1). Cutadapt (version 1.9.1) was used to remove adapter sequences; remove bases whose 5' or 3' end quality value is lower than 20 or contain N; remove sequences whose read length after trim is lower than 75 bp.
Compare and analyze the filtered sequencing CleanData with the reference genome, and use Hisat2 (v2.0.1) software to compare short reads with default parameters.
Gene expression levels in FPKM were quantified using Htseq software (V0.6.1).
Differentially expressed genes were screened using the DESeq2 algorithm. Genes with adjusted P < 0.05 and fold change > 2 were regarded as candidate differential genes.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files includes gene_id, Exonic.gene.sizes, raw counts, Chr, Start, End, Strand, GeneSymbol and Description.
Supplementary files format and content: Tab-delimited text files includes gene_id, fpkms and GeneSymbol.
Supplementary files format and content: Tab-delimited text files includes gene_id, logFC, logCPM, PValue, FDR and GeneSymbol.

organism: Homo sapiens

growth_protocol: HEK293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS; Life Technologies), 100 U/mL penicillin, and 100 µg/mL streptomycin. U87 cells were cultured in DMEM containing 20% FBS, 100 U/mL penicillin, and 100 µg/mL streptomycin. All cells were cultured at 5% CO2 and 37°C.

extract_protocol:
Cells were harvested after 48 hours of transfection, and total RNA was extracted using TRIzol reagent (Invitrogen).
The RNA samples were subsequently sent to GENEWIZ for Illumina sequencing with a 2x150 paired-end (PE) configuration. Before library preparation and sequencing, total RNA integrity was quantified using an Agilent 2100 Bioanalyzer.

treatment_protocol: Transient transfection of cells with plasmids was performed with Lipofectamine 3000 (Invitrgen) according to the manufacturer's instructions.

value: human embryonic kidney cells

value: Cas13a/NT crRNA transfection


title: 293T-13d-mRuby-NT

value: Cas13d/NT crRNA transfection


title: 293T-13d-Fluc-cr4

value: Cas13d/Fluc-cr4 transfection


title: 293T-13a-mRuby-cr2

value: Cas13a/mRuby-cr2 transfection


title: 293T-13a-Fluc-NT


title: WT, IsoL21, 3


title: WT, IsoL21, 4


title: 293T-13a-Fluc-cr4

value: Cas13a/Fluc-cr4 transfection


title: 293T-13d-mRuby-cr2

value: Cas13d/mRuby-cr2 transfection


title: WT, IsoL21, 2


title: U87-13a-mRuby-cr2

source_name: U-87 MG

value: U-87 MG

value: human glioblastoma cells


title: WT, IsoL21, 1

value: heart


title: LN CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 3

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

description:
LN-DKO-14-2_S26
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv

data_processing:
Read quality of sequenced libraries was evaluated with FastQC.
Sequencing reads were aligned to the reference mouse genome assembly GRCm38 using hisat2.
Reads aligned to annotated genes were quantified with featureCounts.
Raw counts normalized with DESEQ2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw gene counts
Supplementary files format and content: csv files include DESEQ2 normalized counts

source_name: Lymph Node

extract_protocol:
OTI cells were sorted from splenocytes and LNs at 7 days post MCMV infection.
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen) according to manufacturer’s instructions. Quality and integrity of total RNA was controlled using 5200 Fragment Analyzer System (Agilent Technologies).
The RNA sequencing libraries were generated using NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol.

value: Lymph Node

value: CD8+ T cell

value: NFAT c1c2 DKO


title: U87-13a-mRuby-NT


title: LN CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 2

description:
LN-DKO-13_S25
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv


title: 293T-13d-Fluc-NT


title: LN CD8+ T cells WT 7 DPI MCMV infection 3

description:
WT-LN-5_S32
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv


title: U87-13a-Fluc-NT


title: U87-13d-mRuby-NT


title: LN CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 1

description:
LN-DKO-12_S24
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv


title: Dp1Tyb, IsoL21, 1


title: U87-13a-Fluc-cr4


title: U87-13d-mRuby-cr2


title: WT, L21, 1


title: U87-13d-Fluc-NT


title: U87-13d-Fluc-cr4


title: SP CD8+ T cells WT 7 DPI MCMV infection 3

description:
WT-SP-5-K_S29
Raw_counts.txt
Normalized_count_spleen.csv

source_name: Spleen

value: Spleen


title: LN CD8+ T cells WT 7 DPI MCMV infection 1

description:
WT-LN-3_S30
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv


title: SP CD8+ T cells WT 7 DPI MCMV infection 2

description:
WT-SP-3-K_S28
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 1

description:
SP-DKO-12-Q_S21
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 2

description:
SP-DKO-13-Q_S22
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc1c2 DKO 7 DPI MCMV infection 3

description:
SP-DKO-14-Q_S23
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc2 KO 7 DPI MCMV infection 2

description:
c2-7-Z_S19
Raw_counts.txt
Normalized_count_spleen.csv

value: NFAT c2 KO


title: SP CD8+ T cells NFATc1 KO 7 DPI MCMV infection 2

description:
c1-2_S15
Raw_counts.txt
Normalized_count_spleen.csv

value: NFAT c1 KO


title: human_DLBCL_region_337

city: Singapore

first: Min

last: Liu

address: 13-02, 14 Medical Drive, Singapore

country: Singapore

institute: National University of Singapore

description: Susan DLBCL TMA B2+tonsil 17-12 right | 047 | CD20

data_processing:
The GeoMx® NGS Pipeline is used to process FASTQ sequencing files from Nanostring GeoMx libraries to produce digital count conversion (.dcc) files. Once complete, all DCC files are packed into a zip file and available to download. This zip file can be uploaded into the GeoMx Digital Spatial Profiler (DSP) system for quality control and normalizaton.
Raw reads were trimmed, stitched, aligned, and deduplicated to transform digital counts data with unique targets. AOIs with fewer than 10,000 raw reads or sequencing saturation <50% were filtered out of the analysis. AOIs with less than 5% of all target genes (18,000+) and target genes that do not achieve the limit of quantitation were removed. The data was then processed with the Q3 normalization method for all the remaining targets. Q3 normalization divides the counts in one segment by the 3rd quartile value for that segment, then subsequently multiplies that value by the geometric mean of the 3rd quartile values of all segments. Q3 normalization rescales the gene expression data such that all segments have similar gene expression ranges. It reduces variance from segment size, segment cellularity, and other technical factors. Underlying the Q3 method is an assumption that, despite biological variation, segments should have similar gene expression count distributions. Thus, Q3 is only appropriate when a probe panel is large and diverse, such as one that targets the full transcriptome.
Assembly: hg38
Supplementary files format and content: The file named processed data (DSP_gene_matrix) showed the genes expression of all DLBCL tissues and 12 tonsil samples, sequencing by illimina hiseq3000.
Supplementary files format and content: The file named processed data2 (DSP_gene_matrix) showed the genes expression of the rest of tonsil samples, sequencing by illimina novaseq 6000.

source_name: DLBCL

extract_protocol:
The slides were incubated with blocking Buffer W (200 μL/slide, NanoString) for 30 min in the humidity chamber at room temperature after hybridization.Each slide was stained with corresponding morophology markers. After immunofluorescent staining, the slides were visualized using the GeoMx® DSP instrument to select regions of interest (ROIs). To acquire representative regions, ROI selection was performed by an expert pathologist. The pathologist was blinded to the group assignment during the ROIs selection. Based on fluorescent staining, each ROI was segmented into corresponding areas of interest (AOIs) - CD68+ regions, CD3+ regions, and CD20+ regions. Subsequently, each AOI was exposed to UV light and photocleaved oligos were aspirated from the solution into the wells of a collection plate.
Collected photocleaved oligos were PCR amplified with the corresponding GeoMx® Seq Code Primer Plate and Master Mix (NanoString). PCR products were pooled and cleaned with AMPure XP beads (Agilent, Santa Clara, California, USA) twice to obtain the libraries. The quality and concentration of libraries were assessed using a high sensitivity DNA Kit (Agilent) and Bioanalyzer. Subsequently, libraries were sequenced on an illumina sequencing platform (Hiseq or NovaSeq) with standard workflow specifications (dual-indexing and paired-end reads (2 × 27 bp)).

value: DLBCL

tag: region cell_type


title: LN CD8+ T cells WT 7 DPI MCMV infection 2

description:
WT-LN-4_S31
Raw_counts.txt
Normalized_count_LN_DKO_WT.csv

value: WT


title: human_RLT_region_476

description: Susan DLBCL TMA B2+tonsil 17-12 right | 046 | CD68

source_name: reactive lympoid tissues

value: reactive lympoid tissues


title: human_RLT_region_474

description: Susan DLBCL TMA B2+tonsil 17-12 right | 045 | CD68


title: human_RLT_region_472

description: Susan DLBCL TMA B2+tonsil 17-12 right | 044 | CD68


title: SP CD8+ T cells NFATc2 KO 7 DPI MCMV infection 1

description:
c2-5-Z_S18
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc2 KO 7 DPI MCMV infection 3

description:
c2-8-Z_S20
Raw_counts.txt
Normalized_count_spleen.csv


title: SP CD8+ T cells NFATc1 KO 7 DPI MCMV infection 3

description:
c1-3_S16
Raw_counts.txt
Normalized_count_spleen.csv


title: human_RLT_region_468

description: Susan DLBCL TMA B2+tonsil 17-12 right | 042 | CD68


title: human_RLT_region_466

description: Susan DLBCL TMA B2+tonsil 17-12 right | 041 | CD68


title: t821-3-LSC

city: Nottingham

first: Sophie

middle: G

last: Kellaway

department: School of Medicine

institute: University of Nottingham

library_source: transcriptomic single cell

data_processing:
Reads from single-cell RNA-Seq experiments were aligned to the human genome (version hg38) and quantified using the count function in CellRanger v6.0.1 from 10x Genomics and using gene models from Ensembl as the reference transcriptome.
Unique Molecular Identifier (UMI) count data was filtered for low quality cells by removing cells with less than 500 and more than 5000 detectable genes. Cells that had more than 20% of UMIs aligned to mitochondrial transcripts were also excluded from further analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated table of cell barcodes, inferred cell type and cell cycle phase
Supplementary files format and content: Supplementary files format and content: HDF5 filtered feature barcode matrix file generated using CellRanger Count

source_name: CD34+CD38- Leukemic stem cells

extract_protocol:
Library generation for scRNA-Seq was performed using the Chromium Single Cell 3' library and gel bead kit v3 (10x Genomics).
Libraries were pair-end sequenced on an Illumina NovaSeq 6000 using the cycle parameters recommended by 10x Genomics

value: CD34+CD38- Leukemic stem cells


title: t821-4-LSC


title: human_RLT_region_470

description: Susan DLBCL TMA B2+tonsil 17-12 right | 043 | CD68


title: t821-4-Blast

source_name: CD34+CD38+ AML blasts

value: CD34+CD38+ AML blasts


title: t821-3-Blast


title: human_RLT_region_465

description: Susan DLBCL TMA B2+tonsil 17-12 right | 040 | CD20


title: SP CD8+ T cells NFATc1 KO 7 DPI MCMV infection 1

description:
c1-1_S14
Raw_counts.txt
Normalized_count_spleen.csv


title: HFD-AT-Macro3

city: Montreal

first: Mike

last: Sapieha

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

data_processing:
Reads were aligned to GRCm38 reference genome using Bowtie2.2.6
PCR duplicates were removed with Picard MarkDuplicates 2.4.1 and reads mapping to mitochondiral DNA were removed.
Deeptools was used to shift reads coordinates to represent the real Tn5 binding site and to remove ENCODE's blacklisted regions (signal artefact regions).
MACS 2.0.10 was used for peak calling using q-value < 0.001 to define peaks
DESeq2 was used to identify DARs (differentially accessible regions).
Genome_build: GRcm38
Supplementary_files_format_and_content: Differentially accessible regions identified by DESeq2

source_name: ATM-specific nuclei from RD-RD mice

growth_protocol: Adult male C57Bl/6J mice were fed a high-fat diet (HFD: 60% lipid content) for 11 weeks and then switched them to a regular diet (RD: 10% lipid content) for 9 weeks to trigger weight loss (HFD-RD mice). Control groups were fed a RD throughout the study (20 weeks; RD-RD mice) or a HFD throughout the study (11weeks; HFD mice).

extract_protocol:
FACS-sorted ATMs were used for ATAC-seq and nuclei were isolated as previously described (Curr Protoc Mol Biol. 2016; 109: 21.29.1–21.29.9). Briefly, isolated cells were centrifuged at 500xg for 5 min at 4°C and then resuspended in ice-cold PBS+0.04% BSA. The cell lysis was performed for 5 minutes on ice by adding 45μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P-40, 0.001% Digitonin, and 1% BSA). After lysis, 50μl ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA) were added and then centrifuged at 500 × g for 5 min at 4 °C. After one more wash, the washed nuclei were counted and used for the transposase reaction.
The library was constructed as cited previously (doi: 10.1002/0471142727.mb2129s109),   using Nextera Tn5 Transposase from Illumina

tag: Stage

value: adult

tag: gender

value: male

tag: diet

value: HFD

value: adipose tissue macrophages


title: human_RLT_region_463

description: Susan DLBCL TMA B2+tonsil 17-12 right | 039 | CD20


title: HFD-AT-Macro1

source_name: ATM-specific nuclei from HFD-RD mice


title: human_RLT_region_464

description: Susan DLBCL TMA B2+tonsil 17-12 right | 040 | CD68


title: HFD-AT-Macro2


title: SP CD8+ T cells WT 7 DPI MCMV infection 1

description:
WT-SP-2-K_S27
Raw_counts.txt
Normalized_count_spleen.csv


title: human_RLT_region_462

description: Susan DLBCL TMA B2+tonsil 17-12 right | 039 | CD68


title: human_RLT_region_461

description: Susan DLBCL TMA B2+tonsil 17-12 right | 038 | CD20


title: RD-RD-AT-Macro2

value: RD-RD


title: RD-RD-AT-Macro1

source_name: ATM-specific nuclei from HFD mice


title: human_RLT_region_460

description: Susan DLBCL TMA B2+tonsil 17-12 right | 038 | CD68


title: human_RLT_region_459

description: Susan DLBCL TMA B2+tonsil 17-12 right | 037 | CD20


title: human_RLT_region_458

description: Susan DLBCL TMA B2+tonsil 17-12 right | 037 | CD68


title: HFD-RD-AT-Macro2

value: HFD-RD


title: human_RLT_region_457

description: Susan DLBCL TMA B2+tonsil 17-12 right | 036 | CD20


title: human_DLBCL_region_287

description: Susan DLBCL TMA B2+tonsil 17-12 right | 017 | CD68


title: human_DLBCL_region_289

description: Susan DLBCL TMA B2+tonsil 17-12 right | 017 | CD20


title: human_DLBCL_region_286

description: Susan DLBCL TMA B2+tonsil 17-12 right | 016 | CD20


title: human_RLT_region_454

description: Susan DLBCL TMA B2+tonsil 17-12 right | 035 | CD68


title: human_DLBCL_region_334

description: Susan DLBCL TMA B2+tonsil 17-12 right | 033 | CD20


title: HFD-RD-AT-Macro1


title: human_DLBCL_region_280

description: Susan DLBCL TMA B2+tonsil 17-12 right | 014 | CD68


title: human_DLBCL_region_284

description: Susan DLBCL TMA B2+tonsil 17-12 right | 016 | CD68


title: human_DLBCL_region_332

description: Susan DLBCL TMA B2+tonsil 17-12 right | 033 | CD68


title: human_DLBCL_region_279

description: Susan DLBCL TMA B2+tonsil 17-12 right | 013 | CD20


title: human_DLBCL_region_330

description: Susan DLBCL TMA B2+tonsil 17-12 right | 032 | CD68


title: human_DLBCL_region_278

description: Susan DLBCL TMA B2+tonsil 17-12 right | 013 | CD68


title: human_DLBCL_region_277

description: Susan DLBCL TMA B2+tonsil 17-12 right | 012 | CD20


title: human_DLBCL_region_335

description: Susan DLBCL TMA B2+tonsil 17-12 right | 034 | CD68


title: human_DLBCL_region_328

description: Susan DLBCL TMA B2+tonsil 17-12 right | 031 | CD68


title: human_DLBCL_region_275

description: Susan DLBCL TMA B2+tonsil 17-12 right | 012 | CD68


title: human_RLT_region_455

description: Susan DLBCL TMA B2+tonsil 17-12 right | 035 | CD20


title: human_RLT_region_456

description: Susan DLBCL TMA B2+tonsil 17-12 right | 036 | CD68


title: human_DLBCL_region_290

description: Susan DLBCL TMA B2+tonsil 17-12 right | 018 | CD68


title: human_DLBCL_region_324

description: Susan DLBCL TMA B2+tonsil 17-12 right | 029 | CD20


title: human_DLBCL_region_283

description: Susan DLBCL TMA B2+tonsil 17-12 right | 015 | CD20


title: human_DLBCL_region_323

description: Susan DLBCL TMA B2+tonsil 17-12 right | 029 | CD68


title: human_DLBCL_region_271

description: Susan DLBCL TMA B2+tonsil 17-12 right | 010 | CD68


title: human_DLBCL_region_272

description: Susan DLBCL TMA B2+tonsil 17-12 right | 011 | CD68


title: human_DLBCL_region_322

description: Susan DLBCL TMA B2+tonsil 17-12 right | 028 | CD20


title: human_DLBCL_region_325

description: Susan DLBCL TMA B2+tonsil 17-12 right | 030 | CD68


title: human_DLBCL_region_282

description: Susan DLBCL TMA B2+tonsil 17-12 right | 014 | CD20


title: human_DLBCL_region_320

description: Susan DLBCL TMA B2+tonsil 17-12 right | 028 | CD68


title: human_DLBCL_region_317

description: Susan DLBCL TMA B2+tonsil 17-12 right | 027 | CD68


title: human_DLBCL_region_267

description: Susan DLBCL TMA B2+tonsil 17-12 right | 008 | CD20


title: human_DLBCL_region_265

description: Susan DLBCL TMA B2+tonsil 17-12 right | 008 | CD68


title: human_DLBCL_region_329

description: Susan DLBCL TMA B2+tonsil 17-12 right | 031 | CD20


title: human_DLBCL_region_316

description: Susan DLBCL TMA B2+tonsil 17-12 right | 026 | CD20


title: human_DLBCL_region_327

description: Susan DLBCL TMA B2+tonsil 17-12 right | 030 | CD20


title: human_DLBCL_region_262

description: Susan DLBCL TMA B2+tonsil 17-12 right | 007 | CD68


title: human_DLBCL_region_314

description: Susan DLBCL TMA B2+tonsil 17-12 right | 026 | CD68


title: human_DLBCL_region_311

description: Susan DLBCL TMA B2+tonsil 17-12 right | 025 | CD68


title: human_DLBCL_region_259

description: Susan DLBCL TMA B2+tonsil 17-12 right | 006 | CD68


title: human_DLBCL_region_261

description: Susan DLBCL TMA B2+tonsil 17-12 right | 006 | CD20


title: human_DLBCL_region_313

description: Susan DLBCL TMA B2+tonsil 17-12 right | 025 | CD20


title: human_DLBCL_region_319

description: Susan DLBCL TMA B2+tonsil 17-12 right | 027 | CD20


title: human_DLBCL_region_274

description: Susan DLBCL TMA B2+tonsil 17-12 right | 011 | CD20


title: human_DLBCL_region_310

description: Susan DLBCL TMA B2+tonsil 17-12 right | 024 | CD20


title: human_DLBCL_region_258

description: Susan DLBCL TMA B2+tonsil 17-12 right | 005 | CD20


title: human_DLBCL_region_256

description: Susan DLBCL TMA B2+tonsil 17-12 right | 004 | CD20


title: human_DLBCL_region_308

description: Susan DLBCL TMA B2+tonsil 17-12 right | 024 | CD68


title: human_DLBCL_region_270

description: Susan DLBCL TMA B2+tonsil 17-12 right | 009 | CD20


title: human_DLBCL_region_305

description: Susan DLBCL TMA B2+tonsil 17-12 right | 023 | CD68


title: human_DLBCL_region_268

description: Susan DLBCL TMA B2+tonsil 17-12 right | 009 | CD68


title: human_DLBCL_region_254

description: Susan DLBCL TMA B2+tonsil 17-12 right | 004 | CD68


title: human_DLBCL_region_302

description: Susan DLBCL TMA B2+tonsil 17-12 right | 022 | CD68


title: human_DLBCL_region_250

description: Susan DLBCL TMA B2+tonsil 17-12 right | 002 | CD20


title: human_DLBCL_region_253

description: Susan DLBCL TMA B2+tonsil 17-12 right | 003 | CD20


title: human_DLBCL_region_299

description: Susan DLBCL TMA B2+tonsil 17-12 right | 021 | CD68


title: human_DLBCL_region_248

description: Susan DLBCL TMA B2+tonsil 17-12 right | 002 | CD68


title: human_DLBCL_region_264

description: Susan DLBCL TMA B2+tonsil 17-12 right | 007 | CD20


title: human_DLBCL_region_247

description: Susan DLBCL TMA B2+tonsil 17-12 right | 001 | CD20


title: human_DLBCL_region_245

description: Susan DLBCL TMA B2+tonsil 17-12 right | 001 | CD68


title: human_DLBCL_region_298

description: Susan DLBCL TMA B2+tonsil 17-12 right | 020 | CD20


title: human_DLBCL_region_296

description: Susan DLBCL TMA B2+tonsil 17-12 right | 020 | CD68


title: human_DLBCL_region_244

description: Susan DLBCL TMA A1+tonsil 17-12 left | 041 | CD20


title: human_DLBCL_region_295

description: Susan DLBCL TMA B2+tonsil 17-12 right | 019 | CD20


title: human_DLBCL_region_293

description: Susan DLBCL TMA B2+tonsil 17-12 right | 019 | CD68


title: human_DLBCL_region_240

description: Susan DLBCL TMA A1+tonsil 17-12 left | 040 | CD68


title: human_DLBCL_region_292

description: Susan DLBCL TMA B2+tonsil 17-12 right | 018 | CD20


title: human_DLBCL_region_242

description: Susan DLBCL TMA A1+tonsil 17-12 left | 041 | CD68


title: human_RLT_region_427

description: TonsilC2+8-1 | 084 | CD68


title: human_DLBCL_region_307

description: Susan DLBCL TMA B2+tonsil 17-12 right | 023 | CD20


title: human_DLBCL_region_235

description: Susan DLBCL TMA A1+tonsil 17-12 left | 038 | CD68


title: human_DLBCL_region_237

description: Susan DLBCL TMA A1+tonsil 17-12 left | 039 | CD68


title: human_RLT_region_425

description: TonsilC2+8-1 | 083 | CD68


title: human_DLBCL_region_239

description: Susan DLBCL TMA A1+tonsil 17-12 left | 039 | CD20


title: human_RLT_region_426

description: TonsilC2+8-1 | 083 | CD20


title: human_DLBCL_region_304

description: Susan DLBCL TMA B2+tonsil 17-12 right | 022 | CD20


title: human_RLT_region_424

description: TonsilC2+8-1 | 082 | CD20


title: human_RLT_region_423

description: TonsilC2+8-1 | 082 | CD68


title: human_DLBCL_region_251

description: Susan DLBCL TMA B2+tonsil 17-12 right | 003 | CD68


title: human_DLBCL_region_301

description: Susan DLBCL TMA B2+tonsil 17-12 right | 021 | CD20


title: human_DLBCL_region_232

description: Susan DLBCL TMA A1+tonsil 17-12 left | 037 | CD68


title: human_DLBCL_region_231

description: Susan DLBCL TMA A1+tonsil 17-12 left | 036 | CD20


title: human_RLT_region_421

description: TonsilC2+8-1 | 081 | CD68


title: human_DLBCL_region_234

description: Susan DLBCL TMA A1+tonsil 17-12 left | 037 | CD20


title: human_DLBCL_region_229

description: Susan DLBCL TMA A1+tonsil 17-12 left | 036 | CD68


title: human_DLBCL_region_226

description: Susan DLBCL TMA A1+tonsil 17-12 left | 035 | CD68


title: human_RLT_region_422

description: TonsilC2+8-1 | 081 | CD20


title: human_RLT_region_420

description: TonsilC2+8-1 | 080 | CD20


title: human_DLBCL_region_225

description: Susan DLBCL TMA A1+tonsil 17-12 left | 034 | CD20


title: human_RLT_region_418

description: TonsilC2+8-1 | 079 | CD20


title: human_DLBCL_region_228

description: Susan DLBCL TMA A1+tonsil 17-12 left | 035 | CD20


title: human_RLT_region_419

description: TonsilC2+8-1 | 080 | CD68


title: human_RLT_region_417

description: TonsilC2+8-1 | 079 | CD68


title: human_DLBCL_region_223

description: Susan DLBCL TMA A1+tonsil 17-12 left | 034 | CD68


title: human_RLT_region_415

description: TonsilC2+8-1 | 078 | CD68


title: human_RLT_region_416

description: TonsilC2+8-1 | 078 | CD20


title: human_DLBCL_region_222

description: Susan DLBCL TMA A1+tonsil 17-12 left | 033 | CD20


title: human_DLBCL_region_220

description: Susan DLBCL TMA A1+tonsil 17-12 left | 033 | CD68


title: human_DLBCL_region_219

description: Susan DLBCL TMA A1+tonsil 17-12 left | 032 | CD20


title: human_DLBCL_region_217

description: Susan DLBCL TMA A1+tonsil 17-12 left | 032 | CD68


title: human_DLBCL_region_214

description: Susan DLBCL TMA A1+tonsil 17-12 left | 031 | CD68


title: human_RLT_region_414

description: TonsilC2+8-1 | 077 | CD20


title: human_RLT_region_410

description: TonsilC2+8-1 | 075 | CD68


title: human_RLT_region_408

description: TonsilC2+8-1 | 074 | CD68


title: human_DLBCL_region_216

description: Susan DLBCL TMA A1+tonsil 17-12 left | 031 | CD20


title: human_RLT_region_412

description: TonsilC2+8-1 | 076 | CD68


title: human_DLBCL_region_213

description: Susan DLBCL TMA A1+tonsil 17-12 left | 030 | CD20


title: human_DLBCL_region_211

description: Susan DLBCL TMA A1+tonsil 17-12 left | 030 | CD68


title: human_RLT_region_406

description: TonsilC2+8-1 | 073 | CD68


title: human_DLBCL_region_204

description: Susan DLBCL TMA A1+tonsil 17-12 left | 027 | CD68


title: human_RLT_region_402

description: TonsilC2+8-1 | 071 | CD68


title: human_DLBCL_region_210

description: Susan DLBCL TMA A1+tonsil 17-12 left | 029 | CD20


title: human_RLT_region_404

description: TonsilC2+8-1 | 072 | CD68


title: human_RLT_region_400

description: TonsilC2+8-1 | 070 | CD68


title: human_RLT_region_392

description: TonsilC2+8-1 | 066 | CD68


title: human_DLBCL_region_197

description: Susan DLBCL TMA A1+tonsil 17-12 left | 024 | CD20


title: human_DLBCL_region_208

description: Susan DLBCL TMA A1+tonsil 17-12 left | 029 | CD68


title: human_RLT_region_394

description: TonsilC2+8-1 | 067 | CD68


title: human_RLT_region_398

description: TonsilC2+8-1 | 069 | CD68


title: human_RLT_region_396

description: TonsilC2+8-1 | 068 | CD68


title: human_DLBCL_region_203

description: Susan DLBCL TMA A1+tonsil 17-12 left | 026 | CD20


title: human_DLBCL_region_194

description: Susan DLBCL TMA A1+tonsil 17-12 left | 023 | CD20


title: human_DLBCL_region_201

description: Susan DLBCL TMA A1+tonsil 17-12 left | 026 | CD68


title: human_RLT_region_386

description: TonsilC2+8-1 | 063 | CD68


title: human_DLBCL_region_191

description: Susan DLBCL TMA A1+tonsil 17-12 left | 022 | CD20


title: human_RLT_region_385

description: TonsilC2+8-1 | 062 | CD20


title: human_RLT_region_390

description: TonsilC2+8-1 | 065 | CD68


title: human_RLT_region_384

description: TonsilC2+8-1 | 062 | CD68


title: human_RLT_region_389

description: TonsilC2+8-1 | 064 | CD20


title: human_DLBCL_region_195

description: Susan DLBCL TMA A1+tonsil 17-12 left | 024 | CD68


title: human_RLT_region_387

description: TonsilC2+8-1 | 063 | CD20


title: human_RLT_region_388

description: TonsilC2+8-1 | 064 | CD68


title: human_RLT_region_383

description: TonsilC2+8-1 | 061 | CD20


title: human_DLBCL_region_189

description: Susan DLBCL TMA A1+tonsil 17-12 left | 022 | CD68


title: human_DLBCL_region_188

description: Susan DLBCL TMA A1+tonsil 17-12 left | 021 | CD20


title: human_RLT_region_382

description: TonsilC2+8-1 | 061 | CD68


title: human_DLBCL_region_198

description: Susan DLBCL TMA A1+tonsil 17-12 left | 025 | CD68


title: human_DLBCL_region_206

description: Susan DLBCL TMA A1+tonsil 17-12 left | 028 | CD68


title: human_RLT_region_381

description: TonsilC2+8-1 | 060 | CD20


title: human_RLT_region_380

description: TonsilC2+8-1 | 060 | CD68


title: human_DLBCL_region_184

description: Susan DLBCL TMA A1+tonsil 17-12 left | 020 | CD68


title: human_DLBCL_region_200

description: Susan DLBCL TMA A1+tonsil 17-12 left | 025 | CD20


title: human_RLT_region_379

description: TonsilC2+8-1 | 059 | CD20


title: human_DLBCL_region_181

description: Susan DLBCL TMA A1+tonsil 17-12 left | 019 | CD68


title: human_DLBCL_region_183

description: Susan DLBCL TMA A1+tonsil 17-12 left | 019 | CD20


title: human_RLT_region_378

description: TonsilC2+8-1 | 059 | CD68


title: human_DLBCL_region_180

description: Susan DLBCL TMA A1+tonsil 17-12 left | 018 | CD20


title: human_RLT_region_377

description: TonsilC2+8-1 | 058 | CD20


title: human_DLBCL_region_192

description: Susan DLBCL TMA A1+tonsil 17-12 left | 023 | CD68


title: human_DLBCL_region_177

description: Susan DLBCL TMA A1+tonsil 17-12 left | 017 | CD20


title: human_DLBCL_region_175

description: Susan DLBCL TMA A1+tonsil 17-12 left | 017 | CD68


title: human_RLT_region_376

description: TonsilC2+8-1 | 058 | CD68


title: human_DLBCL_region_178

description: Susan DLBCL TMA A1+tonsil 17-12 left | 018 | CD68


title: human_RLT_region_375

description: TonsilC2+8-1 | 057 | CD20


title: human_RLT_region_374

description: TonsilC2+8-1 | 057 | CD68


title: human_DLBCL_region_172

description: Susan DLBCL TMA A1+tonsil 17-12 left | 016 | CD68


title: human_DLBCL_region_169

description: Susan DLBCL TMA A1+tonsil 17-12 left | 015 | CD68


title: human_DLBCL_region_171

description: Susan DLBCL TMA A1+tonsil 17-12 left | 015 | CD20


title: human_RLT_region_370

description: TonsilC2+8-1 | 054 | CD68


title: human_RLT_region_371

description: TonsilC2+8-1 | 055 | CD68


title: human_DLBCL_region_174

description: Susan DLBCL TMA A1+tonsil 17-12 left | 016 | CD20


title: human_RLT_region_372

description: TonsilC2+8-1 | 056 | CD68


title: human_DLBCL_region_168

description: Susan DLBCL TMA A1+tonsil 17-12 left | 014 | CD20


title: human_RLT_region_369

description: TonsilC2+8-1 | 053 | CD68


title: human_DLBCL_region_165

description: Susan DLBCL TMA A1+tonsil 17-12 left | 013 | CD20


title: human_RLT_region_367

description: TonsilC2+8-1 | 052 | CD68


title: human_RLT_region_373

description: TonsilC2+8-1 | 056 | CD20


title: human_DLBCL_region_163

description: Susan DLBCL TMA A1+tonsil 17-12 left | 013 | CD68


title: human_DLBCL_region_186

description: Susan DLBCL TMA A1+tonsil 17-12 left | 021 | CD68


title: human_RLT_region_365

description: TonsilC2+8-1 | 051 | CD68


title: human_RLT_region_364

description: TonsilC2+8-1 | 050 | CD20


title: human_DLBCL_region_160

description: Susan DLBCL TMA A1+tonsil 17-12 left | 012 | CD68


title: human_DLBCL_region_159

description: Susan DLBCL TMA A1+tonsil 17-12 left | 011 | CD20


title: human_RLT_region_362

description: TonsilC2+8-1 | 049 | CD20


title: human_RLT_region_363

description: TonsilC2+8-1 | 050 | CD68


title: human_DLBCL_region_166

description: Susan DLBCL TMA A1+tonsil 17-12 left | 014 | CD68


title: human_RLT_region_361

description: TonsilC2+8-1 | 049 | CD68


title: human_DLBCL_region_157

description: Susan DLBCL TMA A1+tonsil 17-12 left | 011 | CD68


title: human_RLT_region_452

description: Susan DLBCL TMA A1+tonsil 17-12 left | 010 | CD68


title: human_RLT_region_450

description: Susan DLBCL TMA A1+tonsil 17-12 left | 009 | CD68


title: human_DLBCL_region_156

description: Susan DLBCL TMA A1+tonsil 17-12 left | 007 | CD20


title: human_RLT_region_358

description: TonsilC2+8-1 | 047 | CD20


title: human_RLT_region_359

description: TonsilC2+8-1 | 048 | CD68


title: human_RLT_region_357

description: TonsilC2+8-1 | 047 | CD68


title: human_RLT_region_356

description: TonsilC2+8-1 | 046 | CD68


title: human_RLT_region_449

description: Susan DLBCL TMA A1+tonsil 17-12 left | 006 | CD20


title: human_RLT_region_448

description: Susan DLBCL TMA A1+tonsil 17-12 left | 006 | CD68


title: human_RLT_region_355

description: TonsilC2+8-1 | 045 | CD68


title: human_RLT_region_447

description: Susan DLBCL TMA A1+tonsil 17-12 left | 005 | CD20


title: human_RLT_region_446

description: Susan DLBCL TMA A1+tonsil 17-12 left | 005 | CD68


title: human_RLT_region_354

description: TonsilC2+8-1 | 044 | CD20


title: human_RLT_region_353

description: TonsilC2+8-1 | 044 | CD68


title: human_RLT_region_352

description: TonsilC2+8-1 | 043 | CD20


title: human_RLT_region_445

description: Susan DLBCL TMA A1+tonsil 17-12 left | 004 | CD20


title: human_DLBCL_region_162

description: Susan DLBCL TMA A1+tonsil 17-12 left | 012 | CD20


title: human_RLT_region_351

description: TonsilC2+8-1 | 042 | CD20


title: human_RLT_region_350

description: TonsilC2+8-1 | 042 | CD68


title: human_RLT_region_443

description: Susan DLBCL TMA A1+tonsil 17-12 left | 003 | CD20


title: human_RLT_region_442

description: Susan DLBCL TMA A1+tonsil 17-12 left | 003 | CD68


title: human_RLT_region_440

description: Susan DLBCL TMA A1+tonsil 17-12 left | 002 | CD68


title: human_RLT_region_441

description: Susan DLBCL TMA A1+tonsil 17-12 left | 002 | CD20


title: human_RLT_region_348

description: TonsilC2+8-1 | 041 | CD68


title: human_RLT_region_360

description: TonsilC2+8-1 | 048 | CD20


title: human_RLT_region_349

description: TonsilC2+8-1 | 041 | CD20


title: human_RLT_region_346

description: TonsilC2+8-1 | 040 | CD68


title: human_RLT_region_439

description: Susan DLBCL TMA A1+tonsil 17-12 left | 001 | CD20


title: human_RLT_region_347

description: TonsilC2+8-1 | 040 | CD20


title: human_RLT_region_345

description: TonsilC2+8-1 | 039 | CD20


title: human_RLT_region_435

description: TonsilC2+8-1 | 088 | CD68


title: human_RLT_region_433

description: TonsilC2+8-1 | 087 | CD68


title: human_RLT_region_438

description: Susan DLBCL TMA A1+tonsil 17-12 left | 001 | CD68


title: human_RLT_region_344

description: TonsilC2+8-1 | 039 | CD68


title: human_RLT_region_343

description: TonsilC2+8-1 | 038 | CD20


title: human_RLT_region_431

description: TonsilC2+8-1 | 086 | CD68


title: human_RLT_region_430

description: TonsilC2+8-1 | 085 | CD20


title: human_RLT_region_342

description: TonsilC2+8-1 | 038 | CD68


title: human_RLT_region_341

description: TonsilC2+8-1 | 037 | CD20


title: human_RLT_region_340

description: TonsilC2+8-1 | 037 | CD68


title: human_RLT_region_444

description: Susan DLBCL TMA A1+tonsil 17-12 left | 004 | CD68


title: human_RLT_region_339

description: TonsilC2+8-1 | 036 | CD20


title: human_RLT_region_428

description: TonsilC2+8-1 | 084 | CD20


title: human_RLT_region_300

description: TonsilC2+8-1 | 017 | CD68


title: human_RLT_region_302

description: TonsilC2+8-1 | 018 | CD68


title: human_RLT_region_336

description: TonsilC2+8-1 | 035 | CD68


title: human_RLT_region_338

description: TonsilC2+8-1 | 036 | CD68


title: human_RLT_region_334

description: TonsilC2+8-1 | 034 | CD68


title: human_RLT_region_298

description: TonsilC2+8-1 | 016 | CD68


title: human_RLT_region_296

description: TonsilC2+8-1 | 015 | CD68


title: human_RLT_region_332

description: TonsilC2+8-1 | 033 | CD68


title: human_RLT_region_294

description: TonsilC2+8-1 | 014 | CD68


title: human_RLT_region_290

description: TonsilC2+8-1 | 012 | CD68


title: human_RLT_region_330

description: TonsilC2+8-1 | 032 | CD68


title: human_RLT_region_291

description: TonsilC2+8-1 | 012 | CD20


title: human_RLT_region_292

description: TonsilC2+8-1 | 013 | CD68


title: human_RLT_region_288

description: TonsilC2+8-1 | 011 | CD68


title: human_RLT_region_289

description: TonsilC2+8-1 | 011 | CD20


title: human_RLT_region_329

description: TonsilC2+8-1 | 031 | CD20


title: human_RLT_region_328

description: TonsilC2+8-1 | 031 | CD68


title: human_RLT_region_327

description: TonsilC2+8-1 | 030 | CD20


title: human_RLT_region_429

description: TonsilC2+8-1 | 085 | CD68


title: human_RLT_region_287

description: TonsilC2+8-1 | 010 | CD20


title: human_RLT_region_325

description: TonsilC2+8-1 | 029 | CD20


title: human_RLT_region_326

description: TonsilC2+8-1 | 030 | CD68


title: human_RLT_region_286

description: TonsilC2+8-1 | 010 | CD68


title: human_RLT_region_324

description: TonsilC2+8-1 | 029 | CD68


title: human_RLT_region_284

description: TonsilC2+8-1 | 009 | CD68


title: human_RLT_region_280

description: TonsilC2+8-1 | 007 | CD68


title: human_RLT_region_282

description: TonsilC2+8-1 | 008 | CD68


title: human_RLT_region_323

description: TonsilC2+8-1 | 028 | CD20


title: human_RLT_region_333

description: TonsilC2+8-1 | 033 | CD20


title: human_RLT_region_322

description: TonsilC2+8-1 | 028 | CD68


title: human_RLT_region_321

description: TonsilC2+8-1 | 027 | CD20


title: human_RLT_region_278

description: TonsilC2+8-1 | 006 | CD68


title: human_RLT_region_331

description: TonsilC2+8-1 | 032 | CD20


title: human_RLT_region_320

description: TonsilC2+8-1 | 027 | CD68


title: human_RLT_region_319

description: TonsilC2+8-1 | 026 | CD20


title: human_RLT_region_276

description: TonsilC2+8-1 | 005 | CD68


title: human_RLT_region_273

description: TonsilC2+8-1 | 003 | CD20


title: human_RLT_region_274

description: TonsilC2+8-1 | 004 | CD68


title: human_RLT_region_272

description: TonsilC2+8-1 | 003 | CD68


title: human_RLT_region_271

description: TonsilC2+8-1 | 002 | CD20


title: human_RLT_region_270

description: TonsilC2+8-1 | 002 | CD68


title: human_RLT_region_316

description: TonsilC2+8-1 | 025 | CD68


title: human_RLT_region_317

description: TonsilC2+8-1 | 025 | CD20


title: human_RLT_region_312

description: TonsilC2+8-1 | 023 | CD68


title: human_RLT_region_268

description: TonsilC2+8-1 | 001 | CD68


title: human_RLT_region_310

description: TonsilC2+8-1 | 022 | CD68


title: human_RLT_region_314

description: TonsilC2+8-1 | 024 | CD68


title: human_RLT_region_269

description: TonsilC2+8-1 | 001 | CD20


title: human_RLT_region_308

description: TonsilC2+8-1 | 021 | CD68


title: human_RLT_region_267

description: 4tonsils + 15-1b | 063 | CD20


title: human_RLT_region_266

description: 4tonsils + 15-1b | 063 | CD68


title: human_RLT_region_265

description: 4tonsils + 15-1b | 062 | CD20


title: human_RLT_region_264

description: 4tonsils + 15-1b | 062 | CD68


title: human_RLT_region_263

description: 4tonsils + 15-1b | 061 | CD20


title: Organoid_line_220523pk_Normoxia_at_establishment_then_switch_to_hypoxia_3_passages_replicate_2

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research

data_processing:
Raw fastq reads for each samples were stitched using UNIX, quality controlled using fastqc (v0.11.9)
adaptor-, poly-A-, and 2 colour-trimmed as paired-end reads using trim_galore (v0.6.5; running python-base v.3.6.10, cutadapt v.2.10, java v.17.0.1, fastqc v.0.11.9, and pigz v.2.4)
Processed fastq results were mapped against the Mus musculus (UCSC/hg38) igenomes STAR index using rna-star (v2.7.10b) using two-pass mapping with quantMode enabled, allowing for soft-clipping (Nmin = 0.2) and splicing (min 20 bp).
Normalisation and differential gene expression analyses were performed as previously described (PMID: 31207090, 31733993, 31595650) using edgeR (v3.40.0) glmQLFTest.
Assembly: hg38
Supplementary files format and content: *.txt - normalised gene expression

source_name: PDAC cT2N2M0, cStageIII (UICC)

growth_protocol: The organoid lines were maintained in Advanced DMEM/F12 (Thermo Fisher Scientific #12634010) supplement with 10mM HEPES (Thermo Fisher Scientific #15630080), 2mM Glutamax (Thermo Fisher Scientific #35050061), 1x Penicillin/Streptomycin (FUJIFILM Wako #168-23191), 1.25 mM N-acetylcysteine (Sigma-Aldrich #A9165), and 0.01 μM gastrin (Sigma-Aldrich #G9145).  Additionally, the medium contained following niche factors: 50 nM mouse recombinant EGF (Thermo Fisher Scientific #PMG8043), 500 nM A83-01 (Tocris #2939), Y-27632 (FUJIFILM Wako #253-00513), 100ng/ml IGF-1 (BioLegend #590904), 100 ng/ml FGF10 (PeproTech #100-26), 100 ng/ml mouse recombinant Noggin (PeproTech #250-38), R-spondin1-conditioned media 10% of the final volume, and Afamin/Wnt3A (#J2-002 MBL)-conditioned media 50% of the final volume. Approximately 2.0E4 cells seeded with 20 µL Matrigel (#356231 BD Biosciences) domes per well on a 48-well plate. The media were changed every 3 or 4 days.

extract_protocol:
Total RNA sample libraries were prepared using (QIAGEN RNeasy Plus Mini Kit #74034) according to manufacturer protocol
Library were prepared and sequenced on NovaSeq6000 using S1 Reagent Kit v1.5 flow cell (200 Cycles).

treatment_protocol: Organoid lines were established directly from clinical specimens surgically resected from patients at University of Tsukuba Hospital (registration number: R01-193) with informed consent after approval by the ethical committees.  Specimens were washed vigorously and minced into 10 mm3-size fragments. The fragments were digested with Liberase TH (Roche life science) at 37℃ for 30min and TrypLE Express Enzyme (Thermo Fisher Scientific #12605020) at 37℃ for 20min. Approximately 2.0E4 cells were seeded in 20 µL Matrigel (BD Biosciences #356231) domes per well on a 48-well plate. Two plates were prepared as described above, one incubated at 20% O2 (normoxia) and the other at 1% O2 (hypoxia). The medium for hypoxia treated plates was preequilibrated in a sealed container with oxygen adsorbent at least 6 hours prior to use.  The media were changed every 3 or 4 days. A total of three passages were performed in medium without EGF for the purpose of enriching pancreatic cancer organoids.  Following establishment and RNA samples collected, lines established under hypoxia were switched to normoxia for three passages and RNA-samples collected. Similarly, lines established under normoxia were also switch to hypoxia for three passages and RNA-samples collected.

value: PDAC cT2N2M0, cStageIII (UICC)

value: Pancreatic ductal adenocarcinoma


title: human_RLT_region_262

description: 4tonsils + 15-1b | 061 | CD68


title: Organoid_line_220523pk_Normoxia_at_establishment_then_switch_to_hypoxia_3_passages_replicate_3


title: human_RLT_region_260

description: 4tonsils + 15-1b | 060 | CD68


title: Organoid_line_220523pk_Normoxia_at_establishment_then_switch_to_hypoxia_3_passages_replicate_1


title: human_RLT_region_256

description: 4tonsils + 15-1b | 058 | CD68


title: Organoid_line_220523pk_Normoxia_at_establishment_replicate_3


title: human_RLT_region_318

description: TonsilC2+8-1 | 026 | CD68


title: human_RLT_region_258

description: 4tonsils + 15-1b | 059 | CD68


title: Organoid_line_220523pk_Normoxia_at_establishment_replicate_2


title: Organoid_line_220523pk_Normoxia_at_establishment_replicate_1


title: Organoid_line_220523pk_Hypoxia_at_establishment_then_switch_to_normoxia_3_passages_replicate_2


title: human_RLT_region_254

description: 4tonsils + 15-1b | 057 | CD68


title: human_RLT_region_250

description: 4tonsils + 15-1b | 055 | CD68


title: Organoid_line_220523pk_Hypoxia_at_establishment_then_switch_to_normoxia_3_passages_replicate_3


title: Organoid_line_220523pk_Hypoxia_at_establishment_then_switch_to_normoxia_3_passages_replicate_1


title: human_RLT_region_249

description: 4tonsils + 15-1b | 054 | CD20


title: human_RLT_region_252

description: 4tonsils + 15-1b | 056 | CD68


title: Organoid_line_220523pk_Hypoxia_at_establishment_replicate_3


title: human_RLT_region_306

description: TonsilC2+8-1 | 020 | CD68


title: human_RLT_region_248

description: 4tonsils + 15-1b | 054 | CD68


title: human_RLT_region_247

description: 4tonsils + 15-1b | 053 | CD20


title: human_RLT_region_304

description: TonsilC2+8-1 | 019 | CD68


title: Organoid_line_220523pk_Hypoxia_at_establishment_replicate_2


title: Organoid_line_220523pk_Hypoxia_at_establishment_replicate_1


title: B1MW092

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

library_source: other

data_processing:
Sequencing reads were trimmed by Trim_galore to remove low-quality nucleotides.
Clean reads were aligned to hg19 reference genome by Bowtie2.
PCR duplicates were removed by Samtools.
Uniquely mapped reads were counted on gene-bodies by FeatureCounts.
Assembly: hg19
Supplementary files format and content: Bigwig files normalized to show RPKM.

molecule: other

source_name: circulating cell-free DNA (cfDNA)

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 10ng cfDNA was used for library construction.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: high-grade serous ovarian cancer (HGSOC)

tag: platinumsensitivity

value: Resistant

tag: chemonaive

value: Y

value: circulating cell-free DNA (cfDNA)


title: B1MW091

value: R


title: human_RLT_region_245

description: 4tonsils + 15-1b | 052 | CD20


title: human_RLT_region_243

description: 4tonsils + 15-1b | 051 | CD20


title: human_RLT_region_244

description: 4tonsils + 15-1b | 052 | CD68


title: B1MW088

value: Intermediate


title: B1MW087

value: N


title: human_RLT_region_242

description: 4tonsils + 15-1b | 051 | CD68

value: reactive lympoid tissues


title: human_RLT_region_241

description: 4tonsils + 15-1b | 050 | CD20


title: B1MW086

value: Sensitive


title: human_RLT_region_240

description: 4tonsils + 15-1b | 050 | CD68


title: B1MW077


title: B1MW090


title: B1MW079


title: human_RLT_region_239

description: 4tonsils + 15-1b | 049 | CD20


title: B1MW076


title: B1MW075


title: human_RLT_region_246

description: 4tonsils + 15-1b | 053 | CD68


title: human_RLT_region_233

description: 4tonsils + 15-1b | 046 | CD20


title: human_RLT_region_236

description: 4tonsils + 15-1b | 048 | CD68


title: human_RLT_region_232

description: 4tonsils + 15-1b | 046 | CD68


title: human_RLT_region_231

description: 4tonsils + 15-1b | 045 | CD20


title: human_RLT_region_234

description: 4tonsils + 15-1b | 047 | CD68


title: human_RLT_region_230

description: 4tonsils + 15-1b | 045 | CD68


title: B1MW063


title: B1MW071


title: B1MW062


title: B1MW060


title: B1MW059


title: B1MW057


title: B1MW056


title: human_RLT_region_226

description: 4tonsils + 15-1b | 043 | CD68


title: B1MW053


title: B1MW052


title: human_RLT_region_225

description: 4tonsils + 15-1b | 042 | CD20


title: human_RLT_region_224

description: 4tonsils + 15-1b | 042 | CD68


title: human_RLT_region_223

description: 4tonsils + 15-1b | 041 | CD20


title: B1MW073


title: human_RLT_region_238

description: 4tonsils + 15-1b | 049 | CD68


title: B1MW048


title: human_RLT_region_222

description: 4tonsils + 15-1b | 041 | CD68


title: human_RLT_region_221

description: 4tonsils + 15-1b | 040 | CD20


title: B1MW047


title: B1MW046


title: B1MW044


title: human_RLT_region_229

description: 4tonsils + 15-1b | 044 | CD20


title: human_RLT_region_218

description: 4tonsils + 15-1b | 039 | CD68


title: human_RLT_region_220

description: 4tonsils + 15-1b | 040 | CD68


title: human_RLT_region_217

description: 4tonsils + 15-1b | 038 | CD20


title: human_RLT_region_219

description: 4tonsils + 15-1b | 039 | CD20


title: human_RLT_region_228

description: 4tonsils + 15-1b | 044 | CD68


title: B1MW038


title: B1MW036


title: human_RLT_region_227

description: 4tonsils + 15-1b | 043 | CD20


title: human_RLT_region_216

description: 4tonsils + 15-1b | 038 | CD68


title: B1MW035


title: human_RLT_region_214

description: 4tonsils + 15-1b | 037 | CD68


title: B1MW034


title: B1MW051


title: human_RLT_region_213

description: 4tonsils + 15-1b | 036 | CD20


title: B1MW026


title: human_RLT_region_211

description: 4tonsils + 15-1b | 035 | CD20


title: B1MW033


title: B1MW022


title: human_RLT_region_210

description: 4tonsils + 15-1b | 035 | CD68


title: B1MW028


title: human_RLT_region_208

description: 4tonsils + 15-1b | 034 | CD68


title: B1MW043


title: B1MW023


title: B1MW020


title: B1MW001


title: B1MW005


title: human_RLT_region_200

description: 4tonsils + 15-1b | 030 | CD68


title: human_RLT_region_204

description: 4tonsils + 15-1b | 032 | CD68


title: human_RLT_region_201

description: 4tonsils + 15-1b | 030 | CD20


title: B1MW006


title: human_RLT_region_215

description: 4tonsils + 15-1b | 037 | CD20


title: human_RLT_region_198

description: 4tonsils + 15-1b | 029 | CD68


title: B3MW083


title: human_RLT_region_212

description: 4tonsils + 15-1b | 036 | CD68


title: human_RLT_region_196

description: 4tonsils + 15-1b | 028 | CD68


title: B3MW078


title: human_RLT_region_197

description: 4tonsils + 15-1b | 028 | CD20


title: B3MW073


title: B3MW088


title: human_RLT_region_194

description: 4tonsils + 15-1b | 027 | CD68


title: B3MW071


title: human_RLT_region_190

description: 4tonsils + 15-1b | 025 | CD68


title: B3MW072


title: B3MW070


title: human_RLT_region_206

description: 4tonsils + 15-1b | 033 | CD68


title: B3MW069


title: human_RLT_region_202

description: 4tonsils + 15-1b | 031 | CD68


title: human_RLT_region_186

description: 4tonsils + 15-1b | 023 | CD68


title: B3MW084


title: human_RLT_region_184

description: 4tonsils + 15-1b | 022 | CD68


title: human_RLT_region_188

description: 4tonsils + 15-1b | 024 | CD68


title: B3MW066


title: B3MW080


title: human_RLT_region_182

description: 4tonsils + 15-1b | 021 | CD68


title: human_RLT_region_199

description: 4tonsils + 15-1b | 029 | CD20


title: B3MW060


title: human_RLT_region_181

description: 4tonsils + 15-1b | 020 | CD20


title: B3MW064


title: B3MW057


title: B3MW056


title: human_RLT_region_183

description: 4tonsils + 15-1b | 021 | CD20


title: human_RLT_region_179

description: 4tonsils + 15-1b | 019 | CD20


title: B3MW052


title: human_RLT_region_178

description: 4tonsils + 15-1b | 019 | CD68


title: B3MW055


title: human_RLT_region_177

description: 4tonsils + 15-1b | 018 | CD20


title: B3MW054


title: human_RLT_region_180

description: 4tonsils + 15-1b | 020 | CD68


title: B3MW049


title: B3MW048


title: B3MW046


title: human_RLT_region_175

description: 4tonsils + 15-1b | 017 | CD20


title: human_RLT_region_176

description: 4tonsils + 15-1b | 018 | CD68


title: B3MW042


title: B3MW043


title: human_RLT_region_172

description: 4tonsils + 15-1b | 016 | CD68


title: B3MW039


title: human_RLT_region_171

description: 4tonsils + 15-1b | 015 | CD20


title: human_RLT_region_170

description: 4tonsils + 15-1b | 015 | CD68


title: B3MW031


title: B3MW032


title: human_RLT_region_168

description: 4tonsils + 15-1b | 014 | CD68


title: human_RLT_region_169

description: 4tonsils + 15-1b | 014 | CD20


title: B3MW026


title: B3MW027


title: human_RLT_region_192

description: 4tonsils + 15-1b | 026 | CD68


title: human_RLT_region_167

description: 4tonsils + 15-1b | 013 | CD20


title: human_RLT_region_166

description: 4tonsils + 15-1b | 013 | CD68


title: B3MW023


title: B3MW016


title: human_RLT_region_163

description: 4tonsils + 15-1b | 011 | CD20


title: human_RLT_region_164

description: 4tonsils + 15-1b | 012 | CD68


title: human_RLT_region_174

description: 4tonsils + 15-1b | 017 | CD68


title: human_RLT_region_162

description: 4tonsils + 15-1b | 011 | CD68


title: B3MW013


title: B3MW018


title: B3MW012


title: B3MW021


title: human_RLT_region_160

description: 4tonsils + 15-1b | 010 | CD68


title: human_RLT_region_161

description: 4tonsils + 15-1b | 010 | CD20


title: human_RLT_region_159

description: 4tonsils + 15-1b | 009 | CD20


title: B3MW009


title: B3MW011


title: human_RLT_region_155

description: 4tonsils + 15-1b | 007 | CD20


title: B4MW088


title: B3MW006


title: B4MW087


title: human_RLT_region_154

description: 4tonsils + 15-1b | 007 | CD68


title: human_RLT_region_157

description: 4tonsils + 15-1b | 008 | CD20


title: B4MW085


title: human_RLT_region_153

description: 4tonsils + 15-1b | 006 | CD20


title: B4MW083


title: human_RLT_region_152

description: 4tonsils + 15-1b | 006 | CD68


title: B4MW082


title: human_RLT_region_165

description: 4tonsils + 15-1b | 012 | CD20


title: human_RLT_region_151

description: 4tonsils + 15-1b | 005 | CD20


title: B4MW080


title: B4MW079


title: B3MW007


title: B4MW072


title: human_RLT_region_150

description: 4tonsils + 15-1b | 005 | CD68


title: human_RLT_region_149

description: 4tonsils + 15-1b | 004 | CD20


title: human_RLT_region_148

description: 4tonsils + 15-1b | 004 | CD68


title: B4MW077


title: human_RLT_region_144

description: 4tonsils + 15-1b | 001 | CD20


title: human_RLT_region_158

description: 4tonsils + 15-1b | 009 | CD68


title: human_RLT_region_143

description: 4tonsils + 15-1b | 001 | CD68


title: B4MW068


title: B4MW076


title: human_DLBCL_region_152

description: Tonsil CD20CD68NGFR|009|CD68

extract_protocol:
The slides were incubated with blocking Buffer W (200 ?L/slide, NanoString) for 30 min in the humidity chamber at room temperature after hybridization.Each slide was stained with corresponding morophology markers. After immunofluorescent staining, the slides were visualized using the GeoMx® DSP instrument to select regions of interest (ROIs). To acquire representative regions, ROI selection was performed by an expert pathologist. The pathologist was blinded to the group assignment during the ROIs selection. Based on fluorescent staining, each ROI was segmented into corresponding areas of interest (AOIs) - CD68+ regions, CD3+ regions, and CD20+ regions. Subsequently, each AOI was exposed to UV light and photocleaved oligos were aspirated from the solution into the wells of a collection plate.
Collected photocleaved oligos were PCR amplified with the corresponding GeoMx® Seq Code Primer Plate and Master Mix (NanoString). PCR products were pooled and cleaned with AMPure XP beads (Agilent, Santa Clara, California, USA) twice to obtain the libraries. The quality and concentration of libraries were assessed using a high sensitivity DNA Kit (Agilent) and Bioanalyzer. Subsequently, libraries were sequenced on an illumina sequencing platform (Hiseq or NovaSeq) with standard workflow specifications (dual-indexing and paired-end reads (2?×?27?bp)).

value: DLBCL


title: human_DLBCL_region_154

description: Tonsil CD20CD68NGFR|011|CD68


title: human_DLBCL_region_151

description: Tonsil CD20CD68NGFR|008|CD68


title: human_RLT_region_156

description: 4tonsils + 15-1b | 008 | CD68


title: human_RLT_region_146

description: 4tonsils + 15-1b | 002 | CD20


title: human_RLT_region_142

description: Tonsil CD20CD68NGFR|006|Full ROI

value: Full ROI


title: B4MW056


title: human_RLT_region_141

description: Tonsil CD20CD68NGFR|005|Full ROI


title: B4MW052


title: B4MW054


title: B4MW060


title: B4MW071


title: human_RLT_region_145

description: 4tonsils + 15-1b | 002 | CD68


title: B4MW049


title: B4MW070


title: B4MW069


title: human_DLBCL_region_155

description: Tonsil CD20CD68NGFR|012|CD68


title: B4MW067


title: human_DLBCL_region_149

description: DLBCL C1|021|CD20


title: human_DLBCL_region_153

description: Tonsil CD20CD68NGFR|010|CD68


title: B4MW044


title: B4MW045


title: B4MW066


title: human_DLBCL_region_144

description: DLBCL C1|020|CD68


title: B2MW088


title: B4MW059


title: human_RLT_region_147

description: 4tonsils + 15-1b | 003 | CD68


title: human_DLBCL_region_150

description: Tonsil CD20CD68NGFR|007|CD68


title: B4MW057


title: human_DLBCL_region_141

description: DLBCL C1|019|CD68


title: human_RLT_region_173

description: 4tonsils + 15-1b | 016 | CD20


title: human_RLT_region_137

description: Tonsil CD20CD68NGFR|001|Full ROI


title: B3MW028


title: B2MW084


title: human_RLT_region_140

description: Tonsil CD20CD68NGFR|004|Full ROI


title: human_RLT_region_139

description: Tonsil CD20CD68NGFR|003|Full ROI


title: B4MW051


title: B2MW083


title: human_DLBCL_region_135

description: DLBCL C1|017|CD68


title: B2MW080


title: human_RLT_region_138

description: Tonsil CD20CD68NGFR|002|Full ROI


title: B4MW050


title: B4MW048


title: human_DLBCL_region_147

description: DLBCL C1|021|CD68


title: cDC, mRNA vaccine, 24h

city: Tsukuba

first: Kenji

last: Kubara

state: Ibaraki

address: Tokodai 5-1-3

department: Tsukuba Research Laboratories

country: Japan

institute: Eisai Co., Ltd.

data_processing:
Raw reads were trimmed for raw quality reads using Trimmomatic.
Reads were mapped to mouse transcriptome annotations and reference genome sequences (Mm10 and Ensembl 84) using STAR.
RSEM was used for estimating gene-level expression reported as transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: Excel file including TPM values for each sample

source_name: Lymph node

extract_protocol:
Total RNA was extracted and purified from the sorted cells (>1000 cells) using an RNeasy micro kit (Qiagen) following the manufacturer’s instructions and converted into cDNA using a SMART-Seq HT kit (Takara).
Sequencing libraries were generated using Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: C57BL/6J mice were injected with mRNA-LNP subcutaneously at the back. After 24 h, brachial lymph nodes were collected, and myeloid cells were sorted by FACS.

value: Lymph node

value: Immune cells

tag: cell subset

value: cDC

value: WT

value: mRNA vaccine


title: human_DLBCL_region_129

description: DLBCL C1|015|CD68


title: human_DLBCL_region_146

description: DLBCL C1|020|CD20


title: B2MW074


title: Monocytes, mRNA vaccine, 24h

value: Monocytes

tag: treatment


title: human_DLBCL_region_143

description: DLBCL C1|019|CD20

tag: tissue


title: human_DLBCL_region_128

description: DLBCL C1|014|CD20


title: Med macrophages, mRNA vaccine, 24h

value: Med macrophages


title: SCS macrophages, mRNA vaccine, 24h

value: SCS macrophages


title: B2MW087

value: high-grade serous ovarian cancer (HGSOC)

value: Y


title: B2MW070

value: circulating cell-free DNA (cfDNA)


title: B2MW086

value: Intermediate


title: human_DLBCL_region_125

description: DLBCL C1|013|CD20


title: B2MW068

value: N


title: human_DLBCL_region_140

description: DLBCL C1|018|CD20


title: Med macrophages, Saline, 24h

value: Saline


title: human_DLBCL_region_123

description: DLBCL C1|013|CD68


title: B2MW067


title: B2MW085

value: Resistant


title: human_DLBCL_region_138

description: DLBCL C1|018|CD68

value: DLBCL


title: human_DLBCL_region_122

description: DLBCL C1|012|CD20


title: pDC, Saline, 24h

value: pDC


title: B2MW065

value: Sensitive


title: human_DLBCL_region_137

description: DLBCL C1|017|CD20


title: human_DLBCL_region_134

description: DLBCL C1|016|CD20


title: human_DLBCL_region_120

description: DLBCL C1|012|CD68


title: macrophage, mfap4 positive/tnfa negative, Salmonella-infected, 4 days, rep 3

city: Montpellier

first: Mai-Eva

last: Nguyen-chi

address: Pl. Eugène Bataillon

country: France

institute: CNRS

data_processing:
production of sequences using software : illumina bcl2fastq  (v 2.20.0.422)
data pre-processing : Image analysis (NovaSeq Control Software) and base calling (Real-Time Analysis 3 software) and demultiplexing (bcl2fastq)  image analysis using NovaSeq Control Software and
Quality control (Sequencing Analysis Viewer) and Contaminant screening (FastQ Screen)  FastQC) and Contaminant screening
Read count extraction and normalization were performed using TopHat2 software v2.1.1, Samtools v1.13
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include geneID| gene symbol and raw counts values for each Sample

organism: Danio rerio

source_name: mfap4positive, tnfa negative

growth_protocol: Tg(mfap4:mCherry-F;tnfa:GFP-F) embryos were maintained in embryo water at 28C during 2 days.

extract_protocol:
Macrophages were sorted by FACS and RNA was harvested using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using kit SMART-Seq v4 Ultra Low Input RNA Kit from Takara and the kit DNA Prep from Illumina following manufacturer's protocols.

treatment_protocol:
At 2 days post-fertilization, Tg(mfap4:mCherry-F;tnfa:GFP-F) embryos were injected in the hind brain ventricule Salmonella Thyphimurium (ATCC14028s strain) or kept intact
Cell dissociation was done at 4 hours post infection and 4 days pos-infection (at 4 dpi, larvae presenting macrophage clusters in the head were selected)

value: mfap4positive, tnfa negative

value: macrophage

value: Salmonella-infected

tag: time

value: 4 days


title: B2MW079


title: human_DLBCL_region_132

description: DLBCL C1|016|CD68


title: macrophage, mfap4 positive/tnfa negative, Salmonella-infected, 4 days, rep 2

tag: cell type


title: human_DLBCL_region_119

description: DLBCL C1|011|CD20


title: B2MW063

value: R


title: human_DLBCL_region_131

description: DLBCL C1|015|CD20


title: B2MW077


title: human_DLBCL_region_117

description: DLBCL C1|011|CD68


title: pDC, mRNA vaccine, 24h

value: Lymph node

value: Immune cells

tag: genotype

value: WT

value: mRNA vaccine


title: B2MW076

value: high-grade serous ovarian cancer (HGSOC)

value: circulating cell-free DNA (cfDNA)


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 days, rep 1

value: non-infected


title: Neutrophils, mRNA vaccine, 24h

tag: strain

value: Neutrophils


title: B2MW073

value: Resistant

value: N


title: human_DLBCL_region_126

description: DLBCL C1|014|CD68

value: DLBCL


title: B2MW058

value: Sensitive

value: Y


title: macrophage, mfap4 positive/tnfa positive, Salmonella-infected, 4 hours, rep 1

source_name: mfap4 positive, tnfa positive

value: mfap4 positive, tnfa positive

value: macrophage

value: 4 hours


title: cDC, Saline, 24h

value: cDC

value: Saline


title: SCS macrophages, Saline, 24h

value: Lymph node

value: Immune cells

value: SCS macrophages


title: Neutrophils, Saline, 24h

value: WT


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 hours, rep 4

value: mfap4positive, tnfa negative


title: human_DLBCL_region_113

description: DLBCL C1|009|CD20


title: macrophage, mfap4 positive/tnfa negative, Salmonella-infected, 4 days, rep 1

value: Salmonella-infected

value: 4 days


title: macrophage, mfap4 positive/tnfa negative, Salmonella-infected, 4 days, rep 4


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 hours, rep 1

value: non-infected


title: B2MW045

value: high-grade serous ovarian cancer (HGSOC)

value: circulating cell-free DNA (cfDNA)


title: B2MW048

value: Sensitive


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 hours, rep 2


title: Monocytes, Saline, 24h

value: Monocytes


title: B2MW064

value: Y


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 days, rep 2

value: macrophage


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 days, rep 3


title: B2MW059


title: macrophage, mfap4 positive/tnfa positive, Salmonella-infected, 4 hours, rep 4

value: mfap4 positive, tnfa positive

value: 4 hours


title: human_DLBCL_region_116

description: DLBCL C1|010|CD20

value: DLBCL


title: human_DLBCL_region_108

description: DLBCL C1|008|CD68


title: macrophage, mfap4 positive/tnfa positive, Salmonella-infected, 4 hours, rep 2


title: macrophage, mfap4 positive/tnfa positive, Salmonella-infected, 4 hours, rep 3


title: human_DLBCL_region_111

description: DLBCL C1|009|CD68


title: human_RLT_region_130

description: Tonsil1+2 CD3CD20CD68|040|CD20

value: reactive lympoid tissues


title: human_DLBCL_region_114

description: DLBCL C1|010|CD68


title: B2MW049

value: Resistant


title: macrophage, mfap4 positive/tnfa negative, non-infected, 4 hours, rep 3


title: CD14+ monocytes, 10 μM DG40:6, 2

city: Amsterdam

first: Jeffrey

last: Kroon

address: Meibergdreef 9

department: Experimental Vascular Medicine

country: Netherlands

institute: Amsterdam UMC

data_processing:
Library construction, quality control and sequencing were performed at Novogene. In brief, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library19. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on a HiSeq instrument (Illumina) with 150-bp paired-end reads and 10 G data per sample. Obtained reads were processed through in-house perl scripts at Novogene and were aligned to the human genome using Hisat2 v2.0.5. Then reads were counted with featureCounts v1.5.0-p320.
Assembly: hg38
Supplementary files format and content: comma delimited text file includes raw counts for each Sample

source_name: Primary monocytes

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats (Sanquin, Amsterdam, Netherlands) by Ficoll density gradient centrifugations (Axis-Shield) as described previously. In brief, after washing PBMC fraction, CD14+ monocytes were isolated using human CD14 magnetic beads and MACS® cell separation columns according to the manufacturer’s instructions (Miltenyi Biotec, Leiden, The Netherlands). All experiments were conducted in RPMI 1640 (Gibco) supplemented with Glutamax, penicillin and streptomycin.

extract_protocol:
Human monocytes were lysed using TriPure Isolation Reagent (Roche, Basel, Switzerland) and stored at -80 prior to RNA isolation. RNA was isolated according to the manufacturer’s instructions, and the quality was determined using Lab-on-a-Chip RNA 6000 Nano on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).
Library construction, quality control and sequencing were performed at Novogene. In brief, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on a HiSeq instrument (Illumina) with 150-bp paired-end reads and 10 G data per sample. Obtained reads were processed through in-house perl scripts at Novogene and were aligned to the human genome using Hisat2 v2.0.5. Then reads were counted with featureCounts v1.5.0-p3.

treatment_protocol: CD14+ monocytes were stimulated with DMSO or 10 μM DG(40:6), DG(38:4) or LPA for 4 hours for RNA sequencing.

tag: individual

value: healthy donors

value: Primary monocytes

value: CD14+ monocytes


title: human_DLBCL_region_110

description: DLBCL C1|008|CD20


title: CD14+ monocytes, Unstimulated, 4

value: WT

value: t=4 hr Unstimulated


title: B2MW044


title: CD14+ monocytes, Unstimulated, 3


title: CD14+ monocytes, 10 μM DG40:6, 3


title: CD14+ monocytes, Unstimulated, 2


title: human_DLBCL_region_107

description: DLBCL C1|007|CD20


title: CD14+ monocytes, 10 μM LPA, 2

value: t=4 hr 10 μM LPA


title: CD14+ monocytes, 10 μM LPA, 3


title: CD14+ monocytes, 10 μM LPA, 1


title: CD14+ monocytes, 10 μM DG38:4, 3


title: CD14+ monocytes, Unstimulated, 1


title: human_RLT_region_127

description: Tonsil1+2 CD3CD20CD68|036|CD20


title: CD14+ monocytes, 10 μM DG38:4, 2


title: CD14+ monocytes, 10 μM DG40:6, 1


title: human_RLT_region_128

description: Tonsil1+2 CD3CD20CD68|037|CD20


title: CD14+ monocytes, 10 μM DG38:4, 1


title: human_RLT_region_129

description: Tonsil1+2 CD3CD20CD68|038|CD20


title: human_DLBCL_region_99

description: DLBCL C1|005|CD68


title: human_DLBCL_region_105

description: DLBCL C1|007|CD68


title: CD14+ monocytes, DMSO control, LPA, 3

value: t=4 hr DMSO


title: CD14+ monocytes, DMSO control, LPA, 2


title: human_RLT_region_126

description: Tonsil1+2 CD3CD20CD68|036|CD68


title: human_DLBCL_region_102

description: DLBCL C1|006|CD68


title: CD14+ monocytes, DMSO control, LPA, 1


title: CD14+ monocytes, DMSO control, 6


title: human_RLT_region_123

description: Tonsil1+2 CD3CD20CD68|033|CD20


title: human_RLT_region_125

description: Tonsil1+2 CD3CD20CD68|035|CD20


title: human_RLT_region_122

description: Tonsil1+2 CD3CD20CD68|033|CD68


title: B4MW062

value: high-grade serous ovarian cancer (HGSOC)

value: Intermediate

value: R

value: circulating cell-free DNA (cfDNA)


title: human_DLBCL_region_97

description:
For this template control, it is only for quality control when we run it on the GeoMx DSP instrument. It will not be converted in processed file .
No Template Control 2

value: template control


title: human_RLT_region_124

description: Tonsil1+2 CD3CD20CD68|034|CD20


title: CD14+ monocytes, DMSO control, 4


title: human_DLBCL_region_104

description: DLBCL C1|006|CD20


title: CD14+ monocytes, DMSO control, 3


title: CD14+ monocytes, DMSO control, 1


title: human_DLBCL_region_101

description: DLBCL C1|005|CD20


title: CD14+ monocytes, DMSO control, 5


title: LAN757A20

description: DS

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCh38 Ensembl release 89
Supplementary_files_format_and_content: table of normalized counts per gene  per sample obtained from DESeq

source_name: Heart

extract_protocol: samples were obtained and snap frozen and kept at -80C. Samples were lysed (buffer RLT Qiagen Rneasy Maxi kit) and homogenised using Macs Milteni M tubes and gentleMACS dissociator followed by RNA extraction using Qiagen Rneasy Maxi kit following the standard protocol

tag: developmental stage

value: 14 pcw

tag: Sex

value: female

tag: number of chromosomes

value: 47 chromosomes


title: human_RLT_region_121

description: Tonsil1+2 CD3CD20CD68|032|CD20

value: reactive lympoid tissues

tag: region cell_type


title: LAN757A19

description: DS

value: male


title: human_DLBCL_region_94

description: DLBCL C1|003|CD20

value: DLBCL


title: LAN757A16

description: DS


title: human_RLT_region_120

description: Tonsil1+2 CD3CD20CD68|031|CD20


title: human_DLBCL_region_92

description: DLBCL C1|003|CD68


title: LAN757A12

description: DS

value: 13 pcw


title: human_DLBCL_region_91

description: DLBCL C1|002|CD20


title: LAN757A18

description: control

value: 46 chromosomes


title: LAN757A15

description: DS


title: human_RLT_region_116

description: Tonsil1+2 CD3CD20CD68|027|CD20


title: human_DLBCL_region_98

description: DLBCL C1|004|CD20


title: human_DLBCL_region_95

description: DLBCL C1|004|CD68


title: human_RLT_region_115

description: Tonsil1+2 CD3CD20CD68|027|CD68


title: LAN757A14

description: control


title: LAN757A17

description: control


title: human_DLBCL_region_89

description: DLBCL C1|002|CD68


title: CD14+ monocytes, DMSO control, 2

value: healthy donors

tag: cell line

value: Primary monocytes

value: CD14+ monocytes

value: WT


title: LAN757A13

description: control


title: human_RLT_region_113

description: Tonsil1+2 CD3CD20CD68|025|CD20


title: LAN757A11

description: control


title: human_DLBCL_region_88

description: DLBCL C1|001|CD20


title: human_RLT_region_112

description: Tonsil1+2 CD3CD20CD68|025|CD68


title: human_DLBCL_region_86

description: DLBCL C1|001|CD68


title: MPN

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

description: FACS-sorted c-kit+ BM cells  (Lin-cKit+Sca1-c-kit+)

data_processing:
Raw data  of fastq format were  processed via in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher).
The RNA sequencing libraries were prepared following standard Illumina protocols.

treatment_protocol: The c-kit+ BM cells were isolated from Gadd45g-deficient mice with MPNs and Ctrl mice.

value: Bone marrow cells

value: c-kit+ BM cells

value: Heterozygous Gadd45g knockout


title: MPN_Ctrl

value: wild type


title: human_RLT_region_110

description: Tonsil1+2 CD3CD20CD68|024|CD68


title: human_DLBCL_region_85

description: DLBCL B2|015|CD20


title: human_RLT_region_111

description: Tonsil1+2 CD3CD20CD68|024|CD20


title: LAN207A7

description: control

data_processing:
Cellranger-2.1.1 was used to deconvolve, align and quantify the per-cell transcriptomes.
Reads were aligned to mouse mm10-1.2.0 (obtained from 10x genomics)
Genome_build: mouse mm10 (mm10-1.2.0 from 10x Genomics)
Supplementary_files_format_and_content: tar file containing 10x counts matrix, features and barcode data from filtered cell ranger outputs

extract_protocol:
Hearts were dissected and dissociated into single cell suspensions using the Neonatal Heart Dissociation kit (Miltenyi Biotech) and gentleMACS Octo Dissociator (Miltenyi Biotech) with gentle MACS C tubes and were subsequently methanol-fixed and stored at -80C.
libraries were prepared with the 10x Chromium 3’ mRNA-Seq kit version 2.  The cells were QC’d with trypan blue viability dye and quantified using the EVE automated cell counter.  Approximately 2000 – 3000 cells were loaded onto the 10x and prepared according to manufacturer’s instructions.


title: human_RLT_region_109

description: Tonsil1+2 CD3CD20CD68|023|CD20


title: human_DLBCL_region_80

description: DLBCL B2|014|CD68


title: human_DLBCL_region_82

description: DLBCL B2|014|CD20


title: LAN207A6

description: rescue


title: human_DLBCL_region_83

description: DLBCL B2|015|CD68


title: human_RLT_region_108

description: Tonsil1+2 CD3CD20CD68|023|CD68


title: LAN207A5

description: rescue


title: JC2307 (DccrM Ptac-ccrM) ATGN+IPTG replicate C

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

data_processing:
bcl2fastq2 Conversion Software (version 2.20, Illumina)
reads mapping on ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1)
reads were filtered for low complexity with reaper (v. 15-065)
reads genome mapping with STAR 42 (v. 23 2.5.3a)
number of read counts per gene locus was summarized with htseq-count 43 (v.0.9.1)
Assembly: Agrobacterium fabrum C58 ASM9202v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Agrobacterium tumefaciens

growth_protocol: Cells were cultivated exponentially for 7 hours in ATGN medium +/-IPTG 1mM.

extract_protocol:
Cells were pelleted from 1-2mL of bacterial cultures and immediately frozen in liquid nitrogen prior to conservation at -80°C. RNA were extracted using an RNeasy Mini-Kit from Qiagen and following the manufacturer’s protocol and including a DNase I (RNase-free DNases set from Qiagen) treatment. Samples were additionally treated with a TURBO DNA-free kit from Invitrogen following the manufacturer’s protocol.
RNA-seq libraries were prepared from 800 ng of total RNA with the TruSeq Stranded mRNA Prep reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on the Sciclone liquid handling robot (PerkinElmer). The polyA selection step was replaced by an rRNA depletion step with the QIAseq FastSelect - 5S/16S/23S bacterial rRNA removal kit (Qiagen).

value: DccrM Ptac-ccrM

value: ATGN + IPTG


title: JC2307 (DccrM Ptac-ccrM) ATGN-IPTG replicate A

value: ATGN - IPTG


title: JC2307 (DccrM Ptac-ccrM) ATGN-IPTG replicate C


title: JC2307 (DccrM Ptac-ccrM) ATGN-IPTG replicate B


title: JC2307 (DccrM Ptac-ccrM) ATGN+IPTG replicate B


title: LAN207A1

description: control


title: LAN207A3

description: DS


title: JC2140 (WT) ATGN-IPTG replicate C


title: JC2140 (WT) ATGN-IPTG replicate B


title: human_RLT_region_106

description: Tonsil1+2 CD3CD20CD68|022|CD68


title: human_DLBCL_region_77

description: DLBCL B2|013|CD68


title: JC2307 (DccrM Ptac-ccrM) ATGN+IPTG replicate A


title: human_DLBCL_region_76

description: DLBCL B2|012|CD20


title: human_RLT_region_107

description: Tonsil1+2 CD3CD20CD68|022|CD20


title: human_RLT_region_103

description: Tonsil1+2 CD3CD20CD68|019|CD20


title: LAN233A20

description: DS model no heart defects

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 86
Supplementary_files_format_and_content: table of normalized counts per gene  per sample obtained from DESeq

extract_protocol:
Hearts were dissected and snap frozen and kept at -80C. Samples were lysed (buffer RLT Qiagen RNeasy Minikit) and homogenised using a battery-operated pestle motor mixer followed by RNA extraction using Qiagen RNeasy Mini kit using the standard protocol.
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 4000  following manufacturer's protocols.


title: LAN233A19

description: control


title: human_DLBCL_region_74

description: DLBCL B2|012|CD68


title: human_RLT_region_105

description: Tonsil1+2 CD3CD20CD68|021|CD20


title: LAN233A18

description: DS model no heart defects


title: LAN233A16

description: DS model no heart defects


title: human_DLBCL_region_71

description: DLBCL B2|011|CD68


title: human_RLT_region_102

description: Tonsil1+2 CD3CD20CD68|019|CD68


title: human_DLBCL_region_73

description: DLBCL B2|011|CD20


title: human_DLBCL_region_79

description: DLBCL B2|013|CD20


title: LAN233A17

description: control


title: LAN233A15

description: control


title: human_RLT_region_101

description: Tonsil1+2 CD3CD20CD68|018|CD20


title: human_RLT_region_99

description: Tonsil1+2 CD3CD20CD68|017|CD68


title: human_DLBCL_region_68

description: DLBCL B2|010|CD68


title: human_RLT_region_98

description: Tonsil1+2 CD3CD20CD68|016|CD20


title: human_DLBCL_region_65

description: DLBCL B2|009|CD68


title: human_RLT_region_97

description: Tonsil1+2 CD3CD20CD68|016|CD68


title: LAN233A14

description: DS model heart defects


title: LAN233A13

description: control


title: human_DLBCL_region_64

description: DLBCL B2|008|CD20


title: human_RLT_region_96

description: Tonsil1+2 CD3CD20CD68|015|CD20


title: human_RLT_region_100

description: Tonsil1+2 CD3CD20CD68|017|CD20


title: LAN233A12

description: DS model heart defects


title: human_DLBCL_region_70

description: DLBCL B2|010|CD20


title: JC2140 (WT) ATGN-IPTG replicate A


title: human_RLT_region_95

description: Tonsil1+2 CD3CD20CD68|015|CD68


title: human_DLBCL_region_59

description: DLBCL B2|007|CD68


title: human_DLBCL_region_62

description: DLBCL B2|008|CD68


title: LAN233A10

description: DS model heart defects


title: human_RLT_region_92

description: Tonsil1+2 CD3CD20CD68|013|CD20


title: LAN233A11

description: control


title: LAN233A9

description: control


title: human_RLT_region_93

description: Tonsil1+2 CD3CD20CD68|014|CD68


title: human_DLBCL_region_58

description: DLBCL B2|006|CD20


title: LAN233A8

description: DS model heart defects


title: human_RLT_region_90

description: Tonsil1+2 CD3CD20CD68|012|CD20


title: human_RLT_region_91

description: Tonsil1+2 CD3CD20CD68|013|CD68


title: LAN233A7

description: control


title: human_RLT_region_89

description: Tonsil1+2 CD3CD20CD68|012|CD68


title: human_DLBCL_region_67

description: DLBCL B2|009|CD20


title: human_DLBCL_region_56

description: DLBCL B2|006|CD68


title: human_DLBCL_region_55

description: DLBCL B2|005|CD20


title: human_RLT_region_88

description: Tonsil1+2 CD3CD20CD68|011|CD20


title: LAN233A6

description: DS model heart defects


title: human_DLBCL_region_53

description: DLBCL B2|005|CD68


title: human_RLT_region_87

description: Tonsil1+2 CD3CD20CD68|011|CD68


title: LAN233A5

description: control


title: human_DLBCL_region_52

description: DLBCL B2|004|CD20


title: human_DLBCL_region_50

description: DLBCL B2|004|CD68


title: human_RLT_region_84

description: Tonsil1+2 CD3CD20CD68|008|CD20


title: human_DLBCL_region_61

description: DLBCL B2|007|CD20


title: LAN233A4

description: DS model heart defects


title: human_RLT_region_83

description: Tonsil1+2 CD3CD20CD68|008|CD68


title: LAN233A3

description: control


title: LAN233A1

description: control