title: [2nd exp] alveolar macrophages, Printex90, non-overload, biol rep1


title: [2nd exp] alveolar macrophages, Printex90, non-overload, biol rep2

status: Public on Apr 30 2025

type: SRA

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

library_source: transcriptomic

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Rattus_norvegicus.Rnor_6.0.cdna.all.fa file.
Assembly: Rattus_norvegicus.Rnor_6.0.cdna.all.fa
Supplementary files format and content: excell file with the counts matrix

molecule: total RNA

organism: Rattus norvegicus

source_name: Primary alveolar macrophages

growth_protocol: Primary alveolar macrophages were maintained during 5 days in DMEM supplemented with 10% fetal bovine serum (FBS) and 1 % antibiotic-antimycotic (AA) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Residual DNA was removed by on-column DNase digestion using the RNAse-Free DNase Set (Qiagen)
The Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

treatment_protocol: Cells were exposed during 4 days to control, non-overload or overload conditions of G1-1, Printex90, G3-1 or Bayertitan particles

tag: cell type

value: Primary alveolar macrophages

tag: strain

value: F344/HanZtmRj rats

tag: Sex

value: Male

tag: treatment

tag: time

value: 4 days


title: [2nd exp] alveolar macrophages, Printex90, control, biol rep3


title: [2nd exp] alveolar macrophages, Printex90, control, biol rep2


title: [2nd exp] alveolar macrophages, Printex90, control, biol rep1


title: [2nd exp] alveolar macrophages, G1-1, overload, biol rep2


title: [2nd exp] alveolar macrophages, G1-1, overload, biol rep1


title: [2nd exp] alveolar macrophages, Printex90, overload, biol rep1


title: [2nd exp] alveolar macrophages, G1-1, non-overload, biol rep3


title: [2nd exp] alveolar macrophages, G1-1, non-overload, biol rep1


title: [2nd exp] alveolar macrophages, G1-1, non-overload, biol rep2


title: [2nd exp] alveolar macrophages, G3-1, non-overload, biol rep2


title: [2nd exp] alveolar macrophages, G1-1, control, biol rep3


title: [2nd exp] alveolar macrophages, Printex90, overload, biol rep3


title: [2nd exp] alveolar macrophages, G1-1, control, biol rep2


title: [2nd exp] alveolar macrophages, G1-1, control, biol rep1


title: alveolar macrophages, Bayertitan, overload, biol rep2

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Rattus_norvegicus.Rnor_6.0.cdna.all.fa file.
Assembly: Rattus_norvegicus.Rnor_6.0.cdna.all.fa
Supplementary files format and content: Excel file with the counts matrix

extract_protocol:
RNA was isolated by liquid-phase separation with TriPure Isolation Reagent according to manufacturer’s instructions (Roche).
The Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

value: F344 rats

value: Bayertitan

tag: condition

value: overload


title: alveolar macrophages, Bayertitan, overload, biol rep1


title: alveolar macrophages, Bayertitan, non-overload, biol rep2

value: non-overload


title: [2nd exp] alveolar macrophages, Printex90, non-overload, biol rep3


title: alveolar macrophages, Bayertitan, non-overload, biol rep1


title: alveolar macrophages, Bayertitan, control, biol rep2

value: control


title: alveolar macrophages, Bayertitan, control, biol rep1


title: alveolar macrophages, Bayertitan, control, biol rep3


title: [2nd exp] alveolar macrophages, G1-1, overload, biol rep3


title: alveolar macrophages, G3-1, non-overload, biol rep2


title: alveolar macrophages, G3-1, overload, biol rep3


title: alveolar macrophages, G3-1, non-overload, biol rep1


title: alveolar macrophages, G3-1, control, biol rep2


title: alveolar macrophages, G3-1, control, biol rep3


title: alveolar macrophages, G3-1, control, biol rep1


title: alveolar macrophages, G3-1, overload, biol rep1


title: alveolar macrophages, G3-1, overload, biol rep2


title: alveolar macrophages, G3-1, non-overload, biol rep3


title: alveolar macrophages, Printex90, overload, biol rep3


title: alveolar macrophages, Printex90, overload, biol rep2


title: alveolar macrophages, Printex90, non-overload, biol rep2


title: alveolar macrophages, Bayertitan, overload, biol rep3


title: alveolar macrophages, Printex90, overload, biol rep1


title: alveolar macrophages, Printex90, non-overload, biol rep1


title: alveolar macrophages, Printex90, control, biol rep1


title: alveolar macrophages, Printex90, control, biol rep3


title: alveolar macrophages, G1-1, overload, biol rep3


title: alveolar macrophages, Bayertitan, non-overload, biol rep3


title: alveolar macrophages, Printex90, control, biol rep2


title: alveolar macrophages, Printex90, non-overload, biol rep3


title: alveolar macrophages, G1-1, non-overload, biol rep3


title: alveolar macrophages, G1-1, overload, biol rep1


title: alveolar macrophages, G1-1, non-overload, biol rep2


title: alveolar macrophages, G1-1, control, biol rep2


title: alveolar macrophages, G1-1, control, biol rep3


title: alveolar macrophages, G1-1, non-overload, biol rep1


title: alveolar macrophages, G1-1, control, biol rep1


title: octr-1_old_25C_rep5

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

country: USA

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.20 was used to convert base-calling files to fastq files and to trim adaptors.
HISAT2 v2.2.1 was used for alignment
featureCounts (from Subrea v2.0.1) was used to quantify genes and transcripts.
DESeq2 v1.31.16 was used for differential gene expression analysis.
Assembly: UCSC ce10
Supplementary files format and content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were cultured at 15⁰C, 20⁰C, or 25⁰C and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: C. elegans were cultured at 15⁰C, 20⁰C, or 25⁰C and collected at the young-adult stage as well as at an old age (Days 24, 14, and 9 of adulthood under 15⁰C, 20⁰C, and 25⁰C, respectively).   .

tag: tissue

value: whole animal

tag: cell line

tag: genotype


title: octr-1_old_25C_rep2


title: octr-1_old_25C_rep1


title: octr-1_old_25C_rep3


title: octr-1_old_15C_rep3


title: octr-1_old_15C_rep4


title: alveolar macrophages, G1-1, overload, biol rep2


title: octr-1_old_15C_rep2


title: octr-1_old_25C_rep4


title: octr-1_old_15C_rep5


title: octr-1_old_20C_repl3


title: octr-1_old_20C_repl2


title: octr-1_old_20C_repl4


title: octr-1_old_20C_repl5


title: octr-1_young_20C_rep5


title: octr-1_old_20C_repl1


title: octr-1_young_20C_rep4


title: octr-1_young_20C_rep3


title: octr-1_young_20C_rep1


title: octr-1_young_20C_rep2


title: WT_old_25C_rep5

value: wild-type N2


title: WT_old_25C_rep4


title: WT_old_25C_rep2


title: WT_old_25C_rep1


title: WT_old_25C_rep3


title: WT_old_15C_rep3


title: WT_old_15C_rep4


title: WT_old_15C_rep2


title: WT_old_15C_rep5


title: WT_old_15C_rep1


title: octr-1_old_15C_rep1


title: WT_old_20C_rep4


title: WT_old_20C_rep1


title: WT_Young_20C_rep5


title: WT_Young_20C_rep4


title: WT_old_20C_rep2


title: WT_old_20C_rep5


title: WT_Young_20C_rep3


title: WT_Young_20C_rep1


title: WT_old_20C_rep3


title: WT_Young_20C_rep2


title: Rv0042c IDAPSeq: 300nM protein, replicate 2

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description: Library name: s4_300nM_42c

library_source: genomic

data_processing:
See publication for complete details. Reads were mapped with bowtie2 to a H37Rv reference genome.
Full extent of PE fragment was mapped to a genome length array adding 1 count for every position a fragment crossed.
Counts were depth normalized using a size factor calculated from the geometric mean of all sample's mapped reads.
Binding signal was calculated as the (mean of + protein replicates / the mean of - protein replicates).
Assembly: NC_000962.3
Supplementary files format and content: csv with each column as a sample's normalized counts or the binding signal and each row as a bp position in the reference genome.

molecule: genomic DNA

organism: Mycobacterium tuberculosis

source_name: bacterial

extract_protocol:
See publication for complete details. Sheared Mtb genomic DNA (mean ~300 bp) was incubated with N-terminal HIS tagged SlfR protein. Protein:gDNA was enriched by binding to Talon resin and washing off unbound gDNA. Bound gDNA was eluted.
Eluted gDNA was prepared for Illumina sequencing using an NEBNext Ultra II DNA Library Prep Kit.

value: bacterial


title: Rv0042c IDAPSeq: 300nM protein, replicate 1

description: Library name: s3_300nM_42c


title: Rv0042c IDAPSeq: 0nM protein, replicate 1

description: Library name: s1_0nM_42c


title: Rv0042c IDAPSeq: 0nM protein, replicate 2

description: Library name: s2_0nM_42c


title: validation mix: lineage 4, replicate 2, input 50ng

description: Library name: l4_r2_50ng

data_processing:
See publication for complete details. Paired end reads were demultiplexed by their inline barcodes using cutadapt and a custom demultiplexer script.
Reads were mapped with bowtie2 to H37Rv reference.
Non-unique reads were removed with picard.
Reads were mapped to H37Rv regions with a custom script, removing low mapq reads. Reported values are log2 transformed and library depth normalized.
Assembly: NC_000962.3
Supplementary files format and content: 2D csvs with gene IDs and sample names

growth_protocol: Mtb was grown in a 1 mL volume in 24-well plates, covered with breathe-easy film, at 37°C x 100 RPM, in 7H9 media supplemented with 0.2% glycerol, 0.05% Tween-80, and 10% OADC. Strains were grown and back diluted as necessary over a 8 day period to achieve a final OD of ~0.4.

extract_protocol:
Crosslinks were reversed by incubating at 70°C. Cells were lysed in Trizol using bead beating tubes. RNA was extracted by adding chloroform and removing the aqueous upper layer. RNA was precipitated onto carboxylate-modified magnetic beads with isopropanol-GuHCl and beads were washed with ethanol. RNA was resuspended into tris-buffered water. See publication for full details.
RNA library preps were prepared for Illumina sequencing using a custom protocol, see publication for complete details. Briefly, cDNA was barcoded using random primers with inline barcodes and an Illumina sequencing adapter. Barcoded, single-stranded cDNA was pooled and a second adapter was added using a splint ligation. Reads corresponding to rRNA were depleted using Taq polymerase's endonuclease activity, combined with a library of guides. Libraries were amplified and sequenced on either a MiSeq or NovaSeq instrument.

treatment_protocol: To halt transcriptome dynamics and sterilize cultures, PFA was added to each 1 mL culture to a final concentration of 2% and allowed to incubate for 1 hour at room temperature.

value: Isolate Mixture


title: validation mix: lineage 4, replicate 3, input 50ng

description: Library name: l4_r3_50ng


title: validation mix: lineage 4, replicate 3, input 10ng

description: Library name: l4_r3_10ng


title: validation mix: lineage 4, replicate 3, input 100ng

description: Library name: l4_r3_100ng


title: validation mix: lineage 4, replicate 2, input 10ng

description: Library name: l4_r2_10ng


title: validation mix: lineage 4, replicate 1, input 100ng

description: Library name: l4_r1_100ng


title: validation mix: lineage 2, replicate 3, input 50ng

description: Library name: l2_r3_50ng


title: validation mix: lineage 4, replicate 2, input 100ng

description: Library name: l4_r2_100ng


title: validation mix: lineage 4, replicate 1, input 10ng

description: Library name: l4_r1_10ng


title: validation mix: lineage 2, replicate 3, input 10ng

description: Library name: l2_r3_10ng


title: validation mix: lineage 2, replicate 2, input 50ng

description: Library name: l2_r2_50ng


title: validation mix: lineage 2, replicate 3, input 100ng

description: Library name: l2_r3_100ng


title: validation mix: lineage 4, replicate 1, input 50ng

description: Library name: l4_r1_50ng


title: validation mix: lineage 2, replicate 2, input 100ng

description: Library name: l2_r2_100ng


title: validation mix: lineage 2, replicate 2, input 10ng

description: Library name: l2_r2_10ng


title: validation mix: lineage 2, replicate 1, input 50ng

description: Library name: l2_r1_50ng


title: validation mix: lineage 2, replicate 1, input 10ng

description: Library name: l2_r1_10ng


title: validation mix: lineage 1, replicate 3, input 50ng

description: Library name: l1_r3_50ng


title: validation mix: lineage 2, replicate 1, input 100ng

description: Library name: l2_r1_100ng


title: validation mix: lineage 1, replicate 3, input 10ng

description: Library name: l1_r3_10ng


title: validation mix: lineage 1, replicate 3, input 100ng

description: Library name: l1_r3_100ng


title: validation mix: lineage 1, replicate 1, input 50ng

description: Library name: l1_r1_50ng


title: validation mix: lineage 1, replicate 2, input 10ng

description: Library name: l1_r2_10ng


title: validation mix: lineage 1, replicate 2, input 100ng

description: Library name: l1_r2_100ng


title: validation mix: lineage 1, replicate 1, input 10ng

description: Library name: l1_r1_10ng


title: 2-AA treated HPMEC cells_2

first: Laurence G

last: Rahme

state: Massachusetts

address: 340 Thier Research Building

institute: Massachusetts General Hospital, Harvard Medical School

description:
Library name: Sample 8
Column name is gene name and row name is samples in raw counts All samples.txt: 2-AA HPMEC

data_processing:
Galaxy (usegalaxy.org)
The paired-end reads obtained were quality-controlled using FastQC (Galaxy version 0.74). Trimming of the 3’adaptor and the low-quality read were removed using the Cutadapt tool (Galaxy version 4.8). The trimmed paired-end reads were joined using the concatenate tool (Galaxy version 9.3).
The reads were mapped to Homo sapiens (release 38) reference sequence (GRCh38) using STAR alignment (galaxy version 2.7.11a).
Reads mapped to the GRCh38 were counted using featureCounts (Galaxy version 2.0.3) with default parameters.
Differential gene expression analysis was implemented using DeSeq2 version (1.40.2) with default parameters.
Assembly: GRCh38
Supplementary files format and content: tab deliminated text file includes raw counts of genes for each sample
Supplementary files format and content: excel files from Deseq2 showing the raw data of log2 fold change, p-value for the genes in each sample

organism: Homo sapiens

source_name: Primary HPMEC cells

growth_protocol: The HPMEC cells were maintained in Endothelial Cell Growth Medium MV2 (Promocell, C-22221) and NHBE cells were maintained in epithelial growth medium (Promocell, C-21260) with 1X Anti-anti in 37C with 5% CO2. The cells were introcdued in the bottom (HPMEC) and top (NHBE) inlets of the organ-on-chip platform. The chips were maintained for 7 days to establish a monolayer. From 8-14 days, the epithelial channel was switched to airway liquid interface by removing the media from the top channel and adding  ALI media with vitaminc C and VEGF in the bottom channel.

extract_protocol:
The top and bottom channels of the chip were lysed with RLT(Qiagen)+BME, NHBE and HPMEC cells were collected separately. RNA extraction from the cells was isolated using the RNeasy Micro Kit (Qiagen).
RNA libraries for RNA-seq using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following manufacturer's instructions.

treatment_protocol: At day 14, 20 μM of the 2-AA compound was added in the ALI media and in the bottom channel with a continuous flow for 20 hrs.

value: Lung-on-chip

value: HPMEC cells

value: 2-AA treated

value: 20 hrs


title: 2-AA treated HPMEC cells_1

description:
Library name: Sample 7
Column name is gene name and row name is samples in raw counts All samples.txt: 2-AA HPMEC


title: Naive HPMEC cells_2

description:
Library name: Sample 6
Column name is gene name and row name is samples in raw counts All samples.txt: Naïve HPMEC

value: No treatment


title: validation mix: lineage 1, replicate 1, input 100ng

description: Library name: l1_r1_100ng


title: Naive HPMEC cells_1

description:
Library name: Sample 5
Column name is gene name and row name is samples in raw counts All samples.txt: Naïve HPMEC


title: PS19_3

city: Rochester

first: Darren

last: Baker

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

description:
Library name: C7500-47
Column name in 8mF_Raw_Counts.csv: C7500-47

data_processing:
Evaluate sequence quality.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 normalization.
Assembly: Mus musculus GRCm38
Supplementary files format and content: csv file includes raw counts for all samples

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from isolated hippocampus using the Qiagen QIAshredder and RNeasy mini prep kits and manufacturer protocols.
Library preparation and initial data processing steps were completed by Genewiz from Azenta Life Sciences.

value: Hippocampus

value: Female

tag: ps19 genotype

tag: p16 genotype

value: wildtype


title: PS19_p16KO_3

description:
Library name: C7038-54
Column name in 8mF_Raw_Counts.csv: C7038-54


title: 2-AA treated NHBE cells_1

description:
Library name: Sample 3
Column name is gene name and row name is samples in raw counts All samples.txt:2-AA NHBE

source_name: Primary NHBE cells

value: NHBE cells


title: PS19_p16KO_2

description:
Library name: C7504-46
Column name in 8mF_Raw_Counts.csv: C7504-46


title: 2-AA treated NHBE cells_2

description:
Library name: Sample 4
Column name is gene name and row name is samples in raw counts All samples.txt:2-AA NHBE


title: PS19_p16KO_4

description:
Library name: C7913-62
Column name in 8mF_Raw_Counts.csv: C7913-62


title: PS19_p16KO_1

description:
Library name: C7035-35
Column name in 8mF_Raw_Counts.csv: C7035-35


title: Naive NHBE cells_1

description:
Library name: Sample 1
Column name is gene name and row name is samples in raw counts All samples.txt: Naïve NHBE


title: PS19_2

description:
Library name: C7499-36
Column name in 8mF_Raw_Counts.csv: C7499-36


title: validation mix: lineage 1, replicate 2, input 50ng

description: Library name: l1_r2_50ng


title: PS19_1

description:
Library name: C6894-63
Column name in 8mF_Raw_Counts.csv: C6894-63


title: p16KO_4

description:
Library name: C7036-60
Column name in 8mF_Raw_Counts.csv: C7036-60


title: p16KO_3

description:
Library name: C7510-52
Column name in 8mF_Raw_Counts.csv: C7510-52


title: A549-shNRF2-BIND-Neh1Del_24hrs_rep1

city: South San Francisco

first: Scott

last: Foster

address: Genentech

institute: Genentech

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
GSNAP: version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap')
Assembly: GrCH38/hg38
Supplementary files format and content: Tab delimited file, contains Ensemble ID, counts and RPKM

extract_protocol:
RNA isolation was performed using the RNeasy Plus Mini Kit (Qiagen) and reverse transcription was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermo) according to the manufacturer’s protocol.
the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies).

value: Non-Small Cell Lung Carcinoma

tag: timepoint

value: 24hr, 2.5ng/mL dox

tag: replicate


title: A549-shNRF2-BIND-Neh1Del_24hrs_rep2


title: p16KO_2

description:
Library name: C7507-42
Column name in 8mF_Raw_Counts.csv: C7507-42


title: A549-shNRF2-BIND-Neh4/5mut_24hrs_rep1


title: A549-shNRF2-BIND-Neh4/5mut_24hrs_rep2


title: A549-shNRF2-BIND-Neh1Del_24hrs_rep3


title: A549-shNRF2-BIND-Neh4/5mut_24hrs_rep3


title: wildtype_4

description:
Library name: C6967-53
Column name in 8mF_Raw_Counts.csv: C6967-53


title: A549-shNRF2-WT NRF2_24hrs_rep3

value: A549-shNRF2-WT NRF2


title: p16KO_1

description:
Library name: C7505-41
Column name in 8mF_Raw_Counts.csv: C7505-41


title: Naive NHBE cells_2

description:
Library name: Sample 2
Column name is gene name and row name is samples in raw counts All samples.txt: Naïve NHBE


title: PS19_4

description:
Library name: C8147-55
Column name in 8mF_Raw_Counts.csv: C8147-55


title: wildtype_3

description:
Library name: C6960-45
Column name in 8mF_Raw_Counts.csv: C6960-45


title: A549-shNRF2-WT NRF2_24hrs_rep2


title: wildtype_2

description:
Library name: C6959-34
Column name in 8mF_Raw_Counts.csv: C6959-34


title: A549-shNRF2-WT NRF2_24hrs_rep1


title: A549-shNRF2-BIND-luc_24hrs_rep1


title: A549-shNRF2-BIND-luc_24hrs_rep2


title: A549-shNRF2-BIND-luc_24hrs_rep3


title: Donor_2_d6_LPS_RNAseq

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: Sample 5

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie2 was used to map reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using HTseq. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .counts files contain unnormalized counts per gene

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were differentiated into resting or trained  macrophages by ex vivo culture in Dutch modified RPMI 1640 culture medium supplemented with gentamicin (50 µg/mL; Centrafarm), glutamax (2 mM; GIBCO), pyruvate (1mM; GIBCO) and 10% (v/v) human pooled serum. Medium was excahenged in days 1, 3 and 6.

extract_protocol:
At the end of differentiation, total RNA was extracted from macrophages using thethe RNeasy mini kit (QIAGEN)  according to manufacturer’s instructions.
Short-insert library was prepared by BGI genomics

treatment_protocol: Trained immunity was induced by exposing cells to BCG vaccine for 24 hours, followed by 5 days culture in RPMI. Cells were cultured with DMSO or LDH inhibitor GSK2837808A (5µM) the first 5 days days. At day 6, LPS 10 ng/ml was added for 4 hours.

value: Adult Human Peripheral Blood

tag: donor

value: Monocyte

value: LPS exposed for 24 hours, culture for 5 days to macrophage


title: Donor_3_d6_LPS_RNAseq

description: Library name: Sample 6


title: A549-shNRF2-BIND-Neh1Del_rep2

value: 24hr, no dox


title: A549-shNRF2-BIND-Neh1Del_rep3


title: A549-shNRF2-BIND-Neh1Del_rep1


title: Donor_2_d1_LPS_RNAseq

description: Library name: Sample 2

value: LPS exposed, collected at 24 hours post exposure


title: Donor_3_d1_LPS_RNAseq

description: Library name: Sample 3


title: Donor_1_d1_LPS_RNAseq

description: Library name: Sample 1


title: A549-shNRF2-BIND-Neh4/5mut_rep3


title: A549-shNRF2-BIND-Neh4/5mut_rep2


title: Donor_G_LPS_GSK_RNAseq

description: Library name: Sample 11

treatment_protocol: Trained immunity was induced by exposing cells to BCG vaccine for 24 hours, followed by 5 days culture in RPMI.  Additionally, tolerance was induced by exposing cells to LPS for 24 hours, followed by 5 days culture in RPMI. Cells were cultured with DMSO or LDH inhibitor GSK2837808A (5µM) the first 5 days days. At day 6, LPS 10 ng/ml was added for 4 hours.

value: LPS exposed for 24h and LDH inhibitor exposed for 5 days, differentiated to macrophage, followed by 4 hours LPS exposure


title: Donor_H_LPS_GSK_RNAseq

description: Library name: Sample 12


title: Donor_F_LPS_GSK_RNAseq

description: Library name: Sample 10


title: A549-shNRF2-BIND-Neh4/5mut_rep1


title: Donor_E_LPS_GSK_RNAseq

description: Library name: Sample 9


title: A549-shNRF2-WT NRF2_rep3


title: wildtype_1

description:
Library name: C6883-61
Column name in 8mF_Raw_Counts.csv: C6883-61


title: A549-shNRF2-WT NRF2_rep1


title: A549-shNRF2-WT NRF2_rep2


title: Donor_1_d6_LPS_RNAseq

description: Library name: Sample 4


title: Donor_H_LPS_RNAseq

description: Library name: Sample 8

value: LPS exposed for 24 hours, culture for 5 days to macrophage, followed by 4 hours LPS exposure


title: Donor_F_LPS_RNAseq

description: Library name: Sample 6


title: A549-shNRF2-BIND-luc_rep2


title: Donor_G_LPS_RNAseq

description: Library name: Sample 7


title: A549-shNRF2-BIND-luc_rep3


title: Donor_E_LPS_RNAseq

description: Library name: Sample 5


title: A549-shNRF2-BIND-luc_rep1


title: Donor_H_RPMI_RNAseq

description: Library name: Sample 4

value: RPMI media only for 6 days to macrophage, followed by 4 hours LPS exposure


title: Donor_G_RPMI_RNAseq

description: Library name: Sample 3


title: AdMSC-EVs, biol rep 3

city: Suita

first: Xiaoqin

last: Li

state: Osaka

department: Ophthalmology

country: Japan

institute: Osaka University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform (Illumina).
Validation of sequencing quality was performed using FastQC v.0.11.7, followed by reads trimming via Trimmomatic v.0.38.
Sequenced reads were mapped onto the human hg38 reference genome by HISAT2 v.2.1.0.
The quantification of raw reads mapped to the exon regions was performed by FeatureCounts v.1.6.3.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each gene and each sample.

source_name: adipose-derived mesenchymal stem cells

growth_protocol: AdMSCs were seeded into T75 flasks at 2500-3000 cells/cm2 and cultured in Cellartis MSC Xeno-Free Culture Medium (Cellartis; Takara Bio, Shiga, Japan) in humidified atmosphere with 5% CO2 at 37℃ for two days. Subsequently, medium was refreshed and cells were cultivated for two days.

extract_protocol:
RNA was harvested using miRNeasy Mini kit
Briefly, the cDNA library was constructed using a SMARTER smRNA-Seq for Illumina Kit. Sequencing was performed on an Illumina HiSeq 2500 platform (Illumina).

treatment_protocol: AdMSC-EVs were isolated from the conditioned medium by differential ultracentrifugation.

value: adipose-derived mesenchymal stem cells

value: WT


title: Donor_E_RPMI_RNAseq

description: Library name: Sample 1


title: AdMSC-EVs, biol rep 4


title: Donor_F_RPMI_RNAseq

description: Library name: Sample 2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1415

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

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'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 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'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').

library_source: transcriptomic single cell

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using 'bcl2fastq2 v2.19' from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.

molecule: polyA RNA

extract_protocol:
Neuronal cultures were treated for 1 hour with 5 µM Y-27632 before dissociation with trypsin or accutase. The cells were resuspended in FACS buffer (HBSS with magnesium and calcium, 2% w/v bovine serum albumine, 2% v/v knockout serum replacement, 2% v/v B-27 supplement, 25 mM D-glucose, 5 µM Y-27632). Single live cells were isolated by fluorescence activated cell sorting (FACS) using Topro-3 iodide and were directly lysed in ice-cold single-cell lysis buffer (0.2% w/v Triton X-100, 0.5% v/v recombinant RNase inhibitor, 10 µM Smarter_oligo-dTVN, 25 mM dNTP, 100 mM DL-dithiothreitol, 4e-5 diluted ERCC spike-in RNAs, in ultrapure water). Protocol according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).
Individual single cell libraries were prepared using the Smart-Seq2 protocol followed by tagmentation using components form the Nextera XT DNA library preparation kit (Illumina). Protocols with adaptations according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).

treatment_protocol:
Heterogenous protocol: Differentiation of adherent cells for two days in medium 1 (200 nM LDN193189, 10 µM SB431542, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid), followed by seven days medium 2 (medium 1 with 3 µM CHIR99021), one day of medium d3 (Medium 2 with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF), and three days of medium 4 (3 µM CHIR99021, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid, with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF). From day 14 onwards, culture was kept in medium 5 (200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT3, and CNTF).
Homogenous protocol according to Nijssen J, et al. 2019. Bioprotocol (PMID: 33654821). The neurons were cultured until day 28.

value: spinal neuron differentiation

value: heterogenous protocol

tag: sequencing batch


title: AKTi replicate 2

city: Charleston

first: Wenjian

last: Gan

state: SC

address: 173 Ashley Ave, BSB507

institute: Medical University of South Carolina

description: Library name: Ipat_2

data_processing:
Raw reads were filtered by software SOAPnuke to obtain clean reads, followed by mapping to the human genome with HISAT2 and Bowtie2. Gene expression level is estimated using FPKM value.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Table-delimited file include FPKM values for each sample

source_name: MDA-MB-231 cells

extract_protocol:
Total RNAs were exacted from MDA-MB-231 cells treated with DMSO, I-BRD9, or Ipatasertib using RNeasy Plus Mini Kit (Qiagen, 74134)
mRNA was purified using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented and then used for synthesis of the first-strand cDNA using random hexamer primers, followed second strand cDNA synthesis using dTTP for library construction

value: MDA-MB-231 cells

value: Breast cancer cells

value: Ipatasertib


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1413


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1412


title: AKTi replicate 1

description: Library name: Ipat_1


title: AdMSC-EVs, biol rep 2


title: I-BRD9 replicate 2

description: Library name: I-BRD9_2


title: I-BRD9 replicate 1

description: Library name: I-BRD9_1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1411


title: AdMSC-EVs, biol rep 1


title: AKTi replicate 3

description: Library name: Ipat_3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1410


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1409


title: DMSO replicate 1

description: Library name: Ctrl_1

value: DMSO


title: DMSO replicate 2

description: Library name: Ctrl_2


title: Donor_D_BCG_GSK_RNAseq

growth_protocol: Monocytes were differentiated into resting or trained  macrophages by ex vivo culture in Dutch modified RPMI 1640 culture medium supplemented with gentamicin (50 µg/mL; Centrafarm), glutamax (2 mM; GIBCO), pyruvate (1mM; GIBCO) and 10% (v/v) human pooled serum.Medium was excahenged in days 1, 3 and 6.

value: BCG exposed for 24h and LDH inhibitor exposed for 5 days, differentiated to macrophage, followed by 4 hours LPS exposure


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1407


title: DMSO replicate 3

description: Library name: Ctrl_3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1408


title: Donor_B_BCG_GSK_RNAseq

value: Adult Human Peripheral Blood


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1404


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1405


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1406


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1403


title: Donor_A_BCG_GSK_RNAseq

value: Monocyte


title: I-BRD9 replicate 3

description: Library name: I-BRD9_3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1401


title: Donor_C_BCG_GSK_RNAseq


title: Donor_B_BCG_RNAseq

value: BCG exposed for 24 hours, culture for 5 days to macrophage, followed by 4 hours LPS exposure


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1400


title: Donor_D_BCG_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1399


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1398


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1397


title: Donor_D_RPMI_GSK_RNAseq

value: RPMI media and LDH inhibitor exposed for 5 days, differentiated to macrophage, followed by 4 hours LPS exposure


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1402


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1396


title: Donor_B_RPMI_GSK_RNAseq


title: Donor_D_RPMI_RNAseq


title: Donor_A_RPMI_GSK_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1395


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1393


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1394


title: Donor_C_RPMI_RNAseq


title: Donor_B_RPMI_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1392


title: Donor_3_d6_BCG_RNAseq

value: BCG exposed for 24 hours, culture for 5 days to macrophage


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1391


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1390


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1389


title: Donor_A_RPMI_RNAseq


title: Donor_C_BCG_RNAseq


title: Donor_A_BCG_RNAseq


title: Donor_3_d1_BCG_RNAseq

value: BCG exposed, collected at 24 hours post exposure


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1388


title: Donor_3_d1_RPMI_RNAseq

value: RPMI media only, collected at 24 hours post culture


title: Donor_C_RPMI_GSK_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1387


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1386


title: Donor_2_d1_BCG_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1385


title: Donor_3_d0_RNAseq

value: Baseline monocytes isolated with beads


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1383


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1414


title: Donor_2_d1_RPMI_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1382


title: Donor_1_d6_BCG_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1380


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1381


title: Donor_3_d6_RPMI_RNAseq

value: RPMI media only for 6 days to macrophage


title: Donor_1_d1_BCG_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1378


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1377


title: Donor_1_d1_RPMI_RNAseq


title: Donor_2_d6_BCG_RNAseq


title: Donor_1_d0_RNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1376


title: Donor_2_d6_RPMI_RNAseq


title: Wild type 2

city: COLLEGE PARK

first: Xudong

last: Zhu

state: Maryland

address: 10300 Baltimore Ave.

institute: USDA-ARS-BARC-FQL

data_processing:
All raw reads were stored in FASTQ(fq) format files and then were filtered to remove the reads which contained adaptors and low quality reads. Filtered reads were mapped to NCBI tomato genome with Bowtie and then normalized using the TPM method (transcripts per million). The reads mapped to reference genome were compared with specific sequences in the miRBase to obtain detailed information and DESeq2 is used to calculate the differential expression level. Significant threshold cutoffs were set to log2 fold change ≥ 1 or ≤ − 1 with q-value ≤ 0.05.
Assembly: Solanum lycopersicum
Supplementary files format and content: tab-delimited text files include the TPM values of each sample

organism: Solanum lycopersicum

source_name: Fruits

growth_protocol: The tomato (Solanum lycopersicum L.) cultivar ‘Micro-Tom’ was used in our study. Both control (wild-type) and transgenic plants were grown under a consistent photoperiod (16 hours light/8 hours dark) with regular fertilizer applications in the greenhouse at 23-26°C. Tomato tissues used for a series of downstream experiments were collected and immediately frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted from terminal leaflets (30 days post germination) and fruits (mature green and red ripe) of wild-type and transgenic plants using TRIzol reagent (Invitrogen, Cat #15596026) according to the manufacturer’s instructions.
Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ ends of small RNA, respectively. Then the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing on Illumina sequencing platform with SE50.

treatment_protocol: In this study, we used short tandem target mimic (STTM) and artificial miRNA (amiRNA) technologies to generate a set of experimental materials with up- or down-regulated miR396 expression and studied the effect of miR396 on fruit size, productivity, and quality in tomatoes.

value: Fruits

value: Red and full ripen stage

tag: cultivar

value: Micro-Tom

value: control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1384

value: spinal neuron differentiation

value: heterogenous protocol


title: Wild type 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1375


title: STTM396  trangenic line 2

value: up-regulated miR396 using short tandem target mimic (STTM) technology


title: STTM396  trangenic line 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1372


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1371


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1374


title: Donor_2_d0_RNAseq


title: amiR396 trangenic line 2

value: down-regulated miR396 using artificial miRNA (amiRNA) technology


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1379


title: 35S::MtCLE35 + S. meliloti, 11 dpi, rep 3

city: Saint-Petersburg

first: Maria

last: Lebedeva

address: 7-9 Universitetskaya Emb.

department: Genetics and Biotechnology

country: Russia

institute: St Petersburg University

data_processing:
*library strategy: 3′ massive analysis of c-DNA ends (MACE) RNA-sequencing
Filtration and TrueQuant-based deduplication of reads were done using the bbduk and dedupe utilities from the BBtools suite
Reads were mapped to the reference genome MtrunA17r5.0-ANR using HISAT2
StringTie was used for transcript counting
Assembly: reference genome MtrunA17r5.0-ANR, GCF_003473485.1
Supplementary files format and content: .csv file include raw counts for each sample

organism: Medicago truncatula

source_name: MtCLE35 transgenic roots

growth_protocol: Composite plants were grown in pots filled with vermiculite supplemented with nitrogen-free Fahraeus medium

extract_protocol:
Total RNA was extracted with TriZol reagent using isopropanol precipitation, followed by DNAse treatment and subsequence cholorophorm extraction and EtOH-NaAc precipitation
MACE-Seq Kit (GenXPro GmbH, Frankfurt, Germany)

value: MtCLE35 transgenic roots

value: S. meliloti 2011, 11 dpi


title: Donor_1_d6_RPMI_RNAseq

value: Adult Human Peripheral Blood

value: Monocyte


title: 35S::MtCLE35 + S. meliloti, 11 dpi, rep 2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1368


title: 35S::MtCLE35 + S. meliloti, 11 dpi, rep 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1367


title: 35S::GUS + S. meliloti, 11 dpi, rep 3

source_name: 35S::GUS transgenic roots

value: 35S::GUS transgenic roots


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1366


title: 35S::GUS + S. meliloti, 11 dpi, rep 2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1365


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1373


title: 35S::GUS + S. meliloti, 11 dpi, rep 1


title: 35S::CLE35, no rhizobia, rep 3

value: no rhizobia, nitrogen-free


title: 35S::CLE35, no rhizobia, rep 2


title: 35S: CLE35, no rhizobia, rep 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1362


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1361


title: amiR396 trangenic line 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1363


title: 35S::GUS, no rhizobia, rep 3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1370


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1358


title: 35S::GUS, no rhizobia, rep 2


title: genomic DNA from dedifferentiated liposarcoma cell line LPS12

type: genomic

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

description:
200467580077_R04C01
genomic DNA from dedifferentiated liposarcoma cell line

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
The data were analyzed using GenomeStudio Methylation Module Software. Beta values were obtained after background correction and normalization to internal controls.
Average Beta, intensity, Detection P-value

label: Cy5 and Cy3

source_name: Cell line of dedifferentiated liposarcoma

label_protocol: Standard Illumina Protocol

growth_protocol: TGW cell line was maintained in MEM medium with 10% FBS.

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

treatment_protocol: Cells were seeded on Day 0. On Days 1, 2, and 3, the medium was replaced with a medium containing 0.3 µM of 5-aza-dC. On Day 4, the cells were collected for genomic DNA extraction.


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1369


title: genomic DNA from dedifferentiated liposarcoma cell line LP6

description:
200467580077_R03C01
genomic DNA from dedifferentiated liposarcoma cell line

value: Cell line of dedifferentiated liposarcoma


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1356


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1357


title: genomic DNA from well-differentiated liposarcoma cell line 94T778

description:
200467580077_R02C01
genomic DNA from well-differentiated liposarcoma cell line

source_name: Cell line of well-differentiated liposarcoma


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1354


description:
201233650059_R08C01
genomic DNA from peripheral blood mononuclear cells of health male

source_name: PBMC from health male

value: PBMC from health male


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1353


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1364


title: genomic DNA from peripheral blood mononuclear cells of healthy female

description:
200514040005_R07C01
genomic DNA from peripheral blood mononuclear cells of healthy femal

source_name: PBMC from health female

value: PBMC from health female


title: blood sample 185

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

institute: Keio University School of Medicine

description:
cfDNA of patient with NSCLC
SAMPLE 185

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio methylation software
Normalized Average Beta is supplementary file

source_name: NSCLC 185

extract_protocol: Five ml of plasma was subjected into cfDNA extraction using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany).

tag: disease

value: non-small cell lung cancer

tag: age bracket

value: male


title: blood sample 183

description:
cfDNA of patient with NSCLC
SAMPLE 183

source_name: NSCLC 183

value: female


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1350

tag: cell type


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1360


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1359


title: blood sample 184

description:
cfDNA of patient with NSCLC
SAMPLE 184

source_name: NSCLC 184

tag: Sex


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1351

tag: treatment


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1348


title: 35S::GUS, no rhizobia, rep 1


title: blood sample 180

description:
cfDNA of patient with NSCLC
SAMPLE 180

source_name: NSCLC 180


title: blood sample 181

description:
cfDNA of patient with NSCLC
SAMPLE 181

source_name: NSCLC 181


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1346


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1347


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1355


title: blood sample 182

description:
cfDNA of patient with NSCLC
SAMPLE 182

source_name: NSCLC 182


title: genomic DNA from well-differentiated liposarcoma cell line 93T449

description:
200467580077_R01C01
genomic DNA from well-differentiated liposarcoma cell line

value: Cell line of well-differentiated liposarcoma


title: blood sample 179

description:
cfDNA of patient with NSCLC
SAMPLE 179

source_name: NSCLC 179


title: blood sample 177

description:
cfDNA of patient with NSCLC
SAMPLE 177

source_name: NSCLC 177


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1349

value: spinal neuron differentiation


title: blood sample 176

description:
cfDNA of patient with NSCLC
SAMPLE 176

source_name: NSCLC 176


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1344

value: heterogenous protocol


title: blood sample 178

description:
cfDNA of patient with NSCLC
SAMPLE 178

source_name: NSCLC 178


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1343


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1342


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1352


title: blood sample 174

description:
cfDNA of patient with NSCLC
SAMPLE 174

source_name: NSCLC 174


title: blood sample 173

description:
cfDNA of patient with NSCLC
SAMPLE 173

source_name: NSCLC 173


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1340


title: blood sample 172

description:
cfDNA of patient with NSCLC
SAMPLE 172

source_name: NSCLC 172


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1338


title: blood sample 171

description:
cfDNA of patient with NSCLC
SAMPLE 171

source_name: NSCLC 171


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1337


title: blood sample 170

description:
cfDNA of patient with NSCLC
SAMPLE 170

source_name: NSCLC 170


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1336


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1345


title: blood sample 169

description:
cfDNA of patient with NSCLC
SAMPLE 169

source_name: NSCLC 169


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1334


title: blood sample 168

description:
cfDNA of patient with NSCLC
SAMPLE 168

source_name: NSCLC 168


title: blood sample 167

description:
cfDNA of patient with NSCLC
SAMPLE 167

source_name: NSCLC 167


title: blood sample 165

description:
cfDNA of patient with NSCLC
SAMPLE 165

source_name: NSCLC 165


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1333


title: blood sample 166

description:
cfDNA of patient with NSCLC
SAMPLE 166

source_name: NSCLC 166


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1332


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1335


title: blood sample 175

description:
cfDNA of patient with NSCLC
SAMPLE 175

source_name: NSCLC 175


title: blood sample 163

description:
cfDNA of patient with NSCLC
SAMPLE 163

source_name: NSCLC 163


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1329


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1331


title: blood sample 164

description:
cfDNA of patient with NSCLC
SAMPLE 164

source_name: NSCLC 164


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1330


title: blood sample 162

description:
cfDNA of patient with NSCLC
SAMPLE 162

source_name: NSCLC 162


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1341


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1328


title: blood sample 161

description:
cfDNA of patient with NSCLC
SAMPLE 161

source_name: NSCLC 161


title: blood sample 160

description:
cfDNA of patient with NSCLC
SAMPLE 160

source_name: NSCLC 160


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1327


title: blood sample 158

description:
cfDNA of patient with NSCLC
SAMPLE 158

source_name: NSCLC 158


title: blood sample 159

description:
cfDNA of patient with NSCLC
SAMPLE 159

source_name: NSCLC 159


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1339


title: blood sample 157

description:
cfDNA of patient with NSCLC
SAMPLE 157

source_name: NSCLC 157


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1325


title: blood sample 156

description:
cfDNA of patient with NSCLC
SAMPLE 156

source_name: NSCLC 156


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1323


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1322


title: blood sample 155

description:
cfDNA of patient with NSCLC
SAMPLE 155

source_name: NSCLC 155


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1321


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1324


title: blood sample 154

description:
cfDNA of patient with NSCLC
SAMPLE 154

source_name: NSCLC 154


title: blood sample 151

description:
cfDNA of patient with NSCLC
SAMPLE 151

source_name: NSCLC 151


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1326


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1318


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1320


title: blood sample 153

description:
cfDNA of patient with NSCLC
SAMPLE 153

source_name: NSCLC 153


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1317


title: blood sample 149

description:
cfDNA of patient with NSCLC
SAMPLE 149

source_name: NSCLC 149


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1316


title: blood sample 152

description:
cfDNA of patient with NSCLC
SAMPLE 152

source_name: NSCLC 152


title: blood sample 147

description:
cfDNA of patient with NSCLC
SAMPLE 147

source_name: NSCLC 147


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1315


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1313


title: blood sample 148

description:
cfDNA of patient with NSCLC
SAMPLE 148

source_name: NSCLC 148


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1314


title: blood sample 150

description:
cfDNA of patient with NSCLC
SAMPLE 150

source_name: NSCLC 150


title: blood sample 146

description:
cfDNA of patient with NSCLC
SAMPLE 146

source_name: NSCLC 146


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1312


title: blood sample 145

description:
cfDNA of patient with NSCLC
SAMPLE 145

source_name: NSCLC 145


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1311


title: blood sample 143

description:
cfDNA of patient with NSCLC
SAMPLE 143

source_name: NSCLC 143


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1310


title: blood sample 144

description:
cfDNA of patient with NSCLC
SAMPLE 144

source_name: NSCLC 144


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1309


title: blood sample 141

description:
cfDNA of patient with NSCLC
SAMPLE 141

source_name: NSCLC 141


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1319


title: blood sample 142

description:
cfDNA of patient with NSCLC
SAMPLE 142

source_name: NSCLC 142


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1306


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1308


title: blood sample 140

description:
cfDNA of patient with NSCLC
SAMPLE 140

source_name: NSCLC 140


title: blood sample 138

description:
cfDNA of patient with NSCLC
SAMPLE 138

source_name: NSCLC 138


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1304


title: blood sample 139

description:
cfDNA of patient with NSCLC
SAMPLE 139

source_name: NSCLC 139


title: blood sample 137

description:
cfDNA of patient with NSCLC
SAMPLE 137

source_name: NSCLC 137


title: blood sample 136

description:
cfDNA of patient with NSCLC
SAMPLE 136

source_name: NSCLC 136


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1303


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1307


title: blood sample 135

description:
cfDNA of patient with NSCLC
SAMPLE 135

source_name: NSCLC 135


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1302


title: blood sample 133

description:
cfDNA of patient with NSCLC
SAMPLE 133

source_name: NSCLC 133


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1300


title: blood sample 131

description:
cfDNA of patient with NSCLC
SAMPLE 131

source_name: NSCLC 131


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1301


title: blood sample 132

description:
cfDNA of patient with NSCLC
SAMPLE 132

source_name: NSCLC 132


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1298


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1299


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_1305


title: blood sample 134

description:
cfDNA of patient with NSCLC
SAMPLE 134

source_name: NSCLC 134


title: blood sample 130

description:
cfDNA of patient with NSCLC
SAMPLE 130

source_name: NSCLC 130


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1296


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1297


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1295


title: blood sample 129

description:
cfDNA of patient with NSCLC
SAMPLE 129

source_name: NSCLC 129


title: blood sample 127

description:
cfDNA of patient with NSCLC
SAMPLE 127

source_name: NSCLC 127


title: blood sample 126

description:
cfDNA of patient with NSCLC
SAMPLE 126

source_name: NSCLC 126


title: blood sample 125

description:
cfDNA of patient with NSCLC
SAMPLE 125

source_name: NSCLC 125


title: blood sample 124

description:
cfDNA of patient with NSCLC
SAMPLE 124

source_name: NSCLC 124


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1292


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1293


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1290


title: blood sample 122

description:
cfDNA of patient with NSCLC
SAMPLE 122

source_name: NSCLC 122


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1289


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1294


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1291


title: blood sample 123

description:
cfDNA of patient with NSCLC
SAMPLE 123

source_name: NSCLC 123


title: blood sample 128

description:
cfDNA of patient with NSCLC
SAMPLE 128

source_name: NSCLC 128


title: blood sample 120

description:
cfDNA of patient with NSCLC
SAMPLE 120

source_name: NSCLC 120


title: blood sample 115

description:
cfDNA of patient with NSCLC
SAMPLE 115

source_name: NSCLC 115


title: blood sample 121

description:
cfDNA of patient with NSCLC
SAMPLE 121

source_name: NSCLC 121


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1287


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1284


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1285


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1286


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1283


title: blood sample 118

description:
cfDNA of patient with NSCLC
SAMPLE 118

source_name: NSCLC 118


title: blood sample 119

description:
cfDNA of patient with NSCLC
SAMPLE 119

source_name: NSCLC 119


title: blood sample 117

description:
cfDNA of patient with NSCLC
SAMPLE 117

source_name: NSCLC 117


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1288


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1282


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1281


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1280


title: blood sample 112

description:
cfDNA of patient with NSCLC
SAMPLE 112

source_name: NSCLC 112


title: blood sample 111

description:
cfDNA of patient with NSCLC
SAMPLE 111

source_name: NSCLC 111


title: blood sample 110

description:
cfDNA of patient with NSCLC
SAMPLE 110

source_name: NSCLC 110


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1279


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1277


title: blood sample 113

description:
cfDNA of patient with NSCLC
SAMPLE 113

source_name: NSCLC 113


title: blood sample 108

description:
cfDNA of patient with NSCLC
SAMPLE 108

source_name: NSCLC 108


title: blood sample 114

description:
cfDNA of patient with NSCLC
SAMPLE 114

source_name: NSCLC 114


title: blood sample 107

description:
cfDNA of patient with NSCLC
SAMPLE 107

source_name: NSCLC 107


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1274


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1275


title: blood sample 109

description:
cfDNA of patient with NSCLC
SAMPLE 109

source_name: NSCLC 109


title: blood sample 116

description:
cfDNA of patient with NSCLC
SAMPLE 116

source_name: NSCLC 116


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1273


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1272


title: blood sample 106

description:
cfDNA of patient with NSCLC
SAMPLE 106

source_name: NSCLC 106


title: blood sample 105

description:
cfDNA of patient with NSCLC
SAMPLE 105

source_name: NSCLC 105


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1278


title: blood sample 104

description:
cfDNA of patient with NSCLC
SAMPLE 104

source_name: NSCLC 104


title: blood sample 103

description:
cfDNA of patient with NSCLC
SAMPLE 103

source_name: NSCLC 103


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1270


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1269


title: blood sample 102

description:
cfDNA of patient with NSCLC
SAMPLE 102

source_name: NSCLC 102


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1267


title: blood sample 101

description:
cfDNA of patient with NSCLC
SAMPLE 101

source_name: NSCLC 101


title: blood sample 100

description:
cfDNA of patient with NSCLC
SAMPLE 100

source_name: NSCLC 100


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1271


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1268


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1276


title: blood sample 98

description:
cfDNA of patient with NSCLC
SAMPLE 98

source_name: NSCLC 98


title: blood sample 99

description:
cfDNA of patient with NSCLC
SAMPLE 99

source_name: NSCLC 99


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1266


title: blood sample 96

description:
cfDNA of patient with NSCLC
SAMPLE 96

source_name: NSCLC 96


title: blood sample 97

description:
cfDNA of patient with NSCLC
SAMPLE 97

source_name: NSCLC 97


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1263


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1262


title: blood sample 95

description:
cfDNA of patient with NSCLC
SAMPLE 95

source_name: NSCLC 95


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1261


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1260


title: blood sample 94

description:
cfDNA of patient with NSCLC
SAMPLE 94

source_name: NSCLC 94


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1265


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1264


title: blood sample 93

description:
cfDNA of patient with NSCLC
SAMPLE 93

source_name: NSCLC 93


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1259


title: blood sample 92

description:
cfDNA of patient with NSCLC
SAMPLE 92

source_name: NSCLC 92


title: blood sample 90

description:
cfDNA of patient with NSCLC
SAMPLE 90

source_name: NSCLC 90


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1258


title: blood sample 89

description:
cfDNA of patient with NSCLC
SAMPLE 89

source_name: NSCLC 89


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1256


title: blood sample 88

description:
cfDNA of patient with NSCLC
SAMPLE 88

source_name: NSCLC 88


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1255


title: blood sample 85

description:
cfDNA of patient with NSCLC
SAMPLE 85

source_name: NSCLC 85


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1253


title: blood sample 87

description:
cfDNA of patient with NSCLC
SAMPLE 87

source_name: NSCLC 87


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1254


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1252


title: blood sample 91

description:
cfDNA of patient with NSCLC
SAMPLE 91

source_name: NSCLC 91


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1251


title: blood sample 86

description:
cfDNA of patient with NSCLC
SAMPLE 86

source_name: NSCLC 86


title: blood sample 84

description:
cfDNA of patient with NSCLC
SAMPLE 84

source_name: NSCLC 84


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1249


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1257


title: blood sample 80

description:
cfDNA of patient with NSCLC
SAMPLE 80

source_name: NSCLC 80


title: blood sample 82

description:
cfDNA of patient with NSCLC
SAMPLE 82

source_name: NSCLC 82


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1250


title: blood sample 83

description:
cfDNA of patient with NSCLC
SAMPLE 83

source_name: NSCLC 83


title: blood sample 81

description:
cfDNA of patient with NSCLC
SAMPLE 81

source_name: NSCLC 81


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1245


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1248


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1246


title: blood sample 79

description:
cfDNA of patient with NSCLC
SAMPLE 79

source_name: NSCLC 79


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1247


title: blood sample 78

description:
cfDNA of patient with NSCLC
SAMPLE 78

source_name: NSCLC 78


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1244


title: blood sample 77

description:
cfDNA of patient with NSCLC
SAMPLE 77

source_name: NSCLC 77


title: blood sample 76

description:
cfDNA of patient with NSCLC
SAMPLE 76

source_name: NSCLC 76


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1243


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1241


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1242


title: blood sample 73

description:
cfDNA of patient with NSCLC
SAMPLE 73

source_name: NSCLC 73


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1239


title: blood sample 70

description:
cfDNA of patient with NSCLC
SAMPLE 70

source_name: NSCLC 70


title: blood sample 71

description:
cfDNA of patient with NSCLC
SAMPLE 71

source_name: NSCLC 71


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1237


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1238


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1240


title: blood sample 74

description:
cfDNA of patient with NSCLC
SAMPLE 74

source_name: NSCLC 74


title: blood sample 68

description:
cfDNA of patient with NSCLC
SAMPLE 68

source_name: NSCLC 68


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1235


title: blood sample 69

description:
cfDNA of patient with NSCLC
SAMPLE 69

source_name: NSCLC 69


title: blood sample 66

description:
cfDNA of patient with NSCLC
SAMPLE 66

source_name: NSCLC 66


title: blood sample 67

description:
cfDNA of patient with NSCLC
SAMPLE 67

source_name: NSCLC 67


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1234


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1233

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_2.17 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.


title: blood sample 65

description:
cfDNA of patient with NSCLC
SAMPLE 65

source_name: NSCLC 65


title: blood sample 64

description:
cfDNA of patient with NSCLC
SAMPLE 64

source_name: NSCLC 64


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1231


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1230


title: blood sample 63

description:
cfDNA of patient with NSCLC
SAMPLE 63

source_name: NSCLC 63


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1229


title: blood sample 62

description:
cfDNA of patient with NSCLC
SAMPLE 62

source_name: NSCLC 62


title: blood sample 75

description:
cfDNA of patient with NSCLC
SAMPLE 75

source_name: NSCLC 75


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1228


title: blood sample 72

description:
cfDNA of patient with NSCLC
SAMPLE 72

source_name: NSCLC 72


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1227


title: blood sample 60

description:
cfDNA of patient with NSCLC
SAMPLE 60

source_name: NSCLC 60


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_1236


title: blood sample 59

description:
cfDNA of patient with NSCLC
SAMPLE 59

source_name: NSCLC 59


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1226


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1225


title: blood sample 57

description:
cfDNA of patient with NSCLC
SAMPLE 57

source_name: NSCLC 57


title: blood sample 58

description:
cfDNA of patient with NSCLC
SAMPLE 58

source_name: NSCLC 58


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1224


title: blood sample 56

description:
cfDNA of patient with NSCLC
SAMPLE 56

source_name: NSCLC 56


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1223


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1221


title: blood sample 55

description:
cfDNA of patient with NSCLC
SAMPLE 55

source_name: NSCLC 55


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1232


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1219


title: blood sample 54

description:
cfDNA of patient with NSCLC
SAMPLE 54

source_name: NSCLC 54


title: blood sample 53

description:
cfDNA of patient with NSCLC
SAMPLE 53

source_name: NSCLC 53


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1218


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1215


title: blood sample 52

description:
cfDNA of patient with NSCLC
SAMPLE 52

source_name: NSCLC 52


title: blood sample 50

description:
cfDNA of patient with NSCLC
SAMPLE 50

source_name: NSCLC 50


title: blood sample 61

description:
cfDNA of patient with NSCLC
SAMPLE 61

source_name: NSCLC 61


title: blood sample 49

description:
cfDNA of patient with NSCLC
SAMPLE 49

source_name: NSCLC 49


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1217


title: blood sample 48

description:
cfDNA of patient with NSCLC
SAMPLE 48

source_name: NSCLC 48


title: blood sample 47

description:
cfDNA of patient with NSCLC
SAMPLE 47

source_name: NSCLC 47


title: blood sample 46

description:
cfDNA of patient with NSCLC
SAMPLE 46

source_name: NSCLC 46


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1214


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1213


title: blood sample 45

description:
cfDNA of patient with NSCLC
SAMPLE 45

source_name: NSCLC 45


title: blood sample 44

description:
cfDNA of patient with NSCLC
SAMPLE 44

source_name: NSCLC 44


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1222


title: blood sample 43

description:
cfDNA of patient with NSCLC
SAMPLE 43

source_name: NSCLC 43


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1220


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1209


title: blood sample 42

description:
cfDNA of patient with NSCLC
SAMPLE 42

source_name: NSCLC 42


title: blood sample 51

description:
cfDNA of patient with NSCLC
SAMPLE 51

source_name: NSCLC 51


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1216


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1207


title: blood sample 41

description:
cfDNA of patient with NSCLC
SAMPLE 41

source_name: NSCLC 41


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1206


title: blood sample 39

description:
cfDNA of patient with NSCLC
SAMPLE 39

source_name: NSCLC 39


title: blood sample 38

description:
cfDNA of patient with NSCLC
SAMPLE 38

source_name: NSCLC 38


title: blood sample 37

description:
cfDNA of patient with NSCLC
SAMPLE 37

source_name: NSCLC 37


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1205


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1204


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1203


title: blood sample 36

description:
cfDNA of patient with NSCLC
SAMPLE 36

source_name: NSCLC 36


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1202


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1212


title: blood sample 34

description:
cfDNA of patient with NSCLC
SAMPLE 34

source_name: NSCLC 34


title: blood sample 33

description:
cfDNA of patient with NSCLC
SAMPLE 33

source_name: NSCLC 33


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1211


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1200


title: blood sample 32

description:
cfDNA of patient with NSCLC
SAMPLE 32

source_name: NSCLC 32


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1210


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1198


title: blood sample 31

description:
cfDNA of patient with NSCLC
SAMPLE 31

source_name: NSCLC 31


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1208


title: blood sample 40

description:
cfDNA of patient with NSCLC
SAMPLE 40

source_name: NSCLC 40


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1197


title: blood sample 29

description:
cfDNA of patient with NSCLC
SAMPLE 29

source_name: NSCLC 29


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1196


title: blood sample 28

description:
cfDNA of patient with NSCLC
SAMPLE 28

source_name: NSCLC 28


title: blood sample 27

description:
cfDNA of patient with NSCLC
SAMPLE 27

source_name: NSCLC 27


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1193


title: blood sample 26

description:
cfDNA of patient with NSCLC
SAMPLE 26

source_name: NSCLC 26


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1195


title: blood sample 35

description:
cfDNA of patient with NSCLC
SAMPLE 35

source_name: NSCLC 35


title: blood sample 24

description:
cfDNA of patient with NSCLC
SAMPLE 24

source_name: NSCLC 24


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1191

value: Control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1194


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1201


title: blood sample 22

description:
cfDNA of patient with NSCLC
SAMPLE 22

source_name: NSCLC 22


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1189


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1199


title: blood sample 21

description:
cfDNA of patient with NSCLC
SAMPLE 21

source_name: NSCLC 21


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1187


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1192


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1186


title: blood sample 20

description:
cfDNA of patient with NSCLC
SAMPLE 20

source_name: NSCLC 20


title: blood sample 30

description:
cfDNA of patient with NSCLC
SAMPLE 30

source_name: NSCLC 30


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1184


title: blood sample 19

description:
cfDNA of patient with NSCLC
SAMPLE 19

source_name: NSCLC 19


title: blood sample 17

description:
cfDNA of patient with NSCLC
SAMPLE 17

source_name: NSCLC 17


title: blood sample 18

description:
cfDNA of patient with NSCLC
SAMPLE 18

source_name: NSCLC 18


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1181


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1183


title: blood sample 16

description:
cfDNA of patient with NSCLC
SAMPLE 16

source_name: NSCLC 16


title: blood sample 25

description:
cfDNA of patient with NSCLC
SAMPLE 25

source_name: NSCLC 25


title: blood sample 14

description:
cfDNA of patient with NSCLC
SAMPLE 14

source_name: NSCLC 14


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1190


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1182


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1180


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1179


title: blood sample 12

description:
cfDNA of patient with NSCLC
SAMPLE 12

source_name: NSCLC 12


title: blood sample 23

description:
cfDNA of patient with NSCLC
SAMPLE 23

source_name: NSCLC 23


title: blood sample 13

description:
cfDNA of patient with NSCLC
SAMPLE 13

source_name: NSCLC 13


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1178


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1188


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1177


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1176


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1175


title: blood sample 11

description:
cfDNA of patient with NSCLC
SAMPLE 11

source_name: NSCLC 11


title: blood sample 9

description:
cfDNA of patient with NSCLC
SAMPLE 9

source_name: NSCLC 9


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1185


title: blood sample 8

description:
cfDNA of patient with NSCLC
SAMPLE 8

source_name: NSCLC 8


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1174


title: blood sample 10

description:
cfDNA of patient with NSCLC
SAMPLE 10

source_name: NSCLC 10


title: blood sample 6

description:
cfDNA of patient with NSCLC
SAMPLE 6

source_name: NSCLC 6


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1173


title: blood sample 15

description:
cfDNA of patient with NSCLC
SAMPLE 15

source_name: NSCLC 15


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1172


title: blood sample 5

description:
cfDNA of patient with NSCLC
SAMPLE 5

source_name: NSCLC 5


title: blood sample 2

description:
cfDNA of patient with NSCLC
SAMPLE 2

source_name: NSCLC 2


title: blood sample 3

description:
cfDNA of patient with NSCLC
SAMPLE 3

source_name: NSCLC 3


title: blood sample 4

description:
cfDNA of patient with NSCLC
SAMPLE 4

source_name: NSCLC 4


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1171


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1170


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1168


title: blood sample 1

description:
cfDNA of patient with NSCLC
SAMPLE 1

source_name: NSCLC 1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1169


title: blood sample 7

description:
cfDNA of patient with NSCLC
SAMPLE 7

source_name: NSCLC 7


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1165


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1167


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1163


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1162


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1164


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1160


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1161


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1159


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1157


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1158


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1155


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1154


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1156


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1166


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1153


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1152


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1151


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1149


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1150