title: Total RNA-seq of old brain replicate 2

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150937
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: SF_con_01

status: Public on Jul 31 2025

type: SRA

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Paired reads were demultiplexed using bcl2fastq (v2.20.0, Illumina) and only R1 used for expression (R2 mostly 3'UTR)
Adapter trimming and quality control was performed with Trim Galore! (v.0.6.4_dev)
Alignment and counting were performed using STAR (v.2.7.6a)
Assembly: Astyanax_mexicanus-2.0
Supplementary files format and content: extended_AstMex_surface_v103.gtf.gz (gzipped gene annotation files based on Ensembl v.103 release with extended 3'UTR)
Supplementary files format and content: ext103_raw_counts.tsv (tab-separated matrix of raw counts)
Supplementary files format and content: ext103_rLog2_counts.tsv (tab-separated matrix of regularized log2 counts)

molecule: total RNA

organism: Astyanax mexicanus

source_name: cardiac ventricle

extract_protocol:
RNA was extracted from individual ventricles using the Quick-RNA MicroPrep kit (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) from Lexogen.

treatment_protocol: Cryo-injury was induced on the tip of the ventricle using a copper probe pre-chilled in liquid nitrogen.

tag: tissue

value: cardiac ventricle

tag: population

value: Surface

tag: treatment

value: uninjured

tag: time (hours)


title: Total RNA-seq of old brain replicate 1

city: Stanford

first: Jae Ho

last: Lee

state: CA

address: 318 Campus Drive E200

department: Biology

country: USA

institute: Stanford University

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150936
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.

organism: Nothobranchius furzeri

source_name: brain

extract_protocol:
Individual brains from the fish were collected and snap-frozen in liquid nitrogen. The protein amount was estimated based on fresh tissue weight (assuming 5% of protein w/w) and ice-cold 1x PBS with protease/ phosphatase inhibitors (Roche,11836170001, 4906837001) was added accordingly to a final concentration of 2 μg/μL. Samples were then vortexed (5 times) before sonication (Bioruptor Plus) for 10 cycles (60 sec ON/30 sec OFF) at the high setting, at 4 °C. The samples were then centrifuged at 3000 xg for 5 min at 4 °C, and the supernatant was transferred to 2 mL Eppendorf tubes. 1.5 mL of ice-cold Qiazol (Qiagen, 79306) reagent was added to 150 μL of homogenate, vortexed five times, and snap-frozen in liquid nitrogen. On the day of the experiment, samples were thawed on ice, vortexed five times, and incubated at room temperature for 5 min before the addition of 300 μL of chloroform. Samples were mixed vigorously, incubated for 3 min at room temperature, and centrifuged at 12000 xg for 20 min at 4 °C. The upper aqueous phase (600 μL) was carefully transferred into a fresh tube and the remaining volume (phenol/chloroform phase) was kept on ice for DNA isolation. The aqueous phase was mixed with 1.1 volume of isopropyl alcohol, 0.16 volumes of sodium acetate (2 M; pH 4.0), and 1 μL of GlycoBlue (Invitrogen, AM9515) to precipitate RNA. After 10 min incubation at room temperature, samples were centrifuged at 12000 xg for 30 min at 4 °C. The supernatant was completely removed, and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500 xg for 5 min at 4 °C. The washing steps were performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 μL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65 °C for 5 min, before storage at -80 °C.
Total RNA library preparation was done by introducing 500 ng total RNA into Illumina’s NEBNext Ultra II directional mRNA (UMI) kit (NEB, E7760S), following the manufacturer’s instructions. The quality and quantity of all libraries were checked using Agilent’s Bioanalyzer 2100 and DNA 7500 kit (Agilent Technologies, 5067-1506).

value: brain

tag: strain

tag: age


title: SKNMC-sgGFP_RNA_7d_REP3_220504_GATCAG_S3

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description: SKNMC-DKO_7d_vs_SKNMC-sgGFP_7d_allSamples_diffexp_sorted_rmdup.csv

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Assembly: Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: DESeq2 differential expression summary data (.csv format)
Supplementary files format and content: .tdf files

organism: Homo sapiens

source_name: Ewing Sarcoma

extract_protocol:
For RNA isolation, cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions.
rRNA depletion and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain unique sequencing paired-end reads

value: Ewing Sarcoma

tag: cell line

value: SK-N-MC

tag: guide rna

value: sgGFP

tag: time

value: 7 days


title: Total RNA-seq of adult brain replicate 4

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150935
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: SKNMC-sgGFP_RNA_7d_REP2_220504_ACTTGA_S2


title: Hypoxia_Dam_rep4

city: Cambridge

first: Emma

last: Rawlins

address: Tennis court road

institute: University of Cambridge

library_source: genomic

data_processing:
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore
Trimmed reads for further processed by damidseq_pipeline to create bedgraph files
bedGraphToBigWig was used to create BigWig fles
Assembly: Ensembl hg38 build 110
Supplementary files format and content: BigWIg files with log2FC of fusion over dam only control
Library strategy: DamID-seq

molecule: genomic DNA

source_name: lung organoids

extract_protocol:
Marshall et al. Nat Protoc, 2016
NEBNext Ultra II DNA Library Prep kit

value: lung organoids

value: Hypoxia


title: Total RNA-seq of adult brain replicate 3

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150934
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: Total RNA-seq of adult brain replicate 2

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150933
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: Hypoxia_HIF2A_rep4


title: Total RNA-seq of adult brain replicate 1

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150932
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: Hypoxia_Dam_rep3


title: Hypoxia_HIF2A_rep3


title: Hypoxia_HIF1A_rep4


title: Hypoxia_HIF1A_rep3


title: SKNMC_RNA_DMSO_6h_REP2_230418_CAGATC_S7

description:
SKNMC_A485_6h_vs_SKNMC_DMSO_6h_diffexp_sorted_rmdup.csv
SKNMC_dCBP1_6h_vs_SKNMC_DMSO_6h_diffexp_sorted_rmdup.csv

value: 6 hours

value: DMSO


title: SKNMC_RNA_dCBP1_100nM_6h_REP2_230418_GATCAG_S9

description: SKNMC_dCBP1_6h_vs_SKNMC_DMSO_6h_diffexp_sorted_rmdup.csv

value: 1uM dCBP1


title: H4K8ac_rep3_Input_peak

city: Kunming

first: Qinyi

last: Wu

state: Yunnan

address: No.1076 Yuhua Road

country: China

institute: Yunnan University of  Chinese Medicine

description: Library name: Sample 12

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bpChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: Caenorhabditis elegans WBcel235
Supplementary files format and content: xlsx files include Peak values for each Sample

organism: Caenorhabditis elegans

source_name: Whole Organism

growth_protocol: C. elegans N2 were maintained on nematode growth media (NGM) and fed with E. coli OP50 at 20°C

extract_protocol:
The worms which fed on E. coli OP50 were collected after reaching to adult stage. The chromatin was sheared into 0.2- to 1-kb fragments. The soluble chromatin fraction was immunoprecipitated using antibodies specific for H4K5ac (Abcam, ab51997) or H4K8ac (Abcam, ab45166).
ChIP-seq libraries were prepared using the NEBNext UltraDNA library prep kit (New England Biolabs) followed with paired-end sequencing on an Illumina NovaSeq6000.

value: Whole Organism

tag: genotype

value: Bristol N2


title: H4K8ac_rep1_Input_peak

description: Library name: Sample 10

treatment_protocol: The worms which fed on E. coli OP50 were collected after reaching to adult stage


title: Hypoxia_HIF2A_rep2


title: Total RNA-seq of young brain replicate 2

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150929
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: SKNMC_RNA_dCBP1_100nM_6h_REP1_230418_TTAGGC_S3


title: Hypoxia_HIF1A_rep2


title: Total RNA-seq of young brain replicate 3

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150930
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: H4K8ac_rep2_IP_peak

description: Library name: Sample 8


title: H4K8ac_rep3_IP_peak

description: Library name: Sample 9


title: SKNMC_RNA_A485_1uM_6h_REP2_230418_ACTTGA_S8

description: SKNMC_A485_6h_vs_SKNMC_DMSO_6h_diffexp_sorted_rmdup.csv


title: Total RNA-seq of young brain replicate 1

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150928
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: H4K8ac_rep2_Input_peak

description: Library name: Sample 11


title: H4K8ac_rep1_IP_peak

description: Library name: Sample 7


title: SKNMC_RNA_A485_1uM_6h_REP1_230418_CGATGT_S2


title: SKNMC-DKO_RNA_7d_REP2_220504_GTGGCC_S11

value: sgMLL3, sgMLL4


title: TXR1 overexrpression strain, with cadmium,replicate 3, OK-seq, single-indexed

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

data_processing:
Sequence reads were identiﬁed and demultiplexed using the standard Illumina software suite and adaptor sequences were removed by Cutadapt (version 3.2). Reads >10 nt were aligned to the reference genome (T_Thermophila_MAC_2021) using the HISAT2(2.1.0) software with default parameters.
Assembly: Tetrahymena genome (SB210, 2021 version, TGD)
Supplementary files format and content: tab-delimited text files include RFD values counted in 200bp window for each Sample
Library strategy: DNA-seq

organism: Tetrahymena thermophila

growth_protocol: The asynchronous exponentially growing Tetrahymena cells cultured in 2% PPYS media to the density of 1.5-3.0 × 10 e5 /ml.

extract_protocol:
Genomic DNA was extracted by a previously described NDS extraction method followed by ethanol precipitation, dissolved in H2O, treated with RNAse A 5µl (10mg/ml) ,98oC heat denatured and chilled on ice. Okazaki fragment were isolated and biotinylated. Sequencing adaptor were ligated and Okazaki fragment capture using Strep-Magnetic beads.
Libraries were ampliﬁed in 15 cycles of PCR using bead suspension as a template, Phusion polymerase (NEB) and the following primers: Amplify F2, Amplify R2. PCR products were gel-purified to select for fragments 150–400 bp using gel elution kit (Qiagen).

treatment_protocol: The asynchronous exponentially growing Tetrahymena cells were labelled by adding 200 µM EdU (5-ethynyl-2’-deoxyuridine, ThermoFisher) for 5 min at 30°C to label newly synthesized DNA.  Cells were washed with 10 mM Tris pH 7.5 and collected by centrifugation (Petryk et al. 2016).

tag: cell type

value: vegetative growing cells

value: TXR1 overexrpression


title: H4K5ac_rep3_Input_peak

description: Library name: Sample 6


title: TXR1 overexrpression strain, with cadmium,replicate 3, OK-seq, paired-indexed


title: H4K5ac_rep2_Input_peak

description: Library name: Sample 5


title: SKNMC-DKO_RNA_7d_REP1_220504_GTAGAG_S10


title: Hypoxia_Dam_rep2


title: TXR1 overexrpression strain, with cadmium,replicate 2, OK-seq, single-indexed


title: Total RNA-seq of young brain replicate 4

data_processing:
Illumina bcl2FastQ v2.20.0.422 was used for base calling and demultiplexing.
Alignment to the reference genome was performed using STAR  with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique
To get the processed data, qlignment to the reference genome was performed using STAR  with the following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150931
Supplementary files format and content: Tab-delimited text files include: Column1: gene ID; Column2: counts for unstranded RNA-seq; Column3: counts for the 1st read strand aligned with RNA; Column 4: counts for the 2nd read strand aligned with RNA.


title: EWS502_RNA_dTAG1_1uM_24h_REP2_230830_GGCTAC_S11

description: EWS502_dTAG_24h_vs_dNEG_24h_diffexp_sorted_rmdup.csv

value: 24 hours

value: 1uM dTAG


title: H4K5ac_rep3_IP_peak

description: Library name: Sample 3


title: TXR1 overexrpression strain, with cadmium,replicate 2, OK-seq, paired-indexed


title: TXR1 overexrpression strain, with cadmium,replicate 1, OK-seq, single-indexed


title: TXR1 overexrpression strain, with cadmium,replicate 1, OK-seq, paired-indexed


title: EWS502_RNA_dNEG_1uM_24h_REP3_230830_GATCAG_S9

value: 1uM dNEG


title: EWS502_RNA_dTAG1_1uM_24h_REP1_230830_TAGCTT_S10

value: Ewing Sarcoma


title: TXR1 overexrpression strain, without cadmium,replicate 3, OK-seq, single-indexed


title: EWS502_RNA_dNEG_1uM_24h_REP2_230830_ACTTGA_S8


title: Total RNA Heart Male 15wph replicate 3

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422.
Reads were aligned to the Nothobranchius furzeri reference genome ((Nfu_20150522, annotation nfurzeri_genebuild_v1.150922) using STAR 2.7.10a (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 2.0.3 (-p -B --countReadPairs -s 2) (PMID: 24227677).
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: Counts of each gene from different samples

source_name: Heart ventricle

extract_protocol:
Total RNA was extracted from Nothobranchius furzeri (strain MZCS-08/122) ventricles using Trizol.
Preparation of libraries was done using NEBNext Ultra II directional RNA library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer‘s description.
Libraries were pooled and sequenced using a HiSeq 2500 system (San Diego, CA, USA) in 51 cycle/single-end/high-output mode.

value: Heart ventricle

tag: Sex

value: M


title: H4K5ac_rep1_Input_peak

description: Library name: Sample 4


title: TXR1 overexrpression strain, without cadmium,replicate 3, OK-seq, paired-indexed


title: EWS502_RNA_dTAG1_1uM_24h_REP3_230830_CTTGTA_S12


title: EWS502_RNA_dNEG_1uM_24h_REP1_230830_CAGATC_S7


title: Total RNA Heart Male 15wph replicate 2


title: H4K5ac_rep2_IP_peak

description: Library name: Sample 2


title: A673-sgLuc_RNA_steadystate_REP2_230830_AGTTCC_S14

description: A673-sgFLI1-1_vs_A673-sgLuc_diffexp_sorted_rmdup.csv

value: sgLuciferase

value: 7 days


title: TXR1 overexrpression strain, without cadmium,replicate 2, OK-seq, single-indexed


title: Total RNA Heart Male 15wph replicate 1


title: H4K5ac_rep1_IP_peak

description: Library name: Sample 1


title: TXR1 overexrpression strain, without cadmium,replicate 2, OK-seq, paired-indexed


title: A673-sgLuc_RNA_steadystate_REP1_230830_AGTCAA_S13


title: TXR1 overexrpression strain, without cadmium,replicate 1, OK-seq, single-indexed


title: Total RNA Heart Male 46wph replicate 2


title: A673-sgGFP_RNA_8d_REP2_211203_TAGCTT_S6

description: A673_DKO_vs_GFP_8d_allSamples_diffexp_sorted_rmdup.csv

value: sgGFP

value: 8 days


title: A673-sgGFP_RNA_8d_REP1_211203_GATCAG_S5


title: Total RNA Heart Male 46wph replicate 1


title: TXR1 overexrpression strain, without cadmium,replicate 1, OK-seq, paired-indexed


title: A673-sgFLI1-2_RNA_steadystate_REP2_230830_GTCCGC_S18


title: TXR1 knockout, replicate 3, OK-seq, single-indexed

value: TXR1 knockout


title: Total RNA Fin Male 5wph replicate 4

data_processing:
Sequence information was extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422, against the Nothobranchius furzeri reference genome (Nfu_20150522, annotation nfurzeri_genebuild_v1.150922). Alignment to the reference genome was performed using STAR with the following parameters: --outSAMmultNmax 1 --outFilterMultimapNmax 1 -- outFilterMismatchNoverLmax 0.04 --sjdbOverhang 99 --alignIntronMax 1000000 -- outSJfilterReads Unique. The deduplication step was performed using the umi_tool v1.1.1, using the following parameters: extract --bcpattern= NNNNNNNNNNN`, `dedup --chimeric-pairs discard --unpaired-reads discard -- paired.
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: Counts of each gene from different samples

source_name: Fin clip

extract_protocol:
Individual brains from the fish were collected and snap-frozen in liquid nitrogen. The protein amount was estimated based on fresh tissue weight (assuming 5% of protein w/w), and ice-cold 1x PBS with protease/ phosphatase inhibitors (Roche,11836170001, 4906837001) was added accordingly to a final concentration of 2 μg/μL. Samples were then vortexed (5 times) before sonication (Bioruptor Plus) for 10 cycles (60 sec ON/30 sec OFF) at the high setting, at 4 °C. The samples were then centrifuged at 3000 xg for 5 min at 4 °C, and the supernatant was transferred to 2 mL Eppendorf tubes. 1.5 mL of ice-cold Qiazol (Qiagen, 79306) reagent was added to 150 μL of homogenate, vortexed five times, and snap-frozen in liquid nitrogen. On the day of the experiment, samples were thawed on ice, vortexed five times, and incubated at room temperature for 5 min before adding 300 μL of chloroform. Samples were mixed vigorously, incubated for 3 min at room temperature, and centrifuged at 12000 xg for 20 min at 4 °C. The upper aqueous phase (600 μL) was carefully transferred into a fresh tube, and the remaining volume (phenol/chloroform phase) was kept on ice for DNA isolation. The aqueous phase was mixed with 1.1 volume of isopropyl alcohol, 0.16 volumes of sodium acetate (2 M; pH 4.0), and 1 μL of GlycoBlue (Invitrogen, AM9515) to precipitate RNA. After 10 min incubation at room temperature, samples were centrifuged at 12000 xg for 30 min at 4 °C. The supernatant was completely removed, and RNA pellets were washed by adding 80% (v/v) ethanol and centrifuging at 7500 xg for 5 min at 4 °C. The washing steps were performed twice. The resulting pellets were air-dried for no more than 5 min and dissolved in 10 μL nuclease-free water. To ensure full dissolution of RNA in water, samples were then incubated at 65 °C for 5 min, before storage at -80 °C.
quality check and quantification of total RNA was done using the Agilent Bioanalyzer 2100 in combination with the RNA 6000 pico kit (Agilent Technologies, 5067-1513). Total RNA library preparation was done by introducing 500 ng total RNA into Illumina’s NEBNext Ultra II directional mRNA (UMI) kit (NEB, E7760S), following the manufacturer’s instructions. The quality and quantity of all libraries were checked using Agilent’s Bioanalyzer 2100 and DNA 7500 kit (Agilent Technologies, 5067-1506).

value: Fin clip


title: Total RNA Heart Male 46wph replicate 3


title: A673-sgFLI1-2_RNA_steadystate_REP1_230830_GTAGAG_S17


title: Total RNA Fin Male 5wph replicate 3


title: TXR1 knockout,replicate 2, OK-seq, single-indexed


title: A673-sgFLI1-1_RNA_steadystate_REP2_230830_CCGTCC_S16


title: TXR1 knockout,replicate 2, OK-seq, paired-indexed


title: ATCC19606 lpxD knockout mutant biol rep 3

city: Yangzhou

first: JIngchen

last: Hao

address: No. 136, Jiangyang Middle Road

institute: Yangzhou University

description: Library name: lpxD_3

data_processing:
featureCounts (2.0.6) 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.
Assembly: Genome assembly ASM903584v1
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Acinetobacter baumannii

source_name: Bacteria

extract_protocol:
Total bacterial RNA extraction was performed using RNAprep PureCell/Bacteria Kit (TIANGEN) following manufacturer's protocols.
Ribosomal RNA was removed from the total RNA and then precipitated with ethanol.   After fragmentation, the first strand cDNA was synthesized using random hexamer primers.   During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer.   The directional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

value: Bacteria

value: Gram-negative coccobacillus


title: Total RNA Fin Male 5wph replicate 2


title: TXR1 knockout, replicate 3, OK-seq, paired-indexed


title: Total RNA Fin Male 5wph replicate 1


title: A673-sgFLI1-1_RNA_steadystate_REP1_230830_ATGTCA_S15


title: TXR1 knockout, replicate 1, OK-seq, single-indexed


title: SKNMC-sgGFP_RNA_7d_REP1_220504_CAGATC_S1

value: SK-N-MC


title: ATCC19606 lpxD knockout mutant biol rep 2

description: Library name: lpxD_2


title: A673-DKO_RNA_8d_REP2_211203_GGTAGC_S8

value: sgMLL3, sgMLL4


title: Total RNA Fin Male 39wph replicate 4


title: A673-DKO_RNA_8d_REP1_211203_CTTGTA_S7


title: SKNMC_RNA_DMSO_6h_REP1_230418_ATCACG_S1

value: 6 hours

value: DMSO


title: Total RNA Fin Male 39wph replicate 3


title: TXR1 knockout, replicate 1, OK-seq, paired-indexed

value: vegetative growing cells


title: ATCC19606 lpxD knockout mutant biol rep 1

description: Library name: lpxD_1


title: ATCC19606 lpxC knockout mutant biol rep 3

description: Library name: lpxC_3


title: Wild type cells, replicate 3, OK-seq, single-indexed

value: WT


title: Total RNA Fin Male 39wph replicate 2


title: A673-dHALO_RNA_VH0032_1uM_24h_REP3_230830_GCCAAT_S6

description: A673-dHALO_VH0032_24h_vs_DMSO_24h_diffexp_sorted_rmdup.csv

value: Ewing Sarcoma

value: 24 hours


title: ATCC19606 lpxC knockout mutant biol rep 2

description: Library name: lpxC_2


title: Wild type cells, replicate 3, OK-seq, paired-indexed


title: Total RNA Fin Male 39wph replicate 1

value: M


title: A673-dHALO_RNA_VH0032_1uM_24h_REP2_230830_ACAGTG_S5


title: ATCC19606 lpxC knockout mutant biol rep 1

description: Library name: lpxC_1


title: Wild type cells, replicate 2, OK-seq, single-indexed


title: A673-dHALO_RNA_VH0032_1uM_24h_REP1_230830_TGACCA_S4


title: Total RNA Fin Male 13wph replicate 4


title: ATCC19606 biol rep 3

description: Library name: ATCC19606_3


title: Wild type cells, replicate 2, OK-seq, paired-indexed


title: A673-dHALO_RNA_DMSO_24h_REP3_230830_TTAGGC_S3


title: Total RNA Fin Male 13wph replicate 3


title: Wild type cells, replicate 1, OK-seq, single-indexed


title: ostrich embryonic stem cells rep2, p14

city: Pasadena

first: Xi

last: Chen

state: California

address: 1200 E. California Blvd

institute: California Institute of Technology

description: Library name: sample6

data_processing:
STAR alignment, RSEM quantification, DESeq for differential expression
Assembly: quail reference genome (Ensembl Coturnix_japonica.Coturnix_japonica_2.0.113), goose reference genome (Ensembl Anser_cygnoides.GooseV1.0.113), Ostrich reference genome (Ensembl Struthio_camelus_australis.ASM69896v1.113)
Supplementary files format and content: txt format, including raw counts, gene length, etc

organism: Struthio camelus australis

source_name: freshly laid EGK.X embryo

growth_protocol: Freshly laid avian fertile eggs at EGK.X-XII stages were kept at 16 °C before extraction. To harvest cells from yolk, a filter paper-based method was applied (Chapman et al., 2001). Filter paper with a hole at center was placed on top of the embryo. The outer edge of the filter paper was cut together with the vitelline membranes. Embryo were then released from yolk together with the filter paper and washed in PBS solution. Next, embryo was transferred into a 15ml tube free of the paper ring and dissociated by pipetting inside N2B27 medium. Dissociated cells were cultured in tissue plates coated with irradiated mouse embryonic fibroblast (MEF) cells as feeder layer. Basal medium used for routine ESC maintenance was N2B27 medium composed of DMEM/F12:Neuralbasal (1:1) plus 0.5x N2, 0.5x B27 supplement and 20ng/ml ovotransferrin with the addition of 1x penicillin-streptomycin. Avian ESC self-renewal was kept with 2µM IWR-1, 2.5µM Gö6983, 2µM SB431542. Quail and goose ESCs were treated with additional chicken LIF at 10ng/ml. ESCs were cultured at 38 °C in 5% CO2 with daily medium change. To passage, TrypLE was used to incubate the cells for 5 min and neutralized with basal medium in triple amount. Cells were handled with 5ml pipette all the time to avoid dissociation into singles.

extract_protocol:
Total RNA of in-vitro expanded cells was extracted using the RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
RNA-seq

value: freshly laid EGK.X embryo

value: oES p14

value: embryonic stem cells


title: Total RNA Fin Male 13wph replicate 2


title: A673-dHALO_RNA_DMSO_24h_REP1_230830_ATCACG_S1


title: Wild type cells, replicate 1, OK-seq, paired-indexed


title: ATCC19606 biol rep 2

description: Library name: ATCC19606_2


title: ostrich embryonic stem cells rep1, p14

description: Library name: sample5


title: Left parotid BCAC

type: genomic

city: Montreal

first: Fiona

last: Chan Pak Choon

state: QC

address: 3755 Côte-Sainte-Catherine

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner and processed with Chromosome Analysis Suite (ChAS) v4.2, following the manufacturer’s standard procedures

data_processing:
Arrays were analysed using Affymetrix Chromosome Analysis Suite (ChAS) v4.2 with the GRCh37/hg19 reference genome. CNVs were called using a minimum threshold of 20 markers and 50 kb in length; LOH regions were called with ≥50 markers and ≥5 Mb. Regions were manually reviewed and filtered using the Database of Genomic Variants (DGV) to exclude common or artefactual events
[primary data description] Raw array data include CEL and OSCHP files for each sample. CEL files contain probe-level intensity data generated from the OncoScan CNV array. OSCHP files represent processed outputs containing summarised signal data, copy number, and loss of heterozygosity (LOH) metrics. Genotype calls include AA, AB, BB, NoCall, and NC

label: Biotin

source_name: Left parotid BCAC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumour tissues using standard protocols for FFPE and fresh frozen samples, followed by quantification and quality control prior to array processing

value: Left parotid BCAC

value: male


title: Right parotid BCAC

source_name: Right parotid BCAC

value: Right parotid BCAC


title: Submandibular BCAC

source_name: Submandibular BCAC

value: Submandibular BCAC


title: Differentiated LUHMES with 4sU Rep2

status: Public on Jul 30 2025

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description: Library name: diff_0h_4sU_2

data_processing:
Quality of the sequencing data was checked using FastQC (version 0.11.9). RNA-seq reads were mapped against the (i) the human genome (GRCh38/hg38), (ii) human rRNA sequences and (iii) the HSV-1 genome (HSV-1 strain 17, GenBank accession code: JN555585), using ContextMap 2 (version 2.7.9) using BWA as short read aligner and with default parameters. SAM output files of ContextMap2 were converted to BAM files using samtools. Number of read fragments per gene were determined from BAM files in a strand-specific manner using featureCounts and gene annotations from Ensembl (version 100). All these steps were implemented and run using the Watchdog workflow management system.
Assembly: GRCh38/hg38, JN555585
Supplementary files format and content: read counts per gene, tab separated file

source_name: LUHMES

extract_protocol:
Cells were lysed in TRIzol and RNA col-lected with the Direct-zol RNA Miniprep kit (Zymo Research #R2050).
Total RNA was treated with DNase I and then Ribo-Zero before fragmentation to 130-160nt.  cDNA synthesis was combined with End Repair Mix, then add A-Tailing Mix,  then the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix before  Ampure XP Beads purification. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which have more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and paired-end 100 base reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

value: LUHMES

value: RNA in 90 microliters of 1xPBS was combined with 90 microliters of 20mM iodoacetamide for 20min at 50 degrees C.  Reactions were quenched with 20 microliters of 1M DTT, and incubated on ice for 30min before purification with Qiagen mRNeasy kit.


title: Differentiated LUHMES Rep2

description: Library name: diff_0h_no4sU_2


title: Undifferentiated LUHMES cells with 4sU Rep2

description: Library name: undiff_4sU_2


title: A673-dHALO_RNA_DMSO_24h_REP2_230830_CGATGT_S2

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Assembly: Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Supplementary files format and content: GRCh38/hg38
Supplementary files format and content: DESeq2 differential expression summary data (.csv format)
Supplementary files format and content: .tdf files


title: Total RNA Fin Male 13wph replicate 1

value: Fin clip


title: Undifferentiated LUHMES cells Rep2

description: Library name: undiff_no4sU_2


title: Differentiated LUHMES with 4sU Rep1

description: Library name: diff_0h_4sU_1


title: Differentiated LUHMES Rep1

description: Library name: diff_0h_no4sU_1


title: Undifferentiated LUHMES cells Rep1

description: Library name: undiff_no4sU_1


title: Undifferentiated LUHMES cells with 4sU Rep1

description: Library name: undiff_4sU_1


title: PG4

city: Shanghai

first: Chenxiao

last: Zhang

state: Shanghai

address: 227 South Chongqing Road

institute: Shanghai Jiao Tong University

description: Library name: PG4

data_processing:
After sequencing, the raw reads were filtered using the SOAPnuke (v1.5.2) with the following parameters: -n 0.01 -I 20 -q 0.4 --adaMR 0.25 –ada_trim –polyX 50 –minReadLen 150 so that the adapter was removed if the read matches 25% or more of the adapter sequence (maximum 2 base pairs mismatches were allowed) and the reads were discarded if matches the following criteria: 1) if the read length is less than 150bp; 2) if the N content in the read accounts for 1% or more of the entire read; 3) if the length of base pair repeats in the read exceeds 50bp; 4) if 40% or more of the base pairs in the read with the quality score less than 20. After quality control, the average clean reads for each sample were approximately 24M with Q30 > 92%. Then the reads were aligned onto the human genome GRCh38 using STAR (v2.7.2a) and counted using featureCounts (v2.0.3).
Assembly: GRCh38
Supplementary files format and content: Raw counts in tab-delimtied format (.txt)

source_name: Peripheral Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from blood in the lavender tube via density gradient centrifugation using Lymphoprep (Serumwerk Bernburg AG, #1858,). Total RNA was extracted using the Takara RNA extraction kit (Takara, TKR-9109).
Eukaryotic mRNA library was constructed and downstream sequencing was performed using the DNBSEQ platform (150 bp paired-end).

value: Peripheral Blood

tag: disease state

value: PG


title: PE3

description: Library name: PE3

value: PE


title: PG2

description: Library name: PG2


title: PG1

description: Library name: PG1


title: PG3

description: Library name: PG3


title: PE2

description: Library name: PE2


title: PE1

description: Library name: PE1


title: GDM5

description: Library name: GDM5

value: GDM


title: GDM4

description: Library name: GDM4


title: GDM3

description: Library name: GDM3


title: GDM2

description: Library name: GDM2


title: CTL5

description: Library name: CTL5

value: CTL


title: CTL4

description: Library name: CTL4


title: CTL1

description: Library name: CTL1


title: CTL2

description: Library name: CTL2


title: PC3 cells, ShARF, vehicle

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

description: According to manufacturer's protocol

data_processing:
RNA sequencing data were analyzed by using Qiagen CLC Genomics Workbench (GWB) V 23.0.5. Sequencing reads were first adapters trimmed with GWB “Trim Reads” tool then mapped to Human hg38 genome with default setting.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for all samples

growth_protocol: PC3 cells were cultured in complete medium (DMEM, supplemented with 10% fetal bovine serum, 1% penicillin/ streptomycin) in humdified atmoposphere with 5% CO2 at 37 degrees

extract_protocol:
Total RNA was extracted using GenElute™ Total RNA Purification Kit
RNA libraries for RNA-seq were prepared following manufacturer's protocols.

treatment_protocol: PC3 cells were treated with MLN4924 or DMSO at a final concentration 1µM

value: prostatic adenocarcinoma

value: Sh ARF

value: DMSO


title: PC3 cells, MLN4924

description: According to manufacturer's protocol

value: wt


title: PC3 cells, ShARF, MLN4924

description: According to manufacturer's protocol


title: Human breast cancer patient270

city: Gothenburg

first: Axel

last: Stenmark Tullberg

address: Bla Straket

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8101.v1_24R07C01

hyb_protocol: Bisulfite-converted DNA was hybridized to the Illumina Infinium Methylation EPIC array (MethylationEPIC_v-1-0_B5) according to the manufacturer's standard Infinium HD Methylation Assay protocol.

scan_protocol: Illumina Infinium-compatible scanner

data_processing:
Raw intensity data (IDAT files) from the Illumina Infinium Methylation EPIC array were processed using GenomeStudio (v2011.1) from Illumina Inc. Data processing included background subtraction and normalization using GenomeStudio's 'Normalization Controls' feature, as per Illumina's recommendations. Samples were considered acceptable if their probe call rate exceeded 98% at a detection p-value of 0.01. Individual marker loci with a detection p-value > 0.01 were excluded. Processed data refers to Beta values mapped to Genome Build 37 (hg19). The final methylation profile is provided in a matrix format.
Processed values are reported as Beta values, representing the methylation level at each CpG site. Beta values range from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

source_name: Breast cancer

label_protocol: Genomic DNA (250 ng per sample) underwent bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Product No: D5004) according to the manufacturer's protocol. Bisulfite-converted DNA was eluted in 15µl, evaporated to a volume of <4µl, and then processed for the Illumina Infinium Methylation EPIC array.

growth_protocol: Samples were cryopreserved

extract_protocol: Genomic DNA was extracted from fresh-frozen or formalin-fixed paraffin-embedded samples using a standard spin-column based DNA extraction method, according to established laboratory protocols.

treatment_protocol: No treatment

value: Breast cancer

value: Pretreatment

value: Positive

tag: proliferativeindex

tag: immunescore


title: PC3 cells, vehicle

description: According to manufacturer's protocol


title: GDM1

description: Library name: GDM1


title: Human breast cancer patient269

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9448.v1_24R06C01


title: CTL3

description: Library name: CTL3


title: Human breast cancer patient267

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9227.v1_24R01C01


title: Human breast cancer patient268

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9247.v1_24R04C01


title: Human breast cancer patient265

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8439.v1_23R07C01


title: Human breast cancer patient264

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7919.v1_23R06C01


title: Human breast cancer patient262

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9361.v1_23R03C01


title: Human breast cancer patient263

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7591.v1_23R04C01


title: Human breast cancer patient260

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10225.v1_23R01C01


title: Human breast cancer patient261

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8073.v1_23R02C01


title: Human breast cancer patient259

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8947.v1_22R07C01


title: Human breast cancer patient257

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8009.v1_22R03C01


title: Human breast cancer patient258

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8966.v1_22R06C01


title: Human breast cancer patient255

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10501.v1_21R07C01


title: Human breast cancer patient266

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7484.v1_23R08C01


title: Human breast cancer patient254

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8490.v1_21R06C01


title: Human breast cancer patient256

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8596.v1_22R01C01


title: Human breast cancer patient252

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10903.v1_21R04C01


title: Human breast cancer patient253

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7456.v1_21R05C01


title: Human breast cancer patient250

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6866.v1_21R01C01


title: Human breast cancer patient251

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7854.v1_21R02C01


title: Human breast cancer patient245

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9192.v1_20R01C01


title: Human breast cancer patient247

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8390.v1_20R05C01


title: Human breast cancer patient246

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6782.v1_20R04C01


title: Human breast cancer patient249

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8156.v1_20R08C01


title: Human breast cancer patient244

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11009.v1_19R08C01


title: ATCC19606 under phage pressure biol rep 1

description: Library name: pATCC19606_1

value: Bacteria

value: Gram-negative coccobacillus


title: ATCC19606 lpxD knockout mutant under phage pressure biol rep 1

description: Library name: plpxD_1


title: ATCC19606 lpxD knockout mutant under phage pressure biol rep 2

description: Library name: plpxD_2


title: ATCC19606 under phage pressure biol rep 3

description: Library name: pATCC19606_3


title: ATCC19606 lpxD knockout mutant under phage pressure biol rep 3

description: Library name: plpxD_3


title: ATCC19606 lpxC knockout mutant under phage pressure biol rep 2

description: Library name: plpxC_2


title: ATCC19606 lpxC knockout mutant under phage pressure biol rep 3

description: Library name: plpxC_3


title: ATCC19606 under phage pressure biol rep 2

description: Library name: pATCC19606_2


title: Human breast cancer patient243

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10175.v1_19R07C01


title: ATCC19606 lpxC knockout mutant under phage pressure biol rep 1

description: Library name: plpxC_1


title: Human breast cancer patient248

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9212.v1_20R06C01


title: Human breast cancer patient241

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11217.v1_19R05C01


title: Human breast cancer patient239

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9099.v1_18R08C01


title: Human breast cancer patient240

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_5474.v1_19R02C01


title: Human breast cancer patient237

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7569.v1_18R06C01


title: Human breast cancer patient236

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11127.v1_18R04C01


title: Human breast cancer patient235

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8199.v1_18R03C01


title: Human breast cancer patient234

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8816.v1_18R02C01


title: Human breast cancer patient232

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7442.v1_17R08C01


title: Human breast cancer patient231

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11020.v1_17R07C01


title: Human breast cancer patient233

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7374.v1_18R01C01


title: Human breast cancer patient230

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7711.v1_17R06C01


title: Human breast cancer patient227

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8242.v1_17R01C01


title: Human breast cancer patient226

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8982.v1_16R08C01


title: Human breast cancer patient229

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6211.v1_17R04C01


title: Human breast cancer patient228

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_5522.v1_17R02C01


title: Human breast cancer patient222

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9894.v1_16R04C01


title: Human breast cancer patient225

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8021.v1_16R07C01


title: Human breast cancer patient223

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11355.v1_16R05C01


title: Human breast cancer patient242

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7715.v1_19R06C01


title: Human breast cancer patient221

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8304.v1_16R03C01


title: Human breast cancer patient220

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8143.v1_16R02C01


title: Human breast cancer patient219

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9719.v1_16R01C01


title: Human breast cancer patient218

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6898.v1_15R06C01


title: Human breast cancer patient217

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6671.v2_15R04C01


title: Human breast cancer patient216

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10633.v1_15R03C01


title: Human breast cancer patient215

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6893.v1_14R08C01


title: Human breast cancer patient214

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_4282.v1_14R06C01


title: Human breast cancer patient212

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11353.v1_14R04C01


title: Human breast cancer patient210

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9386.v1_14R02C01


title: Human breast cancer patient209

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6688.v1_14R01C01


title: Human breast cancer patient224

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8398.v1_16R06C01


title: Human breast cancer patient207

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7454.v2_13R04C01


title: Human breast cancer patient205

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8049.v1_13R01C01


title: Human breast cancer patient206

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7847.v1_13R02C01


title: Human breast cancer patient198

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7450.v1_11R08C01


title: Human breast cancer patient202

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9387.v1_12R06C01


title: Human breast cancer patient201

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_4272.v1_12R05C01


title: Human breast cancer patient196

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9492.v1_11R06C01


title: Human breast cancer patient194

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9248.v1_11R02C01


title: Human breast cancer patient211

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11196.v1_14R03C01


title: Human breast cancer patient200

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9762.v1_12R02C01


title: Human breast cancer patient190

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9311.v1_10R05C01


title: Human breast cancer patient197

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_10297.v1_11R07C01


title: Human breast cancer patient204

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9468.v1_12R08C01


title: Human breast cancer patient199

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7545.v1_12R01C01


title: Human breast cancer patient213

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8527.v2_14R05C01


title: Human breast cancer patient195

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7878.v1_11R04C01


title: Human breast cancer patient186

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8891.v1_10R01C01


title: Human breast cancer patient182

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_4742.v1_9R02C01


title: Human breast cancer patient180

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8716.v1_8R08C01


title: Human breast cancer patient193

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9964.v1_11R01C01


title: Human breast cancer patient208

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_4675.v1_13R07C01


title: Human breast cancer patient189

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11209.v1_10R04C01


title: Human breast cancer patient178

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_8628.v1_8R05C01


title: Human breast cancer patient192

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9869.v1_10R07C01


title: Human breast cancer patient177

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9585.v1_8R04C01


title: Human breast cancer patient203

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7135.v1_12R07C01


title: Human breast cancer patient188

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_6662.v2_10R03C01


title: Human breast cancer patient175

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7334.v1_8R02C01


title: Human breast cancer patient176

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_11015.v1_8R03C01


title: Human breast cancer patient185

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7121.v1_9R08C01


title: Human breast cancer patient174

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_7525.v1_7R08C01


title: Human breast cancer patient184

description:
Single-base extension was performed using hapten-labeled dideoxynucleotides, followed by multi-layered fluorescent staining with streptavidin-Cy3 and anti-DNP-Cy5 to detect incorporated labels.
Methylation analysis was performed of ER-positive tumors to identify tumor-intrinsic characteristics associated with immune responsiveness. The S04 epithelial cell state was associated with immune responsiveness while the S05 epithelial cell trate predicted immune evasion.
Illumina EPIC v1-0_B5 array
KAPE1_9602.v1_9R07C01