title: control ASO treatment, biological recplicate 1

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2 (-Q 5)
RNA-seq read quantification was performed using Kallisto 0.44.0 (-b 50 –single -l 200 -s 20)
DEG calling was performed using Sleuth 0.28.1 (Control contrast)
Genome_build: GRCh38
Supplementary_files_format_and_content: expression.tsv: tsv (Gene quantifications)
Supplementary_files_format_and_content: base-nontg_FUS-wt-homo_gene.tsv: tsv (DE calls for homozygous vs nontransgenic)
Supplementary_files_format_and_content: base-nontg_FUS-wt-het_gene.tsv: tsv (DE calls for heterozygous vs nontransgenic)
Supplementary_files_format_and_content: bs-control_fus-ko_wt_gene.tsv: tsv (DE calls for Fus KO vs control)

source_name: Spinal cord

extract_protocol:
Spinal cords were removed, flash frozen under liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared using Illumina TruSeq RNA Sample Prep Kit as per manufacturer directions

value: spinal cord

value: C57BL/6 wild type mice


title: control ASO treatment, biological recplicate 2

status: Public on Jan 16 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

tag: genotype


title: ASO Fus knockdown, biological recplicate 1


title: 740nm(1-24h)_alternating_10min(25-48h)_Rep5

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Ensembl (release: 75) annotation using TopHat2 (v2.0.13) with the options mate-inner-dist, mate-std-dev and library-type (fr- firststrand).
The distance between read mates (mate-inner-dist and mate-std-dev) were assessed individually using RSeQC (v2.6.1).
After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting.
DESeq2 was used for differential expression analysis of all replicates for each condition. In this analysis, all libraries were compared in a pairwise manner.
Genome_build: hg19

organism: Homo sapiens

source_name: hMSC

growth_protocol: hMSCs were cultivated on the indicated substrates.

extract_protocol: The cells were lysed using 1 ml peqGOLD Trifast (VWR International, Erlangen, Germany, cat. no. 30-2020) per hydrogel and RNA was extracted from the aqueous phase using the RNA purification kit R1013 (Zymo Research, Irvine, CA) according to the manufacturer’s protocol.

treatment_protocol: Samples were exposed to the indicated illumination.

tag: condition

value: phytochrome-based hydrogels

tag: illumination


title: ASO Fus knockdown, biological recplicate 2


title: control ASO treatment, biological recplicate 3


title: 740nm(1-24h)_alternating_10min(25-48h)_Rep2


title: 660nm(48h)_Rep5


title: 740nm(1-24h)_alternating_10min(25-48h)_Rep1


title: 660nm(48h)_Rep4


title: genomic DNA from sample596

type: genomic

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples, resultng in 249874 data rows out of a possible 485577 (provided in the matrix_normalized.txt)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: case_whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

tag: diagnosis

value: case

tag: Sex

value: F

value: whole blood

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: Ufo1_5_seedling

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: aboveground tissue of V2 stage seedling

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: maize AGPv3 genome
Supplementary_files_format_and_content: tag count file

organism: Zea mays

source_name: Ufo1-1 expressser, seedling  sample 5

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed with Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNAseq libraries were constructed with Illumina Truseq RNA sample preparation kit (RS-122-2001) . Script-Seq libraries (strand-specific RNAseq) were constructed with Illumina ScriptSeq RNA-seq library preparation kit (SSV21106).

value: aboveground seedling tissue

value: Ufo1-1 expresser

tag: developmental stage


title: hFUS overexpression Homo (line 101), mouse ID 166

description:
base-nontg_FUS_wt_homo_gene.tsv
expression.tsv

value: wt-FUS transgene homozygote


title: wt_2_seedling

description: aboveground tissue of V2 stage seedling

source_name: wildtype segregate, seedling  sample 2

value: wt


title: wt_4_seedling

description: aboveground tissue of V2 stage seedling

source_name: wildtype segregate, seedling  sample 4


title: wt_1_seedling

description: aboveground tissue of V2 stage seedling

source_name: wildtype segregate, seedling  sample 1


title: 660nm(48h)_Rep3


title: genomic DNA from sample569

description: whole blood control sample

source_name: control_whole blood

value: control

value: M


title: Ufo1_4_seedling

description: aboveground tissue of V2 stage seedling

source_name: Ufo1-1 expressser, seedling  sample 4


title: hFUS overexpression Homo (line 101), mouse ID 882


title: hFUS overexpression Het (line 101), mouse ID 545

description:
base-nontg_FUS_wt_het_gene.tsv
expression.tsv

value: wt-FUS transgene hemizygote


title: 660nm(48h)_Rep1


title: Ufo1_2_seedling

description: aboveground tissue of V2 stage seedling

source_name: Ufo1-1 expressser, seedling  sample 2


title: hFUS overexpression Het (line 101), mouse ID 825


title: genomic DNA from sample618

description: whole blood case sample


title: Ufo1_3_seedling

description: aboveground tissue of V2 stage seedling

source_name: Ufo1-1 expressser, seedling  sample 3


title: 660nm(48h)_Rep2


title: genomic DNA from sample571

description: whole blood control sample


title: hFUS overexpression Het (line 101), mouse ID 540


title: 660nm(1-24h)_alternating_160min(25-48h)_Rep5


title: hFUS overexpression Homo (line 101), mouse ID 858


title: Nontransgenic, mouse ID 821

value: non-transgenic control


title: Ufo1_3_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 3, batch 2

value: pericarp

value: 18 days after pollination


title: Ufo1_1_seedling

description: aboveground tissue of V2 stage seedling

source_name: Ufo1-1 expressser, seedling  sample 1


title: 660nm(1-24h)_alternating_160min(25-48h)_Rep4


title: Ufo1_2_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 2, batch 2


title: Nontransgenic, mouse ID 157


title: Nontransgenic, mouse ID 163


title: 660nm(1-24h)_alternating_160min(25-48h)_Rep3


title: 2_mo_BMC_2

city: Durham

first: Yasuhito

last: Yahara

state: NC

address: Duke Hospital South, 200 Trent Drive, Orange Zone 5th floor

institute: Duke Univ

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of samples: Csf1r_1, Csf1r_2, Cx3cr1_1, and Cx3cr1_2, using 10X Cellranger v2.1.1 with default parameters.
Alignment, counting, filtering, of single cell RNA-Seq of 2_mo_BMC_1 and 2_mo_BMC_2, using 10X Cellranger v2.1.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BMC.matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus 2_mo_BMC_1 and Mus musculus 2_mo_BMC_1 total bone marrow cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: BMC.genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: BMC.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.
Supplementary_files_format_and_content: Cx3cr1_Csf1r.matrix.mtx:  Gene-barcode matrix in Market Exchange Format (MEX) for Mus musculus Csf1r_1, Csf1r_2, Cx3cr1_1, and Cx3cr1_2 total bone marrow cells. Columns correspond to individual cells(barcodes), while rows correspond to genes.
Supplementary_files_format_and_content: Cx3cr1_Csf1r.genes.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column.
Supplementary_files_format_and_content: Cx3cr1_Csf1rbarcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.

source_name: Total bone marrow cells

growth_protocol: Macrophage/ monocyte lineage cells were isolated from E14.5 whole body cell suspensions. Total bone marrow cells were isolated from 2-month-old C57BL6 mice.

extract_protocol:
Cell were prepared for 10X Genomics Single Cell RNA-Seq using Chromium Single Cell 3′ Library & Gel Bead Kit v1.
10X Single Cell 3'

treatment_protocol: Pregnant female carrying Cx3cr1CreER; R26tdTomato or Csf1r-Mer-iCre-Mer; Csf1r-EGFP; R26tdTomato pups were injected with 4 hydroxytamoxifen at either E8.5 or 9.5.

value: wildtype

tag: 4 hydroxytamoxifen


title: 660nm(1-24h)_alternating_160min(25-48h)_Rep2


title: genomic DNA from sample676

description: whole blood case sample


title: Ufo1_1_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 expressser, 18 Day-after-pollination pericarp  sample 1, batch 2


title: 660nm(1-24h)_alternating_160min(25-48h)_Rep1


title: sil_3_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 3, batch 2

value: Ufo1-1 silent


title: 2_mo_BMC_1


title: 660nm(1-24h)_alternating_10min(25-48h)_Rep5


title: 660nm(1-24h)_alternating_10min(25-48h)_Rep4


title: sil_2_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 2, batch 2


title: wt_3_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: wildtype segregate, 18 Day-after-pollination pericarp  sample 3, batch, 2


title: genomic DNA from sample630

description: whole blood case sample

source_name: case_whole blood


title: sil_1_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: Ufo1-1 silent, 18 Day-after-pollination pericarp  sample 1, batch 2


title: wt_2_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: wildtype segregate, 18 Day-after-pollination pericarp  sample 2, batch 2


title: 660nm(1-24h)_alternating_10min(25-48h)_Rep1

source_name: hMSC


title: Tim-3-PD-1- CD8+ antiTim3+antiPD1 treated (scRNA-seq)

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

institute: BWH

description:
data_mat_CD8_counts_WT_iso_treated.txt
data_mat_CD8_scaled_WT_iso_treated.txt
CD8_Tils_B
S2

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome using CellRanger software (v1.3 10× Genomics). To remove doublets and poor-quality cells, we removed cells that contained more than 10% mitochondrially derived transcripts, or where less than 500 genes were detected. Among the retained cells, we considered only genes that are present in >30 cells and have >60 transcripts summed across all the selected cells, yielding 5,457 cells and 9,505 genes.
Genome_build: mm10
Supplementary_files_format_and_content: Transcript count for each library was normalized to the median of the transcript counts across all cells. For PCA and clustering, we used a log-transformed expression matrix. The top 13 PCs were included for subsequent tSNE analysis, determined by a drop in the proportion of variance explained by subsequent PCs. We confirmed that the resulting analyses were not particularly sensitive to this choice.
Column names ending with "1" belongs to sample number 1 (isotype treated) and column names ending with "2" blong to sample number 2 (anti-Tim3-anti-PD1 treated)

source_name: Tumor MC38-OVA

extract_protocol:
Tim-3-PD-1- CD8+ TILs were sorted from MC38-OVA tumor-bearing mice that were treated with anti-PD-1 and anti-Tim-3 antibodies or isotype controls and were encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer’s protocol (10× Genomics). The generated single cell RNA-seq libraries were sequenced using a 75 cycle Nextseq 500 high output V2 kit.

treatment_protocol: On day 12 post tumor implantation, Tim-3-PD-1- CD8+ TILs were isolated by cell sorting (BD FACS Aria II) from MC38-OVA tumor-bearing mice that were treated with anti-PD-1 and anti-Tim-3 antibodies or isotype controls.

value: Tumor MC38-OVA

value: wild type

tag: cell type

value: Tim-3-PD-1- CD8+ TILs

tag: treatment

value: antiTim3+antiPD1 treated


title: 660nm(1-24h)_alternating_10min(25-48h)_Rep2

value: phytochrome-based hydrogels


title: 660nm(1-24h)_alternating_10min(25-48h)_Rep3


title: wt_1_pericarp_2

description: 18 Day-after-pollination pericarp

source_name: wildtype segregate, 18 Day-after-pollination pericarp  sample 1, batch 2


title: Tim-3-PD-1- CD8+ isotype treated (scRNA-seq)

description:
data_mat_CD8_counts_WT_iso_treated.txt
data_mat_CD8_scaled_WT_iso_treated.txt
CD8_Tils_A
S1

value: isotype treated


title: Input Hypoxia n2

city: Liverpool

first: Sonia

last: Rocha

address: Crown Street

country: United Kingdom

institute: University of Liverool

library_source: genomic

data_processing:
Fastq data files were passed through the quality control tool FASTQC and aligned to the human genome annotation hg19_73 using the subread package
RPKM normalised bigwig files were generated using Deeptools 3.1
H3K4me3 peaks for individual replicates and merged bam files for each condition (normoxia and hypoxia) were called using the MACS2 peak caller  in narrow peak mode with the IP sample bam files set as treatment and corresponding input bam files set as control. Peaks called in 3 out of 3 replicates per condition were designated as high stringency peaks. To call H3K4me3 peaks enriched in hypoxia over normoxia (upregulated), the merged hypoxia bam file was used as the treatment and merged normoxia bam file as the control in MACS2 peak caller narrow peak mode. To call H3K4me3 peaks enriched in normoxia over hypoxia (downregulated), the merged normoxia bam file was used as the treatment and the merged hypoxia bam file as the control in MACS2 peak caller narrow peak mode. An FDR of 0.05 was used as the cut off for MACS2 peak calls.
H3K36me3 peaks for individual replicates and merge bam files for each condition were called using the using the SICER peak caller with the IP sample bam files set as treatment and corresponding input bams file set as control. SICER is a peak caller which specializes in calling broad peaks and was deemed more suitable than MACS2 for calling H3K36me3 peaks. To call H3K36me3 peaks enriched in hypoxia over normoxia, the merged hypoxia bam file was used as the treatment and merged normoxia bam file as the control. To call H3K36me3 peaks enriched in hypoxia over normoxia, the merged normoxia bam file was used as the treatment and the merged hypoxia bam file as the control. FDR of 0.01 was used as the cut off for all SICER calls   and a fold change cut off of 0.2 for peaks called as enriched in one condition over another was applied
H3K4me3 and H3K36me3 hypoxia upregulated and downregulated peaks were further filtered to only include high stringency peaks (peaks called in 3 out of 3 replicates) for the condition they are the enriched in.
Genome_build: hg19_73
Supplementary_files_format_and_content: Bigwig files= RPKM normalised alignment data. Bam files= alignment data to hg19_73. Narrow peak files= Seqnames, start  ,end, name, score ,strand, sigValue, pvalue, qvalue, peak. BED files = Seqnames, start, end, name, score, strand.

source_name: Cervical cancer

growth_protocol: HeLa were maintained in Dulbecco’s modified Eagle's medium (DMEM) (Sigma), supplemented with 2mM L- glutamine, 10% (v/v) Foetal Bovine Serum (FBS) (Gibco), 50 units/mL penicillin (Lonza) and 50 μg/mL streptomycin (Lonza)

extract_protocol:
see SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression, Biddlestone J et al 2018. PMID: 29784889
DNA libraries for ChIP sequening were prepared  using standard Illumina protocols

value: 1H of 1% O2

tag: cell line

value: HeLa


title: Input Hypoxia n3


title: Input Hypoxia n1


title: Input n2


title: Input n1


title: Input n3


title: H3K36me3 Hypoxia n2

tag: chip antibody

value: H3K36me3 (61101, Active Motif)


title: Sample 5: Src_SH4_C2

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE, Foege Building, S041

department: Genome Sciences

institute: University of Washington

description: Targeted barcode amplification from extracted plasmid DNA

data_processing:
Sample 1 was sequenced on MiSeq (Illumina). Samples 2-5 were sequenced on NextSeq 500 (Illumina).
All reads were processed using  bcl2fastq v.2.16 and ea-utils v.1.1.2-537.
Sample 1: R2 files were trimmed to 230bp and replicates for both R1 and R2 were concatenated into single files.
Samples 2-5: Functional scores were calculated using Enrich2 v1.2 software and Src_Barcode_Map.txt.
Samples 4-5: Paired reads were collapsed into a single consensus read using PEAR v.0.9.5.
Supplementary_files_format_and_content: Src_Barcode_Map.txt provides the linkage between the barcode sequence (first column) and the full length variant sequence of Src's catalytic domain (second column). This document was generated through the following steps: 1) Custom subassembly scripts to link barcode sequence with full length catalytic domain sequence. 2) Custom subassembly filtering script for high quality reads. 3) Filtering out WT barcodes with aberrant activity score using 2x Std. Dev. of WT barcode mean activity score. 4) Spike in of 6 barcode sequences of control Src variants (3 each for K298M and T341I).
Supplementary_files_format_and_content: CD_Scores.csv and SH4_Scores.csv are the output of Enrich2 v1.2. Each variant has a corresponding functional score and standard error measurement. Reads from Src_CD_1 and Src_CD_2 are used in CD_Scores.csv. Reads from Src_SH4_1 and Src_SH4_2 are used in SH4_Scores.csv.

organism: Saccharomyces cerevisiae

source_name: Synthetic sequence

growth_protocol: TOP10 E.coli were grown in LB supplemented with 100 ug/mL Ampicillin. BY4741 Green Monster S. cerevisiae were grown in C-Leu media supplemented with 2% galactose.

extract_protocol:
Harvested cells (4 OD units worth) at each sampled time point were pelleted and stored at -20ºC. Plasmid DNA was extracted using Zymogen Yeast Miniprep Kit I following supplied protocol.
Extracted barcodes were amplifed and sample indices appended using 2x KAPA2G Robust HotStart ReadyMix with Thermocycler conditions of: Initial denaturation at 95ºC for 3 min, followed by 17 cycles of 95ºC for 15s, 60ºC for 15s, and 72ºC for 15s. Amplicons were quantified using KAPA Library Quantification Kit.

treatment_protocol: S. cerevisiae harboring Src variant library were grown in 2% galactose containing media to induce Src expression. Library was grown and 4 OD unit timepoints were harvested throughout growth.

tag: strain

value: Green Monster BY4741

tag: molecule

value: Plasmid DNA


title: H3K36me3 n3


title: H3K36me3 n2


title: H3K36me3 Hypoxia n3


title: H3K36me3 n1


title: s412_extracted DNA_n=3

city: Yokohama

first: Naoyuki

last: Togawa

state: Kanagawa

country: Japan

institute: Mitsubishi Chemical Corporation

hyb_protocol: Two hundred μl hybridization solution was prepared from the PCR products with 0.24 M Tris/HCl (pH 7.5), 0.24 M NaCl, and 0.05% Tween®20. Hybridization and washing were performed by DNA chip Instrument Systems (Mitsubishi Chemical Co., Ltd.) for 16 h, after which the DNA chips were further washed with wash solution (0.24 M Tris/HCl pH 7.5 and 0.24 M NaCl) for 5 min at room temperature.

scan_protocol: Hybridization signals were examined by Genopal Reader™ (Mitsubishi Chemical Co., Ltd.) with multi-beam excitation technology (Yokogawa Electric, Tokyo, Japan). Fluorescence signals were detected with exposure times of 0.1, 1, 4, and 40 s using this instrument, and the longest exposure images without saturated pixels in the spots were adopted as spot images and quantified as the fluorescence signal intensity per second.

data_processing:
The probe signal intensity was determined from the fluorescence signal intensity. The mean and standard deviation of the fluorescence signal intensity of the background spot without the probe were calculated, and the sum of the mean and standard deviation of three repetitions was defined as the background signal intensity. Probe signal intensity was calculated by subtracting the background signal intensity from the median of the fluorescence signal intensity of the five spots of each probe.
BLANK array features are not represented in the data table.

source_name: dental plaque from patient (oral sample)

label_protocol: Cy5 labeled PCR primer

extract_protocol: Genomic DNA was extracted from the samples using a Wizard Genome DNA Purification Kit (Promega).

treatment_protocol: Human dental plaque samples were collected from the erupted teeth of a person by brushing for 1 min with a sterile toothbrush. The plaques attached to the brush were removed by washing several times in 5 ml sterile distilled water in 15 ml test tubes then collected by centrifugation at 1,600×g for 20 min.

tag: sample type

value: dental plaque


title: s409_extracted DNA_n=2


title: s409_extracted DNA_n=3


title: s412_extracted DNA_n=1


title: s12-1_extracted DNA_n=2


title: s412_extracted DNA_n=2


title: s12-1_extracted DNA_n=1


title: H3K4me3 Hypoxia n3

value: H3K4me3 (39915, Active Motif)


title: Sample 5: Src_SH4_B2


title: H3K36me3 Hypoxia n1


title: genomic DNA from sample584

description: whole blood case sample

value: case

tag: age

value: F

tag: tissue

value: whole blood


title: s48_extracted DNA_n=1


title: s48_extracted DNA_n=2


title: s409_extracted DNA_n=1


title: s48_extracted DNA_n=3


title: s12-1_extracted DNA_n=3


title: Sample 4: Src_SH4_A1


title: genomic DNA from sample544

description: whole blood case sample

tag: diagnosis

value: M


title: s47_extracted DNA_n=3


title: Streptococcus mutans_0.01amol (16SrRNA gene)_n=1

organism: Streptococcus mutans


title: H3K4me3 n2


title: Sample 5: Src_SH4_A2


title: Sample 5: Src_SH4_Input2


title: Streptococcus mutans_0.001amol (16SrRNA gene)_n=2


title: s47_extracted DNA_n=2


title: Sample 3: Src_CD_B2


title: Sample 3: Src_CD_A2


title: DIO and control MDA-MB-468 Tumors, replicates 2 of 3

type: RNA

city: Detroit

first: Emily

middle: A.

last: Teslow

state: MI

address: 4100 John R St.

department: Oncology

institute: Wayne State University School of Medicine

hyb_protocol: Whole-genome expression was measured by a 2-color microarray approach using Agilent SurePrint G3 Human GE 8X60K arrays. DIO and control samples were randomly assigned.

scan_protocol: GE2_1200_Jun14 protocol and Agilent SureScan System

data_processing:
Probe intensity, background and detection quality data were extracted with Agilent Feature Extraction software. The limma package in R was used to perform normal-exponential convolution (with an offset of 50) background correction; loess normalization within arrays; and quantile normalization across arrays.
Results of differential expression analysis of pooled replicates, effect size expressed as DIO/Control log10 ratio are in Series supplementary file

source_name: DIO replicate 2

label_protocol: Labeling reaction used the Low Input Quick Amp Labeling Kit from Agilent Technologies, Inc. following the recommended protocol to produce cRNA for a two-color microarray experiment

growth_protocol: Established human breast cancer cell line MDA-MB-468 was maintained in adherent monolayer conditions for 3 passages, prior to inoculation in female 11 week old B6.Rag1-/- mice that were maintained on purified high-fat diet or formula matched low-fat diet (Research Diets). Resulting tumors at approximately 1,000 mg in size were harvested, immediately flash frozen and stored at -80C.

extract_protocol: Tumors were flash frozen with liquid nitrogen and pulverized for total RNA extraction using RNeasy mini Kit (Qiagen). Quantity and quality of all mRNA samples was estimated using the NanoDrop 1000.

treatment_protocol: Female B6.Rag1-/- mice were fed a control (kcal fat%=10, gram%=4.3) or  high-fat DIO diet (kcal fat%=60, gram%=35) diet  5 weeks prior to innoculation and post-innoculation (cat # D12492 and D12450B, Research Diets, New Brunswick, NJ)

value: MDA-MB-468 tumor formed in DIO mice

source_name: Control replicate 2

value: MDA-MB-468 tumor formed in lean control mice


title: DIO and control MDA-MB-468 Tumors, replicates 1 of 3

source_name: DIO replicate 1

source_name: Control replicate 1


title: Streptococcus mutans_0.1amol (16SrRNA gene)_n=2


title: DIO and control MDA-MB-468 Tumors, replicates 3 of 3

source_name: DIO replicate 3

source_name: Control replicate 3


title: s47_extracted DNA_n=1


title: Sample 4: Src_SH4_C1


title: Sample 2: Src_CD_B1


title: H3K4me3 Hypoxia n2


title: Sample 4: Src_SH4_B1


title: Streptococcus intermedius_0.001amol (16SrRNA gene)_n=2

organism: Streptococcus intermedius


title: Streptococcus mutans_1amol (16SrRNA gene)_n=2


title: Streptococcus mutans_0.1amol (16SrRNA gene)_n=1


title: Streptococcus mutans_0.001amol (16SrRNA gene)_n=1


title: Sample 2: Src_CD_Input1


title: Sample 2: Src_CD_C1


title: Streptococcus mutans_0.01amol (16SrRNA gene)_n=2


title: H3K4me3 n3


title: Spb1_pulldown_B

city: New Haven

first: Wendy

last: Gilbert

state: CT

address: 333 Cedar Street, P.O. Box 208024

institute: Yale University

description:
UV-crosslinked RNA
TableS14.Spb1_eCLIP.csv
Spb1_B

data_processing:
Read demultiplexing: removed the first 10-nt of the forward reads, and adding them to the sequence name for later use
Use cutadapt (version 1.7.1) to trim 3’ adapter, requiring a minimum trimmed read length of 18-nt.
Map reads using STAR(version 2.5.1b) to a repeat-masked yeast genome.
Collapse PCR duplicates: use the 10-nt barcode from step 1 to merge reads that map to the same position and share the same barcode.
Call peaks using CLIPper
Normalize peaks from pulldown libraries by peaks in size-matched input library
Genome_build: sacCer3
Supplementary_files_format_and_content: *.csv files are tables of normalized peak heights
*.bed files represent raw peaks

growth_protocol: For ePAR-CLIP assays yeast were grown at 30°C in minimal media with reduced uracil (SCUra120uM) to an A600nm=0.4-0.5, supplemented with 4-thiouracil to a final concentration of 500uM and cultured for 3 more hours before harvest.

extract_protocol:
Cells were resuspened in 1.5 mL iCLIP lysis buffer (50 mM Tris-HCl pH7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1X protease inhibitor cocktail (Millipore), 400U/mL Murine RNase inhibitor (NEB)) per g of cell pellet and lysed by vortexing with glass beads (Manufacturer). Lysates were clarified by centrifugation, flash frozen in liquid N2 and stored at -80°C.
Lysates were diluted in iCLIP lysis buffer to 26 ODU/2 mL and treated with Turbo DNase (Lifetech) and RNase I (Lifetech) for 15min at 22°C before placing on ice. Treated lysates were centrifuged (15,000 x g 15min) and added to Protein G magnetic beads (Dynabeads) pre-bound with 10 µg of antibody (anti-Myc or anti-FLAG, Sigma) and rotated for 2.5hr at 4°C. 4% of the binding reaction was saved as input before extensive washing of bead-bound protein-RNA complexes. Bound RNA 3′ ends were dephosphorylated with FastAP (Lifetech) and PNK (NEB) before on-bead ligation of a 3′ RNA linker with T4 Rnl (NEB) at 16°C overnight. After washing, 10% of bound RNA was labeled by PNK with 32P ATP for diagnostic gels. The remainder was eluted from the beads by incubation in 1X NuPAGE loading buffer with 0.1M DTT at 70°C for 10min. CLIP eluates and paired inputs were electrophoresed on 4-12% Bis-Tris NuPAGE and transferred to nitrocellulose membranes. Tagged protein MW was determined by western blot of 2% input before CLIP and size-matched input (SMI) membranes were cut, taking a 75kDa region just above the target protein size. RNA was released with proteinase K, extracted with phenol:chloroform:isoamy alcohol, and purified on RNA Clean & Concentrator-5 columns (Zymo). SMI RNA was dephosphorylated, a 3′ linker ligated, and purified on silane beads (Dynabeads). CLIP and SMI RNA was reverse transcribed with SuperScript IV, hydrolyzed with NaOH, neutralized with HCl, and cDNA was purified on silane beads. A 5′ linker was ligated with T4 Rnl (NEB) overnight at 16°C. Linker-ligated cDNA was purified on silane beads before diagnostic PCRs to determine the minimum number of cycles. Final PCR products were gel-purified, precipitated and sequenced on an Illumina HiSeq 2000.

treatment_protocol: Cells were harvested by centrifugation, resuspended in ice cold water, and UV irradiated on ice in a Stratalinker (365 nm, energy = 7.2J/cm2). Crosslinked cells were washed in ice water, flash frozen in liquid N2, and stored at -80°C until lysis.

tag: pulldown

value: pulldown

tag: genotype

tag: affinity tag

value: FLAG

tag: rip antibody

value: anti-FLAG, Sigma, catalog # F3165, lot # SLBN-8915V


title: Sample 4: Src_SH4_Input1


title: Sample 3: Src_CD_C2


title: genomic DNA from sample591

description: whole blood case sample

tag: Sex

tag: cellcount-nk

tag: cellcount-bcell

tag: cellcount-mono

tag: cellcount-gran


title: genomic DNA from sample686

description: whole blood case sample


title: Streptococcus mutans_1amol (16SrRNA gene)_n=1


title: H3K4me3 n1

tag: treatment

tag: cell line


title: Streptococcus intermedius_0.1amol (16SrRNA gene)_n=1


title: NI_48h_rep2_vs_Ctr_48h_rep2

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted dual-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and within-array normalized using method LOESS was applied.

source_name: C.trachomatis infection, 48h, replicate 2

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: End1/E6E7 (End1) [American Type Culture Collection (ATCC) CRL-2615] and cells were cultured in Hepes-buffered growth medium [DMEM (GibCo) supplemented with 10% fetal calf serum (FCS) (Biochrome), 2mM glutamine, and 1 mM sodium pyruvate], at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany).

treatment_protocol: End1/E6E7 cells in six-well plates were infected with C. trachomatis L2 for 24 or 48h.

tag: replicate

tag: time p.i.

value: Ctr

source_name: uninfected control, 48h, replicate 2

value: NI


title: Streptococcus intermedius_0.1amol (16SrRNA gene)_n=2

tag: sample type


title: Sample 3: Src_CD_Input2

tag: strain

tag: molecule


title: Sample 2: Src_CD_A1


title: Streptococcus intermedius_0.001amol (16SrRNA gene)_n=1


title: Streptococcus intermedius_0.01amol (16SrRNA gene)_n=2


title: Streptococcus intermedius_1amol (16SrRNA gene)_n=2


title: Streptococcus intermedius_0.01amol (16SrRNA gene)_n=1


title: Spb1_pulldown_A

description:
UV-crosslinked RNA
TableS14.Spb1_eCLIP.csv
Spb1_A


title: genomic DNA from sample622

description: whole blood case sample

source_name: case_whole blood

tag: diagnosis

tag: age

tag: tissue


title: Streptococcus gordonii_0.001amol (16SrRNA gene)_n=2

organism: Streptococcus gordonii


title: Rpb3_Nocodazole_0h_Input_B

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

data_processing:
Sequencing data were aligned to the yeast genome (SacCer3) using Bowtie2 with default settings.
Occupancy profiles in bedGraph format were generated using bedtools.
For further analyses the aligned reads were size-selected as described in the article.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph

growth_protocol: Wild type yeast strain YDC111 was grown in synthetic complete medium to OD600 ~0.25. A control sample ("0 h") was removed from the culture before nocodazole addition.

extract_protocol:
ChIP-seq experiments: cells were formaldehyde cross-linked before harvesting (1% for 15 minutes). The IP was performed with anti-Rpb3 antibody (Neoclone WP012)
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

treatment_protocol: Nocodazole (Abcam ab120630) was added (6 ug/ml). Cells were monitored by microscopy for 2 h, by which time the large majority displayed the dumbbell shape characteristic of G2/M arrest ("2h" samples). Arrest was confirmed using fluorescence microscopy after staining for DNA using propidium iodide.

value: YDC111 (wild type)

tag: genotype/variation

value: control

tag: time

tag: chip antibody

tag: biological replicate


title: Ctr_24h_rep2_vs_NI_24h_rep2

source_name: uninfected control, 24h, replicate 2

source_name: C.trachomatis infection, 24h, replicate 2


title: Rpb3_Nocodazole_2h_IP_B

value: Nocodazole

value: anti-Rpb3 antibody (Neoclone WP012)


title: H3K4me3 Hypoxia n1

value: 1H of 1% O2

value: HeLa


title: Rpb3_Nocodazole_2h_Input_B


title: genomic DNA from sample696

description: whole blood case sample

value: case

tag: Sex

tag: cellcount-nk

tag: cellcount-bcell


title: Rpb3_Nocodazole_0h_IP_B

tag: treatment


title: Streptococcus intermedius_1amol (16SrRNA gene)_n=1


title: Streptococcus gordonii_0.001amol (16SrRNA gene)_n=1


title: Streptococcus gordonii_0.01amol (16SrRNA gene)_n=2


title: Rpb3_Nocodazole_0h_IP_A


title: Ctr_48h_rep1_vs_NI_48h_rep1

source_name: uninfected control, 48h, replicate 1

source_name: C.trachomatis infection, 48h, replicate 1


title: genomic DNA from sample646

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: Ctr_48h_rep2_vs_NI_48h_rep2

tag: replicate

tag: time p.i.


title: Rpb3_Nocodazole_2h_IP_A

tag: strain


title: Rpb3_Nocodazole_0h_Input_A


title: Streptococcus gordonii_0.1amol (16SrRNA gene)_n=2

tag: sample type


title: Streptococcus gordonii_0.01amol (16SrRNA gene)_n=1


title: Ctr_24h_rep1_vs_NI_24h_rep1

source_name: uninfected control, 24h, replicate 1

source_name: C.trachomatis infection, 24h, replicate 1


title: genomic DNA from sample693

description: whole blood case sample

tag: diagnosis


title: Streptococcus gordonii_0.1amol (16SrRNA gene)_n=1


title: NI_24h_rep2_vs_Ctr_24h_rep2


title: K2PT B

city: Edinburgh

first: Martha

last: Lopez Yrigoyen

address: 5 Little France Dr

institute: Centre for Regenerative Medicine

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-001_TP-D5-004

data_processing:
Sequence data was generated in HiSeq 4000 75PE (Illumina) to yield at least 290M + 290M reads (1 lane)
Reads were trimmed using Cutadapt version 1.121. Reads were trimmed for quality at the 3’ end using a quality threshold of 30and for adapter sequences of the TruSeq stranded mRNA kit (AGATCGGAAGAGC). Reads after trimming were required to have a minimum length of 50.
The reference used for mapping was the Homo sapiens genome from Ensembl, assembly GRCh38, annotation version 84.
Reads were aligned to the reference genome using STAR2 version 2.5.2b specifying paired-end reads and the option ‘–outSAMtype BAM Unsorted’. All other parameters were left at default.
Genome_build: GRCh38, annotation version 84.

source_name: tamoxifen treated iKLF1.2 iPSC derived macrophages

growth_protocol: Human iPSC-derived macrophages wre produced in a step-wise manner. IPSC Maintenance media was replaced with Day 0 mix:  StemPro hESC SFM (Gibco) supplemented with 50ng/ml BMP4 (R&D), 50ng/ml VEGF (R&D) and 20ng/ml SCF (Life Technologies). Colonies were cut using the EZPassageTM tool into two wells and cultured in Ultralow Attachment 6 well plates (Greiner) for four days to induce embryoid body (EB) formation. On day 2, cytokine top-up was carried out. On day 4, 10-15 EBs were transferred to one gelatin-coated well of a 6-well tissue culture grade plate containing 3ml Day 4 mix (X-VIVO15 media supplemented with 100ng/ml CSF1 (Biolegend), 25ng/ml IL-3 (Preprotech), 2mM Glutamax (Gibco), 1% Penicillin-Streptomycin (Life Technologies) and 0.055mM β-mercaptoethanol. Media was changed every 3-4 days. After 3 weeks, the EBs started releasing non-adherent monocyte-like precursors that were harvested from the supernatant and plated into untreated bacteriological plates or six-well plates in Maturation mix (X-VIVO15 media supplemented with 100ng/ml CSF1, 2mM Glutamax and 1% Penicillin-Streptomycin for 9-11 days.

extract_protocol:
RNA extraction was carried out using the RNAeasy Mini Kit (Qiagen) following manufacturer instructions. DNA removal from samples was carried out using the RNAse-free DNAse Set (Qiagen) on the RNA extraction columns. RNA quantity and quality was assessed using the Agilent Technologies TapeStation
Edinburgh Genomics generated 8 TruSeq stranded mRNA-seq libraries (Illumina) from total RNA samples

treatment_protocol: To activate KLF1 transcription factor in iKLF1.2 IiPSC-DMs, 100nM Tamoxifen was added to the matured macrophage population for the last 4 days of the differentiation process

tag: parental line

tag: cell type

value: KLF1 inducible iPSC-derived macrophages

value: Tamoxifen added, KLF1 Activation


title: Rpb3_Nocodazole_2h_Input_A

tag: genotype/variation


title: K2PT D

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-002_TP-D5-004


title: Streptococcus gordonii_1amol (16SrRNA gene)_n=2


title: K2PT A

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-001_TP-D5-002


title: NI_48h_rep1_vs_Ctr_48h_rep1


title: FoxO1 wt tumor tissue_mouse 1

city: Cologne

first: thomas

last: wunderlich

state: NRW

address: Gleueler Str. 50

institute: MPI for Metabolism Research

description: WT_OST667 [701/779]; LogSignal

hyb_protocol: GeneChip® Hybridization Control Kit; GeneChip® Hybridization Oven 645

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: Expression Console v 1.4

label: biotin

source_name: colorectal tumors isolated 62 days after chemical induction of CAC development

label_protocol: GeneChip® WT Terminal Labeling Kit

growth_protocol: CAC was induced by a injection of 10 mg/kg AOM at day 1 and administration of 1.5% DSS via the drinking water at day 5-11. Tumours were isolated 62 days after AOM injection.

extract_protocol: RNA was extracted using Trizol according to manufacture's instructions

treatment_protocol: Tumour tissue was snap-frozen in liquid nitrogen and stored at -80°C until RNA isolation.

tag: gender

value: female

value: wildtype

tag: tissue

value: pure colorectal adenoma tissue


title: FoxO1 wt tumor tissue_mouse 2

description: WT_OST2513 [702/780]; LogSignal


title: genomic DNA from sample570

description: whole blood control sample

source_name: control_whole blood

tag: age

value: M

value: whole blood


title: K2PT C

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-002_TP-D5-002


title: FoxO1 wt tumor tissue_mouse 3

description: WT_OST2854 [703/781]; LogSignal


title: Capnocytophaga gingivalis_0.001amol (16SrRNA gene)_n=2

organism: Capnocytophaga gingivalis


title: NI_24h_rep1_vs_Ctr_24h_rep1


title: Streptococcus gordonii_1amol (16SrRNA gene)_n=1


title: FoxO1ADA tumor tissue_mouse 2

description: KO_OST2809 [705/783]; LogSignal


title: K2MT C

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-002_TP-D5-001

source_name: untreated iKLF1.2 derived macrophages

value: No Tamoxifen added


title: K2MT A

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-001_TP-D5-001


title: Capnocytophaga gingivalis_0.001amol (16SrRNA gene)_n=1


title: Capnocytophaga gingivalis_1amol (16SrRNA gene)_n=2


title: Capnocytophaga gingivalis_0.1amol (16SrRNA gene)_n=1


title: FoxO1ADA tumor tissue_mouse 3

description: KO_OST2855 [706/784]; LogSignal


title: Capnocytophaga gingivalis_0.1amol (16SrRNA gene)_n=2


title: K2MT D

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-002_TP-D5-003


title: Colon cancer Tumor xenograft sample normal glucose, 459

city: Madrid

first: Pablo

last: Minguez

state: Madrid

address: Av. Reyes Catolicos 2

department: Genetics and Genomics

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz (IIS-FJD), UAM

description: Colon cancer Xenograft Tumor sample non-diabetic mouse

hyb_protocol: WT Pico reagent kit

scan_protocol: GeneChip System of Affymetrix

data_processing:
CEL files are background corrected and normalized using the RMA method implemented in the oligo R package and annotated with hugene20sttranscriptcluster R package
probe group file: HuGene-2_0-st.pgf
meta-probeset file: HuGene-2_0-st.mps

label: WT Pico reagent kit

label_protocol: WT Pico reagent kit

extract_protocol: RNeasy Mini Kit (Qiagen)

value: Colon cancer Xenograft Tumor

value: no diabetes

tag: blood glucose level


title: K2MT B

description: 170313_K00166_0193_BHHMJYBBXX_7_TP-D7-001_TP-D5-003


title: Capnocytophaga gingivalis_0.01amol (16SrRNA gene)_n=2


title: Capnocytophaga gingivalis_0.01amol (16SrRNA gene)_n=1


title: Colon cancer Tumor xenograft sample normal glucose, 458


title: FoxO1ADA tumor tissue_mouse 1

description: KO_OST2654 [704/782]; LogSignal


title: genomic DNA from sample619

description: whole blood case sample

tag: Sex

tag: cellcount-nk


title: Aggregatibacter actinomycetemcomitans_0.001amol (16SrRNA gene)_n=1

organism: Aggregatibacter actinomycetemcomitans


title: Colon cancer Tumor xenograft sample high glucose, 478

description: Colon cancer Xenograft Tumor sample diabetic mouse

value: diabetes


title: Colon cancer Tumor xenograft sample normal glucose, 457


title: Colon cancer Tumor xenograft sample high glucose, 479


title: Aggregatibacter actinomycetemcomitans_0.01amol (16SrRNA gene)_n=1


title: Colon cancer Tumor xenograft sample normal glucose, 456


title: Aggregatibacter actinomycetemcomitans_0.001amol (16SrRNA gene)_n=2


title: Capnocytophaga gingivalis_1amol (16SrRNA gene)_n=1


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 8

description: Colon cancer Tumor sample (FFPE) non-diabetic patient

data_processing:
CEL files are background corrected and normalized using the RMA method implemented in the oligo R package and annotated with hugene20sttranscriptcluster R package
probe_group_file: HuGene-2_0-st.pgf
meta-probeset_file:  HuGene-2_0-st.mps

extract_protocol: RNeasy FFPE Kit (Qiagen)

value: Colon cancer Tumor

value: non-diabetic patient


title: Colon cancer Tumor xenograft sample normal glucose, 455


title: Aggregatibacter actinomycetemcomitans_0.01amol (16SrRNA gene)_n=2


title: Aggregatibacter actinomycetemcomitans_0.1amol (16SrRNA gene)_n=2


title: genomic DNA from sample631

description: whole blood case sample

tag: cellcount-bcell


title: cirmtuzumab4

city: La Jolla

first: suping

last: zhang

state: CA

address: 8955 health science Dr

department: Medical school

institute: UCSD

data_processing:
adapters were removed and reads were trimmed off bases with low quality scores in late sequencing cycles using Cutadapt
the reads to human genome build 38 using the STAR aligner was mapped
RSEM (v1.3.0)   was used to get the raw gene counts from the read alignments and Ensembl gene models (v83).
Two different packages DEseq2 and limma  were used to normalize the read count data and assess differential expression
Genome_build: human genome build 38
Supplementary_files_format_and_content: excel file containing normalized gene expression value

source_name: breast cancer patient-derived xenograft (PDX4)

growth_protocol: Equal number of single cell suspension isolated from PDX4 tumors  were implanted in Rag2-/-γc-/- mice.

extract_protocol:
Total RNA was prepared from tumor tissues excised from mice received either hIgG or Cirmtuzumab treatment using Trizol RNA extracting protocol, followed with RNeasy column (Qiagen kit) purification.
RNA libraries were generated from 1 µg of RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes

treatment_protocol: Mice bearing PDX tumors were treated with eithor control antibody or cirmtuzuma at 10mg/Kg biweekly

value: breast cancer patient-derived xenograft


title: Aggregatibacter actinomycetemcomitans_0.1amol (16SrRNA gene)_n=1


title: Aggregatibacter actinomycetemcomitans_1amol (16SrRNA gene)_n=2


title: Aggregatibacter actinomycetemcomitans_1amol (16SrRNA gene)_n=1


title: Prevotella nigrescens_0.001amol (16SrRNA gene)_n=2

organism: Prevotella nigrescens


title: cirmtuzumab3


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 9

description: Normal colonic mucosa sample (FFPE) non-diabetic patient

value: Normal colonic mucosa


title: cirmtuzumab1


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 8

source_name: Normal colonic mucosa sample (FFPE) non-diabetic patient


title: Prevotella nigrescens_0.01amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 7

source_name: Colon cancer Tumor sample (FFPE) non-diabetic patient


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 4


title: cirmtuzumab2


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 5


title: Colon cancer Tumor sample (FFPE) diabetic, patient 50

description: Colon cancer Tumor sample (FFPE) diabetic patient

value: diabetic patient


title: Prevotella nigrescens_0.001amol (16SrRNA gene)_n=1


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 9


title: Normal colonic mucosa sample (FFPE) diabetic, patient 50

description: Normal colonic mucosa sample (FFPE) diabetic patient


title: Normal colonic mucosa sample (FFPE) diabetic, patient 49

source_name: Normal colonic mucosa sample (FFPE) diabetic patient


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 7


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 4


title: Prevotella nigrescens_0.1amol (16SrRNA gene)_n=1


title: control2


title: control3


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 5


title: Normal colonic mucosa sample (FFPE) diabetic, patient 48


title: control4


title: Colon cancer Tumor sample (FFPE) diabetic, patient 48

source_name: Colon cancer Tumor sample (FFPE) diabetic patient


title: Prevotella nigrescens_0.1amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) diabetic, patient 49


title: genomic DNA from sample606

description: whole blood case sample

value: case

value: F

tag: cellcount-mono


title: Prevotella nigrescens_0.01amol (16SrRNA gene)_n=1


title: genomic DNA from sample642

description: whole blood case sample

tag: cellcount-gran


title: Prevotella nigrescens_1amol (16SrRNA gene)_n=2


title: Prevotella intermedia_0.001amol (16SrRNA gene)_n=2

organism: Prevotella intermedia


title: Prevotella nigrescens_1amol (16SrRNA gene)_n=1


title: Prevotella intermedia_0.001amol (16SrRNA gene)_n=1


title: Prevotella intermedia_0.01amol (16SrRNA gene)_n=2


title: genomic DNA from sample545

description: whole blood case sample


title: Prevotella intermedia_0.01amol (16SrRNA gene)_n=1


title: control1


title: Normal colonic mucosa sample (FFPE) diabetic, patient 47


title: Prevotella intermedia_0.1amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) diabetic, patient 46


title: genomic DNA from sample538

description: whole blood control sample

value: control


title: Normal colonic mucosa sample (FFPE) diabetic, patient 46


title: Colon cancer Tumor sample (FFPE) diabetic, patient 47


title: Normal colonic mucosa sample (FFPE) diabetic, patient 45


title: Colon cancer Tumor sample (FFPE) diabetic, patient 45


title: Prevotella intermedia_1amol (16SrRNA gene)_n=2


title: Prevotella intermedia_0.1amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) diabetic, patient 44


title: Fusobacterium nucleatum subsp. nucleatum_0.01amol (16SrRNA gene)_n=1

organism: Fusobacterium nucleatum


title: Fusobacterium nucleatum subsp. nucleatum_0.001amol (16SrRNA gene)_n=1


title: Fusobacterium nucleatum subsp. nucleatum_0.01amol (16SrRNA gene)_n=2


title: Fusobacterium nucleatum subsp. nucleatum_0.1amol (16SrRNA gene)_n=2


title: Fusobacterium nucleatum subsp. nucleatum_0.1amol (16SrRNA gene)_n=1


title: Fusobacterium nucleatum subsp. nucleatum_1amol (16SrRNA gene)_n=2


title: Fusobacterium nucleatum subsp. nucleatum_0.001amol (16SrRNA gene)_n=2


title: Normal colonic mucosa sample (FFPE) diabetic, patient 43


title: Normal colonic mucosa sample (FFPE) diabetic, patient 42


title: Colon cancer Tumor sample (FFPE) diabetic, patient 44


title: Colon cancer Tumor sample (FFPE) diabetic, patient 41


title: Colon cancer Tumor sample (FFPE) diabetic, patient 42


title: Colon cancer Tumor sample (FFPE) diabetic, patient 40


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 3


title: Normal colonic mucosa sample (FFPE) diabetic, patient 40


title: Colon cancer Tumor sample (FFPE) diabetic, patient 43


title: Prevotella intermedia_1amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) diabetic, patient 41


title: 5633P3L

city: Galway

first: Marc

last: Higgins

address: University Road

department: Discipline of Biochemistry

country: Ireland

institute: NUI Galway

data_processing:
Basecalls performed using CASAVA (v1.8)
FastQC (v0.11.5) was used to check read quality
Reads were aligned to the reference genome (UMD3.1) using STAR (v2.5.3a). The STAR command "quantMode GeneCounts" was used to map sequenced fragments to protein coding genes of the Bovine genome, according to the Ensembl release 87.
Raw reads generated by STAR were quantified by DESeq2's (v1.16.1) internal analysis pipeline via the command "DESeq")
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Processed data files are in .csv format.
Supplementary_files_format_and_content: First row contains sample I.D.s, column A contains gene I.D.s in Ensembl format with the number of raw reads that map to each specified gene per sample in the other rows.

organism: Bos taurus

source_name: Liver

growth_protocol: Charolais (n=90) and Holstein Friesian (n=77) steers were allowed ad libitum access to feed. The type of feed animals were allowed varied depending on experimental phase as outlined in the Samples section.

extract_protocol:
Total RNA was extracted from 50mg of frozen biopsy sample by homogenisation in Trizol using manual disruption. Total RNA was purified using Rneasy plus Universal Kits (Qiagen)
Single-end mRNA-seq libraries were generated using the Illumina TruSeq sample prep kit

tag: diet

value: Zero Grazed Grass (Digestable dry matter:196g/kg)

tag: breed

value: Holstein Friesian

tag: rfi status

value: High RFI


title: 5635P3L

value: Low RFI


title: 5632P3L


title: genomic DNA from sample575

description: whole blood control sample

data_processing: Microarray methylation analysis was performed in R. Quality control, including intensity read outs, filtering as well as beta value calculation was done using the minfi Bioconductor package. Functional normalization onto control probes was then used to normalized the raw intensity values across all the arrays and to remove part of the variance attributable to technical batches. We excluded any CpG containing SNPs or cross-hybridizing probes and CpGs with a detection p-value > 0.01 in at least 50% of the samples, resultng in 249874 data rows out of a possible 485577 (provided in the matrix_normalized.txt)

extract_protocol: genomic DNA was extracted using the Allprep mini kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer’s instructions

value: whole blood


title: genomic DNA from sample627

description: whole blood case sample

source_name: case_whole blood

value: M


title: Fusobacterium nucleatum subsp. nucleatum_1amol (16SrRNA gene)_n=1

tag: sample type


title: Campylobacter rectus_0.001amol (16SrRNA gene)_n=2

organism: Campylobacter rectus


title: 5616P3L


title: 2272P3L


title: 5612P3L


title: Colon cancer Tumor sample (FFPE) diabetic, patient 39


title: Campylobacter rectus_0.01amol (16SrRNA gene)_n=1


title: Campylobacter rectus_0.01amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 3


title: 2242P3L


title: Campylobacter rectus_0.001amol (16SrRNA gene)_n=1


title: Campylobacter rectus_0.1amol (16SrRNA gene)_n=1


title: 2094P3L


title: 2069P3L


title: Campylobacter rectus_0.1amol (16SrRNA gene)_n=2


title: 2065P3L


title: Normal colonic mucosa sample (FFPE) diabetic, patient 39


title: Campylobacter rectus_1amol (16SrRNA gene)_n=1


title: Campylobacter rectus_1amol (16SrRNA gene)_n=2


title: 1961P3L


title: Colon cancer Tumor sample (FFPE) diabetic, patient 38


title: Treponema denticola_0.001amol (16SrRNA gene)_n=2

organism: Treponema denticola


title: 1834P3L


title: Treponema denticola_0.01amol (16SrRNA gene)_n=2


title: 1909P3L


title: Treponema denticola_0.001amol (16SrRNA gene)_n=1


title: 1798P3L


title: Normal colonic mucosa sample (FFPE) diabetic, patient 38


title: Colon cancer Tumor sample (FFPE) diabetic, patient 36


title: Normal colonic mucosa sample (FFPE) diabetic, patient 36


title: Colon cancer Tumor sample (FFPE) diabetic, patient 35


title: Normal colonic mucosa sample (FFPE) diabetic, patient 37


title: 1668P3L


title: Normal colonic mucosa sample (FFPE) diabetic, patient 35


title: Treponema denticola_0.1amol (16SrRNA gene)_n=2


title: Normal colonic mucosa sample (FFPE) diabetic, patient 34


title: Colon cancer Tumor sample (FFPE) diabetic, patient 37


title: genomic DNA from sample589

description: whole blood case sample

tag: diagnosis


title: Treponema denticola_0.01amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) diabetic, patient 33


title: Treponema denticola_0.1amol (16SrRNA gene)_n=1


title: Colon cancer Tumor sample (FFPE) diabetic, patient 34


title: Colon cancer Tumor sample (FFPE) diabetic, patient 33


title: 788P3L

value: Charolais


title: Treponema denticola_1amol (16SrRNA gene)_n=1


title: 1683P3L


title: 437P3L


title: Tannerella forsythia_0.001amol (16SrRNA gene)_n=2

organism: Tannerella forsythia


title: Normal colonic mucosa sample (FFPE) diabetic, patient 32


title: Tannerella forsythia_0.01amol (16SrRNA gene)_n=2


title: 307P3L


title: genomic DNA from sample608

description: whole blood case sample


title: 1639P3L


title: 1212P3L


title: 5632P4L

value: High Concentrate Two (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).


title: Treponema denticola_1amol (16SrRNA gene)_n=2


title: genomic DNA from sample560

description: whole blood case sample


title: Tannerella forsythia_1amol (16SrRNA gene)_n=2


title: Tannerella forsythia_0.01amol (16SrRNA gene)_n=1


title: Tannerella forsythia_0.001amol (16SrRNA gene)_n=1


title: Tannerella forsythia_0.1amol (16SrRNA gene)_n=2


title: 1831P3L


title: Normal colonic mucosa sample (FFPE) diabetic, patient 30


title: 5612P4L


title: 1816P3L


title: Colon cancer Tumor sample (FFPE) diabetic, patient 32


title: Normal colonic mucosa sample (FFPE) diabetic, patient 29


title: Colon cancer Tumor sample (FFPE) diabetic, patient 30


title: Colon cancer Tumor sample (FFPE) diabetic, patient 27


title: Colon cancer Tumor sample (FFPE) diabetic, patient 29


title: Normal colonic mucosa sample (FFPE) diabetic, patient 27


title: Tannerella forsythia_0.1amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) diabetic, patient 26


title: 5617P4L


title: 357P3L


title: Colon cancer Tumor sample (FFPE) diabetic, patient 26


title: Tannerella forsythia_1amol (16SrRNA gene)_n=1


title: Porphyromonas gingivalis_0.001amol (16SrRNA gene)_n=2

organism: Porphyromonas gingivalis


title: genomic DNA from sample543

description: whole blood case sample


title: Porphyromonas gingivalis_0.001amol (16SrRNA gene)_n=1


title: 2101P4L


title: Porphyromonas gingivalis_0.1amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 25


title: 5609P4L


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 25


title: 5588P4L


title: 2071P4L


title: Porphyromonas gingivalis_1amol (16SrRNA gene)_n=2


title: Porphyromonas gingivalis_0.01amol (16SrRNA gene)_n=2


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 24


title: 2220P4L


title: Porphyromonas gingivalis_0.01amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 24


title: genomic DNA from sample574

description: whole blood control sample


title: ATCC MSA-1003_dilution_step10_n=2

description: 11 serial 4-fold dilutions of 20 Strains Staggered Mix Genomic Material (ATCC MSA-1003™)

organism:
Helicobacter pylori
Pseudomonas aeruginosa
Acinetobacter baumannii
Neisseria meningitidis
Escherichia coli
Phocaeicola vulgatus
Porphyromonas gingivalis
Cereibacter sphaeroides
Staphylococcus aureus
Staphylococcus epidermidis
Deinococcus radiodurans
Streptococcus mutans
Streptococcus agalactiae
Enterococcus faecalis
Bacillus cereus
Clostridium beijerinckii
Lactobacillus gasseri
Schaalia odontolytica
Bifidobacterium adolescentis
Cutibacterium acnes

source_name: ATCC MSA-1003_dilution_step10

value: ATCC MSA-1003_dilution_step10


title: 1797P4L


title: genomic DNA from sample558

description: whole blood control sample

organism: Homo sapiens


title: Porphyromonas gingivalis_0.1amol (16SrRNA gene)_n=1


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 21


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 23


title: 1661P4L


title: Porphyromonas gingivalis_1amol (16SrRNA gene)_n=1


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 23

value: Colon cancer Tumor


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 22

value: non-diabetic patient


title: 1492P4L


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 22


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 20


title: 860P4L


title: 1657P4L


title: ATCC MSA-1003_dilution_step9_n=1

source_name: ATCC MSA-1003_dilution_step9

value: ATCC MSA-1003_dilution_step9


title: genomic DNA from sample674

description: whole blood case sample


title: 1645P4L


title: 1639P4L


title: 493P4L


title: 546P4L


title: ATCC MSA-1003_dilution_step9_n=2


title: genomic DNA from sample553

description: whole blood case sample


title: genomic DNA from sample540

description: whole blood control sample


title: ATCC MSA-1003_dilution_step8_n=1

source_name: ATCC MSA-1003_dilution_step8

value: ATCC MSA-1003_dilution_step8


title: ATCC MSA-1003_dilution_step7_n=2

source_name: ATCC MSA-1003_dilution_step7

value: ATCC MSA-1003_dilution_step7


title: ATCC MSA-1003_dilution_step8_n=2


title: 454P4L


title: ATCC MSA-1003_dilution_step7_n=1


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 19


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 19

value: Normal colonic mucosa


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 20


title: ATCC MSA-1003_dilution_step10_n=1


title: 419P4L


title: 364P4L


title: genomic DNA from sample550

description: whole blood case sample

value: case


title: ATCC MSA-1003_dilution_step6_n=2

source_name: ATCC MSA-1003_dilution_step6

value: ATCC MSA-1003_dilution_step6


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 21


title: ATCC MSA-1003_dilution_step6_n=1


title: 359P4L


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 16


title: ATCC MSA-1003_dilution_step5_n=2

source_name: ATCC MSA-1003_dilution_step5

value: ATCC MSA-1003_dilution_step5


title: genomic DNA from sample594

description: whole blood case sample


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 18


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 15


title: 307P4L


title: 310P4L


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 16


title: ATCC MSA-1003_dilution_step5_n=1


title: ATCC MSA-1003_dilution_step4_n=2

source_name: ATCC MSA-1003_dilution_step4

value: ATCC MSA-1003_dilution_step4


title: 1844P4L


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 14


title: 1840P4L

value: High RFI


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 15


title: ATCC MSA-1003_dilution_step4_n=1


title: 1484P4L


title: 1483P4L

value: Low RFI


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 14


title: ATCC MSA-1003_dilution_step3_n=1

source_name: ATCC MSA-1003_dilution_step3

value: ATCC MSA-1003_dilution_step3


title: ATCC MSA-1003_dilution_step3_n=2


title: ATCC MSA-1003_dilution_step2_n=2

source_name: ATCC MSA-1003_dilution_step2

value: ATCC MSA-1003_dilution_step2


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 13


title: 1320P4L

value: Charolais


title: 1316P4L

value: High Concentrate Two (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).


title: Tim-3+PD-1+ CD8+_antiTim3+antiPD1 rep1

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK7DP_T/P

data_processing:
RNA-seq reads were aligned using Tophat and RSEM-based quantification using known transcripts, followed by further processing using the Bioconductor package DESeq in R.
Genome_build: mm9
Supplementary_files_format_and_content: The data was normalized using TMM normalization. The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis. Post-processing and statistical analysis was carried out in R.

organism: Mus musculus

source_name: Tumor MC38-OVA

extract_protocol:
5uL of lysate from bulk CD8+ T cells as the input for each sample during RNA cleanup via SPRI beads (~2,000 cells lysed on average in RLT).
Tumor infiltrating CD8+ T cells were processed using an adaptation of the SMART-Seq 2 protocol.

treatment_protocol: On day 12 post tumor implantation, Tim-3+PD-1+ and Tim-3-PD-1- CD8+ TILs were isolated by cell sorting (BD FACS Aria II) from MC38-OVA tumor-bearing mice that were treated with anti-PD-1 and anti-Tim-3 antibodies or isotype controls.

tag: strain

value: Tumor MC38-OVA

tag: genotype

value: wild type

value: Tim-3+PD-1+ CD8+ TILs

tag: treatment

value: antiTim3+antiPD1 treated


title: 1100P4L


title: Tim-3+PD-1+ CD8+_antiTim3+antiPD1 rep3

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK9DP_T/P

tag: cell type


title: Tim-3+PD-1+ CD8+_antiTim3+antiPD1 rep2

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK8DP_T/P

tag: tissue


title: Tim-3+PD-1+ CD8+_iso rep3

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK2DP_iso

value: isotype treated


title: 5632P1L

value: High Concentrate One (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).

value: Holstein Friesian


title: 5624P1L


title: Tim-3+PD-1+ CD8+_iso rep2

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK3DP_iso


title: ATCC MSA-1003_dilution_step2_n=1


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 10

value: Colon cancer Tumor

value: non-diabetic patient


title: 5613P1L


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 13


title: Normal colonic mucosa sample (FFPE) non-diabetic, patient 10

value: Normal colonic mucosa


title: 5608P1L


title: Colon cancer Tumor sample (FFPE) non-diabetic, patient 18


title: Tim-3-PD-1- CD8+_antiTim3+antiPD1 rep3

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK8DN_T/P

value: Tim-3-PD-1- CD8+ TILs


title: 2266P1L


title: ATCC MSA-1003_dilution_step1_n=2

source_name: ATCC MSA-1003_dilution_step1

value: ATCC MSA-1003_dilution_step1


title: ATCC MSA-1002_dilution_step8_n=3

description: 9 serial 4-fold dilutions of 20 Strains Even Mix Genomic Material (ATCC MSA-1002™)

source_name: ATCC MSA-1002_dilution_step8

value: ATCC MSA-1002_dilution_step8


title: ATCC MSA-1003_dilution_step0_n=2

source_name: ATCC MSA-1003_dilution_step0

value: ATCC MSA-1003_dilution_step0


title: ATCC MSA-1003_dilution_step0_n=1


title: ATCC MSA-1003_dilution_step1_n=1


title: Tim-3+PD-1+ CD8+_iso rep1

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK1DP_iso


title: ATCC MSA-1002_dilution_step7_n=3

source_name: ATCC MSA-1002_dilution_step7

value: ATCC MSA-1002_dilution_step7


title: ATCC MSA-1002_dilution_step8_n=1


title: 2101P1L

value: High RFI


title: Tim-3-PD-1- CD8+_iso rep2

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK2DN_iso


title: ATCC MSA-1002_dilution_step7_n=2


title: Tim-3-PD-1- CD8+_antiTim3+antiPD1 rep2

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK7DN_T/P


title: ATCC MSA-1002_dilution_step8_n=2


title: ATCC MSA-1002_dilution_step6_n=3

source_name: ATCC MSA-1002_dilution_step6

value: ATCC MSA-1002_dilution_step6


title: genomic DNA from sample691

description: whole blood case sample

value: case

tag: age

value: F

value: whole blood


title: genomic DNA from sample648

description: whole blood case sample

value: M


title: 2220P1L

source_name: Liver

value: Low RFI


title: Tim-3-PD-1- CD8+_antiTim3+antiPD1 rep1

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK9DN_T/P

value: Tumor MC38-OVA

value: wild type

value: antiTim3+antiPD1 treated


title: 2071P1L

value: High Concentrate One (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).

value: Holstein Friesian


title: ATCC MSA-1002_dilution_step7_n=1


title: Tim-3-PD-1- CD8+_iso rep3

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK3DN_iso

value: Tim-3-PD-1- CD8+ TILs

value: isotype treated


title: 2068P1L


title: 2065P1L


title: genomic DNA from sample541

description: whole blood control sample

source_name: control_whole blood

value: control


title: Naïve-like rep3

description:
Data_norm_DN1_DN3_DN4.txt
S26_3_DN1_20170130

source_name: Tumor  MC38-OVA

treatment_protocol: Tumor infiltrating PD1-CD8+ T cells were isolated from WT MC38-OVA bearing mice.

value: Tumor


title: ATCC MSA-1002_dilution_step6_n=1


title: 2095P1L


title: ATCC MSA-1002_dilution_step5_n=3

source_name: ATCC MSA-1002_dilution_step5

value: ATCC MSA-1002_dilution_step5


title: Naïve-like rep6

description:
Data_norm_DN1_DN3_DN4.txt
S29_6_DN1_20170130


title: ATCC MSA-1002_dilution_step6_n=2


title: ATCC MSA-1002_dilution_step5_n=2


title: 1877P1L


title: Naïve-like rep4

description:
Data_norm_DN1_DN3_DN4.txt
S27_4_DN1_20170130


title: Naïve-like rep1

description:
Data_norm_DN1_DN3_DN4.txt
S24_1_DN1_20170130


title: Tim-3-PD-1- CD8+_iso rep1

description:
Data_WT_counts_ordered.txt
Data_WT_norm_ordered.txt
SK1DN_iso


title: 1656P1L


title: 950P1L

value: Charolais


title: 2069P1L

value: High RFI


title: Effector-like rep3

description:
Data_norm_DN1_DN3_DN4.txt
S23_5_DN4_20170127


title: ATCC MSA-1002_dilution_step4_n=2

source_name: ATCC MSA-1002_dilution_step4

value: ATCC MSA-1002_dilution_step4


title: ATCC MSA-1002_dilution_step4_n=3


title: Naïve-like rep5

description:
Data_norm_DN1_DN3_DN4.txt
S28_5_DN1_20170130


title: 871P1L


title: ATCC MSA-1002_dilution_step5_n=1


title: Effector-like rep2

description:
Data_norm_DN1_DN3_DN4.txt
S22_4_5_6_DN4_20170127


title: Effector-like rep1

description:
Data_norm_DN1_DN3_DN4.txt
S21_1_2_3_DN4_20170127


title: ATCC MSA-1002_dilution_step4_n=1


title: 856P1L


title: 2064P1L


title: 1811P1L


title: Memory-like rep5

description:
Data_norm_DN1_DN3_DN4.txt
S20_6_DN3_20170127


title: 854P1L


title: Naïve-like rep2

description:
Data_norm_DN1_DN3_DN4.txt
S25_2_DN1_20170130


title: Memory-like rep4

description:
Data_norm_DN1_DN3_DN4.txt
S19_5_DN3_20170127


title: ATCC MSA-1002_dilution_step3_n=3

description: 9 serial 4-fold dilutions of 20 Strains Even Mix Genomic Material (ATCC MSA-1002™)

source_name: ATCC MSA-1002_dilution_step3

value: ATCC MSA-1002_dilution_step3


title: Memory-like rep3

description:
Data_norm_DN1_DN3_DN4.txt
S18_4_DN3_20170127


title: genomic DNA from sample601

description: whole blood case sample

source_name: case_whole blood

value: case

value: whole blood


title: ATCC MSA-1002_dilution_step3_n=2


title: genomic DNA from sample668

description: whole blood case sample

value: F


title: Memory-like rep2

description:
Data_norm_DN1_DN3_DN4.txt
S17_3_DN3_20170127


title: ATCC MSA-1002_dilution_step2_n=3

source_name: ATCC MSA-1002_dilution_step2

value: ATCC MSA-1002_dilution_step2


title: 555P1L

value: Low RFI


title: ATCC MSA-1002_dilution_step3_n=1


title: ATCC MSA-1002_dilution_step2_n=2


title: 449P1L


title: Memory-like rep1

description:
Data_norm_DN1_DN3_DN4.txt
S16_2_DN3_20170127

value: wild type


title: ATCC MSA-1002_dilution_step2_n=1


title: Dnm2_Mut_3

city: Zurich

first: Daniel

last: Gerber

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
adapter sequences were removed, low quality ends trimmed, and reads with low quality (phred quality<20) filtered using Trimmomatic (Bolger et al., Bioinformatics, 2014)
high-quality reads were mapped to the mouse reference genome and quantification of gene level expression was carried out using RSEM (version 1.2.22)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample

source_name: Dnm2_Mut_sciatic nerve

extract_protocol:
Nerves were extracted, flash frozen in liquid nitrogen after mechanical removal of the epineurium, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 4 weeks post tamoxifen

tag: genotype/variation

value: Dnm2 knockout

tag: additional protocol

value: animals were injected with tamoxifen at 2 month of age

value: Sciatic nerve


title: Dnm2_Mut_2


title: 443P1L

value: High Concentrate One (860g/kg rolled barley, 60g/kg soya bean meal, 60g/kg molasses, and 20g/kg minerals and vitamins plus restricted grass silage for healthy rumen function).


title: 364P1L


title: genomic DNA from sample682

city: Munich

first: Janine

last: Arloth

institute: Max Planck Institute of Psychiatry

description: whole blood case sample

tag: Sex

value: M

tag: cellcount-nk

tag: cellcount-bcell


title: ATCC MSA-1002_dilution_step1_n=1

source_name: ATCC MSA-1002_dilution_step1

value: ATCC MSA-1002_dilution_step1


title: ATCC MSA-1002_dilution_step1_n=2


title: ATCC MSA-1002_dilution_step1_n=3


title: Dnm2_Mut_1


title: 307P1L

tag: diet

value: Charolais


title: Dnm2_Ctr_3

source_name: Dnm2_Ctr_sciatic nerve

value: Control


title: 579P1L

tag: breed


title: 1846P1L

tag: rfi status


title: Dnm2_Ctr_2


title: 1831P1L


title: Dnm2_Ctr_1


title: genomic DNA from sample675

description: whole blood case sample

tag: cellcount-mono

tag: cellcount-gran


title: ATCC MSA-1002_dilution_step0_n=3

source_name: ATCC MSA-1002_dilution_step0

tag: sample type

value: ATCC MSA-1002_dilution_step0


title: ATCC MSA-1002_dilution_step0_n=2


title: genomic DNA from sample546

description: whole blood case sample

tag: diagnosis


title: P5_dnm2KO2

source_name: P5_dnm2KO_sciatic nerve


title: 1797P1L


title: 447P1L

value: High RFI


title: 1792P1L


title: 8 kinds of bacterial genomic DNA mixture_dilution_step5_n=3

description: 6 serial 16-fold dilutions of eight kinds of genomic DNA mixture solution.

organism:
Treponema denticola
Aggregatibacter actinomycetemcomitans
Porphyromonas gingivalis
Fusobacterium nucleatum
Streptococcus gordonii
Streptococcus mutans
Tannerella forsythia
Prevotella intermedia


title: P5_dnm2KO1


title: 8 kinds of bacterial genomic DNA mixture_dilution_step5_n=2


title: 8 kinds of bacterial genomic DNA mixture_dilution_step4_n=3


title: 1320P1L


title: P5_wt2

source_name: P5_wt_sciatic nerve


title: 8 kinds of bacterial genomic DNA mixture_dilution_step5_n=1


title: genomic DNA from sample557

description: whole blood case sample

value: case


title: 1496P1L


title: 1100P1L


title: P5_wt3


title: 1078P1L


title: 8 kinds of bacterial genomic DNA mixture_dilution_step4_n=2


title: P5_wt1


title: 1816P1L


title: 8 kinds of bacterial genomic DNA mixture_dilution_step4_n=1


title: 8 kinds of bacterial genomic DNA mixture_dilution_step3_n=3


title: P5_dnm2KO3


title: ATCC MSA-1002_dilution_step0_n=1


title: genomic DNA from sample635

description: whole blood case sample

value: whole blood


title: P1_dnm2KO2

source_name: P1_dnm2KO_sciatic nerve


title: ZC-S10

first: Robert

middle: Blake

last: Billmyre

state: North Carolina

address: 312 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

description: total sRNA

data_processing:
Data was trimmed using TrimGalore
Reads were then mapped using Bowtie.
Cufflinks was utilized to count reads mapping to annotated genes.
Genome_build: Mucor_circinelloides_v2_scaffolds
https://genome.jgi.doe.gov/portal/Mucci2/download/Mucor_circinelloides_v2_  scaffolds.fasta.gz
Supplementary_files_format_and_content: Gene by gene fpkm values from cufflinks

organism: Mucor circinelloides

source_name: vegetative hyphae

extract_protocol:
mirVana Kit (Ambion) was used to extract RNA from hyphae grown on top of cellulose film overlaid on agar plates.
Illumina TruSeq Small RNA Library Prep K

value: vegetative hyphae

tag: epimutation

tag: genotype

value: WT

tag: ura status

value: URA+


title: genomic DNA from sample623

address: Kraepelinstr. 2-10

description: whole blood case sample

tag: age

tag: tissue


title: P1_dnm2KO3

tag: strain background

tag: genotype/variation


title: 8 kinds of bacterial genomic DNA mixture_dilution_step3_n=2


title: genomic DNA from sample687

description: whole blood case sample

tag: Sex


title: P1_dnm2KO1


title: ZC-S8

description: total sRNA

value: pyrG revertant

value: rdrp1 ko


title: ZC-S9

description: total sRNA


title: 8 kinds of bacterial genomic DNA mixture_dilution_step3_n=1


title: 8 kinds of bacterial genomic DNA mixture_dilution_step2_n=2


title: genomic DNA from sample613

description: whole blood case sample

tag: cellcount-nk


title: 8 kinds of bacterial genomic DNA mixture_dilution_step2_n=3


title: P1_wt1

source_name: P1_wt_sciatic nerve


title: P1_wt2


title: genomic DNA from sample664

description: whole blood case sample

value: F

tag: cellcount-bcell


title: ZC-S5

description: total sRNA

value: rdrp3 ko


title: ZC-S6

description: total sRNA


title: 8 kinds of bacterial genomic DNA mixture_dilution_step2_n=1


title: Sample 1: Src_Variant_Library2

description: Library and barcode sequencing from DNA

organism: Escherichia coli

source_name: Synthetic sequence

tag: strain

tag: molecule

value: Plasmid DNA


title: ZC-S4

description: total sRNA

value: pyrF epimutant


title: ZC-S3

description: total sRNA

value: URA-


title: 8 kinds of bacterial genomic DNA mixture_dilution_step1_n=2


title: 8 kinds of bacterial genomic DNA mixture_dilution_step1_n=3


title: Sample 1: Src_Variant_Library1

description: Library and barcode sequencing from DNA


title: genomic DNA from sample611

description: whole blood case sample


title: genomic DNA from sample612

description: whole blood case sample

value: M


title: ZC-S2

description: total sRNA


title: Sample 3_HBoV1 infected HAE-3

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

data_processing:
Illumina bcl2fastq software was used for basecalling.
Cutadapt  was  used to trim reads adaptor at 3’-end
Bowtie 2  was used to align smRNA-seq reads to HBoV1 genome for identification of all small RNAs. The count of HBoV1 mapping reads was extracted using an in-house-developed script from alignment file.
Genome_build: HBoV1 genome
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism:
Homo sapiens
Human bocavirus

source_name: HAE-ALI_HBoV1 infected

growth_protocol: Primary human airway epithelial cells were cultured on collagen-coated, semipermeable membrane inserts of 0.33 cm2, and then were polarized/differentiated at an ALI for 3-4 weeks. Briefly, in the first 2 to 3 days after 2 ×104 airway epithelial cells were seeded onto the Transwell insert, SAGM-H media were fed in both the apical and basolateral chambers of the insert to start the culture, then the SAGM-H media were aspirated from both chambers, and the cells were fed with 500 µl of PneumaCultTM-ALI medium (StemCell, Vancouver, BC, Canada) in the basolateral chamber. The medium was changed every 3-4 days. The ALI-cultured HAE took 3-4 weeks for full differentiation. We chose the cultures with a transepithelial electrical resistance (TEER) of over 1,000 Ω∙cm2, as determined with an epithelial Ohm-voltmeter (Millicell-ERS; EMD-Millipore, Billerica, MA), for subsequent HBoV1 infection.

extract_protocol:
At 7 days post-infection, HBoV1 infected-cell were collected and RNA samples were extracted using the miRNeasy Mini Kit by following the manufacturer’s instruction
TailorMix miRNA V2 library preparation kit was used to prepare the small RNA library with the special RNA length between 100-200 nucleotides.

treatment_protocol: The differentiated HAE cells were infected by HBoV1 at a MOI of 1000 viral genome copies (vgc)/cell

tag: cell type

value: Primary human airway epithelial (HAE) cells

tag: infected with

value: Human Bocavirus 1 (HBoV1)

tag: time point

value: 7 days post-infection


title: Sample 2_HBoV1 infected HAE-2


title: 8 kinds of bacterial genomic DNA mixture_dilution_step1_n=1

tag: sample type


title: Sample 1_HBoV1 infected HAE-1


title: ZC-S1

city: Durham

description: total sRNA


title: ZC-S7

description: total sRNA

value: pyrG epimutant


title: P1_wt3

value: Control

value: Sciatic nerve


title: 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=2


title: L1T3: Spinal cord

status: Public on Jan 15 2019

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

data_processing:
The raw sequence reads were aligned to the rat reference genome (Rnor_6.0) using HISAT2 (version 2.0.4).
Read counting was performed with HTSeq (version 0.6.0) so that UMI duplicates were removed.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The txt file contains UMI count matrix.

organism: Rattus norvegicus

source_name: Spinal cord

extract_protocol:
Spinal cords were removed, flash frozen in liquid nitrogen, and RNA was harvested.
Library were constructed in accordance with the CEL-Seq2 protocol and prepared on the Illumina HiSeq1500 platform.

value: Sprague Dawley

value: Upper spinal cord

tag: group

value: 23 days-post injury with training


title: L1N4: Spinal cord

value: 23 days-post injury without training


title: L1N3: Spinal cord


title: L1T2: Spinal cord


title: L1N2: Spinal cord


title: L1T1: Spinal cord


title: 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=3

data_processing:
The probe signal intensity was determined from the fluorescence signal intensity. The mean and standard deviation of the fluorescence signal intensity of the background spot without the probe were calculated, and the sum of the mean and standard deviation of three repetitions was defined as the background signal intensity. Probe signal intensity was calculated by subtracting the background signal intensity from the median of the fluorescence signal intensity of the five spots of each probe.
BLANK array features are not represented in the data table.

extract_protocol: Genomic DNA was extracted from the samples using a Wizard Genome DNA Purification Kit (Promega).


title: L1N1: Spinal cord


title: SLE40_IFNb

city: Ann Arbor

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
We used STAR-2.5.2 (28) to align the reads to the human reference genome (build 37)
We then used HTSeq-0.6.1 (29) to count the number of uniquely mapped reads for each gene
The gene expression level was modeled using a negative binomial distribution and normalized in DESeq2
Genome_build: build 37
Supplementary_files_format_and_content: count matrix

molecule: polyA RNA

source_name: keratinocytes

extract_protocol:
Cells were harvested in Tripure (Sigma-Aldrich, St. Louis, MO).  RNA was isolated from cell cultures using Qiagen RNeasy kit (Cat # 74136).
Libraries for RNA-seq were generated from polyadenylated RNA and sequenced at six libraries per lane on Illumina HiSeq4000

tag: disease status

value: SLE

tag: stimulation

value: IFNb

tag: patient


title: SLE71_control

value: control


title: SLE71_IFNb


title: SLE66_IFNa6


title: SLE66_IFNg

value: IFNg


title: SLE71_IFNa6


title: SLE71_IFNg


title: SLE39_IFNb


title: SLE40_IFNg


title: SLE71_IFNa2


title: SLE66_control


title: SLE66_IFNb


title: SLE39_IFNa6


title: SLE40_IFNa6


title: SLE24_IFNa6


title: SLE66_IFNa2


title: L1T4: Spinal cord


title: SLE39_IFNg


title: 8 kinds of bacterial genomic DNA mixture_dilution_step0_n=1


title: SLE24_IFNg


title: SLE24_IFNa2


title: SLE24_IFNb


title: SLE24_control


title: N68_IFNb

value: normal


title: N68_IFNa2


title: N68_IFNg


title: N68_control


title: N50_IFNg


title: N50_IFNb


title: N49_IFNa2


title: N50_control


title: N49_IFNb


title: N49_IFNg


title: N44_IFNa2


title: N50_IFNa2


title: N44_IFNa6


title: N49_IFNa6


title: SLE52_IFNa2


title: SLE52_IL18


title: N38_IFNg


title: SLE52_IFNa2_IL18


title: N38_IFNb


title: N44_control


title: N44_IFNg


title: SLE52_control


title: N49_control


title: N50_IFNa6


title: SLE40_control

description:
73997
57780


title: N68_IFNa6


title: SLE39_IFNa2

description:
74009
57765


title: SLE40_IFNa2_IL18


title: SLE39_IFNa2_IL18


title: SLE39_IL18


title: SLE39_control

description:
74007
57764


title: SLE36_IL18


title: N44_IFNb


title: N38_IFNa6


title: SLE40_IL18


title: SLE40_IFNa2

description:
73998
57781


title: SLE36_control


title: SLE36_IFNa2


title: SLE36_IFNa2_IL18


title: N51_IL18

description:
57762
57770


title: N38_IFNa2

description:
73964
57777


title: N40MK_IFNa2_IL18


title: N38_IFNa2_IL18


title: N40MK_IL18


title: N51_control

description:
57760
57768


title: N38_IL18


title: N40MK_control


title: N51_IFNa2_IL18

description:
57763
57771


title: N51_IFNa2

description:
57761
57769


title: N40MK_IFNa2


title: Cal33_WT_4Gy_rep3

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

institute: OncoRay

description: Gene expression of wild type clone irradiated with 4Gy X-ray dose

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v3 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C wit GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using protocol GE1_107_Sep09 and Grid: 072363_D_F_20150612 to obtain background subtracted and spatially detrended Processed Signal intensities

source_name: Cal33 wild type clone, irradiated with 4 Gy, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard tissue culture at 37 ºC in a humidified incubator with 5% CO2, in DMEM supplemented with 10% FBS, 10mM HEPES, and 1x Pen/Strep

extract_protocol: RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations

treatment_protocol: Call33 cell line was gene edited using CRISPR/Cas9 approach.Two regions flanking SLC3A2 gene were targeted simultaneously to achieve deletion of entire gene. Individual clones were isolated and screened for presence and copy number of SLC3A2 gene. Monoallelic knockout (1 copy of SLC3A2) and wild type (3 copies of SLC3A2) clones were selected for study. Both clones were either non-irradiated or irradiated with 4Gy X-ray dose.

tag: slc3a2 gene status

value: 3 alleles present

tag: cell line

value: wild type


title: Cal33_WT_0Gy_rep1

description: Gene expression of  non-irradiated wild type clone

source_name: Cal33 wild type clone, non-irradiated, replicate 1


title: Cal33_WT_0Gy_rep3

source_name: Cal33 wild type clone, non-irradiated, replicate 3


title: Cal33_MAKO_4Gy_rep1

description: Gene expression of monoallelic knockout clone irradiated with 4Gy X-ray dose

source_name: Cal33 monoallelic knockout clone, irradiated with 4Gy, replicate 1

value: 1 allele present, 2 alleles deleted

value: monoallelic knockout


title: Cal33_MAKO_0Gy_rep2

description: Gene expression of  non-irradiated monoallelic knockout clone

source_name: Cal33 monoallelic knockout clone, non-irradiated, replicate 2


title: Cal33_WT_0Gy_rep2

source_name: Cal33 wild type clone, non-irradiated, replicate 2


title: Control-untreated-01BM

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

description:
BMDMs untreated n1
Control_untreated_rep1

data_processing:
Raw fastq reads were trimmed to remove low quality base pairs using Trimmomatic-0.33 with the following parameters: SE –threads 20 –phred33 TRAILING:30 MINLEN:20.  This made sure that all the reads had base pairs with Phred scores above 30 and a minimum length of 20.
The reads were then aligned to the mouse genome mm10 using STAR with the following parameters: —runThreadN 20 —readFilesCommand zcat –c —outSAMtype BAM Unsorted —chimSegmentMin 20 —quantMode TranscriptomeSAM —outReadsUnmapped Fastq —outMultimapperOrder Random —outFilterMultimapNmax 20 —outFilterMismatchNmax 2.
Aligned bam files were then sorted using samtools.
Reads at exons were counted using htseq-count with the following parameters: -f bam –q –m intersection-nonempty –s no –t exon –i gene_id.
Coverage tracks were generated using the R package Rsamtools and the coverage function.
Finally, gene differential analysis was done using the EdgeR statistical package in R.  Differentially expressed genes were called if they had an FDR < 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: htseq output raw counts and normalized counts in .txt files tab delimited and EdgeR differentially expressed genes in .txt files tab delimited.

source_name: Murine macrophages

growth_protocol: Bone marrow was isolated from C57BL/6J mice and subjected to red blood cell lysis with ACK lysis buffer prior to neutralization and resupsension in RPMI media. Cells were counted using a hemocytometer and plated in 10cm tissue culture plates at a density of 3-million cells/ plate. Cells were cultured with 20ng/mL mCSF to induce differentiation into BMDMs. Media was changed every 3 days and BMDMs were harvested by scraping on day 6 and plated in MEM media for the experiments.

extract_protocol:
RNA was isolated 4 hrs post LPS. Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen) following manufacturer's protocol.
RNA-seq library was prepared using NEBNext Ultra RNA Library Prep Kit from New England Biolabs.
Libraries were pooled and sequenced on an Illumina Nextseq500 platform using the 75bp high output sequencing kit NextSeq 500/550 High Output Kit v2 (75 cycles Illumina).

treatment_protocol: BMDMs were cultured in complete MEM, MEM without serine, MEM with 100ng/mL LPS, MEM without serine but with 100ng/mL LPS.


title: Dropout-untreated-04BM

description:
BMDMs serine deprivation n4
Dropout_untreated_rep4


title: Dropout-LPS-04BM

description:
BMDMs serine deprivation LPS n4
Dropout_LPS_rep4


title: Control-LPS-03BM

description:
BMDMs LPS n3
Control_LPS_rep3


title: Control-LPS-04BM

description:
BMDMs LPS n4
Control_LPS_rep4


title: Control-LPS-02BM

description:
BMDMs LPS n2
Control_LPS_rep2


title: Dropout-untreated-03BM

description:
BMDMs serine deprivation n3
Dropout_untreated_rep3


title: Control-untreated-03BM

description:
BMDMs untreated n3
Control_untreated_rep3


title: Dropout-LPS-02BM

description:
BMDMs serine deprivation LPS n2
Dropout_LPS_rep2


title: Cal33_WT_4Gy_rep1

source_name: Cal33 wild type clone, irradiated with 4 Gy, replicate 1


title: Control-untreated-04BM

description:
BMDMs untreated n4
Control_untreated_rep4


title: Control-untreated-02BM

description:
BMDMs untreated n2
Control_untreated_rep2


title: Dropout-untreated-02BM

description:
BMDMs serine deprivation n2
Dropout_untreated_rep2


title: Dropout-untreated-01BM

description:
BMDMs serine deprivation n1
Dropout_untreated_rep1


title: Dropout-LPS-03BM

description:
BMDMs serine deprivation LPS n3
Dropout_LPS_rep3


title: Cal33_MAKO_0Gy_rep3

source_name: Cal33 monoallelic knockout clone, non-irradiated, replicate 3


title: Cal33_MAKO_4Gy_rep2

source_name: Cal33 monoallelic knockout clone, irradiated with 4Gy, replicate 2


title: Cal33_WT_4Gy_rep2

source_name: Cal33 wild type clone, irradiated with 4 Gy, replicate 2


title: Cal33_MAKO_4Gy_rep3

source_name: Cal33 monoallelic knockout clone, irradiated with 4Gy, replicate 3


title: Cal33_MAKO_0Gy_rep1

source_name: Cal33 monoallelic knockout clone, non-irradiated, replicate 1


title: Dropout-LPS-01BM

description:
BMDMs serine deprivation LPS n1
Dropout_LPS_rep1


title: Control-LPS-01BM

description:
BMDMs LPS n1
Control_LPS_rep1


title: LHA female

city: Farmington

first: William

last: Flynn

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: freshly disscted mouse tissue, all 5 animals in study were littermates

data_processing:
Fastqs were generated using 10X Genomics CellRanger mkfastq (version 1.3.0)
R1 = 16bp cell barcode + 10bp UMI barcode.
R2 = biological
Digital expression matrices were generated using 10X Genomics CellRanger count (version 2.2.0) against the 10X Genomics mm10 reference build (version 2.1.0, GRCm38.84).
Genome_build: GRCm38.84
Supplementary_files_format_and_content: Counts matrices in Matrix Market CSR format.  Rows correspond to genes in the order provided in genes.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv

source_name: lateral hypothalamic area

extract_protocol:
tissue collection protocol:  LHA were microdissected from 225 μm thick brain slices, 3 to 4 slices per animal.
cell dissociation protocol: Cells from slices were triturated with a series of small bore fire-polished glass Pasteur pipettes in a volume of 400-600 µL trypsin inhibitor/BSA sucrose dissociation solution. Single cell suspensions were passed through 60 μm nylon mesh filters to remove any cell aggregates, and kept on ice until loaded onto the Chromium system.
Chromium System (10XGenomics) v2 chemistry

tag: tissue

value: brain

tag: brain region

value: lateral hypothalamic area

value: female

tag: animal numbers

tag: age


title: N38_control

description:
73962
57776


title: LHA male

tag: Sex

value: male


title: RMDB_912

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

institute: University of Leeds

description: REMoDLB trial

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

label: Biotin

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: GCB

tag: molecular coo subtype


title: RMDB_928

description: REMoDLB trial


title: RMDB_919

description: REMoDLB trial


title: RMDB_922

description: REMoDLB trial


title: RMDB_925

description: REMoDLB trial

value: MHG


title: RMDB_907

description: REMoDLB trial


title: RMDB_916

description: REMoDLB trial

value: UNC


title: RMDB_923

description: REMoDLB trial


title: RMDB_921

description: REMoDLB trial


title: RMDB_914

description: REMoDLB trial

value: ABC


title: RMDB_915

description: REMoDLB trial


title: RMDB_902

description: REMoDLB trial


title: RMDB_910

description: REMoDLB trial


title: RMDB_911

description: REMoDLB trial


title: RMDB_904

description: REMoDLB trial


title: RMDB_920

description: REMoDLB trial


title: RMDB_918

description: REMoDLB trial


title: RMDB_926

description: REMoDLB trial


title: RMDB_906

description: REMoDLB trial


title: RMDB_913

description: REMoDLB trial


title: RMDB_908

description: REMoDLB trial


title: RMDB_927

description: REMoDLB trial


title: RMDB_900

description: REMoDLB trial


title: RMDB_905

description: REMoDLB trial


title: RMDB_903

description: REMoDLB trial


title: RMDB_917

description: REMoDLB trial


title: RMDB_901

description: REMoDLB trial


title: RMDB_899

description: REMoDLB trial


title: RMDB_924

description: REMoDLB trial


title: RMDB_909

description: REMoDLB trial


title: RMDB_896

description: REMoDLB trial


title: RMDB_897

description: REMoDLB trial


title: RMDB_894

description: REMoDLB trial


title: RMDB_891

description: REMoDLB trial


title: RMDB_895

description: REMoDLB trial


title: RMDB_879

description: REMoDLB trial


title: RMDB_898

description: REMoDLB trial


title: RMDB_880

description: REMoDLB trial


title: RMDB_889

description: REMoDLB trial


title: RMDB_888

description: REMoDLB trial


title: RMDB_883

description: REMoDLB trial


title: RMDB_873

description: REMoDLB trial


title: RMDB_892

description: REMoDLB trial


title: RMDB_875

description: REMoDLB trial


title: RMDB_878

description: REMoDLB trial


title: RMDB_882

description: REMoDLB trial


title: RMDB_876

description: REMoDLB trial


title: RMDB_877

description: REMoDLB trial


title: RMDB_874

description: REMoDLB trial


title: RMDB_868

description: REMoDLB trial


title: RMDB_886

description: REMoDLB trial


title: RMDB_893

description: REMoDLB trial


title: RMDB_890

description: REMoDLB trial


title: RMDB_887

description: REMoDLB trial


title: RMDB_872

description: REMoDLB trial


title: RMDB_869

description: REMoDLB trial


title: RMDB_884

description: REMoDLB trial


title: RMDB_865

description: REMoDLB trial


title: RMDB_863

description: REMoDLB trial


title: RMDB_881

description: REMoDLB trial


title: RMDB_866

description: REMoDLB trial


title: RMDB_871

description: REMoDLB trial


title: RMDB_862

description: REMoDLB trial