title: T23 Hepatocyte RIPK1 konck out mouse liver, Fasted 12h

city: Nanjing

first: Dan

last: Weng

address: 200 Xiaolingwei Street

institute: Nanjing University of Science and Technology

description:
Library name: Sample 10
T23

data_processing:
The quality information of raw data in FASTQ  format was calculated and then the raw data was filtered using fastp(0.22.0) software. data processing step：Reference genome index was built by HISAT2 (v2.1.0) and the filtered reads were mapping to the reference genome using HISAT2.
Assembly: mm10
Supplementary files format and content: text fIles include raw counts for each Sample

source_name: liver

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the  concentration, quality and integrity were determined using a NanoDrop spectrophotometer  (Thermo Scientific).
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA  was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

value: liver

value: Hepatocyte RIPK1 knock out mouse

value: Fasted 12h


title: M51V3-NT

status: Public on Jan 11 2025

type: SRA

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
RNA was sequenced using Illumina NextSeq (HO) 150 cycle Sequencing.
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Reference and Annotation: GRCh38 from ENSEMBL
Assembly: GRCh38 from ENSEMBL
Supplementary files format and content: tab delimited text file of Raw counts of each smples  Generated using Bioconductor R package Rsubread and featureCounts function
Supplementary files format and content: tab delimited text file of counts per million of each smples

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Cells were lysed with RLT Plus Buffer (QIAGEN, Cat. No. 1053393)followed by RNA purifcationusing RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to manufacturer’s protocol.
RNA-seq libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen; Cat. No. 015) with the UMI add-on kit.

treatment_protocol: PBMC from PCSK9_inhibitor treated subjects (n = 3) and placebo controls (n = 3) and stimulated them with the TLR4 ligand LPS (1 ug /ml for 2 hours).TLR ligand (LPS) were obtained from InvivoGen

tag: tissue

value: Blood

tag: patient visit

tag: cell type

value: peripheral blood mononuclear cells

tag: sample type

value: placebo

tag: treatment

value: NO treatment(NT)


title: T22 Hepatocyte RIPK1 konck out mouse liver, Fasted 12h

country: China

description:
Library name: Sample 9
T22

organism: Mus musculus

tag: genotype


title: T12 WT control mouse liver, Fasted 12h

description:
Library name: Sample 6
T12

value: WT control mouse


title: M51V2-NT


title: M50V3-LPS

value: LPS treatment(LPS)


title: M50V3-NT


title: T11 WT control mouse liver, Fasted 12h

description:
Library name: Sample 5
T11


title: CKZ2 Hepatocyte RIPK1 konck out mouse liver,Fed

description:
Library name: Sample 4
CKZ2

value: Fed


title: M50V2-LPS


title: CKZ1 Hepatocyte RIPK1 konck out mouse liver,Fed

description:
Library name: Sample 3
CKZ1


title: M50V2-NT


title: M49V3-LPS


title: CK2 WT control mouse liver, Fed

description:
Library name: Sample 2
CK2


title: M49V3-NT


title: CK1 WT control mouse liver, Fed

description:
Library name: Sample 1
CK1


title: M49V2-NT


title: WT control mouse liver, Fasted 12h

description:
Library name: Sample 1
10 x Genomics

library_source: transcriptomic single cell

data_processing:
Mapping to mm10 mouse genome, quality control and read counting of Ensembl genes was performed by cellranger software with default parameter (v2.1.0)
Cells with more than or equal 200 genes and less than or equal 10% percentage of mitochondrial genes detected were retained for subsequent analyses
Normalization, dimensionality reduction and clustering of single cells were also performed by cellranger.
Assembly: mm10
Supplementary files format and content: TSV

molecule: polyA RNA

extract_protocol:
Tissues were dissociated using Miltenyi-Tumor Dissociation Kit.The cells were washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics Chromium.
GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling.The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: WT control


title: Hepatocyte RIPK1 konck out mouse liver, Fasted 12h

description:
Library name: Sample 2
10 x Genomics

value: Hepatocyte RIPK1 knock out


title: 6m-WT,replicate 3

city: shanghai

first: danhong

last: wu

address: 3rd Floor, Building 2, 801 Heqing Road, Shanghai

department: Department of Neurology

institute: Shanghai Fifth People’s Hospital, Fudan University

description: Library name: sample6

data_processing:
The quality of the sequencing data was evaluated using Q30 metrics. Low-quality reads and 3' adapter sequences were removed using the Cutadapt software (version 1.9.3).
The remaining high-quality reads were then aligned to the reference genome using the HISAT2 software (v2.0.4). The raw counts were generated using HTSeq software (version 0.9.1).
Transcripts per kilobase million (TPM) were calculated to assess similarities and differences between samples.
The identification of differentially expressed genes (DEGs) was conducted using the edgeR (v3.16.5) software, which involved the normalization of raw counts and the calculation of fold change between the two sample groups. A gene was considered to be differentially expressed if the p-value was less than 0.05 and the fold change was greater than or equal to 2.
Assembly: mm10
Supplementary files format and content: gene expression for all samples  Column A: gene_id, the gene identifier. Column B ~ G: counts of all samples of the gene. Column H ~ M: normalized counts by edgeR. Column N ~ W: annotation of the genes.
Supplementary files format and content: The table contains the mRNA raw count and normalized counts identified by each sample

source_name: Hippocampus

extract_protocol:
total RNA was initially subjected to ribosomal RNA (rRNA) depletion through the use of the GenSeq® rRNA Removal Kit (GenSeq, Inc.), in accordance with the instructions provided by the manufacturer. Subsequently, the rRNA-depleted samples were processed for library construction using the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.).
The quality and quantity of the library were evaluated using the Agilent Bioanalyzer 2100 system (Agilent Technologies, Inc., USA). The sequencing was conducted on an Illumina NovaSeq platform, resulting in the generation of 150 bp paired-end reads.

value: Hippocampus

tag: age

value: 6 months

value: WT


title: M45V3-LPS


title: M45V3-NT


title: M51V2-LPS


title: M45V2-LPS


title: 6m-WT,replicate 1

description: Library name: sample4


title: T13 WT control mouse liver, Fasted 12h

description:
Library name: Sample 7
T13


title: M45V2-NT


title: T21 Hepatocyte RIPK1 konck out mouse liver, Fasted 12h

description:
Library name: Sample 8
T21


title: 6m-5xFAD,replicate 3

description: Library name: sample3


title: M42V3-LPS


title: 6m-5xFAD,replicate 2

description: Library name: sample2


title: 6m-5xFAD,replicate 1

description: Library name: sample1


title: M42V2-LPS


title: M42V2-NT


title: Stem recipient-P14 donor cells, chronic LCMV, day 15 post-transfer

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

description:
Library name: Sample 3
10x genomics

data_processing:
Following sequencying samples were aligned using Cellranger 7.0.1 exculding intron reads
Count data was analyzed using Seurat V4 R package
Assembly: mm10
Supplementary files format and content: HDF5

source_name: spleen

extract_protocol:
Flow sorted CD8 T cells were captured using 10x chromium according to manufacture's protocol
cDNA library pepared using 10x genomics 5' V2 library prep

value: spleen

value: CD8 T cell

tag: sample group

value: chronic LCMV, day 15 post-transfer


title: M37V3-LPS


title: M49V2-LPS


title: M37V3-NT


title: Sample29_Naïve 3

description:
Library name: Sample29
combined_counts_Sub.csv

data_processing:
Reads were aligned using HISAT2 version 2.0.5 and count data was from featurecounts from the subread package
Count Data was analyzed using DESeq2
Assembly: mm10 genome
Supplementary files format and content: CSV (comma seperated values)

extract_protocol:
RNA was isolated using AllPrep DNA/RNA micro kit (Qiagen) according to manufacturers protocol
TakaraBio's SMART-Seq v4 Ultra Low Input RNA Kit with Illumina's Nextera XT DNA Library Preparation Kit

treatment_protocol: Cells were sorted from LCMV infected mice. Armstrong or Clone 13. Day 5 or Day 45.

value: Naïve


title: M37V2-LPS


title: Stem recipient- Endogenous GP33+ CD8+ T cells, chronic LCMV, day 15 post-transfer

description:
Library name: Sample 4
10x genomics


title: 6m-WT,replicate 2

description: Library name: sample5


title: LCMV-specific GP33+ CD8+ T cells, chronic LCMV, day >45 post-infection

description:
Library name: Sample 2
10x genomics

value: chronic LCMV, day >45 post-infection


title: Sample27_Naïve 1

description:
Library name: Sample27
combined_counts_Sub.csv


title: LCMV-specific GP33+ CD8+ T cells, chronic LCMV, day 5 post-infection

description:
Library name: Sample 1
10x genomics

value: chronic LCMV, day 5 post-infection


title: M36V3-LPS

value: Blood

value: peripheral blood mononuclear cells


title: Sample26_Arm hi Day5 TD 3

description:
Library name: Sample26
combined_counts_Sub.csv

value: Arm hi Day5 TD


title: Sample24_Arm hi Day5 TD 1

description:
Library name: Sample24
combined_counts_Sub.csv


title: M36V3-NT

value: placebo

value: NO treatment(NT)


title: Sample25_Arm hi Day5 TD 2

description:
Library name: Sample25
combined_counts_Sub.csv


title: M36V2-NT


title: Sample23_Arm hi Day5 Stem 3

description:
Library name: Sample23
combined_counts_Sub.csv

value: Arm hi Day5 Stem


title: Sample22_Arm hi Day5 Stem 2

description:
Library name: Sample22
combined_counts_Sub.csv


title: M36V2-LPS

value: LPS treatment(LPS)


title: M35V3-LPS


title: M35V3-NT


title: Sample21_Arm hi Day5 Stem 1

description:
Library name: Sample21
combined_counts_Sub.csv


title: M42V3-NT


title: M35V2-LPS


title: Sample18_Clone 13 Day5 Stem 3

description:
Library name: Sample18
combined_counts_Sub.csv

value: Clone 13 Day5 Stem


title: M35V2-NT


title: Sample20_Clone 13 Day5 TD 3

description:
Library name: Sample20
combined_counts_Sub.csv

value: Clone 13 Day5 TD


title: Sample28_Naïve 2

description:
Library name: Sample28
combined_counts_Sub.csv


title: Sample19_Clone 13 Day5 TD 1

description:
Library name: Sample19
combined_counts_Sub.csv


title: M32V3-LPS


title: M32V3-NT


title: M32V2-LPS


title: M37V2-NT


title: M31V3-LPS


title: Sample17_Clone 13 Day5 Stem 2

description:
Library name: Sample17
combined_counts_Sub.csv


title: Sample16_Clone 13 Day5 Stem 1

description:
Library name: Sample16
combined_counts_Sub.csv


title: M32V2-NT


title: M31V2-NT


title: Sample15_Naïve (CD44lo PD-1- uninfected mouse) 3

description:
Library name: Sample15
Dan_RNAseq_Raw_Counts.csv
p20177-s015_15_S48

value: Naïve (CD44lo PD-1- uninfected mouse)


title: M31V2-LPS


title: Sample14_Naïve (CD44lo PD-1- uninfected mouse) 2

description:
Library name: Sample14
Dan_RNAseq_Raw_Counts.csv
p20177-s014_14_S47


title: M31V3-NT


title: Sample11_day 48 TD (Tim-3+) 2

description:
Library name: Sample11
Dan_RNAseq_Raw_Counts.csv
p20177-s011_11_S44

value: day 48 TD (Tim-3+)


title: M28V3-LPS


title: Sample12_day 48 TD (Tim-3+) 3

description:
Library name: Sample12
Dan_RNAseq_Raw_Counts.csv
p20177-s012_12_S45

value: spleen


title: Sample13_Naïve (CD44lo PD-1- uninfected mouse) 1

description:
Library name: Sample13
Dan_RNAseq_Raw_Counts.csv
p20177-s013_13_S46

value: CD8 T cell


title: Sample9_day 48 stem (CD73+) 3

description:
Library name: Sample9
Dan_RNAseq_Raw_Counts.csv
p20177-s009_9_S42

value: day 48 stem (CD73+)


title: M28V2-NT


title: M28V3-NT


title: M28V2-LPS


title: Sample7_day 48 stem (CD73+) 1

description:
Library name: Sample7
Dan_RNAseq_Raw_Counts.csv
p20177-s007_7_S40


title: M27V3-LPS


title: Sample6_GK day 5.5 TD (Tim-3+) 3

description:
Library name: Sample6
Dan_RNAseq_Raw_Counts.csv
p20177-s006_6_S39

value: GK day 5.5 TD (Tim-3+)


title: M27V2-NT


title: Sample3_GK day 5.5 stem (CD73+) 3

description:
Library name: Sample3
Dan_RNAseq_Raw_Counts.csv
p20177-s003_3_S36

value: GK day 5.5 stem (CD73+)


title: M27V2-LPS


title: Sample5_GK day 5.5 TD (Tim-3+) 2

description:
Library name: Sample5
Dan_RNAseq_Raw_Counts.csv
p20177-s005_5_S38


title: Sample4_GK day 5.5 TD (Tim-3+) 1

description:
Library name: Sample4
Dan_RNAseq_Raw_Counts.csv
p20177-s004_4_S37


title: M26V3-NT


title: Sample2_GK day 5.5 stem (CD73+) 2

description:
Library name: Sample2
Dan_RNAseq_Raw_Counts.csv
p20177-s002_2_S35


title: Sample1_GK day 5.5 stem (CD73+) 1

description:
Library name: Sample1
Dan_RNAseq_Raw_Counts.csv
p20177-s001_1_S34


title: Sample10_day 48 TD (Tim-3+) 1

description:
Library name: Sample10
Dan_RNAseq_Raw_Counts.csv
p20177-s010_10_S43


title: M26V3-LPS


title: Sample8_day 48 stem (CD73+) 2

description:
Library name: Sample8
Dan_RNAseq_Raw_Counts.csv
p20177-s008_8_S41


title: M26V2-LPS


title: M26V2-NT


title: RAW264.7, infected_3

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: cell line

tag: infection


title: M25V3-NT


title: RAW264.7, infected_1


title: RAW264.7, control_3

value: control


title: wt [R11489]

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to  GRCm38 genome build
Gene counts were obtained using featureCounts on GENCODE vM22 annotations
Assembly: GRCm38
Supplementary files format and content: gene_counts

source_name: neutrophils

extract_protocol:
Mice were perfused with PBS, then lungs were harvested, and digested by mincing and liberase treatment to obtain single cell suspensions, which were then submitted for flow cytometry-assisted cell sorting to obtain purified Ly6G-positive neutrophils. Cells were then centrifuged, and total RNA was extracted from pellet with PicoPure RNA Isolation Kit.
cDNA libraries preparation utilized 2 ng of total RNA and 1 µl of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion) using SMARTSeq v2 protocol, with modifications: (1) 20 µM TSO; and (2) 250 pg of cDNA with 1/5 reaction of Illumina Nextera XT kit. Length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent kit on the Perkin Elmer Labchip. Samples were subjected to an indexed PE sequencing run of 2 × 151 cycles on an Illumina HiSeq 4000 system

tag: genotype/variation

value: Cre-negative TGFbR2-fl/fl littermate control mice (wt)

value: Lung neutrophils


title: RAW264.7, infected_2


title: M25V3-LPS

value: Blood

value: peripheral blood mononuclear cells


title: M25V2-LPS


title: M27V3-NT

value: placebo

value: NO treatment(NT)


title: KYSE150, siANLN for 48 hours, biol rep 3

city: Shantou

first: yufei

last: Cao

address: No. 22, Xinling Road

institute: Shantou University Medical College

description:
Library name: siANLN_48h_3
siANLN_48h_3

data_processing:
For RNA-Seq data analysis, the paired-end sequencing fastq files were removed adaptors and low-quality reads with Cutadapt V1.18. Whole-transcriptome reads were aligned using the STAR V 2.7.3a with the Ensembl Homo_sapiens_Ensembl_GRCh38. The bam files after removing duplicates were used to count the genes with the featureCounts method in Subred V2.0.058. Differential analysis was performed with DESeq2 V1.44.0.
Assembly: Homo_sapiens_Ensembl_GRCh38
Supplementary files format and content: Excel file containing raw counts and FPKM values for all samples.

source_name: Cells are commercialized

extract_protocol:
Cells were lysed with Trizol reagent and total RNA was extracted according to the manufacturer's instructions, the concentration of RNA was measured by Nanodrop 2000.
RNA samples were delivered to Novogene (Beijing) for poly(A) RNA library generation, and the final libraries were sequenced using Illumina HiSeq Xten PE150.

value: Cells are commercialized

value: KYSE150 cells

value: esophageal squamous cell carcinoma cells

value: ANLN knockdown

value: Cells were transfected with siRNA of ANLN for 48 hours


title: RAW264.7, control_2


title: mutant [R11488]

value: Mrp8-Cre;TGFbR2-fl/fl (mutant)


title: M25V2-NT


title: wt [R11487]


title: KYSE150, siANLN for 48 hours, biol rep 2

description:
Library name: siANLN_48h_2
siANLN_48h_2


title: RAW264.7, control_1


title: M23V3-NT


title: KYSE150, siANLN for 48 hours, biol rep 1

description:
Library name: siANLN_48h_1
siANLN_48h_1


title: mutant [R11486]


title: KYSE150, siNC for 48 hours, biol rep 3

description:
Library name: siNC_48h_3
siNC_48h_3

value: WT

value: Cells were transfected with NC for 48 hours


title: Naive_2

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

library_source: genomic

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2
bigWig files were normalized to reads per million and generated using GenomicRanges and bedGraphToBigWig function from the UCSC genome browser
Assembly: mm10
Supplementary files format and content: reads per million normalized bigWig files

molecule: genomic DNA

source_name: Spleen

extract_protocol:
10,000 cells were sorted into complete media.
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: Spleen

tag: strain

tag: time point

value: Day 0

tag: sorting markers


title: wt [R11485]


title: M23V2-LPS

value: LPS treatment(LPS)


title: KYSE150, siNC for 48 hours, biol rep 2

description:
Library name: siNC_48h_2
siNC_48h_2


title: Naive_1


title: mutant [R11484]


title: M23V2-NT


title: GK_Cl13_TD_2

value: Day 45

value: LCMV Clone13


title: ATC28-Liquid

city: Taoyuan

first: Chiao-Ping

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Raw reads were mapped to the hg19 reference genome using the Ion Torrent Suites.
Coverage depth was calculated using Torrent Coverage Analysis plug-in.
Single nucleotide variants (SNVs) and short insertions/deletions (InDels) were identified using the Torrent Variant Caller plug-in.
VEP (Variant Effect Predictor) was used to annotate every variant using databases from Clinvar, COSMIC and Genome Aggregation database.
Assembly: hg19
Supplementary files format and content: The excel file contains raw data on nucleotide variation changes for 41 samples

source_name: Plasma

extract_protocol:
DNA was harvested using the QIAmp DNA FFPE Tissue Kit (Qiagen).
Quality and quantity of amplified library were determined using the fragment analyzer (AATI) and Qubit (Invitrogen). Barcoded libraries were prepared using Ion Chef system (Thermo Fisher Scientific) according to the Ion PI Hi-Q Chef Kit protocol (Thermo Fisher Scientific) or Ion 540 Kit-Chef protocol (Thermo Fisher Scientific) following manufacture's protocols.

value: Plasma


title: KYSE150, siNC for 48 hours, biol rep 1

description:
Library name: siNC_48h_1
siNC_48h_1


title: KYSE150, siANLN for 24 hours, biol rep 3

description:
Library name: siANLN_24h_3
siANLN_24h_3

value: Cells were transfected with siRNA of ANLN for 24 hours


title: M22V3-NT

value: Blood

value: peripheral blood mononuclear cells


title: ATC27-Liquid


title: GK_Cl13_TD_1


title: M22V3-LPS


title: ATC13-Liquid


title: KYSE150, siANLN for 24 hours, biol rep 2

description:
Library name: siANLN_24h_2
siANLN_24h_2

value: Cells are commercialized


title: M22V2-LPS


title: M23V3-LPS


title: GK_Cl13_Stem_1


title: Naive_3


title: M22V2-NT

value: NO treatment(NT)


title: GK_Cl13_Stem_2


title: d5_Arm_effect_2

value: Day 5

value: LCMV Armstrong


title: KYSE150, siNC for 24 hours, biol rep 2

description:
Library name: siNC_24h_2
siNC_24h_2

value: KYSE150 cells

value: esophageal squamous cell carcinoma cells

value: Cells were transfected with NC for 24 hours


title: M20V3-LPS


title: ATC11-Liquid


title: ATC10-Liquid


title: M20V3-NT


title: KYSE150, siNC for 24 hours, biol rep 1

description:
Library name: siNC_24h_1
siNC_24h_1

value: WT


title: d5_Arm_Stem_2

value: Spleen


title: M20V2-LPS


title: d5_Arm_Stem_1


title: KYSE150, siANLN for 24 hours, CUT&Tag analysis H3K27ac

description: Library name: siANLN_24h_H3K27ac_CUTTag

data_processing:
The paired-end reads were aligned to the human genome build GRCh38/hg38 using Bowtie. The MACS2 software was used for peak identification. Alignment files in the bam format were transformed into read coverage files (bigwig format) using DeepTools for visualization in Integrative Genome Viewer.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

source_name: KYSE150 cells

growth_protocol: KYSE150 cells were maintained in RPMI1640 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (GIBCO), 100 U/mL penicillin G, and streptomycin.

extract_protocol: We performed CUT&Tag experiments according to the manufacturer's instructions (Vazyme, TD904).

treatment_protocol: No treatment, or transfection of NC or transfection of ANLN siRNA.

value: ANLN knockdown


title: M20V2-NT


title: d5_Cl13_effect_2


title: ATC08-Liquid


title: KYSE150, siNC for 24 hours, CUT&Tag analysis H3K27ac

description: Library name: siNC_24h_H3K27ac_CUTTag


title: M12V3-LPS

value: placebo

value: LPS treatment(LPS)


title: ATC09-Liquid


title: d5_Cl13_effect_1

value: LCMV Clone13


title: KYSE150, siANLN for 24 hours, CUT&Tag analysis Pol II

description: Library name: siANLN_24h_PolII_CUTTag


title: KYSE150, siANLN for 24 hours, biol rep 1

description:
Library name: siANLN_24h_1
siANLN_24h_1


title: M12V3-NT


title: d5_Cl13_Stem_2


title: KYSE150, siNC for 24 hours, CUT&Tag analysis Pol II

description: Library name: siNC_24h_PolII_CUTTag


title: ATC04-Liquid

value: Plasma


title: KYSE150, siNC for 24 hours, biol rep 3

description:
Library name: siNC_24h_3
siNC_24h_3


title: ATC05-Liquid


title: ATC12-Liquid


title: M12V2-LPS


title: d5_Arm_effect_1


title: Wild type KYSE150 cells, CUT&Tag analysis Pol II

description: Library name: PolII_CUTTag


title: ATC03-Liquid


title: d5_Cl13_Stem_1


title: GSDMD-NTki/wt & Alb-creki/wt，treatment 5 ，day 42

city: Chengdu

first: Wang

last: Xue

address: South Section of Yangliu West Rd.1880#

institute: GemPharmatech Chengdu Co.,Ltd.,

data_processing:
High-quality reads were obtained after removing the low-quality reads, adaptor sequences, empty reads by fastp 0.23.2
The processed reads were mapped to the mouse reference genome (GRCm39) using HISAT2 2.1.0
Assembly: GRCm39
Supplementary files format and content: xlsx file inculdes raw counts for each Sample

extract_protocol:
RNA was extracted from liver with GSDMD-NTki/wt and GSDMD-NTki/wt & Alb-creki/wt mice. The purity of the RNA was determined using a NanoPhotometer® (Implen, CA, USA), and RNA integrity and concentration were determined using the Agilent Bioanalyzer 2100 system with an RNA Nano 6000 Assay kit (Agilent Technologies, CA, USA).
We generated strand-specific libraries after depleting rRNA using the Ribo-Zero™ Gold Kit (Illumina, San Diego, CA, USA). The libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA) using paired-end 150 bp sequencing reads (PE150) at Annoroad Gene Technology Co. Ltd. (Beijing, China).

value: liver

value: NTki/wt & Alb-creki/wt


title: M12V2-NT

value: Blood

value: peripheral blood mononuclear cells


title: Wild type KYSE150 cells, CUT&Tag analysis ANLN

description: Library name: ANLN_CUTTag


title: ATC02-Liquid


title: M25V6-LPS


title: ATC06-Liquid


title: M04V3-LPS


title: ATC07-Liquid


title: GSDMD-NTki/wt & Alb-creki/wt，treatment 4 ，day 42


title: GSDMD-NTki/wt & Alb-creki/wt，treatment 3 ，day 42


title: ATC25-Tissue

source_name: Tissue

value: Tissue


title: ATC26-Tissue


title: ATC22-Tissue


title: GSDMD-NTki/wt & Alb-creki/wt，treatment 2，day 42


title: ATC24-Tissue


title: ATC23-Tissue


title: ATC21-Tissue


title: GSDMD-NTki/wt & Alb-creki/wt，treatment 1 ，day 42


title: ATC20-Tissue


title: primary hypertrophic scar fibroblasts, Scramble control-rep3, 24 h

first: Jingyun

last: Li

address: 123rd Tianfei Street, Mochou Road, Nanjing 210004, China.

institute: Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Seqtk.
Trimmed sequence reads were mapped to GRCh38 using Hisat2 (version:2.0.4).
Read count extraction and normalization were performed using Stringtie (version:1.3.0), TMM (trimmed mean of M values)and perl.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary hypertrophic scar fibroblasts

growth_protocol: Primary hypertrophic scar fibroblasts were cultured in Fibroblast Medium consisting of basal medium, a low concentration of fetal bovine serum and fibroblast growth supplement at 37°C in a 5% CO2 incubator

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen) following the manufacturer’s instructions. 1.3 ug of total RNA was used for the construction of sequencing.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Peptides (>98% pure) were synthesized by Shanghai Science Peptide Biological Technology Co., Ltd and dissolved in distilled water.Hypertrophic scar fibroblasts were treated with 25 μM Sc or ADSCP2 in triplicates and collected for transcriptome library preparation and sequencing

value: primary hypertrophic scar fibroblasts

value: peptide scramble control


title: GSDMD-NTki/wt，control 4，day 42

value: NTki/wt


title: primary hypertrophic scar fibroblasts, Scramble control-rep2, 24 h


title: ATC16-Tissue


title: GSDMD-NTki/wt，control 3，day 42


title: ATC14-Tissue


title: primary hypertrophic scar fibroblasts, Scramble control-rep1, 24 h


title: GSDMD-NTki/wt，control 2，day 42


title: ATC18-Tissue


title: ATC01-Liquid


title: primary hypertrophic scar fibroblasts, ADSCP2-rep3, 24 h

value: peptide ADSCP2


title: M04V3-NT

value: NO treatment(NT)


title: ATC17-Tissue


title: ATC12-Tissue


title: GSDMD-NTki/wt，control 1，day 42


title: M04V2-NT


title: M04V2-LPS


title: ATC11-Tissue


title: ATC15-Tissue


title: primary hypertrophic scar fibroblasts, ADSCP2-rep2, 24 h


title: Monascus purpureus mycelia under optimized metal ion, Sample 3, Day1

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

institute: Changzhou University

data_processing:
The clean reads that were filtered from the raw reads were mapped to M. purpureus genome using Tophat2 software.
Assembly: ASM2599979v1
Supplementary files format and content: FPKM values for each sample

organism: Monascus purpureus

source_name: mycelia

extract_protocol:
RNA was harvested using TRlzol Reagent (Life technologies, California, USA). 0.1-1.0 μg of total RNA was used for the construction of sequencing libraries.
The library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500).
In briefly, the enriched mRNA was fragmented into approximately 200 nt RNA inserts, which were used to synthesize the first-strand cDNA and the second cDNA. The double-stranded cDNA were performed end-repair/dA-tail and adaptor ligation. The suitable fragments were isolated by Agencourt AMPure XP beads (Beckman Coulter, Inc.), and enriched by PCR amplification. Finally, the constructed cDNA libraries of M. purpureus were sequenced on a flow cell using an Illumina HiSeq™ sequencing platform.

value: mycelia

value: Monascus purpureus MP2022

value: WT

value: Treated with 0.0 g/L ZnSO4·2H2O and 2.5 g/L MgSO4·2H2O


title: ATC10-Tissue


title: Monascus purpureus mycelia under optimized metal ion, Sample 2, Day1

value: Treated with 0.0 g/L ZnSO4·2H2Oand 2.5 g/L MgSO4·2H2O


title: ATC07-Tissue


title: ATC09-Tissue


title: primary hypertrophic scar fibroblasts, ADSCP2-rep1, 24 h


title: HCT15vecC2

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

institute: National Yang Ming Chiao Tung University

data_processing:
The bcl2fastq conversion software v2.20 was used to convert BCL files from Illumina sequencing platforms into FASTQ reads.
Both adaptor clipping and sequence quality trimming (Q20) were performed using Trimmomatic v0.36 with a sliding-window approach.
HISAT2 was utilized for alignment.
TPM values was generated using StringTie (StringTir v2.1.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include Gene_ID, Gene Symbol, and TPM values for each sample.

source_name: colorectal cancer cell lines

growth_protocol: Cells were routinely passaged every 5 days on 10 cm2 dish under RPMI 1640 medium containing 10% FBS and 1% P/S.

extract_protocol:
Total RNA was isolated using Trizol reagent accoeding to manufacture's protocol and dissolved in nuclease-free water for library preparation.
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection. The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA).

treatment_protocol: The transductant cells were selected under 0.2 μg/ml puromycin for 2 weeks.

tag: transduction

value: Lentivirus (vector)

value: 0.2 mg/ml puromycin

tag: color

value: mCherry-labeling


title: ATC19-Tissue


title: Monascus purpureus mycelia under optimized metal ion, Sample 1, Day1


title: HCT15CTV2

value: Lentivirus (CT45A1)

value: Venus-labeling


title: ATC04-Tissue


title: ATC06-Tissue


title: ATC08-Tissue


title: Monascus purpureus mycelia, Control 3, day1

value: Untreated with 2.0 g/L ZnSO4 ·2H2O and 1.0 g/L MgSO4·2H2O


title: DLD1CT45V2


title: Monascus purpureus mycelia, Control 2, day1

value: Untreated with 2.0 g/L ZnSO4·2H2O and 1.0 g/L MgSO4·2H2O


title: ATC05-Tissue

value: Tissue


title: ATC03-Tissue


title: Monascus purpureus mycelia, Control 1, day1


title: DLD1VeCC2


title: ATC02-Tissue


title: ATC01-Tissue


title: VAT from late active rats (Exercise) rep6

status: Public on Jan 10 2025

city: Barcelona

first: Luis

middle: P

last: Iniguez

state: Barcelona

address: 88 Dr. Aiguader

department: Computational Biology and Health Genomics

country: Spain

institute: Centre for Genomic Regulation

description: Library name: VAT_PM_Exp_f

data_processing:
RNA-seq samples were mapped with Salmon (version 1.4.0) to the transcriptome reported in ensemble in the release-104 from Rattus_norvegicus (rn6 assembly)
Assembly: rn6 (ensembl release 105)
Supplementary files format and content: Comma separated file with raw gene counts

organism: Rattus norvegicus

source_name: visceral adipose tissue (VAT)

extract_protocol:
Approximately 80mg of adipose tissue was collected and stored in 2ml Precellys tubes (Bertin Instruments, CK28 - 2mL for adipose tissue), filled with the reagents according to the NZY Total RNA isolation kit protocol (NZY, MB1340). The tubes were immediately frozen by contact with dry ice and stored in a -80Cº freezer until further processing. Prior to further processing, the samples were homogenized (Precellys Evolution Homogenizer, Bertin Instruments, France) for 20 seconds at 4500RPM. After RNA isolation, samples were analyzed to determine the RIN score for RNA integrity (Agilent Technologies, 2100 Bioanalyzer). Only samples with a RIN score over 9 were used in all experiments.
mRNA sequencing:  Purified RNA from VAT and SAT samples collected from EAC (n=6), EAE (n=6), LAC (n=6) and LAE (n=6) rats on P61, 24 hours after the last exercise session, were used to prepare polyA-selected Illumina short-read libraries following standard protocols at the Genomics Unit of the Centre for Genomic Regulation. Samples were sequenced on a HiSeq2500 and an average of 21 million 50-nt single-end reads were produced.

value: visceral adipose tissue (VAT)

tag: Sex

value: male

tag: group

value: late active phase exercise (LAE)


title: VAT from late active rats (Exercise) rep5

description: Library name: VAT_PM_Exp_e

tag: tissue


title: VAT from late active rats (Exercise) rep2

description: Library name: VAT_PM_Exp_b


title: VAT from late active rats (Exercise) rep4

description: Library name: VAT_PM_Exp_d


title: VAT from late active rats (Exercise) rep1

description: Library name: VAT_PM_Exp_a


title: VAT from late active rats (Control) rep4

description: Library name: VAT_PM_Cont_d

value: late active phase control (LAC)


title: VAT from late active rats (Exercise) rep3

description: Library name: VAT_PM_Exp_c


title: VAT from late active rats (Control) rep3

description: Library name: VAT_PM_Cont_c


title: VAT from late active rats (Control) rep1

description: Library name: VAT_PM_Cont_a


title: VAT from late active rats (Control) rep2

description: Library name: VAT_PM_Cont_b


title: VAT from early active rats (Exercise) rep5

description: Library name: VAT_AM_Exp_e

value: early active phase exercise (EAE)


title: VAT from early active rats (Exercise) rep2

description: Library name: VAT_AM_Exp_b


title: VAT from early active rats (Exercise) rep4

description: Library name: VAT_AM_Exp_d


title: VAT from early active rats (Exercise) rep6

description: Library name: VAT_AM_Exp_f


title: VAT from early active rats (Exercise) rep3

description: Library name: VAT_AM_Exp_c


title: VAT from early active rats (Control) rep6

description: Library name: VAT_AM_Cont_f

value: early active phase control (EAC)


title: VAT from early active rats (Exercise) rep1

description: Library name: VAT_AM_Exp_a


title: VAT from early active rats (Control) rep5

description: Library name: VAT_AM_Cont_e


title: VAT from early active rats (Control) rep4

description: Library name: VAT_AM_Cont_d


title: VAT from early active rats (Control) rep3

description: Library name: VAT_AM_Cont_c


title: ATC13-Tissue


title: VAT from early active rats (Control) rep2

description: Library name: VAT_AM_Cont_b


title: VAT from early active rats (Control) rep1

description: Library name: VAT_AM_Cont_a


title: SAT from late active rats (Exercise) rep6

description: Library name: SAT_PM_Exp_f

source_name: subcutaneous adipose tissue (SAT)

value: subcutaneous adipose tissue (SAT)


title: SAT from late active rats (Exercise) rep4

description: Library name: SAT_PM_Exp_d


title: SAT from late active rats (Exercise) rep2

description: Library name: SAT_PM_Exp_b


title: SAT from late active rats (Exercise) rep5

description: Library name: SAT_PM_Exp_e


title: SAT from late active rats (Exercise) rep3

description: Library name: SAT_PM_Exp_c


title: VAT from late active rats (Control) rep6

description: Library name: VAT_PM_Cont_f


title: SAT from late active rats (Exercise) rep1

description: Library name: SAT_PM_Exp_a


title: VAT from late active rats (Control) rep5

description: Library name: VAT_PM_Cont_e


title: SAT from late active rats (Control) rep5

description: Library name: SAT_PM_Cont_e


title: SAT from late active rats (Control) rep4

description: Library name: SAT_PM_Cont_d


title: SAT from late active rats (Control) rep6

description: Library name: SAT_PM_Cont_f


title: SAT from late active rats (Control) rep2

description: Library name: SAT_PM_Cont_b


title: SAT from late active rats (Control) rep1

description: Library name: SAT_PM_Cont_a


title: SAT from early active rats (Exercise) rep4

description: Library name: SAT_AM_Exp_d


title: SAT from early active rats (Exercise) rep3

description: Library name: SAT_AM_Exp_c


title: SAT from early active rats (Exercise) rep1

description: Library name: SAT_AM_Exp_a


title: SAT from early active rats (Exercise) rep2

description: Library name: SAT_AM_Exp_b


title: SAT from early active rats (Control) rep5

description: Library name: SAT_AM_Cont_e


title: SAT from early active rats (Control) rep4

description: Library name: SAT_AM_Cont_d


title: SAT from early active rats (Exercise) rep5

description: Library name: SAT_AM_Exp_e


title: SAT from early active rats (Exercise) rep6

description: Library name: SAT_AM_Exp_f


title: SAT from early active rats (Control) rep2

description: Library name: SAT_AM_Cont_b


title: SAT from early active rats (Control) rep3

description: Library name: SAT_AM_Cont_c


title: tumor DNA from breast cancer patient S004654.l.d.mth

type: genomic

city: Lund

first: Johan

last: Staaf

address: Medicon Village

country: Sweden

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC beadchip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing: Beta values, representing the level of methylation, were computed in a sample-by-sample context using the minfi R package v1.44 function preprocessNoob() and next Infinium probe normalized using the approach described by PMID:26923702

label: Cy3 and Cy5

source_name: breast cancer

label_protocol: Standard Illumina protocol

growth_protocol: not relevant

extract_protocol: Tumor DNA was extracted from RNAlater preserved tissue using Qiagen AllPrep kit according to manufacturer's instructions.

treatment_protocol: not relevant

value: breast cancer

value: Female


title: tumor DNA from breast cancer patient S003500.l.d.mth


title: tumor DNA from breast cancer patient S003636.l.d.mth


title: tumor DNA from breast cancer patient S003952.l.d.mth


title: tumor DNA from breast cancer patient S001232.l.d.mth


title: tumor DNA from breast cancer patient S004116.l.d.mth


title: tumor DNA from breast cancer patient S004779.l.d.mth


title: tumor DNA from breast cancer patient S003302.l.d.mth


title: tumor DNA from breast cancer patient S002442.l.d.mth


title: tumor DNA from breast cancer patient S003945.l.d.mth


title: tumor DNA from breast cancer patient S002464.l.d.mth


title: tumor DNA from breast cancer patient S003186.l.d.mth


title: tumor DNA from breast cancer patient S005305.l.d.mth


title: tumor DNA from breast cancer patient S004380.l.d.mth


title: SAT from late active rats (Control) rep3

description: Library name: SAT_PM_Cont_c


title: tumor DNA from breast cancer patient S004527.l.d.mth


title: tumor DNA from breast cancer patient S003544.l.d.mth


title: tumor DNA from breast cancer patient S003498.l.d.mth


title: tumor DNA from breast cancer patient S002763.l.d.mth


title: tumor DNA from breast cancer patient S000327.l.d.mth


title: SAT from early active rats (Control) rep6

description: Library name: SAT_AM_Cont_f


title: tumor DNA from breast cancer patient S003095.l.d.mth


title: tumor DNA from breast cancer patient S004051.l.d.mth


title: tumor DNA from breast cancer patient S005126.l.d.mth


title: SAT from early active rats (Control) rep1

description: Library name: SAT_AM_Cont_a


title: tumor DNA from breast cancer patient S001072.l.d.mth


title: tumor DNA from breast cancer patient S002432.l.d.mth


title: tumor DNA from breast cancer patient S002850.l.d.mth


title: tumor DNA from breast cancer patient S002422.l.d.mth


title: tumor DNA from breast cancer patient S006018.l.d.mth


title: tumor DNA from breast cancer patient S005373.l.d.mth


title: tumor DNA from breast cancer patient S000299.l.d.mth


title: tumor DNA from breast cancer patient S004304.l.d.mth


title: tumor DNA from breast cancer patient S004329.l.d.mth


title: tumor DNA from breast cancer patient S003735.l.d.mth


title: tumor DNA from breast cancer patient S002918.l.d.mth


title: tumor DNA from breast cancer patient S000207.l.d.mth


title: tumor DNA from breast cancer patient S004646.l.d.mth


title: tumor DNA from breast cancer patient S002434.l.d.mth


title: tumor DNA from breast cancer patient S002804.l.d.mth


title: tumor DNA from breast cancer patient S004269.l.d.mth


title: tumor DNA from breast cancer patient S000733.l.d.mth


title: tumor DNA from breast cancer patient S006526.l.d.mth


title: tumor DNA from breast cancer patient S004379.l.d.mth


title: tumor DNA from breast cancer patient S004582.l.d.mth


title: tumor DNA from breast cancer patient S006441.l.d.mth


title: tumor DNA from breast cancer patient S005015.l.d.mth


title: tumor DNA from breast cancer patient S001534.l.d.mth


title: tumor DNA from breast cancer patient S004672.l.d.mth


title: tumor DNA from breast cancer patient S006215.l.d.mth


title: tumor DNA from breast cancer patient S003576.l.d.mth


title: tumor DNA from breast cancer patient S001415.l.d.mth


title: tumor DNA from breast cancer patient S000250.l.d.mth


title: tumor DNA from breast cancer patient S002636.l2.d.mth


title: tumor DNA from breast cancer patient S005136.l.d.mth


title: tumor DNA from breast cancer patient S003557.l.d.mth


title: tumor DNA from breast cancer patient S002138.l.d.mth


title: tumor DNA from breast cancer patient S002935.l.d.mth


title: tumor DNA from breast cancer patient S006105.l.d.mth


title: tumor DNA from breast cancer patient S003275.l.d.mth


title: tumor DNA from breast cancer patient S002355.l.d.mth


title: tumor DNA from breast cancer patient S000212.l.d.mth


title: tumor DNA from breast cancer patient S003289.l2.d.mth


title: tumor DNA from breast cancer patient S005241.l.d.mth


title: tumor DNA from breast cancer patient S003556.l.d.mth


title: tumor DNA from breast cancer patient S004727.l.d.mth


title: tumor DNA from breast cancer patient S004677.l.d.mth


title: tumor DNA from breast cancer patient S004149.l.d.mth


title: tumor DNA from breast cancer patient S004673.l.d.mth


title: tumor DNA from breast cancer patient S004454.l.d.mth


title: tumor DNA from breast cancer patient S005406.l2.d.mth


title: tumor DNA from breast cancer patient S003280.l2.d.mth


title: tumor DNA from breast cancer patient S003951.l.d.mth


title: tumor DNA from breast cancer patient S002374.l.d.mth


title: tumor DNA from breast cancer patient S003328.l.d.mth


title: tumor DNA from breast cancer patient S001240.l.d.mth


title: tumor DNA from breast cancer patient S005616.l.d.mth


title: tumor DNA from breast cancer patient S006011.l.d.mth


title: tumor DNA from breast cancer patient S000006.l.d.mth


title: tumor DNA from breast cancer patient S004581.l.d.mth


title: tumor DNA from breast cancer patient S005049.l.d.mth


title: tumor DNA from breast cancer patient S004873.l.d.mth


title: tumor DNA from breast cancer patient S004173.l.d.mth


title: tumor DNA from breast cancer patient S003111.l.d.mth


title: tumor DNA from breast cancer patient S005062.l.d.mth


title: tumor DNA from breast cancer patient S005013.l.d.mth


title: tumor DNA from breast cancer patient S001531.l.d.mth


title: tumor DNA from breast cancer patient S003130.l.d.mth


title: tumor DNA from breast cancer patient S004682.l.d.mth


title: tumor DNA from breast cancer patient S003254.l.d.mth


title: tumor DNA from breast cancer patient S003591.l.d.mth


title: tumor DNA from breast cancer patient S003620.l.d.mth


title: tumor DNA from breast cancer patient S002605.l.d.mth


title: tumor DNA from breast cancer patient S002945.l.d.mth


title: tumor DNA from breast cancer patient S000498.l.d.mth


title: tumor DNA from breast cancer patient S004641.l.d.mth


title: tumor DNA from breast cancer patient S002853.l.d.mth


title: tumor DNA from breast cancer patient S002940.l.d.mth


title: tumor DNA from breast cancer patient S005990.l.d.mth


title: tumor DNA from breast cancer patient S000601.l.d.mth


title: tumor DNA from breast cancer patient S002283.l.d.mth


title: tumor DNA from breast cancer patient S002243.l.d.mth


title: tumor DNA from breast cancer patient S003847.l.d.mth


title: tumor DNA from breast cancer patient S006566.l.d.mth

value: Male


title: tumor DNA from breast cancer patient S003217.l.d.mth


title: tumor DNA from breast cancer patient S000152.l.d.mth


title: tumor DNA from breast cancer patient S004821.l.d.mth


title: tumor DNA from breast cancer patient S003028.l.d.mth


title: tumor DNA from breast cancer patient S004065.l.d.mth


title: tumor DNA from breast cancer patient S005139.l.d.mth


title: tumor DNA from breast cancer patient S004272.l.d.mth


title: tumor DNA from breast cancer patient S004549.l.d.mth


title: tumor DNA from breast cancer patient S006607.l2.d.mth


title: tumor DNA from breast cancer patient S002325.l.d.mth


title: tumor DNA from breast cancer patient S005425.l.d.mth


title: tumor DNA from breast cancer patient S000915.l.d.mth


title: tumor DNA from breast cancer patient S002271.l.d.mth


title: tumor DNA from breast cancer patient S004132.l.d.mth


title: tumor DNA from breast cancer patient S002244.l.d.mth


title: tumor DNA from breast cancer patient S004206.l.d.mth


title: tumor DNA from breast cancer patient S005567.l.d.mth


title: tumor DNA from breast cancer patient S003684.l.d.mth


title: tumor DNA from breast cancer patient S005528.l.d.mth


title: tumor DNA from breast cancer patient S004118.l.d.mth


title: tumor DNA from breast cancer patient S004647.l.d.mth


title: tumor DNA from breast cancer patient S005169.l.d.mth


title: tumor DNA from breast cancer patient S000266.l.d.mth


title: tumor DNA from breast cancer patient S003192.l.d.mth


title: tumor DNA from breast cancer patient S003642.l.d.mth


title: tumor DNA from breast cancer patient S003133.l.d.mth


title: tumor DNA from breast cancer patient S006116.l.d.mth


title: tumor DNA from breast cancer patient S000179.l.d.mth


title: tumor DNA from breast cancer patient S003255.l.d.mth


title: tumor DNA from breast cancer patient S004558.l.d.mth


title: tumor DNA from breast cancer patient S003102.l.d.mth


title: tumor DNA from breast cancer patient S005963.l.d.mth


title: tumor DNA from breast cancer patient S003592.l.d.mth


title: tumor DNA from breast cancer patient S002803.l.d.mth


title: tumor DNA from breast cancer patient S000471.l.d.mth


title: tumor DNA from breast cancer patient S003189.l.d.mth


title: tumor DNA from breast cancer patient S003383.l.d.mth


title: tumor DNA from breast cancer patient S001143.l.d.mth


title: tumor DNA from breast cancer patient S002947.l.d.mth


title: tumor DNA from breast cancer patient S005782.l.d.mth


title: tumor DNA from breast cancer patient S002400.l.d.mth


title: tumor DNA from breast cancer patient S004406.l.d.mth


title: tumor DNA from breast cancer patient S003715.l.d.mth


title: tumor DNA from breast cancer patient S003058.l.d.mth


title: tumor DNA from breast cancer patient S004740.l.d.mth


title: tumor DNA from breast cancer patient S005619.l.d.mth


title: tumor DNA from breast cancer patient S004050.l.d.mth


title: tumor DNA from breast cancer patient S000259.l.d.mth


title: tumor DNA from breast cancer patient S004781.l.d.mth


title: tumor DNA from breast cancer patient S005644.l.d.mth


title: tumor DNA from breast cancer patient S001118.l.d.mth


title: tumor DNA from breast cancer patient S000722.l.d.mth


title: tumor DNA from breast cancer patient S002491.l.d.mth


title: tumor DNA from breast cancer patient S002906.l.d.mth


title: tumor DNA from breast cancer patient S000225.l.d.mth


title: tumor DNA from breast cancer patient S005549.l.d.mth


title: tumor DNA from breast cancer patient S003138.l.d.mth


title: tumor DNA from breast cancer patient S005059.l.d.mth


title: tumor DNA from breast cancer patient S003429.l.d.mth


title: tumor DNA from breast cancer patient S003259.l.d.mth


title: tumor DNA from breast cancer patient S001486.l.d.mth


title: tumor DNA from breast cancer patient S004921.l2.d.mth


title: tumor DNA from breast cancer patient S003617.l.d.mth


title: tumor DNA from breast cancer patient S004725.l.d.mth


title: tumor DNA from breast cancer patient S002760.l.d.mth


title: tumor DNA from breast cancer patient S003069.l.d.mth


title: tumor DNA from breast cancer patient S000632.l.d.mth


title: tumor DNA from breast cancer patient S003213.l.d.mth


title: tumor DNA from breast cancer patient S002282.l.d.mth


title: tumor DNA from breast cancer patient S006161.l.d.mth


title: tumor DNA from breast cancer patient S004629.l.d.mth


title: tumor DNA from breast cancer patient S004571.l.d.mth


title: tumor DNA from breast cancer patient S002990.l.d.mth


title: tumor DNA from breast cancer patient S003925.l2.d.mth


title: tumor DNA from breast cancer patient S003027.l.d.mth


title: tumor DNA from breast cancer patient S003014.l.d.mth


title: tumor DNA from breast cancer patient S003474.l.d.mth


title: tumor DNA from breast cancer patient S003273.l.d.mth


title: tumor DNA from breast cancer patient S005634.l.d.mth


title: tumor DNA from breast cancer patient S004122.l.d.mth


title: tumor DNA from breast cancer patient S005845.l.d.mth


title: tumor DNA from breast cancer patient S005288.l.d.mth


title: tumor DNA from breast cancer patient S005850.l.d.mth


title: tumor DNA from breast cancer patient S005626.l.d.mth


title: tumor DNA from breast cancer patient S002405.l.d.mth


title: tumor DNA from breast cancer patient S003851.l.d.mth


title: tumor DNA from breast cancer patient S002096.l.d.mth


title: tumor DNA from breast cancer patient S003815.l.d.mth


title: tumor DNA from breast cancer patient S001020.l.d.mth


title: tumor DNA from breast cancer patient S000643.l.d.mth


title: tumor DNA from breast cancer patient S005105.l.d.mth


title: tumor DNA from breast cancer patient S002761.l.d.mth


title: tumor DNA from breast cancer patient S000226.l.d.mth


title: tumor DNA from breast cancer patient S002487.l.d.mth


title: tumor DNA from breast cancer patient S002369.l.d.mth


title: tumor DNA from breast cancer patient S000422.l.d.mth


title: tumor DNA from breast cancer patient S005446.l.d.mth


title: tumor DNA from breast cancer patient S005151.l.d.mth


title: tumor DNA from breast cancer patient S000657.l.d.mth


title: tumor DNA from breast cancer patient S003173.l.d.mth


title: tumor DNA from breast cancer patient S003562.l.d.mth


title: tumor DNA from breast cancer patient S001412.l.d.mth


title: tumor DNA from breast cancer patient S001550.l.d.mth


title: tumor DNA from breast cancer patient S006158.l.d.mth


title: tumor DNA from breast cancer patient S002590.l.d.mth


title: tumor DNA from breast cancer patient S006233.l.d.mth


title: tumor DNA from breast cancer patient S003814.l.d.mth


title: tumor DNA from breast cancer patient S002666.l.d.mth


title: tumor DNA from breast cancer patient S002705.l.d.mth


title: tumor DNA from breast cancer patient S003846.l.d.mth


title: tumor DNA from breast cancer patient S005855.l.d.mth


title: tumor DNA from breast cancer patient S001623.l.d.mth


title: tumor DNA from breast cancer patient S004742.l.d.mth


title: tumor DNA from breast cancer patient S004545.l.d.mth


title: tumor DNA from breast cancer patient S005693.l.d.mth


title: tumor DNA from breast cancer patient S002366.l.d.mth


title: tumor DNA from breast cancer patient S005286.l.d.mth


title: tumor DNA from breast cancer patient S001426.l.d.mth


title: tumor DNA from breast cancer patient S003473.l.d.mth


title: tumor DNA from breast cancer patient S002173.l.d.mth


title: tumor DNA from breast cancer patient S005633.l.d.mth


title: tumor DNA from breast cancer patient S003834.l.d.mth


title: tumor DNA from breast cancer patient S001312.l.d.mth


title: tumor DNA from breast cancer patient S004176.l.d.mth


title: tumor DNA from breast cancer patient S004645.l.d.mth


title: tumor DNA from breast cancer patient S005388.l.d.mth


title: tumor DNA from breast cancer patient S001511.l.d.mth


title: tumor DNA from breast cancer patient S000725.l.d.mth


title: tumor DNA from breast cancer patient S002380.l.d.mth


title: tumor DNA from breast cancer patient S003828.l.d.mth


title: tumor DNA from breast cancer patient S003430.l.d.mth


title: tumor DNA from breast cancer patient S003374.l.d.mth


title: tumor DNA from breast cancer patient S001348.l.d.mth


title: tumor DNA from breast cancer patient S002253.l.d.mth


title: tumor DNA from breast cancer patient S001389.l.d.mth


title: tumor DNA from breast cancer patient S003243.l.d.mth


title: tumor DNA from breast cancer patient S005458.l.d.mth


title: tumor DNA from breast cancer patient S003830.l.d.mth


title: tumor DNA from breast cancer patient S004200.l.d.mth


title: tumor DNA from breast cancer patient S000690.l.d.mth


title: tumor DNA from breast cancer patient S003393.l.d.mth


title: tumor DNA from breast cancer patient S004074.l.d.mth


title: tumor DNA from breast cancer patient S006349.l.d.mth


title: tumor DNA from breast cancer patient S004117.l.d.mth


title: tumor DNA from breast cancer patient S002137.l.d.mth


title: tumor DNA from breast cancer patient S001547.l.d.mth


title: tumor DNA from breast cancer patient S002171.l.d.mth


title: tumor DNA from breast cancer patient S000803.l.d.mth


title: tumor DNA from breast cancer patient S004444.l.d.mth


title: tumor DNA from breast cancer patient S003481.l.d.mth


title: tumor DNA from breast cancer patient S005624.l.d.mth


title: tumor DNA from breast cancer patient S002686.l.d.mth


title: tumor DNA from breast cancer patient S002950.l.d.mth


title: tumor DNA from breast cancer patient S002720.l.d.mth


title: tumor DNA from breast cancer patient S005950.l.d.mth


title: tumor DNA from breast cancer patient S004859.l.d.mth


title: tumor DNA from breast cancer patient S003791.l.d.mth


title: tumor DNA from breast cancer patient S003560.l.d.mth


title: tumor DNA from breast cancer patient S002917.l.d.mth


title: tumor DNA from breast cancer patient S003176.l.d.mth


title: tumor DNA from breast cancer patient S003109.l.d.mth


title: tumor DNA from breast cancer patient S002339.l.d.mth


title: tumor DNA from breast cancer patient S003125.l.d.mth


title: tumor DNA from breast cancer patient S001023.l.d.mth


title: tumor DNA from breast cancer patient S006509.l.d.mth


title: tumor DNA from breast cancer patient S000393.l.d.mth


title: tumor DNA from breast cancer patient S001342.l.d.mth


title: tumor DNA from breast cancer patient S002889.l.d.mth


title: tumor DNA from breast cancer patient S005150.l.d.mth


title: tumor DNA from breast cancer patient S003134.l.d.mth


title: tumor DNA from breast cancer patient S005709.l.d.mth


title: tumor DNA from breast cancer patient S004378.l.d.mth


title: tumor DNA from breast cancer patient S003831.l.d.mth


title: tumor DNA from breast cancer patient S005142.l.d.mth


title: tumor DNA from breast cancer patient S003080.l.d.mth


title: tumor DNA from breast cancer patient S005137.l.d.mth


title: tumor DNA from breast cancer patient S004657.l.d.mth


title: tumor DNA from breast cancer patient S004265.l.d.mth


title: tumor DNA from breast cancer patient S005569.l.d.mth


title: tumor DNA from breast cancer patient S002531.l.d.mth


title: tumor DNA from breast cancer patient S005893.l.d.mth


title: tumor DNA from breast cancer patient S004787.l.d.mth


title: tumor DNA from breast cancer patient S000763.l.d.mth


title: tumor DNA from breast cancer patient S001193.l.d.mth


title: tumor DNA from breast cancer patient S006177.l.d.mth


title: tumor DNA from breast cancer patient S004516.l.d.mth


title: tumor DNA from breast cancer patient S003703.l.d.mth


title: tumor DNA from breast cancer patient S002236.l.d.mth


title: tumor DNA from breast cancer patient S005631.l.d.mth


title: tumor DNA from breast cancer patient S003432.l.d.mth


title: tumor DNA from breast cancer patient S004351.l.d.mth


title: tumor DNA from breast cancer patient S003301.l.d.mth


title: tumor DNA from breast cancer patient S006051.l.d.mth


title: tumor DNA from breast cancer patient S006071.l.d.mth


title: tumor DNA from breast cancer patient S003665.l.d.mth


title: tumor DNA from breast cancer patient S006291.l.d.mth


title: tumor DNA from breast cancer patient S002664.l.d.mth


title: tumor DNA from breast cancer patient S006157.l.d.mth


title: tumor DNA from breast cancer patient S006024.l.d.mth


title: tumor DNA from breast cancer patient S003825.l.d.mth


title: tumor DNA from breast cancer patient S003022.l.d.mth


title: tumor DNA from breast cancer patient S003067.l.d.mth


title: tumor DNA from breast cancer patient S004523.l.d.mth


title: tumor DNA from breast cancer patient S001339.l.d.mth


title: tumor DNA from breast cancer patient S003933.l.d.mth


title: tumor DNA from breast cancer patient S004301.l.d.mth


title: tumor DNA from breast cancer patient S005602.l.d.mth


title: tumor DNA from breast cancer patient S004935.l.d.mth


title: tumor DNA from breast cancer patient S003129.l.d.mth


title: tumor DNA from breast cancer patient S002072.l.d.mth


title: tumor DNA from breast cancer patient S006466.l.d.mth


title: tumor DNA from breast cancer patient S002133.l.d.mth


title: tumor DNA from breast cancer patient S004922.l.d.mth


title: tumor DNA from breast cancer patient S005361.l.d.mth


title: tumor DNA from breast cancer patient S000589.l.d.mth


title: tumor DNA from breast cancer patient S001022.l.d.mth


title: tumor DNA from breast cancer patient S001237.l.d.mth


title: tumor DNA from breast cancer patient S000594.l.d.mth


title: tumor DNA from breast cancer patient S000933.l.d.mth


title: tumor DNA from breast cancer patient S004959.l.d.mth


title: tumor DNA from breast cancer patient S006525.l.d.mth


title: tumor DNA from breast cancer patient S000377.l.d.mth


title: tumor DNA from breast cancer patient S003209.l.d.mth


title: tumor DNA from breast cancer patient S006221.l.d.mth


title: tumor DNA from breast cancer patient S003575.l.d.mth


title: tumor DNA from breast cancer patient S001247.l.d.mth


title: tumor DNA from breast cancer patient S002306.l.d.mth


title: tumor DNA from breast cancer patient S003427.l.d.mth


title: tumor DNA from breast cancer patient S002871.l.d.mth


title: tumor DNA from breast cancer patient S001347.l.d.mth


title: tumor DNA from breast cancer patient S002677.l.d.mth


title: tumor DNA from breast cancer patient S004868.l.d.mth


title: tumor DNA from breast cancer patient S003433.l.d.mth


title: tumor DNA from breast cancer patient S005630.l.d.mth


title: tumor DNA from breast cancer patient S000646.l.d.mth


title: tumor DNA from breast cancer patient S003518.l.d.mth


title: tumor DNA from breast cancer patient S003351.l.d.mth


title: tumor DNA from breast cancer patient S003789.l.d.mth


title: tumor DNA from breast cancer patient S000037.l.d.mth


title: tumor DNA from breast cancer patient S003079.l.d.mth


title: tumor DNA from breast cancer patient S004127.l.d.mth


title: tumor DNA from breast cancer patient S001457.l.d.mth


title: tumor DNA from breast cancer patient S003258.l.d.mth


title: tumor DNA from breast cancer patient S002572.l.d.mth


title: tumor DNA from breast cancer patient S004451.l.d.mth


title: tumor DNA from breast cancer patient S000199.l.d.mth


title: tumor DNA from breast cancer patient S004670.l.d.mth


title: tumor DNA from breast cancer patient S005378.l.d.mth


title: tumor DNA from breast cancer patient S000127.l.d.mth


title: tumor DNA from breast cancer patient S003268.l.d.mth


title: tumor DNA from breast cancer patient S002190.l.d.mth


title: tumor DNA from breast cancer patient S002533.l.d.mth


title: tumor DNA from breast cancer patient S003057.l.d.mth


title: tumor DNA from breast cancer patient S002078.l.d.mth


title: tumor DNA from breast cancer patient S005392.l.d.mth


title: tumor DNA from breast cancer patient S003428.l.d.mth


title: tumor DNA from breast cancer patient S003136.l.d.mth


title: tumor DNA from breast cancer patient S002150.l.d.mth


title: tumor DNA from breast cancer patient S003218.l.d.mth


title: tumor DNA from breast cancer patient S001334.l.d.mth


title: tumor DNA from breast cancer patient S003068.l.d.mth


title: tumor DNA from breast cancer patient S002552.l.d.mth


title: tumor DNA from breast cancer patient S001398.l.d.mth


title: tumor DNA from breast cancer patient S002869.l.d.mth


title: tumor DNA from breast cancer patient S003513.l.d.mth


title: tumor DNA from breast cancer patient S005601.l.d.mth


title: tumor DNA from breast cancer patient S005829.l.d.mth


title: tumor DNA from breast cancer patient S004967.l.d.mth


title: tumor DNA from breast cancer patient S000560.l.d.mth


title: tumor DNA from breast cancer patient S005376.l.d.mth


title: tumor DNA from breast cancer patient S003340.l.d.mth


title: tumor DNA from breast cancer patient S001318.l.d.mth


title: tumor DNA from breast cancer patient S001135.l.d.mth


title: tumor DNA from breast cancer patient S000898.l.d.mth


title: tumor DNA from breast cancer patient S002756.l.d.mth


title: tumor DNA from breast cancer patient S005443.l.d.mth


title: tumor DNA from breast cancer patient S005459.l.d.mth


title: tumor DNA from breast cancer patient S006318.l.d.mth


title: tumor DNA from breast cancer patient S000724.l.d.mth


title: tumor DNA from breast cancer patient S003350.l.d.mth


title: tumor DNA from breast cancer patient S005467.l.d.mth


title: tumor DNA from breast cancer patient S002375.l.d.mth


title: tumor DNA from breast cancer patient S005783.l.d.mth


title: tumor DNA from breast cancer patient S003241.l.d.mth


title: tumor DNA from breast cancer patient S003410.l.d.mth


title: tumor DNA from breast cancer patient S005620.l.d.mth


title: tumor DNA from breast cancer patient S003565.l.d.mth


title: tumor DNA from breast cancer patient S004634.l.d.mth


title: tumor DNA from breast cancer patient S004060.l.d.mth


title: tumor DNA from breast cancer patient S003326.l.d.mth


title: tumor DNA from breast cancer patient S004822.l.d.mth


title: tumor DNA from breast cancer patient S006620.l.d.mth


title: tumor DNA from breast cancer patient S003397.l.d.mth


title: tumor DNA from breast cancer patient S003126.l.d.mth


title: tumor DNA from breast cancer patient S003656.l.d.mth


title: tumor DNA from breast cancer patient S003190.l.d.mth


title: tumor DNA from breast cancer patient S003119.l.d.mth


title: tumor DNA from breast cancer patient S003499.l.d.mth


title: tumor DNA from breast cancer patient S001461.l.d.mth


title: tumor DNA from breast cancer patient S005465.l.d.mth


title: tumor DNA from breast cancer patient S003100.l.d.mth


title: tumor DNA from breast cancer patient S005039.l.d.mth


title: tumor DNA from breast cancer patient S000151.l.d.mth


title: tumor DNA from breast cancer patient S005042.l.d.mth


title: tumor DNA from breast cancer patient S000681.l.d.mth


title: tumor DNA from breast cancer patient S005541.l.d.mth


title: tumor DNA from breast cancer patient S003613.l.d.mth


title: tumor DNA from breast cancer patient S002410.l.d.mth


title: tumor DNA from breast cancer patient S001145.l.d.mth


title: tumor DNA from breast cancer patient S003090.l.d.mth


title: tumor DNA from breast cancer patient S005245.l.d.mth


title: tumor DNA from breast cancer patient S005050.l.d.mth


title: tumor DNA from breast cancer patient S003643.l.d.mth


title: tumor DNA from breast cancer patient S006287.l2.d.mth


title: tumor DNA from breast cancer patient S002134.l.d.mth


title: tumor DNA from breast cancer patient S005394.l.d.mth


title: tumor DNA from breast cancer patient S006162.l.d.mth


title: tumor DNA from breast cancer patient S000939.l.d.mth


title: tumor DNA from breast cancer patient S000964.l.d.mth


title: tumor DNA from breast cancer patient S004437.l.d.mth


title: tumor DNA from breast cancer patient S003083.l.d.mth


title: tumor DNA from breast cancer patient S005529.l.d.mth


title: tumor DNA from breast cancer patient S002688.l.d.mth


title: tumor DNA from breast cancer patient S006103.l.d.mth


title: tumor DNA from breast cancer patient S003178.l.d.mth


title: tumor DNA from breast cancer patient S001310.l.d.mth


title: tumor DNA from breast cancer patient S000873.l.d.mth


title: tumor DNA from breast cancer patient S002129.l.d.mth


title: tumor DNA from breast cancer patient S005978.l.d.mth


title: tumor DNA from breast cancer patient S000910.l.d.mth


title: tumor DNA from breast cancer patient S001168.l.d.mth


title: tumor DNA from breast cancer patient S004348.l.d.mth


title: tumor DNA from breast cancer patient S006214.l.d.mth


title: tumor DNA from breast cancer patient S003417.l.d.mth


title: tumor DNA from breast cancer patient S004864.l.d.mth


title: tumor DNA from breast cancer patient S003247.l.d.mth


title: tumor DNA from breast cancer patient S001282.l.d.mth


title: tumor DNA from breast cancer patient S003743.l.d.mth


title: tumor DNA from breast cancer patient S005574.l.d.mth


title: tumor DNA from breast cancer patient S004047.l.d.mth


title: tumor DNA from breast cancer patient S002606.l.d.mth


title: tumor DNA from breast cancer patient S006087.l.d.mth


title: tumor DNA from breast cancer patient S000981.l.d.mth


title: tumor DNA from breast cancer patient S005563.l.d.mth


title: tumor DNA from breast cancer patient S003008.l.d.mth


title: tumor DNA from breast cancer patient S006490.l.d.mth


title: tumor DNA from breast cancer patient S002970.l.d.mth


title: tumor DNA from breast cancer patient S003050.l.d.mth


title: tumor DNA from breast cancer patient S003779.l.d.mth


title: tumor DNA from breast cancer patient S004055.l.d.mth


title: tumor DNA from breast cancer patient S000472.l.d.mth


title: tumor DNA from breast cancer patient S000965.l.d.mth


title: tumor DNA from breast cancer patient S005027.l.d.mth


title: tumor DNA from breast cancer patient S006178.l.d.mth


title: tumor DNA from breast cancer patient S003185.l.d.mth


title: tumor DNA from breast cancer patient S005570.l.d.mth


title: tumor DNA from breast cancer patient S003257.l.d.mth


title: tumor DNA from breast cancer patient S005405.l2.d.mth


title: tumor DNA from breast cancer patient S003091.l.d.mth


title: tumor DNA from breast cancer patient S005452.l.d.mth


title: tumor DNA from breast cancer patient S003716.l.d.mth


title: tumor DNA from breast cancer patient S004145.l.d.mth


title: tumor DNA from breast cancer patient S003987.l.d.mth


title: tumor DNA from breast cancer patient S006414.l.d.mth


title: tumor DNA from breast cancer patient S002975.l.d.mth


title: tumor DNA from breast cancer patient S003516.l.d.mth


title: tumor DNA from breast cancer patient S002347.l.d.mth


title: tumor DNA from breast cancer patient S003733.l.d.mth


title: tumor DNA from breast cancer patient S005026.l.d.mth


title: tumor DNA from breast cancer patient S004270.l.d.mth


title: tumor DNA from breast cancer patient S003571.l.d.mth


title: tumor DNA from breast cancer patient S000621.l.d.mth


title: tumor DNA from breast cancer patient S003780.l.d.mth


title: tumor DNA from breast cancer patient S005179.l.d.mth


title: tumor DNA from breast cancer patient S003279.l2.d.mth


title: tumor DNA from breast cancer patient S005632.l.d.mth


title: tumor DNA from breast cancer patient S004913.l.d.mth


title: tumor DNA from breast cancer patient S002097.l.d.mth


title: tumor DNA from breast cancer patient S005548.l.d.mth


title: tumor DNA from breast cancer patient S004939.l.d.mth


title: tumor DNA from breast cancer patient S004382.l.d.mth


title: tumor DNA from breast cancer patient S000180.l.d.mth


title: tumor DNA from breast cancer patient S004745.l.d.mth


title: tumor DNA from breast cancer patient S001484.l.d.mth


title: tumor DNA from breast cancer patient S001596.l.d.mth


title: tumor DNA from breast cancer patient S003097.l.d.mth


title: tumor DNA from breast cancer patient S004777.l.d.mth


title: tumor DNA from breast cancer patient S000984.l.d.mth


title: tumor DNA from breast cancer patient S003321.l.d.mth


title: tumor DNA from breast cancer patient S002168.l.d.mth


title: tumor DNA from breast cancer patient S000602.l.d.mth


title: tumor DNA from breast cancer patient S004776.l.d.mth


title: tumor DNA from breast cancer patient S003372.l.d.mth


title: tumor DNA from breast cancer patient S003384.l.d.mth


title: tumor DNA from breast cancer patient S002151.l.d.mth


title: tumor DNA from breast cancer patient S001157.l.d.mth


title: tumor DNA from breast cancer patient S000284.l.d.mth


title: tumor DNA from breast cancer patient S003108.l.d.mth


title: FTOi-treated HeLa replicate 2

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Genomic DNA (300–800 ng) was converted with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research), and it was hybridized with the Illumina MouseMethylation BeadChip array according to the manufacturer’s protocol.

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

data_processing: Raw Infinium 850k data were preprocessed following the published guidelines: CpG probes of low quality (detection p-value threshold of 0.05) or targeting X and Y-chromosomes were removed from the analysis. Additionally, probes targeting methylation sites located at common single-nucleotide polymorphism as well as cross-reactive probes (i.e. targeting several genomic locations) were filtered out based on the extended annotation of McCartney et al. Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction.

source_name: FTOi-treated HeLa

label_protocol: Standard Illumina Protocol

growth_protocol: HeLa cells were cultured at 37°C under 5% CO2 in DMEM (Gibco) media supplemented with 10% FBS and 1% 100X Pen Strep (Gibco).

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Mini Kit (from QIAGEN) following the manufacturer’s protocol.

treatment_protocol: (METTL3KO) HeLa METTL3 KO cell lines were generated with the CRISPR-Cas9 nuclease system via homology-directed repair (HDR) as previously described. Briefly, sgRNAs were designed to target the start codon (ATG) and the first intron of METTL3 using the guidelines described in the online tool (http://crispor.tefor.net). Then they were cloned into the pX461 vector (Addgene). In parallel, a donor vector (pUC18) containing gene sequences homologous to those flanking the sgRNA targeting sites bordering a selectable marker (either mCherry or puromycin resistance gene) and mammalian transcriptional terminator (bGH, synthesized by GENEWIZ) was constructed. Next, the co-transfection of the donor vectors and gRNAs was performed by using Lipofectamine™ 2000 according to the manufacturer’s instructions (Invitrogen). After 24 hours, cells were selected by puromycin at a concentration of 2 µg/ml for at least 10 days, and sorted into 96-well plates (1 cell per well) by fluorescence-activated cell sorting (FACS). After proliferation, clones were analysed for the METTL3 KO by quantitative reverse transcription PCR (RT-qPCR) and western blotting. Subsequently, the CRISPR-Cas9-targeted genomic regions were PCR-amplified and sequenced in positive clones. (METTL3i) HeLa cells were seeded and treated with METTL3 inhibitor STM-2457 (MedChemExpress, HY-134836) at 25 μM, (FTOi) with FTO inhibitor (MedChemExpress, HY-127103) at 20 μM, or with the corresponding vehicle control.

tag: experiment

value: FTOi-vs-Mock-control

value: WT

tag: drug treatment

value: FTOi

tag: biologicalreplicate

tag: technicalreplicate


title: FTOi-treated HeLa replicate 3

tag: genotype


title: Mock-treated HeLa replicate 3 (METTL3i control)

source_name: Mock-treated HeLa

value: Mock


title: METTL3 knocked out HeLa clone 2 replicate 3

source_name: METTL3 knocked out HeLa


title: Mock-treated HeLa replicate 1  (FTOi control)


title: METTL3 knocked out HeLa clone 2 replicate 1


title: FTOi-treated HeLa replicate 1


title: METTL3 knocked out HeLa clone 2 replicate 2


title: Wild Type HeLa replicate 3.3

hyb_protocol: Genomic DNA (300–800 ng) was converted with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research), and it was hybridized with the Illumina HumanMethylation850 BeadChip 850K array according to the manufacturer’s protocol.

source_name: Wild Type HeLa

treatment_protocol: HeLa METTL3 KO cell lines were generated with the CRISPR-Cas9 nuclease system via homology-directed repair (HDR) as previously described. Briefly, sgRNAs were designed to target the start codon (ATG) and the first intron of METTL3 using the guidelines described in the online tool (http://crispor.tefor.net). Then they were cloned into the pX461 vector (Addgene). In parallel, a donor vector (pUC18) containing gene sequences homologous to those flanking the sgRNA targeting sites bordering a selectable marker (either mCherry or puromycin resistance gene) and mammalian transcriptional terminator (bGH, synthesized by GENEWIZ) was constructed. Next, the co-transfection of the donor vectors and gRNAs was performed by using Lipofectamine™ 2000 according to the manufacturer’s instructions (Invitrogen). After 24 hours, cells were selected by puromycin at a concentration of 2 µg/ml for at least 10 days, and sorted into 96-well plates (1 cell per well) by fluorescence-activated cell sorting (FACS). After proliferation, clones were analysed for the METTL3 KO by quantitative reverse transcription PCR (RT-qPCR) and western blotting. Subsequently, the CRISPR-Cas9-targeted genomic regions were PCR-amplified and sequenced in positive clones.

value: HeLa


title: METTL3 knocked out HeLa replicate 3.1


title: Wild Type HeLa replicate 2.2


title: METTL3i-treated HeLa replicate 3

source_name: METTL3i-treated HeLa


title: METTL3i-treated HeLa replicate 2


title: Wild Type HeLa replicate 2 (METTL3 KO clone 2 control)


title: S99

city: LYON

first: Benjamin

last: Gibert

address: 28 promenade Léa et Napoléon Bullukian

country: France

institute: CRCL – UMR 1052 / CNRS 5286

hyb_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)

data_processing: Data were analyzed using the methylkey R package (accessible at https://github.com/IARCbioinfo/methylkey).   Briefly, raw intensity data files were preprocessed and normalized using the minfi Bioconductor package.   Beta-values, which measure the proportion of methylated alleles at any given locus, were generated for each CpG site.   CpG sites for which detected signals were not significantly different from background levels (p > 0.02) and for which data were missing in >20% of the samples were excluded.   Cross-reactive probes, probes located on the X and Y chromosomes and at chromosome locations associated with known SNPs were also excluded, resulting in a final dataset of 792,079 CpG probes.

label: Cy3, Cy5

source_name: Tumor

extract_protocol: genomic DNA was extracted and purified from frozen tissue using Qiagen All prep DNA/RNA Extraction kit according to standard instructions.

tag: tumor type

value: multifocal

tag: primary tumor site

value: ILEUM

tag: discovery cohort

value: YES


title: Wild Type HeLa replicate 2.3

tag: cell line


title: Wild Type HeLa replicate 3 (METTL3 KO clone 2 control)


title: S98

scan_protocol: Infinium MethylationEPIC BeadChip (850K) array were carried out following Infinium HD Methylation Assay Protocol by the Infinium MethylationEPIC Array Service (Diagenode Cat# G02090000)


title: METTL3 knocked out HeLa replicate 3.3


title: S97

value: unifocal

value: DUODENUM


title: S94


title: S95


title: S96


title: S93


title: Mock-treated HeLa replicate 1 (METTL3i control)


title: S92


title: S91


title: S90

value: NO


title: Wild Type HeLa replicate 1 (METTL3 KO clone 2 control)


title: S88


title: S87


title: S86


title: S83

source_name: Liver metastasis


title: S82


title: METTL3i-treated HeLa replicate 1


title: S81


title: S79

source_name: Mesenteric Lymph Node


title: Mock-treated HeLa replicate 2  (FTOi control)


title: METTL3 knocked out HeLa replicate 2.2


title: Wild Type HeLa replicate 2.1


title: S78


title: S77


title: S75

value: JEJUNUM


title: S70


title: Wild Type HeLa replicate 3.2


title: S67


title: METTL3 knocked out HeLa replicate 2.1


title: S66


title: S59


title: S85


title: S60


title: S63


title: METTL3 knocked out HeLa replicate 1.1


title: S61


title: S57


title: METTL3 knocked out HeLa replicate 3.2


title: S56


title: S68


title: S55


title: S54


title: Mock-treated HeLa replicate 3  (FTOi control)


title: S69


title: S72


title: S74


title: S52


title: S53


title: S71


title: S45


title: METTL3 knocked out HeLa replicate 2.3


title: S43


title: S40


title: S47


title: Wild Type HeLa replicate 1.1


title: S44


title: S39


title: S73


title: S65


title: S38


title: METTL3 knocked out HeLa replicate 1.2


title: S41


title: S49


title: S36


title: Mock-treated HeLa replicate 2 (METTL3i control)


title: S35


title: S33


title: S37


title: S34


title: S280


title: S28


title: S279


title: Wild Type HeLa replicate 3.1


title: S29


title: S270


title: S272

source_name: Adenoma


title: S32


title: S283

source_name: Normal


title: S284


title: S271


title: S282


title: S268


title: S276


title: S274


title: S275


title: S277


title: S281


title: Wild Type HeLa replicate 1.2


title: METTL3 knocked out HeLa replicate 1.3


title: Wild Type HeLa replicate 1.3


title: S27


title: S266


title: S267


title: S273


title: S265


title: S264


title: S269


title: S262


title: S260

source_name: Lymph Node


title: S259


title: S261


title: S26


title: S257


title: S255


title: S254


title: RNA-seq of queen hindgut L7

city: Tucson

first: Duan

last: Copeland

state: AZ

address: 2000 E. Allen Rd.

institute: USDA-ARS

description:
Library name: L7
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low

data_processing:
All paired-end raw reads were filtered and trimmed using Trimmomatic v0.38 (Bolger et al., 2014) with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15  MINLEN:75.  FASTQC was used to ensure quality control (Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data).  Kraken2 was used to map and split reads to the Apis mellifera genome assembly Amel_HAv3.1 (PRJNA471592) and the gut symbiont Commensalibacter melissae (PRJNA495947) (Wood et al., 2019).  A. mellifera  reads were mapped against A. mellifera genome using STAR v2.7.10b (Dobin et al., 2013) and C. melissae reads were mapped to C. melissae genome using Bowtie 2 v2.5.2 (Langmead and Salzberg, 2012).  Gene counts were obtained using Subread v2.0.4 package FeatureCounts (Liao et al., 2013).  Genes with read counts below 4 were removed, and genes with variance less than 15% across samples were filtered out.  Final counts were normalized by employing a log2-counts per million (logCPM) transformation.
Assembly: Kraken2 was used to map and split reads to the Apis mellifera genome assembly Amel_HAv3.1 (PRJNA471592) and the gut symbiont Commensalibacter melissae (PRJNA495947) (Wood et al., 2019).  A. mellifera  reads were mapped against A. mellifera genome using STAR v2.7.10b (Dobin et al., 2013) and C. melissae reads were mapped to C. melissae genome using Bowtie 2 v2.5.2 (Langmead and Salzberg, 2012).
Supplementary files format and content: Files are in text format and contain all samples.

organism: Apis mellifera

source_name: queen hindgut (ileum+rectum)

extract_protocol:
RNA from extracted samples was processed for sequencing by depleting the rRNA from samples using a RiboFree cDNA Kit (Zymo Research).
Samples were pooled in equimolar concentrations and libraries were prepared for sequencing using an Adept Rapid PCR-Plus Kit (Element Biosciences).

tag: cell type

value: queen hindgut (ileum+rectum)

tag: age

value: YOUNG

tag: carbonyl expression

tag: a2.1 relative_abundance

tag: a2.1 high/low

value: LOW


title: S256


title: S252


title: RNA-seq of queen hindgut L5

description:
Library name: L5
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low

value: HIGH


title: S258


title: S251


title: RNA-seq of queen hindgut L9

description:
Library name: L9
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L40

description:
Library name: L40
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L6

description:
Library name: L6
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L4

description:
Library name: L4
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S250


title: S263


title: S249


title: RNA-seq of queen hindgut L38

description:
Library name: L38
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L37

description:
Library name: L37
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S246


title: RNA-seq of queen hindgut L36

description:
Library name: L36
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low

value: OLD


title: S245


title: RNA-seq of queen hindgut L8

description:
Library name: L8
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S244


title: S243


title: RNA-seq of queen hindgut L35

description:
Library name: L35
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S240


title: S238


title: S242


title: RNA-seq of queen hindgut L33

description:
Library name: L33
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S237


title: RNA-seq of queen hindgut L32

description:
Library name: L32
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L34

description:
Library name: L34
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L3

description:
Library name: L3
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S248


title: RNA-seq of queen hindgut L28

description:
Library name: L28
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L29

description:
Library name: L29
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L26

description:
Library name: L26
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L31

description:
Library name: L31
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S233


title: RNA-seq of queen hindgut L39

description:
Library name: L39
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S226


title: S23


title: RNA-seq of queen hindgut L27

description:
Library name: L27
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L30

description:
Library name: L30
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S232


title: S225


title: RNA-seq of queen hindgut L25

description:
Library name: L25
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L24

description:
Library name: L24
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S241


title: S224


title: RNA-seq of queen hindgut L23

description:
Library name: L23
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S223


title: S216


title: S220


title: S217


title: RNA-seq of queen hindgut L22

description:
Library name: L22
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L20

description:
Library name: L20
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S213


title: RNA-seq of queen hindgut L21

description:
Library name: L21
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L2

description:
Library name: L2
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S203


title: RNA-seq of queen hindgut L16

description:
Library name: L16
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L14

description:
Library name: L14
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L18

description:
Library name: L18
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S212


title: S200


title: RNA-seq of queen hindgut L19

description:
Library name: L19
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S206


title: RNA-seq of queen hindgut L12

description:
Library name: L12
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S198


title: RNA-seq of queen hindgut L13

description:
Library name: L13
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S196


title: RNA-seq of queen hindgut L11

description:
Library name: L11
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: RNA-seq of queen hindgut L10

description:
Library name: L10
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S195


title: RNA-seq of queen hindgut L1

description:
Library name: L1
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S194


title: KD, 1218-1

city: Kaohsiung

first: Kuang-Den

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

institute: Kaohsiung Chang Gung Memorial Hospital

description: Library name: 1218-1_S80

data_processing:
After demultiplexing the 16S sequence reads based on sample-specific indices, primer sequences were trimmed using Cutadapt v.1.15. The trimmed reads were then processed using the DADA2 R package v.1.18.0 to construct amplicon sequence variants (ASVs). This was achieved using the filterAndTrim function with the standard parameters (maxN = 0, truncQ = 2, and maxEE = 2). Possible chimeric reads were removed using the remote Bimera Denovo function of DADA2. Taxonomic assignment of each amplicon sequence variant (ASV) was performed by similarity searching against the Greengene v13.8 database with a threshold of 97% similarity. The rarefied feature table was then converted into the linear discriminant analysis effect size (LEfSe) format using tools available on Galaxy Hutlab (http://huttenhower.sph.harvard.edu/galaxy/) and MicrobiomeAnalyst (https://www.microbiomeanalyst.ca/MicrobiomeAnalyst/home.xhtml).
Supplementary files format and content: Excel, Phylum-, Genus- and Species-Level Taxonomy Tables
Library strategy: 16S rRNA-seq

organism: human feces metagenome

source_name: fecal matter (not tissue)

extract_protocol:
Stool DNA extraction was performed according to the manufacturer’s protocol using a QiAamp DNA Stool Mini Kit (Qiagen). The extracted DNA was stored in 1X ATE buffer (10 mM Tris-Cl pH 8.3, 0.1 mM EDTA, and 0.04% NaN3) at -20°C for subsequent 16S rRNA-targeted sequencing.
PCR was performed using the forward primer 5′- TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′ and reverse primer 5′- GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′ for the V3–V4 region of the 16S rRNA gene. Amplicons generated from each sample (~ 330 bp) were purified using AMPure XP magnetic beads (Beckman Coulter).

value: fecal matter (not tissue)


title: S187


title: KD, 1209-1

description: Library name: 1209-1_S78


title: S205


title: KD, 1200-1

description: Library name: 1200-1_S76


title: S192


title: S202


title: RNA-seq of queen hindgut L17

description:
Library name: L17
Age, Carbonyl, A2.1 relative abundance, A2.1 high/low


title: S190


title: S182


title: KD, 1199-1

description: Library name: 1199-1_S75


title: S178


title: KD, 1180-1

description: Library name: 1180-1_S72


title: KD, 1196-1

description: Library name: 1196-1_S74


title: S180


title: S169


title: KD, 1190-1

description: Library name: 1190-1_S73


title: S176


title: S167


title: KD, 1164-1

description: Library name: 1164-1_S70


title: KD, KD87

description: Library name: KD87_S74


title: S166


title: KD, KD8

description: Library name: KD8_S63


title: Trametes versicolor, WT wood, 3 weeks, Bio Rep 2

city: Charleston

first: Thomas

last: Canam

state: IL

address: 600 Lincoln Avenue, Life Sciences Building 2070

department: Biological Sciences

institute: Eastern Illinois University

description:
Library name: WT2
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

data_processing:
The raw sequence files generated by RNA-Seq were processed by ArrayStar software (DNASTAR, Inc.).
Trave1_GeneCatalog_proteins_20101111_ GO.tab
The ANOVA function in ArrayStar with false discovery rate (FDR) P value adjustment was used to identify transcripts with significant variation between all sample types (LSX, LSHG, HS, WT) with P<0.05 considered significant.
Total RPKM below 8 (across 8 samples) was removed from data.
Assembly: Trave1_GeneCatalog_transcripts_20101111.nt.fasta
Supplementary files format and content: RPKM data with annotations in CSV format (with stats)

organism: Trametes versicolor

source_name: Mycelia

growth_protocol: Trametes versicolor was grown on wood discs for 3 weeks in Petri plates.

extract_protocol:
RNA was extracted using a modified version of the Kolosova et al. (2004) procedure for woody material.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand.

treatment_protocol: Wood discs were from one of four different phenotypes: WT, LSHG, HS, LSX

value: Mycelia

tag: treatment

value: on WT poplar wood


title: S191


title: S165


title: KD, 1211-1

description: Library name: 1211-1_S79


title: KD, KD85

description: Library name: KD85_S72


title: KD, KD86

description: Library name: KD86_S73


title: S163


title: KD, KD84

description: Library name: KD84_S71


title: Trametes versicolor, WT wood, 3 weeks, Bio Rep 1

description:
Library name: WT1
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).


title: Trametes versicolor, LSX wood, 3 weeks, Bio Rep 2

description:
Library name: LSX2
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

value: on LSX poplar wood


title: KD, KD81

description: Library name: KD81_S68


title: KD, KD83

description: Library name: KD83_S70


title: KD, KD82

description: Library name: KD82_S69


title: KD, 1170-1

description: Library name: 1170-1_S71


title: S160


title: S161


title: KD, KD80

description: Library name: KD80_S67


title: S159


title: KD, KD78

description: Library name: KD78_S65


title: Trametes versicolor, LSHG wood, 3 weeks, Bio Rep 1

description:
Library name: LSHG1
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

value: on LSHG poplar wood


title: KD, KD79

description: Library name: KD79_S66


title: Trametes versicolor, LSHG wood, 3 weeks, Bio Rep 2

description:
Library name: LSHG2
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).


title: KD, KD76

description: Library name: KD76_S63


title: KD, KD77

description: Library name: KD77_S64


title: KD, KD75

description: Library name: KD75_S62


title: Trametes versicolor, HS wood, 3 weeks, Bio Rep 2

description:
Library name: HS2
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

value: on HS poplar wood


title: S158

value: multifocal

value: ILEUM


title: KD, KD74

description: Library name: KD74_S61


title: S157


title: Trametes versicolor, HS wood, 3 weeks, Bio Rep 1

description:
Library name: HS1
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).


title: KD, KD73

description: Library name: KD73_S60


title: KD, KD6

description: Library name: KD6_S61


title: S156


title: KD, KD5

description: Library name: KD5_S60


title: Trametes versicolor, LSX wood, 3 weeks, Bio Rep 1

description:
Library name: LSX1
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).


title: S155

value: YES


title: S30

value: unifocal


title: KD, KD58

description: Library name: KD58_S81